Diff for /imach/src/imach.c between versions 1.39 and 1.135

version 1.39, 2002/04/05 15:45:00 version 1.135, 2009/10/29 15:33:14
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.135  2009/10/29 15:33:14  brouard
      (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
   This program computes Healthy Life Expectancies from  
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    Revision 1.134  2009/10/29 13:18:53  brouard
   first survey ("cross") where individuals from different ages are    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
   interviewed on their health status or degree of disability (in the  
   case of a health survey which is our main interest) -2- at least a    Revision 1.133  2009/07/06 10:21:25  brouard
   second wave of interviews ("longitudinal") which measure each change    just nforces
   (if any) in individual health status.  Health expectancies are  
   computed from the time spent in each health state according to a    Revision 1.132  2009/07/06 08:22:05  brouard
   model. More health states you consider, more time is necessary to reach the    Many tings
   Maximum Likelihood of the parameters involved in the model.  The  
   simplest model is the multinomial logistic model where pij is the    Revision 1.131  2009/06/20 16:22:47  brouard
   probability to be observed in state j at the second wave    Some dimensions resccaled
   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 1.130  2009/05/26 06:44:34  brouard
   'age' is age and 'sex' is a covariate. If you want to have a more    (Module): Max Covariate is now set to 20 instead of 8. A
   complex model than "constant and age", you should modify the program    lot of cleaning with variables initialized to 0. Trying to make
   where the markup *Covariates have to be included here again* invites    V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
   you to do it.  More covariates you add, slower the  
   convergence.    Revision 1.129  2007/08/31 13:49:27  lievre
     Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
   The advantage of this computer programme, compared to a simple  
   multinomial logistic model, is clear when the delay between waves is not    Revision 1.128  2006/06/30 13:02:05  brouard
   identical for each individual. Also, if a individual missed an    (Module): Clarifications on computing e.j
   intermediate interview, the information is lost, but taken into  
   account using an interpolation or extrapolation.      Revision 1.127  2006/04/28 18:11:50  brouard
     (Module): Yes the sum of survivors was wrong since
   hPijx is the probability to be observed in state i at age x+h    imach-114 because nhstepm was no more computed in the age
   conditional to the observed state i at age x. The delay 'h' can be    loop. Now we define nhstepma in the age loop.
   split into an exact number (nh*stepm) of unobserved intermediate    (Module): In order to speed up (in case of numerous covariates) we
   states. This elementary transition (by month or quarter trimester,    compute health expectancies (without variances) in a first step
   semester or year) is model as a multinomial logistic.  The hPx    and then all the health expectancies with variances or standard
   matrix is simply the matrix product of nh*stepm elementary matrices    deviation (needs data from the Hessian matrices) which slows the
   and the contribution of each individual to the likelihood is simply    computation.
   hPijx.    In the future we should be able to stop the program is only health
     expectancies and graph are needed without standard deviations.
   Also this programme outputs the covariance matrix of the parameters but also  
   of the life expectancies. It also computes the prevalence limits.    Revision 1.126  2006/04/28 17:23:28  brouard
      (Module): Yes the sum of survivors was wrong since
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    imach-114 because nhstepm was no more computed in the age
            Institut national d'études démographiques, Paris.    loop. Now we define nhstepma in the age loop.
   This software have been partly granted by Euro-REVES, a concerted action    Version 0.98h
   from the European Union.  
   It is copyrighted identically to a GNU software product, ie programme and    Revision 1.125  2006/04/04 15:20:31  lievre
   software can be distributed freely for non commercial use. Latest version    Errors in calculation of health expectancies. Age was not initialized.
   can be accessed at http://euroreves.ined.fr/imach .    Forecasting file added.
   **********************************************************************/  
      Revision 1.124  2006/03/22 17:13:53  lievre
 #include <math.h>    Parameters are printed with %lf instead of %f (more numbers after the comma).
 #include <stdio.h>    The log-likelihood is printed in the log file
 #include <stdlib.h>  
 #include <unistd.h>    Revision 1.123  2006/03/20 10:52:43  brouard
     * imach.c (Module): <title> changed, corresponds to .htm file
 #define MAXLINE 256    name. <head> headers where missing.
 #define GNUPLOTPROGRAM "wgnuplot"  
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/    * imach.c (Module): Weights can have a decimal point as for
 #define FILENAMELENGTH 80    English (a comma might work with a correct LC_NUMERIC environment,
 /*#define DEBUG*/    otherwise the weight is truncated).
 #define windows    Modification of warning when the covariates values are not 0 or
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    1.
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    Version 0.98g
   
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    Revision 1.122  2006/03/20 09:45:41  brouard
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    (Module): Weights can have a decimal point as for
     English (a comma might work with a correct LC_NUMERIC environment,
 #define NINTERVMAX 8    otherwise the weight is truncated).
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    Modification of warning when the covariates values are not 0 or
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    1.
 #define NCOVMAX 8 /* Maximum number of covariates */    Version 0.98g
 #define MAXN 20000  
 #define YEARM 12. /* Number of months per year */    Revision 1.121  2006/03/16 17:45:01  lievre
 #define AGESUP 130    * imach.c (Module): Comments concerning covariates added
 #define AGEBASE 40  
     * imach.c (Module): refinements in the computation of lli if
     status=-2 in order to have more reliable computation if stepm is
 int erreur; /* Error number */    not 1 month. Version 0.98f
 int nvar;  
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    Revision 1.120  2006/03/16 15:10:38  lievre
 int npar=NPARMAX;    (Module): refinements in the computation of lli if
 int nlstate=2; /* Number of live states */    status=-2 in order to have more reliable computation if stepm is
 int ndeath=1; /* Number of dead states */    not 1 month. Version 0.98f
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  
 int popbased=0;    Revision 1.119  2006/03/15 17:42:26  brouard
     (Module): Bug if status = -2, the loglikelihood was
 int *wav; /* Number of waves for this individuual 0 is possible */    computed as likelihood omitting the logarithm. Version O.98e
 int maxwav; /* Maxim number of waves */  
 int jmin, jmax; /* min, max spacing between 2 waves */    Revision 1.118  2006/03/14 18:20:07  brouard
 int mle, weightopt;    (Module): varevsij Comments added explaining the second
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    table of variances if popbased=1 .
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 double jmean; /* Mean space between 2 waves */    (Module): Function pstamp added
 double **oldm, **newm, **savm; /* Working pointers to matrices */    (Module): Version 0.98d
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    Revision 1.117  2006/03/14 17:16:22  brouard
 FILE *ficgp,*ficresprob,*ficpop;    (Module): varevsij Comments added explaining the second
 FILE *ficreseij;    table of variances if popbased=1 .
   char filerese[FILENAMELENGTH];    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
  FILE  *ficresvij;    (Module): Function pstamp added
   char fileresv[FILENAMELENGTH];    (Module): Version 0.98d
  FILE  *ficresvpl;  
   char fileresvpl[FILENAMELENGTH];    Revision 1.116  2006/03/06 10:29:27  brouard
     (Module): Variance-covariance wrong links and
 #define NR_END 1    varian-covariance of ej. is needed (Saito).
 #define FREE_ARG char*  
 #define FTOL 1.0e-10    Revision 1.115  2006/02/27 12:17:45  brouard
     (Module): One freematrix added in mlikeli! 0.98c
 #define NRANSI  
 #define ITMAX 200    Revision 1.114  2006/02/26 12:57:58  brouard
     (Module): Some improvements in processing parameter
 #define TOL 2.0e-4    filename with strsep.
   
 #define CGOLD 0.3819660    Revision 1.113  2006/02/24 14:20:24  brouard
 #define ZEPS 1.0e-10    (Module): Memory leaks checks with valgrind and:
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    datafile was not closed, some imatrix were not freed and on matrix
     allocation too.
 #define GOLD 1.618034  
 #define GLIMIT 100.0    Revision 1.112  2006/01/30 09:55:26  brouard
 #define TINY 1.0e-20    (Module): Back to gnuplot.exe instead of wgnuplot.exe
   
 static double maxarg1,maxarg2;    Revision 1.111  2006/01/25 20:38:18  brouard
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    (Module): Lots of cleaning and bugs added (Gompertz)
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    (Module): Comments can be added in data file. Missing date values
      can be a simple dot '.'.
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  
 #define rint(a) floor(a+0.5)    Revision 1.110  2006/01/25 00:51:50  brouard
     (Module): Lots of cleaning and bugs added (Gompertz)
 static double sqrarg;  
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    Revision 1.109  2006/01/24 19:37:15  brouard
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    (Module): Comments (lines starting with a #) are allowed in data.
   
 int imx;    Revision 1.108  2006/01/19 18:05:42  lievre
 int stepm;    Gnuplot problem appeared...
 /* Stepm, step in month: minimum step interpolation*/    To be fixed
   
 int estepm;    Revision 1.107  2006/01/19 16:20:37  brouard
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/    Test existence of gnuplot in imach path
   
 int m,nb;    Revision 1.106  2006/01/19 13:24:36  brouard
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    Some cleaning and links added in html output
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  
 double **pmmij, ***probs, ***mobaverage;    Revision 1.105  2006/01/05 20:23:19  lievre
 double dateintmean=0;    *** empty log message ***
   
 double *weight;    Revision 1.104  2005/09/30 16:11:43  lievre
 int **s; /* Status */    (Module): sump fixed, loop imx fixed, and simplifications.
 double *agedc, **covar, idx;    (Module): If the status is missing at the last wave but we know
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    that the person is alive, then we can code his/her status as -2
     (instead of missing=-1 in earlier versions) and his/her
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    contributions to the likelihood is 1 - Prob of dying from last
 double ftolhess; /* Tolerance for computing hessian */    health status (= 1-p13= p11+p12 in the easiest case of somebody in
     the healthy state at last known wave). Version is 0.98
 /**************** split *************************/  
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    Revision 1.103  2005/09/30 15:54:49  lievre
 {    (Module): sump fixed, loop imx fixed, and simplifications.
    char *s;                             /* pointer */  
    int  l1, l2;                         /* length counters */    Revision 1.102  2004/09/15 17:31:30  brouard
     Add the possibility to read data file including tab characters.
    l1 = strlen( path );                 /* length of path */  
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    Revision 1.101  2004/09/15 10:38:38  brouard
 #ifdef windows    Fix on curr_time
    s = strrchr( path, '\\' );           /* find last / */  
 #else    Revision 1.100  2004/07/12 18:29:06  brouard
    s = strrchr( path, '/' );            /* find last / */    Add version for Mac OS X. Just define UNIX in Makefile
 #endif  
    if ( s == NULL ) {                   /* no directory, so use current */    Revision 1.99  2004/06/05 08:57:40  brouard
 #if     defined(__bsd__)                /* get current working directory */    *** empty log message ***
       extern char       *getwd( );  
     Revision 1.98  2004/05/16 15:05:56  brouard
       if ( getwd( dirc ) == NULL ) {    New version 0.97 . First attempt to estimate force of mortality
 #else    directly from the data i.e. without the need of knowing the health
       extern char       *getcwd( );    state at each age, but using a Gompertz model: log u =a + b*age .
     This is the basic analysis of mortality and should be done before any
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    other analysis, in order to test if the mortality estimated from the
 #endif    cross-longitudinal survey is different from the mortality estimated
          return( GLOCK_ERROR_GETCWD );    from other sources like vital statistic data.
       }  
       strcpy( name, path );             /* we've got it */    The same imach parameter file can be used but the option for mle should be -3.
    } else {                             /* strip direcotry from path */  
       s++;                              /* after this, the filename */    Agnès, who wrote this part of the code, tried to keep most of the
       l2 = strlen( s );                 /* length of filename */    former routines in order to include the new code within the former code.
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  
       strcpy( name, s );                /* save file name */    The output is very simple: only an estimate of the intercept and of
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    the slope with 95% confident intervals.
       dirc[l1-l2] = 0;                  /* add zero */  
    }    Current limitations:
    l1 = strlen( dirc );                 /* length of directory */    A) Even if you enter covariates, i.e. with the
 #ifdef windows    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    B) There is no computation of Life Expectancy nor Life Table.
 #else  
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }    Revision 1.97  2004/02/20 13:25:42  lievre
 #endif    Version 0.96d. Population forecasting command line is (temporarily)
    s = strrchr( name, '.' );            /* find last / */    suppressed.
    s++;  
    strcpy(ext,s);                       /* save extension */    Revision 1.96  2003/07/15 15:38:55  brouard
    l1= strlen( name);    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
    l2= strlen( s)+1;    rewritten within the same printf. Workaround: many printfs.
    strncpy( finame, name, l1-l2);  
    finame[l1-l2]= 0;    Revision 1.95  2003/07/08 07:54:34  brouard
    return( 0 );                         /* we're done */    * imach.c (Repository):
 }    (Repository): Using imachwizard code to output a more meaningful covariance
     matrix (cov(a12,c31) instead of numbers.
   
 /******************************************/    Revision 1.94  2003/06/27 13:00:02  brouard
     Just cleaning
 void replace(char *s, char*t)  
 {    Revision 1.93  2003/06/25 16:33:55  brouard
   int i;    (Module): On windows (cygwin) function asctime_r doesn't
   int lg=20;    exist so I changed back to asctime which exists.
   i=0;    (Module): Version 0.96b
   lg=strlen(t);  
   for(i=0; i<= lg; i++) {    Revision 1.92  2003/06/25 16:30:45  brouard
     (s[i] = t[i]);    (Module): On windows (cygwin) function asctime_r doesn't
     if (t[i]== '\\') s[i]='/';    exist so I changed back to asctime which exists.
   }  
 }    Revision 1.91  2003/06/25 15:30:29  brouard
     * imach.c (Repository): Duplicated warning errors corrected.
 int nbocc(char *s, char occ)    (Repository): Elapsed time after each iteration is now output. It
 {    helps to forecast when convergence will be reached. Elapsed time
   int i,j=0;    is stamped in powell.  We created a new html file for the graphs
   int lg=20;    concerning matrix of covariance. It has extension -cov.htm.
   i=0;  
   lg=strlen(s);    Revision 1.90  2003/06/24 12:34:15  brouard
   for(i=0; i<= lg; i++) {    (Module): Some bugs corrected for windows. Also, when
   if  (s[i] == occ ) j++;    mle=-1 a template is output in file "or"mypar.txt with the design
   }    of the covariance matrix to be input.
   return j;  
 }    Revision 1.89  2003/06/24 12:30:52  brouard
     (Module): Some bugs corrected for windows. Also, when
 void cutv(char *u,char *v, char*t, char occ)    mle=-1 a template is output in file "or"mypar.txt with the design
 {    of the covariance matrix to be input.
   int i,lg,j,p=0;  
   i=0;    Revision 1.88  2003/06/23 17:54:56  brouard
   for(j=0; j<=strlen(t)-1; j++) {    * 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.
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  
   }    Revision 1.87  2003/06/18 12:26:01  brouard
     Version 0.96
   lg=strlen(t);  
   for(j=0; j<p; j++) {    Revision 1.86  2003/06/17 20:04:08  brouard
     (u[j] = t[j]);    (Module): Change position of html and gnuplot routines and added
   }    routine fileappend.
      u[p]='\0';  
     Revision 1.85  2003/06/17 13:12:43  brouard
    for(j=0; j<= lg; j++) {    * imach.c (Repository): Check when date of death was earlier that
     if (j>=(p+1))(v[j-p-1] = t[j]);    current date of interview. It may happen when the death was just
   }    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
 /********************** nrerror ********************/    interview.
     (Repository): Because some people have very long ID (first column)
 void nrerror(char error_text[])    we changed int to long in num[] and we added a new lvector for
 {    memory allocation. But we also truncated to 8 characters (left
   fprintf(stderr,"ERREUR ...\n");    truncation)
   fprintf(stderr,"%s\n",error_text);    (Repository): No more line truncation errors.
   exit(1);  
 }    Revision 1.84  2003/06/13 21:44:43  brouard
 /*********************** vector *******************/    * imach.c (Repository): Replace "freqsummary" at a correct
 double *vector(int nl, int nh)    place. It differs from routine "prevalence" which may be called
 {    many times. Probs is memory consuming and must be used with
   double *v;    parcimony.
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
   if (!v) nrerror("allocation failure in vector");  
   return v-nl+NR_END;    Revision 1.83  2003/06/10 13:39:11  lievre
 }    *** empty log message ***
   
 /************************ free vector ******************/    Revision 1.82  2003/06/05 15:57:20  brouard
 void free_vector(double*v, int nl, int nh)    Add log in  imach.c and  fullversion number is now printed.
 {  
   free((FREE_ARG)(v+nl-NR_END));  */
 }  /*
      Interpolated Markov Chain
 /************************ivector *******************************/  
 int *ivector(long nl,long nh)    Short summary of the programme:
 {    
   int *v;    This program computes Healthy Life Expectancies from
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
   if (!v) nrerror("allocation failure in ivector");    first survey ("cross") where individuals from different ages are
   return v-nl+NR_END;    interviewed on their health status or degree of disability (in the
 }    case of a health survey which is our main interest) -2- at least a
     second wave of interviews ("longitudinal") which measure each change
 /******************free ivector **************************/    (if any) in individual health status.  Health expectancies are
 void free_ivector(int *v, long nl, long nh)    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
   free((FREE_ARG)(v+nl-NR_END));    Maximum Likelihood of the parameters involved in the model.  The
 }    simplest model is the multinomial logistic model where pij is the
     probability to be observed in state j at the second wave
 /******************* imatrix *******************************/    conditional to be observed in state i at the first wave. Therefore
 int **imatrix(long nrl, long nrh, long ncl, long nch)    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    '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
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    where the markup *Covariates have to be included here again* invites
   int **m;    you to do it.  More covariates you add, slower the
      convergence.
   /* allocate pointers to rows */  
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    The advantage of this computer programme, compared to a simple
   if (!m) nrerror("allocation failure 1 in matrix()");    multinomial logistic model, is clear when the delay between waves is not
   m += NR_END;    identical for each individual. Also, if a individual missed an
   m -= nrl;    intermediate interview, the information is lost, but taken into
      account using an interpolation or extrapolation.  
    
   /* allocate rows and set pointers to them */    hPijx is the probability to be observed in state i at age x+h
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    conditional to the observed state i at age x. The delay 'h' can be
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    split into an exact number (nh*stepm) of unobserved intermediate
   m[nrl] += NR_END;    states. This elementary transition (by month, quarter,
   m[nrl] -= ncl;    semester or year) is modelled as a multinomial logistic.  The hPx
      matrix is simply the matrix product of nh*stepm elementary matrices
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    and the contribution of each individual to the likelihood is simply
      hPijx.
   /* return pointer to array of pointers to rows */  
   return m;    Also this programme outputs the covariance matrix of the parameters but also
 }    of the life expectancies. It also computes the period (stable) prevalence. 
     
 /****************** free_imatrix *************************/    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
 void free_imatrix(m,nrl,nrh,ncl,nch)             Institut national d'études démographiques, Paris.
       int **m;    This software have been partly granted by Euro-REVES, a concerted action
       long nch,ncl,nrh,nrl;    from the European Union.
      /* free an int matrix allocated by imatrix() */    It is copyrighted identically to a GNU software product, ie programme and
 {    software can be distributed freely for non commercial use. Latest version
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    can be accessed at http://euroreves.ined.fr/imach .
   free((FREE_ARG) (m+nrl-NR_END));  
 }    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
     or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
 /******************* matrix *******************************/    
 double **matrix(long nrl, long nrh, long ncl, long nch)    **********************************************************************/
 {  /*
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    main
   double **m;    read parameterfile
     read datafile
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    concatwav
   if (!m) nrerror("allocation failure 1 in matrix()");    freqsummary
   m += NR_END;    if (mle >= 1)
   m -= nrl;      mlikeli
     print results files
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    if mle==1 
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");       computes hessian
   m[nrl] += NR_END;    read end of parameter file: agemin, agemax, bage, fage, estepm
   m[nrl] -= ncl;        begin-prev-date,...
     open gnuplot file
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    open html file
   return m;    period (stable) prevalence
 }     for age prevalim()
     h Pij x
 /*************************free matrix ************************/    variance of p varprob
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    forecasting if prevfcast==1 prevforecast call prevalence()
 {    health expectancies
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    Variance-covariance of DFLE
   free((FREE_ARG)(m+nrl-NR_END));    prevalence()
 }     movingaverage()
     varevsij() 
 /******************* ma3x *******************************/    if popbased==1 varevsij(,popbased)
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    total life expectancies
 {    Variance of period (stable) prevalence
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;   end
   double ***m;  */
   
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;   
   m -= nrl;  #include <math.h>
   #include <stdio.h>
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  #include <stdlib.h>
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  #include <string.h>
   m[nrl] += NR_END;  #include <unistd.h>
   m[nrl] -= ncl;  
   #include <limits.h>
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  #include <sys/types.h>
   #include <sys/stat.h>
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  #include <errno.h>
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  extern int errno;
   m[nrl][ncl] += NR_END;  
   m[nrl][ncl] -= nll;  /* #include <sys/time.h> */
   for (j=ncl+1; j<=nch; j++)  #include <time.h>
     m[nrl][j]=m[nrl][j-1]+nlay;  #include "timeval.h"
    
   for (i=nrl+1; i<=nrh; i++) {  /* #include <libintl.h> */
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  /* #define _(String) gettext (String) */
     for (j=ncl+1; j<=nch; j++)  
       m[i][j]=m[i][j-1]+nlay;  #define MAXLINE 256
   }  
   return m;  #define GNUPLOTPROGRAM "gnuplot"
 }  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
   #define FILENAMELENGTH 132
 /*************************free ma3x ************************/  
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 {  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  #define MAXPARM 128 /* Maximum number of parameters for the optimization */
   free((FREE_ARG)(m+nrl-NR_END));  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
 }  
   #define NINTERVMAX 8
 /***************** f1dim *************************/  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 extern int ncom;  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
 extern double *pcom,*xicom;  #define NCOVMAX 20 /* Maximum number of covariates */
 extern double (*nrfunc)(double []);  #define MAXN 20000
    #define YEARM 12. /* Number of months per year */
 double f1dim(double x)  #define AGESUP 130
 {  #define AGEBASE 40
   int j;  #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
   double f;  #ifdef UNIX
   double *xt;  #define DIRSEPARATOR '/'
    #define CHARSEPARATOR "/"
   xt=vector(1,ncom);  #define ODIRSEPARATOR '\\'
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  #else
   f=(*nrfunc)(xt);  #define DIRSEPARATOR '\\'
   free_vector(xt,1,ncom);  #define CHARSEPARATOR "\\"
   return f;  #define ODIRSEPARATOR '/'
 }  #endif
   
 /*****************brent *************************/  /* $Id$ */
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  /* $State$ */
 {  
   int iter;  char version[]="Imach version 0.98l, October 2009, INED-EUROREVES-Institut de longevite ";
   double a,b,d,etemp;  char fullversion[]="$Revision$ $Date$"; 
   double fu,fv,fw,fx;  char strstart[80];
   double ftemp;  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
   double p,q,r,tol1,tol2,u,v,w,x,xm;  int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
   double e=0.0;  int nvar=0, nforce=0; /* Number of variables, number of forces */
    int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov=0; /* Number of covariates, of covariates with '*age' */
   a=(ax < cx ? ax : cx);  int npar=NPARMAX;
   b=(ax > cx ? ax : cx);  int nlstate=2; /* Number of live states */
   x=w=v=bx;  int ndeath=1; /* Number of dead states */
   fw=fv=fx=(*f)(x);  int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   for (iter=1;iter<=ITMAX;iter++) {  int popbased=0;
     xm=0.5*(a+b);  
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  int *wav; /* Number of waves for this individuual 0 is possible */
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  int maxwav=0; /* Maxim number of waves */
     printf(".");fflush(stdout);  int jmin=0, jmax=0; /* min, max spacing between 2 waves */
 #ifdef DEBUG  int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);  int gipmx=0, gsw=0; /* Global variables on the number of contributions 
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */                     to the likelihood and the sum of weights (done by funcone)*/
 #endif  int mle=1, weightopt=0;
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
       *xmin=x;  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
       return fx;  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
     }             * wave mi and wave mi+1 is not an exact multiple of stepm. */
     ftemp=fu;  double jmean=1; /* Mean space between 2 waves */
     if (fabs(e) > tol1) {  double **oldm, **newm, **savm; /* Working pointers to matrices */
       r=(x-w)*(fx-fv);  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
       q=(x-v)*(fx-fw);  FILE *fic,*ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
       p=(x-v)*q-(x-w)*r;  FILE *ficlog, *ficrespow;
       q=2.0*(q-r);  int globpr=0; /* Global variable for printing or not */
       if (q > 0.0) p = -p;  double fretone; /* Only one call to likelihood */
       q=fabs(q);  long ipmx=0; /* Number of contributions */
       etemp=e;  double sw; /* Sum of weights */
       e=d;  char filerespow[FILENAMELENGTH];
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  FILE *ficresilk;
       else {  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
         d=p/q;  FILE *ficresprobmorprev;
         u=x+d;  FILE *fichtm, *fichtmcov; /* Html File */
         if (u-a < tol2 || b-u < tol2)  FILE *ficreseij;
           d=SIGN(tol1,xm-x);  char filerese[FILENAMELENGTH];
       }  FILE *ficresstdeij;
     } else {  char fileresstde[FILENAMELENGTH];
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  FILE *ficrescveij;
     }  char filerescve[FILENAMELENGTH];
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  FILE  *ficresvij;
     fu=(*f)(u);  char fileresv[FILENAMELENGTH];
     if (fu <= fx) {  FILE  *ficresvpl;
       if (u >= x) a=x; else b=x;  char fileresvpl[FILENAMELENGTH];
       SHFT(v,w,x,u)  char title[MAXLINE];
         SHFT(fv,fw,fx,fu)  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
         } else {  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
           if (u < x) a=u; else b=u;  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
           if (fu <= fw || w == x) {  char command[FILENAMELENGTH];
             v=w;  int  outcmd=0;
             w=u;  
             fv=fw;  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
             fw=fu;  
           } else if (fu <= fv || v == x || v == w) {  char filelog[FILENAMELENGTH]; /* Log file */
             v=u;  char filerest[FILENAMELENGTH];
             fv=fu;  char fileregp[FILENAMELENGTH];
           }  char popfile[FILENAMELENGTH];
         }  
   }  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
   nrerror("Too many iterations in brent");  
   *xmin=x;  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
   return fx;  struct timezone tzp;
 }  extern int gettimeofday();
   struct tm tmg, tm, tmf, *gmtime(), *localtime();
 /****************** mnbrak ***********************/  long time_value;
   extern long time();
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  char strcurr[80], strfor[80];
             double (*func)(double))  
 {  char *endptr;
   double ulim,u,r,q, dum;  long lval;
   double fu;  double dval;
    
   *fa=(*func)(*ax);  #define NR_END 1
   *fb=(*func)(*bx);  #define FREE_ARG char*
   if (*fb > *fa) {  #define FTOL 1.0e-10
     SHFT(dum,*ax,*bx,dum)  
       SHFT(dum,*fb,*fa,dum)  #define NRANSI 
       }  #define ITMAX 200 
   *cx=(*bx)+GOLD*(*bx-*ax);  
   *fc=(*func)(*cx);  #define TOL 2.0e-4 
   while (*fb > *fc) {  
     r=(*bx-*ax)*(*fb-*fc);  #define CGOLD 0.3819660 
     q=(*bx-*cx)*(*fb-*fa);  #define ZEPS 1.0e-10 
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  
     ulim=(*bx)+GLIMIT*(*cx-*bx);  #define GOLD 1.618034 
     if ((*bx-u)*(u-*cx) > 0.0) {  #define GLIMIT 100.0 
       fu=(*func)(u);  #define TINY 1.0e-20 
     } else if ((*cx-u)*(u-ulim) > 0.0) {  
       fu=(*func)(u);  static double maxarg1,maxarg2;
       if (fu < *fc) {  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
           SHFT(*fb,*fc,fu,(*func)(u))    
           }  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  #define rint(a) floor(a+0.5)
       u=ulim;  
       fu=(*func)(u);  static double sqrarg;
     } else {  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
       u=(*cx)+GOLD*(*cx-*bx);  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
       fu=(*func)(u);  int agegomp= AGEGOMP;
     }  
     SHFT(*ax,*bx,*cx,u)  int imx; 
       SHFT(*fa,*fb,*fc,fu)  int stepm=1;
       }  /* Stepm, step in month: minimum step interpolation*/
 }  
   int estepm;
 /*************** linmin ************************/  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
   
 int ncom;  int m,nb;
 double *pcom,*xicom;  long *num;
 double (*nrfunc)(double []);  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
    double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  double **pmmij, ***probs;
 {  double *ageexmed,*agecens;
   double brent(double ax, double bx, double cx,  double dateintmean=0;
                double (*f)(double), double tol, double *xmin);  
   double f1dim(double x);  double *weight;
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  int **s; /* Status */
               double *fc, double (*func)(double));  double *agedc, **covar, idx;
   int j;  int **nbcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
   double xx,xmin,bx,ax;  double *lsurv, *lpop, *tpop;
   double fx,fb,fa;  
    double ftol=FTOL; /* Tolerance for computing Max Likelihood */
   ncom=n;  double ftolhess; /* Tolerance for computing hessian */
   pcom=vector(1,n);  
   xicom=vector(1,n);  /**************** split *************************/
   nrfunc=func;  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   for (j=1;j<=n;j++) {  {
     pcom[j]=p[j];    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
     xicom[j]=xi[j];       the name of the file (name), its extension only (ext) and its first part of the name (finame)
   }    */ 
   ax=0.0;    char  *ss;                            /* pointer */
   xx=1.0;    int   l1, l2;                         /* length counters */
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    l1 = strlen(path );                   /* length of path */
 #ifdef DEBUG    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
 #endif    if ( ss == NULL ) {                   /* no directory, so determine current directory */
   for (j=1;j<=n;j++) {      strcpy( name, path );               /* we got the fullname name because no directory */
     xi[j] *= xmin;      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
     p[j] += xi[j];        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
   }      /* get current working directory */
   free_vector(xicom,1,n);      /*    extern  char* getcwd ( char *buf , int len);*/
   free_vector(pcom,1,n);      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
 }        return( GLOCK_ERROR_GETCWD );
       }
 /*************** powell ************************/      /* got dirc from getcwd*/
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,      printf(" DIRC = %s \n",dirc);
             double (*func)(double []))    } else {                              /* strip direcotry from path */
 {      ss++;                               /* after this, the filename */
   void linmin(double p[], double xi[], int n, double *fret,      l2 = strlen( ss );                  /* length of filename */
               double (*func)(double []));      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
   int i,ibig,j;      strcpy( name, ss );         /* save file name */
   double del,t,*pt,*ptt,*xit;      strncpy( dirc, path, l1 - l2 );     /* now the directory */
   double fp,fptt;      dirc[l1-l2] = 0;                    /* add zero */
   double *xits;      printf(" DIRC2 = %s \n",dirc);
   pt=vector(1,n);    }
   ptt=vector(1,n);    /* We add a separator at the end of dirc if not exists */
   xit=vector(1,n);    l1 = strlen( dirc );                  /* length of directory */
   xits=vector(1,n);    if( dirc[l1-1] != DIRSEPARATOR ){
   *fret=(*func)(p);      dirc[l1] =  DIRSEPARATOR;
   for (j=1;j<=n;j++) pt[j]=p[j];      dirc[l1+1] = 0; 
   for (*iter=1;;++(*iter)) {      printf(" DIRC3 = %s \n",dirc);
     fp=(*fret);    }
     ibig=0;    ss = strrchr( name, '.' );            /* find last / */
     del=0.0;    if (ss >0){
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);      ss++;
     for (i=1;i<=n;i++)      strcpy(ext,ss);                     /* save extension */
       printf(" %d %.12f",i, p[i]);      l1= strlen( name);
     printf("\n");      l2= strlen(ss)+1;
     for (i=1;i<=n;i++) {      strncpy( finame, name, l1-l2);
       for (j=1;j<=n;j++) xit[j]=xi[j][i];      finame[l1-l2]= 0;
       fptt=(*fret);    }
 #ifdef DEBUG  
       printf("fret=%lf \n",*fret);    return( 0 );                          /* we're done */
 #endif  }
       printf("%d",i);fflush(stdout);  
       linmin(p,xit,n,fret,func);  
       if (fabs(fptt-(*fret)) > del) {  /******************************************/
         del=fabs(fptt-(*fret));  
         ibig=i;  void replace_back_to_slash(char *s, char*t)
       }  {
 #ifdef DEBUG    int i;
       printf("%d %.12e",i,(*fret));    int lg=0;
       for (j=1;j<=n;j++) {    i=0;
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);    lg=strlen(t);
         printf(" x(%d)=%.12e",j,xit[j]);    for(i=0; i<= lg; i++) {
       }      (s[i] = t[i]);
       for(j=1;j<=n;j++)      if (t[i]== '\\') s[i]='/';
         printf(" p=%.12e",p[j]);    }
       printf("\n");  }
 #endif  
     }  char *trimbb(char *out, char *in)
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  { /* Trim multiple blanks in line */
 #ifdef DEBUG    char *s;
       int k[2],l;    s=out;
       k[0]=1;    while (*in != '\0'){
       k[1]=-1;      while( *in == ' ' && *(in+1) == ' ' && *(in+1) != '\0'){
       printf("Max: %.12e",(*func)(p));        in++;
       for (j=1;j<=n;j++)      }
         printf(" %.12e",p[j]);      *out++ = *in++;
       printf("\n");    }
       for(l=0;l<=1;l++) {    *out='\0';
         for (j=1;j<=n;j++) {    return s;
           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]);  
         }  int nbocc(char *s, char occ)
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  {
       }    int i,j=0;
 #endif    int lg=20;
     i=0;
     lg=strlen(s);
       free_vector(xit,1,n);    for(i=0; i<= lg; i++) {
       free_vector(xits,1,n);    if  (s[i] == occ ) j++;
       free_vector(ptt,1,n);    }
       free_vector(pt,1,n);    return j;
       return;  }
     }  
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  void cutv(char *u,char *v, char*t, char occ)
     for (j=1;j<=n;j++) {  {
       ptt[j]=2.0*p[j]-pt[j];    /* cuts string t into u and v where u ends before first occurence of char 'occ' 
       xit[j]=p[j]-pt[j];       and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
       pt[j]=p[j];       gives u="abcedf" and v="ghi2j" */
     }    int i,lg,j,p=0;
     fptt=(*func)(ptt);    i=0;
     if (fptt < fp) {    for(j=0; j<=strlen(t)-1; j++) {
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
       if (t < 0.0) {    }
         linmin(p,xit,n,fret,func);  
         for (j=1;j<=n;j++) {    lg=strlen(t);
           xi[j][ibig]=xi[j][n];    for(j=0; j<p; j++) {
           xi[j][n]=xit[j];      (u[j] = t[j]);
         }    }
 #ifdef DEBUG       u[p]='\0';
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  
         for(j=1;j<=n;j++)     for(j=0; j<= lg; j++) {
           printf(" %.12e",xit[j]);      if (j>=(p+1))(v[j-p-1] = t[j]);
         printf("\n");    }
 #endif  }
       }  
     }  /********************** nrerror ********************/
   }  
 }  void nrerror(char error_text[])
   {
 /**** Prevalence limit ****************/    fprintf(stderr,"ERREUR ...\n");
     fprintf(stderr,"%s\n",error_text);
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)    exit(EXIT_FAILURE);
 {  }
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit  /*********************** vector *******************/
      matrix by transitions matrix until convergence is reached */  double *vector(int nl, int nh)
   {
   int i, ii,j,k;    double *v;
   double min, max, maxmin, maxmax,sumnew=0.;    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
   double **matprod2();    if (!v) nrerror("allocation failure in vector");
   double **out, cov[NCOVMAX], **pmij();    return v-nl+NR_END;
   double **newm;  }
   double agefin, delaymax=50 ; /* Max number of years to converge */  
   /************************ free vector ******************/
   for (ii=1;ii<=nlstate+ndeath;ii++)  void free_vector(double*v, int nl, int nh)
     for (j=1;j<=nlstate+ndeath;j++){  {
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);    free((FREE_ARG)(v+nl-NR_END));
     }  }
   
    cov[1]=1.;  /************************ivector *******************************/
    int *ivector(long nl,long nh)
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */  {
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){    int *v;
     newm=savm;    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
     /* Covariates have to be included here again */    if (!v) nrerror("allocation failure in ivector");
      cov[2]=agefin;    return v-nl+NR_END;
    }
       for (k=1; k<=cptcovn;k++) {  
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  /******************free ivector **************************/
         /*      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]]);*/  void free_ivector(int *v, long nl, long nh)
       }  {
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    free((FREE_ARG)(v+nl-NR_END));
       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]]];  
   /************************lvector *******************************/
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/  long *lvector(long nl,long nh)
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/  {
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/    long *v;
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
     if (!v) nrerror("allocation failure in ivector");
     savm=oldm;    return v-nl+NR_END;
     oldm=newm;  }
     maxmax=0.;  
     for(j=1;j<=nlstate;j++){  /******************free lvector **************************/
       min=1.;  void free_lvector(long *v, long nl, long nh)
       max=0.;  {
       for(i=1; i<=nlstate; i++) {    free((FREE_ARG)(v+nl-NR_END));
         sumnew=0;  }
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  
         prlim[i][j]= newm[i][j]/(1-sumnew);  /******************* imatrix *******************************/
         max=FMAX(max,prlim[i][j]);  int **imatrix(long nrl, long nrh, long ncl, long nch) 
         min=FMIN(min,prlim[i][j]);       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
       }  { 
       maxmin=max-min;    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
       maxmax=FMAX(maxmax,maxmin);    int **m; 
     }    
     if(maxmax < ftolpl){    /* allocate pointers to rows */ 
       return prlim;    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
     }    if (!m) nrerror("allocation failure 1 in matrix()"); 
   }    m += NR_END; 
 }    m -= nrl; 
     
 /*************** transition probabilities ***************/    
     /* allocate rows and set pointers to them */ 
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
 {    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
   double s1, s2;    m[nrl] += NR_END; 
   /*double t34;*/    m[nrl] -= ncl; 
   int i,j,j1, nc, ii, jj;    
     for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
     for(i=1; i<= nlstate; i++){    
     for(j=1; j<i;j++){    /* return pointer to array of pointers to rows */ 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    return m; 
         /*s2 += param[i][j][nc]*cov[nc];*/  } 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/  /****************** free_imatrix *************************/
       }  void free_imatrix(m,nrl,nrh,ncl,nch)
       ps[i][j]=s2;        int **m;
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/        long nch,ncl,nrh,nrl; 
     }       /* free an int matrix allocated by imatrix() */ 
     for(j=i+1; j<=nlstate+ndeath;j++){  { 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    free((FREE_ARG) (m+nrl-NR_END)); 
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/  } 
       }  
       ps[i][j]=s2;  /******************* matrix *******************************/
     }  double **matrix(long nrl, long nrh, long ncl, long nch)
   }  {
     /*ps[3][2]=1;*/    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
     double **m;
   for(i=1; i<= nlstate; i++){  
      s1=0;    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     for(j=1; j<i; j++)    if (!m) nrerror("allocation failure 1 in matrix()");
       s1+=exp(ps[i][j]);    m += NR_END;
     for(j=i+1; j<=nlstate+ndeath; j++)    m -= nrl;
       s1+=exp(ps[i][j]);  
     ps[i][i]=1./(s1+1.);    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()");
       ps[i][j]= exp(ps[i][j])*ps[i][i];    m[nrl] += NR_END;
     for(j=i+1; j<=nlstate+ndeath; j++)    m[nrl] -= ncl;
       ps[i][j]= exp(ps[i][j])*ps[i][i];  
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   } /* end i */    return m;
     /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){     */
     for(jj=1; jj<= nlstate+ndeath; jj++){  }
       ps[ii][jj]=0;  
       ps[ii][ii]=1;  /*************************free matrix ************************/
     }  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   }  {
     free((FREE_ARG)(m[nrl]+ncl-NR_END));
     free((FREE_ARG)(m+nrl-NR_END));
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){  }
     for(jj=1; jj<= nlstate+ndeath; jj++){  
      printf("%lf ",ps[ii][jj]);  /******************* ma3x *******************************/
    }  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
     printf("\n ");  {
     }    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
     printf("\n ");printf("%lf ",cov[2]);*/    double ***m;
 /*  
   for(i=1; i<= npar; i++) printf("%f ",x[i]);    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   goto end;*/    if (!m) nrerror("allocation failure 1 in matrix()");
     return ps;    m += NR_END;
 }    m -= nrl;
   
 /**************** Product of 2 matrices ******************/    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)    m[nrl] += NR_END;
 {    m[nrl] -= ncl;
   /* 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(...) */    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   /* in, b, out are matrice of pointers which should have been initialized  
      before: only the contents of out is modified. The function returns    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
      a pointer to pointers identical to out */    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
   long i, j, k;    m[nrl][ncl] += NR_END;
   for(i=nrl; i<= nrh; i++)    m[nrl][ncl] -= nll;
     for(k=ncolol; k<=ncoloh; k++)    for (j=ncl+1; j<=nch; j++) 
       for(j=ncl,out[i][k]=0.; j<=nch; j++)      m[nrl][j]=m[nrl][j-1]+nlay;
         out[i][k] +=in[i][j]*b[j][k];    
     for (i=nrl+1; i<=nrh; i++) {
   return out;      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
 }      for (j=ncl+1; j<=nch; j++) 
         m[i][j]=m[i][j-1]+nlay;
     }
 /************* Higher Matrix Product ***************/    return m; 
     /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
 {    */
   /* 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.  /*************************free ma3x ************************/
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
      (typically every 2 years instead of every month which is too big).  {
      Model is determined by parameters x and covariates have to be    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
      included manually here.    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     free((FREE_ARG)(m+nrl-NR_END));
      */  }
   
   int i, j, d, h, k;  /*************** function subdirf ***********/
   double **out, cov[NCOVMAX];  char *subdirf(char fileres[])
   double **newm;  {
     /* Caution optionfilefiname is hidden */
   /* Hstepm could be zero and should return the unit matrix */    strcpy(tmpout,optionfilefiname);
   for (i=1;i<=nlstate+ndeath;i++)    strcat(tmpout,"/"); /* Add to the right */
     for (j=1;j<=nlstate+ndeath;j++){    strcat(tmpout,fileres);
       oldm[i][j]=(i==j ? 1.0 : 0.0);    return tmpout;
       po[i][j][0]=(i==j ? 1.0 : 0.0);  }
     }  
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */  /*************** function subdirf2 ***********/
   for(h=1; h <=nhstepm; h++){  char *subdirf2(char fileres[], char *preop)
     for(d=1; d <=hstepm; d++){  {
       newm=savm;    
       /* Covariates have to be included here again */    /* Caution optionfilefiname is hidden */
       cov[1]=1.;    strcpy(tmpout,optionfilefiname);
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;    strcat(tmpout,"/");
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    strcat(tmpout,preop);
       for (k=1; k<=cptcovage;k++)    strcat(tmpout,fileres);
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    return tmpout;
       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]]];  
   /*************** function subdirf3 ***********/
   char *subdirf3(char fileres[], char *preop, char *preop2)
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/  {
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/    
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,    /* Caution optionfilefiname is hidden */
                    pmij(pmmij,cov,ncovmodel,x,nlstate));    strcpy(tmpout,optionfilefiname);
       savm=oldm;    strcat(tmpout,"/");
       oldm=newm;    strcat(tmpout,preop);
     }    strcat(tmpout,preop2);
     for(i=1; i<=nlstate+ndeath; i++)    strcat(tmpout,fileres);
       for(j=1;j<=nlstate+ndeath;j++) {    return tmpout;
         po[i][j][h]=newm[i][j];  }
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);  
          */  /***************** f1dim *************************/
       }  extern int ncom; 
   } /* end h */  extern double *pcom,*xicom;
   return po;  extern double (*nrfunc)(double []); 
 }   
   double f1dim(double x) 
   { 
 /*************** log-likelihood *************/    int j; 
 double func( double *x)    double f;
 {    double *xt; 
   int i, ii, j, k, mi, d, kk;   
   double l, ll[NLSTATEMAX], cov[NCOVMAX];    xt=vector(1,ncom); 
   double **out;    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
   double sw; /* Sum of weights */    f=(*nrfunc)(xt); 
   double lli; /* Individual log likelihood */    free_vector(xt,1,ncom); 
   long ipmx;    return f; 
   /*extern weight */  } 
   /* We are differentiating ll according to initial status */  
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/  /*****************brent *************************/
   /*for(i=1;i<imx;i++)  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
     printf(" %d\n",s[4][i]);  { 
   */    int iter; 
   cov[1]=1.;    double a,b,d,etemp;
     double fu,fv,fw,fx;
   for(k=1; k<=nlstate; k++) ll[k]=0.;    double ftemp;
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){    double p,q,r,tol1,tol2,u,v,w,x,xm; 
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];    double e=0.0; 
     for(mi=1; mi<= wav[i]-1; mi++){   
       for (ii=1;ii<=nlstate+ndeath;ii++)    a=(ax < cx ? ax : cx); 
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);    b=(ax > cx ? ax : cx); 
       for(d=0; d<dh[mi][i]; d++){    x=w=v=bx; 
         newm=savm;    fw=fv=fx=(*f)(x); 
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;    for (iter=1;iter<=ITMAX;iter++) { 
         for (kk=1; kk<=cptcovage;kk++) {      xm=0.5*(a+b); 
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
         }      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
              printf(".");fflush(stdout);
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,      fprintf(ficlog,".");fflush(ficlog);
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));  #ifdef DEBUG
         savm=oldm;      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);
         oldm=newm;      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
              /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
          #endif
       } /* end mult */      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
              *xmin=x; 
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);        return fx; 
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/      } 
       ipmx +=1;      ftemp=fu;
       sw += weight[i];      if (fabs(e) > tol1) { 
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;        r=(x-w)*(fx-fv); 
     } /* end of wave */        q=(x-v)*(fx-fw); 
   } /* end of individual */        p=(x-v)*q-(x-w)*r; 
         q=2.0*(q-r); 
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];        if (q > 0.0) p = -p; 
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */        q=fabs(q); 
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */        etemp=e; 
   return -l;        e=d; 
 }        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
           d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
         else { 
 /*********** Maximum Likelihood Estimation ***************/          d=p/q; 
           u=x+d; 
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))          if (u-a < tol2 || b-u < tol2) 
 {            d=SIGN(tol1,xm-x); 
   int i,j, iter;        } 
   double **xi,*delti;      } else { 
   double fret;        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   xi=matrix(1,npar,1,npar);      } 
   for (i=1;i<=npar;i++)      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
     for (j=1;j<=npar;j++)      fu=(*f)(u); 
       xi[i][j]=(i==j ? 1.0 : 0.0);      if (fu <= fx) { 
   printf("Powell\n");        if (u >= x) a=x; else b=x; 
   powell(p,xi,npar,ftol,&iter,&fret,func);        SHFT(v,w,x,u) 
           SHFT(fv,fw,fx,fu) 
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));          } else { 
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));            if (u < x) a=u; else b=u; 
             if (fu <= fw || w == x) { 
 }              v=w; 
               w=u; 
 /**** Computes Hessian and covariance matrix ***/              fv=fw; 
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))              fw=fu; 
 {            } else if (fu <= fv || v == x || v == w) { 
   double  **a,**y,*x,pd;              v=u; 
   double **hess;              fv=fu; 
   int i, j,jk;            } 
   int *indx;          } 
     } 
   double hessii(double p[], double delta, int theta, double delti[]);    nrerror("Too many iterations in brent"); 
   double hessij(double p[], double delti[], int i, int j);    *xmin=x; 
   void lubksb(double **a, int npar, int *indx, double b[]) ;    return fx; 
   void ludcmp(double **a, int npar, int *indx, double *d) ;  } 
   
   hess=matrix(1,npar,1,npar);  /****************** mnbrak ***********************/
   
   printf("\nCalculation of the hessian matrix. Wait...\n");  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
   for (i=1;i<=npar;i++){              double (*func)(double)) 
     printf("%d",i);fflush(stdout);  { 
     hess[i][i]=hessii(p,ftolhess,i,delti);    double ulim,u,r,q, dum;
     /*printf(" %f ",p[i]);*/    double fu; 
     /*printf(" %lf ",hess[i][i]);*/   
   }    *fa=(*func)(*ax); 
      *fb=(*func)(*bx); 
   for (i=1;i<=npar;i++) {    if (*fb > *fa) { 
     for (j=1;j<=npar;j++)  {      SHFT(dum,*ax,*bx,dum) 
       if (j>i) {        SHFT(dum,*fb,*fa,dum) 
         printf(".%d%d",i,j);fflush(stdout);        } 
         hess[i][j]=hessij(p,delti,i,j);    *cx=(*bx)+GOLD*(*bx-*ax); 
         hess[j][i]=hess[i][j];        *fc=(*func)(*cx); 
         /*printf(" %lf ",hess[i][j]);*/    while (*fb > *fc) { 
       }      r=(*bx-*ax)*(*fb-*fc); 
     }      q=(*bx-*cx)*(*fb-*fa); 
   }      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
   printf("\n");        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
       ulim=(*bx)+GLIMIT*(*cx-*bx); 
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");      if ((*bx-u)*(u-*cx) > 0.0) { 
          fu=(*func)(u); 
   a=matrix(1,npar,1,npar);      } else if ((*cx-u)*(u-ulim) > 0.0) { 
   y=matrix(1,npar,1,npar);        fu=(*func)(u); 
   x=vector(1,npar);        if (fu < *fc) { 
   indx=ivector(1,npar);          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
   for (i=1;i<=npar;i++)            SHFT(*fb,*fc,fu,(*func)(u)) 
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];            } 
   ludcmp(a,npar,indx,&pd);      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
         u=ulim; 
   for (j=1;j<=npar;j++) {        fu=(*func)(u); 
     for (i=1;i<=npar;i++) x[i]=0;      } else { 
     x[j]=1;        u=(*cx)+GOLD*(*cx-*bx); 
     lubksb(a,npar,indx,x);        fu=(*func)(u); 
     for (i=1;i<=npar;i++){      } 
       matcov[i][j]=x[i];      SHFT(*ax,*bx,*cx,u) 
     }        SHFT(*fa,*fb,*fc,fu) 
   }        } 
   } 
   printf("\n#Hessian matrix#\n");  
   for (i=1;i<=npar;i++) {  /*************** linmin ************************/
     for (j=1;j<=npar;j++) {  
       printf("%.3e ",hess[i][j]);  int ncom; 
     }  double *pcom,*xicom;
     printf("\n");  double (*nrfunc)(double []); 
   }   
   void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
   /* Recompute Inverse */  { 
   for (i=1;i<=npar;i++)    double brent(double ax, double bx, double cx, 
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];                 double (*f)(double), double tol, double *xmin); 
   ludcmp(a,npar,indx,&pd);    double f1dim(double x); 
     void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
   /*  printf("\n#Hessian matrix recomputed#\n");                double *fc, double (*func)(double)); 
     int j; 
   for (j=1;j<=npar;j++) {    double xx,xmin,bx,ax; 
     for (i=1;i<=npar;i++) x[i]=0;    double fx,fb,fa;
     x[j]=1;   
     lubksb(a,npar,indx,x);    ncom=n; 
     for (i=1;i<=npar;i++){    pcom=vector(1,n); 
       y[i][j]=x[i];    xicom=vector(1,n); 
       printf("%.3e ",y[i][j]);    nrfunc=func; 
     }    for (j=1;j<=n;j++) { 
     printf("\n");      pcom[j]=p[j]; 
   }      xicom[j]=xi[j]; 
   */    } 
     ax=0.0; 
   free_matrix(a,1,npar,1,npar);    xx=1.0; 
   free_matrix(y,1,npar,1,npar);    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
   free_vector(x,1,npar);    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
   free_ivector(indx,1,npar);  #ifdef DEBUG
   free_matrix(hess,1,npar,1,npar);    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   #endif
 }    for (j=1;j<=n;j++) { 
       xi[j] *= xmin; 
 /*************** hessian matrix ****************/      p[j] += xi[j]; 
 double hessii( double x[], double delta, int theta, double delti[])    } 
 {    free_vector(xicom,1,n); 
   int i;    free_vector(pcom,1,n); 
   int l=1, lmax=20;  } 
   double k1,k2;  
   double p2[NPARMAX+1];  char *asc_diff_time(long time_sec, char ascdiff[])
   double res;  {
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;    long sec_left, days, hours, minutes;
   double fx;    days = (time_sec) / (60*60*24);
   int k=0,kmax=10;    sec_left = (time_sec) % (60*60*24);
   double l1;    hours = (sec_left) / (60*60) ;
     sec_left = (sec_left) %(60*60);
   fx=func(x);    minutes = (sec_left) /60;
   for (i=1;i<=npar;i++) p2[i]=x[i];    sec_left = (sec_left) % (60);
   for(l=0 ; l <=lmax; l++){    sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
     l1=pow(10,l);    return ascdiff;
     delts=delt;  }
     for(k=1 ; k <kmax; k=k+1){  
       delt = delta*(l1*k);  /*************** powell ************************/
       p2[theta]=x[theta] +delt;  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
       k1=func(p2)-fx;              double (*func)(double [])) 
       p2[theta]=x[theta]-delt;  { 
       k2=func(p2)-fx;    void linmin(double p[], double xi[], int n, double *fret, 
       /*res= (k1-2.0*fx+k2)/delt/delt; */                double (*func)(double [])); 
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */    int i,ibig,j; 
          double del,t,*pt,*ptt,*xit;
 #ifdef DEBUG    double fp,fptt;
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);    double *xits;
 #endif    int niterf, itmp;
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */  
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){    pt=vector(1,n); 
         k=kmax;    ptt=vector(1,n); 
       }    xit=vector(1,n); 
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */    xits=vector(1,n); 
         k=kmax; l=lmax*10.;    *fret=(*func)(p); 
       }    for (j=1;j<=n;j++) pt[j]=p[j]; 
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){    for (*iter=1;;++(*iter)) { 
         delts=delt;      fp=(*fret); 
       }      ibig=0; 
     }      del=0.0; 
   }      last_time=curr_time;
   delti[theta]=delts;      (void) gettimeofday(&curr_time,&tzp);
   return res;      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);
        fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec); fflush(ficlog);
 }  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
      for (i=1;i<=n;i++) {
 double hessij( double x[], double delti[], int thetai,int thetaj)        printf(" %d %.12f",i, p[i]);
 {        fprintf(ficlog," %d %.12lf",i, p[i]);
   int i;        fprintf(ficrespow," %.12lf", p[i]);
   int l=1, l1, lmax=20;      }
   double k1,k2,k3,k4,res,fx;      printf("\n");
   double p2[NPARMAX+1];      fprintf(ficlog,"\n");
   int k;      fprintf(ficrespow,"\n");fflush(ficrespow);
       if(*iter <=3){
   fx=func(x);        tm = *localtime(&curr_time.tv_sec);
   for (k=1; k<=2; k++) {        strcpy(strcurr,asctime(&tm));
     for (i=1;i<=npar;i++) p2[i]=x[i];  /*       asctime_r(&tm,strcurr); */
     p2[thetai]=x[thetai]+delti[thetai]/k;        forecast_time=curr_time; 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;        itmp = strlen(strcurr);
     k1=func(p2)-fx;        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
            strcurr[itmp-1]='\0';
     p2[thetai]=x[thetai]+delti[thetai]/k;        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
     k2=func(p2)-fx;        for(niterf=10;niterf<=30;niterf+=10){
            forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
     p2[thetai]=x[thetai]-delti[thetai]/k;          tmf = *localtime(&forecast_time.tv_sec);
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  /*      asctime_r(&tmf,strfor); */
     k3=func(p2)-fx;          strcpy(strfor,asctime(&tmf));
            itmp = strlen(strfor);
     p2[thetai]=x[thetai]-delti[thetai]/k;          if(strfor[itmp-1]=='\n')
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          strfor[itmp-1]='\0';
     k4=func(p2)-fx;          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);
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */          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);
 #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);      }
 #endif      for (i=1;i<=n;i++) { 
   }        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
   return res;        fptt=(*fret); 
 }  #ifdef DEBUG
         printf("fret=%lf \n",*fret);
 /************** Inverse of matrix **************/        fprintf(ficlog,"fret=%lf \n",*fret);
 void ludcmp(double **a, int n, int *indx, double *d)  #endif
 {        printf("%d",i);fflush(stdout);
   int i,imax,j,k;        fprintf(ficlog,"%d",i);fflush(ficlog);
   double big,dum,sum,temp;        linmin(p,xit,n,fret,func); 
   double *vv;        if (fabs(fptt-(*fret)) > del) { 
            del=fabs(fptt-(*fret)); 
   vv=vector(1,n);          ibig=i; 
   *d=1.0;        } 
   for (i=1;i<=n;i++) {  #ifdef DEBUG
     big=0.0;        printf("%d %.12e",i,(*fret));
     for (j=1;j<=n;j++)        fprintf(ficlog,"%d %.12e",i,(*fret));
       if ((temp=fabs(a[i][j])) > big) big=temp;        for (j=1;j<=n;j++) {
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
     vv[i]=1.0/big;          printf(" x(%d)=%.12e",j,xit[j]);
   }          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
   for (j=1;j<=n;j++) {        }
     for (i=1;i<j;i++) {        for(j=1;j<=n;j++) {
       sum=a[i][j];          printf(" p=%.12e",p[j]);
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];          fprintf(ficlog," p=%.12e",p[j]);
       a[i][j]=sum;        }
     }        printf("\n");
     big=0.0;        fprintf(ficlog,"\n");
     for (i=j;i<=n;i++) {  #endif
       sum=a[i][j];      } 
       for (k=1;k<j;k++)      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
         sum -= a[i][k]*a[k][j];  #ifdef DEBUG
       a[i][j]=sum;        int k[2],l;
       if ( (dum=vv[i]*fabs(sum)) >= big) {        k[0]=1;
         big=dum;        k[1]=-1;
         imax=i;        printf("Max: %.12e",(*func)(p));
       }        fprintf(ficlog,"Max: %.12e",(*func)(p));
     }        for (j=1;j<=n;j++) {
     if (j != imax) {          printf(" %.12e",p[j]);
       for (k=1;k<=n;k++) {          fprintf(ficlog," %.12e",p[j]);
         dum=a[imax][k];        }
         a[imax][k]=a[j][k];        printf("\n");
         a[j][k]=dum;        fprintf(ficlog,"\n");
       }        for(l=0;l<=1;l++) {
       *d = -(*d);          for (j=1;j<=n;j++) {
       vv[imax]=vv[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]);
     indx[j]=imax;            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
     if (a[j][j] == 0.0) a[j][j]=TINY;          }
     if (j != n) {          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
       dum=1.0/(a[j][j]);          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
       for (i=j+1;i<=n;i++) a[i][j] *= dum;        }
     }  #endif
   }  
   free_vector(vv,1,n);  /* Doesn't work */  
 ;        free_vector(xit,1,n); 
 }        free_vector(xits,1,n); 
         free_vector(ptt,1,n); 
 void lubksb(double **a, int n, int *indx, double b[])        free_vector(pt,1,n); 
 {        return; 
   int i,ii=0,ip,j;      } 
   double sum;      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
        for (j=1;j<=n;j++) { 
   for (i=1;i<=n;i++) {        ptt[j]=2.0*p[j]-pt[j]; 
     ip=indx[i];        xit[j]=p[j]-pt[j]; 
     sum=b[ip];        pt[j]=p[j]; 
     b[ip]=b[i];      } 
     if (ii)      fptt=(*func)(ptt); 
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];      if (fptt < fp) { 
     else if (sum) ii=i;        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
     b[i]=sum;        if (t < 0.0) { 
   }          linmin(p,xit,n,fret,func); 
   for (i=n;i>=1;i--) {          for (j=1;j<=n;j++) { 
     sum=b[i];            xi[j][ibig]=xi[j][n]; 
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];            xi[j][n]=xit[j]; 
     b[i]=sum/a[i][i];          }
   }  #ifdef DEBUG
 }          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
           fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
 /************ Frequencies ********************/          for(j=1;j<=n;j++){
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)            printf(" %.12e",xit[j]);
 {  /* Some frequencies */            fprintf(ficlog," %.12e",xit[j]);
            }
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;          printf("\n");
   double ***freq; /* Frequencies */          fprintf(ficlog,"\n");
   double *pp;  #endif
   double pos, k2, dateintsum=0,k2cpt=0;        }
   FILE *ficresp;      } 
   char fileresp[FILENAMELENGTH];    } 
    } 
   pp=vector(1,nlstate);  
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);  /**** Prevalence limit (stable or period prevalence)  ****************/
   strcpy(fileresp,"p");  
   strcat(fileresp,fileres);  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
   if((ficresp=fopen(fileresp,"w"))==NULL) {  {
     printf("Problem with prevalence resultfile: %s\n", fileresp);    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
     exit(0);       matrix by transitions matrix until convergence is reached */
   }  
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    int i, ii,j,k;
   j1=0;    double min, max, maxmin, maxmax,sumnew=0.;
      double **matprod2();
   j=cptcoveff;    double **out, cov[NCOVMAX+1], **pmij();
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    double **newm;
      double agefin, delaymax=50 ; /* Max number of years to converge */
   for(k1=1; k1<=j;k1++){  
     for(i1=1; i1<=ncodemax[k1];i1++){    for (ii=1;ii<=nlstate+ndeath;ii++)
       j1++;      for (j=1;j<=nlstate+ndeath;j++){
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         scanf("%d", i);*/      }
       for (i=-1; i<=nlstate+ndeath; i++)    
         for (jk=-1; jk<=nlstate+ndeath; jk++)       cov[1]=1.;
           for(m=agemin; m <= agemax+3; m++)   
             freq[i][jk][m]=0;   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
          for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
       dateintsum=0;      newm=savm;
       k2cpt=0;      /* Covariates have to be included here again */
       for (i=1; i<=imx; i++) {       cov[2]=agefin;
         bool=1;    
         if  (cptcovn>0) {        for (k=1; k<=cptcovn;k++) {
           for (z1=1; z1<=cptcoveff; z1++)          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])          /*      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]]);*/
               bool=0;        }
         }        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
         if (bool==1) {        for (k=1; k<=cptcovprod;k++)
           for(m=firstpass; m<=lastpass; m++){          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
             k2=anint[m][i]+(mint[m][i]/12.);  
             if ((k2>=dateprev1) && (k2<=dateprev2)) {        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
               if(agev[m][i]==0) agev[m][i]=agemax+1;        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
               if(agev[m][i]==1) agev[m][i]=agemax+2;        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
               if (m<lastpass) {      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];  
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];      savm=oldm;
               }      oldm=newm;
                    maxmax=0.;
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {      for(j=1;j<=nlstate;j++){
                 dateintsum=dateintsum+k2;        min=1.;
                 k2cpt++;        max=0.;
               }        for(i=1; i<=nlstate; i++) {
             }          sumnew=0;
           }          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
         }          prlim[i][j]= newm[i][j]/(1-sumnew);
       }          max=FMAX(max,prlim[i][j]);
                  min=FMIN(min,prlim[i][j]);
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        }
         maxmin=max-min;
       if  (cptcovn>0) {        maxmax=FMAX(maxmax,maxmin);
         fprintf(ficresp, "\n#********** Variable ");      }
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);      if(maxmax < ftolpl){
         fprintf(ficresp, "**********\n#");        return prlim;
       }      }
       for(i=1; i<=nlstate;i++)    }
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);  }
       fprintf(ficresp, "\n");  
        /*************** transition probabilities ***************/ 
       for(i=(int)agemin; i <= (int)agemax+3; i++){  
         if(i==(int)agemax+3)  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
           printf("Total");  {
         else    double s1, s2;
           printf("Age %d", i);    /*double t34;*/
         for(jk=1; jk <=nlstate ; jk++){    int i,j,j1, nc, ii, jj;
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)  
             pp[jk] += freq[jk][m][i];      for(i=1; i<= nlstate; i++){
         }        for(j=1; j<i;j++){
         for(jk=1; jk <=nlstate ; jk++){          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
           for(m=-1, pos=0; m <=0 ; m++)            /*s2 += param[i][j][nc]*cov[nc];*/
             pos += freq[jk][m][i];            s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
           if(pp[jk]>=1.e-10)  /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);          }
           else          ps[i][j]=s2;
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);  /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
         }        }
         for(j=i+1; j<=nlstate+ndeath;j++){
         for(jk=1; jk <=nlstate ; jk++){          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)            s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
             pp[jk] += freq[jk][m][i];  /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
         }          }
           ps[i][j]=s2;
         for(jk=1,pos=0; jk <=nlstate ; jk++)        }
           pos += pp[jk];      }
         for(jk=1; jk <=nlstate ; jk++){      /*ps[3][2]=1;*/
           if(pos>=1.e-5)      
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);      for(i=1; i<= nlstate; i++){
           else        s1=0;
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);        for(j=1; j<i; j++){
           if( i <= (int) agemax){          s1+=exp(ps[i][j]);
             if(pos>=1.e-5){          /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);        }
               probs[i][jk][j1]= pp[jk]/pos;        for(j=i+1; j<=nlstate+ndeath; j++){
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/          s1+=exp(ps[i][j]);
             }          /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
             else        }
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);        ps[i][i]=1./(s1+1.);
           }        for(j=1; j<i; j++)
         }          ps[i][j]= exp(ps[i][j])*ps[i][i];
                for(j=i+1; j<=nlstate+ndeath; j++)
         for(jk=-1; jk <=nlstate+ndeath; jk++)          ps[i][j]= exp(ps[i][j])*ps[i][i];
           for(m=-1; m <=nlstate+ndeath; m++)        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);      } /* end i */
         if(i <= (int) agemax)      
           fprintf(ficresp,"\n");      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
         printf("\n");        for(jj=1; jj<= nlstate+ndeath; jj++){
       }          ps[ii][jj]=0;
     }          ps[ii][ii]=1;
   }        }
   dateintmean=dateintsum/k2cpt;      }
        
   fclose(ficresp);  
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);  /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
   free_vector(pp,1,nlstate);  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
    /*         printf("ddd %lf ",ps[ii][jj]); */
   /* End of Freq */  /*       } */
 }  /*       printf("\n "); */
   /*        } */
 /************ Prevalence ********************/  /*        printf("\n ");printf("%lf ",cov[2]); */
 void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)         /*
 {  /* Some frequencies */        for(i=1; i<= npar; i++) printf("%f ",x[i]);
          goto end;*/
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;      return ps;
   double ***freq; /* Frequencies */  }
   double *pp;  
   double pos, k2;  /**************** Product of 2 matrices ******************/
   
   pp=vector(1,nlstate);  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);  {
      /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
   j1=0;    /* in, b, out are matrice of pointers which should have been initialized 
         before: only the contents of out is modified. The function returns
   j=cptcoveff;       a pointer to pointers identical to out */
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    long i, j, k;
      for(i=nrl; i<= nrh; i++)
  for(k1=1; k1<=j;k1++){      for(k=ncolol; k<=ncoloh; k++)
     for(i1=1; i1<=ncodemax[k1];i1++){        for(j=ncl,out[i][k]=0.; j<=nch; j++)
       j1++;          out[i][k] +=in[i][j]*b[j][k];
    
       for (i=-1; i<=nlstate+ndeath; i++)      return out;
         for (jk=-1; jk<=nlstate+ndeath; jk++)    }
           for(m=agemin; m <= agemax+3; m++)  
             freq[i][jk][m]=0;  
        /************* Higher Matrix Product ***************/
       for (i=1; i<=imx; i++) {  
         bool=1;  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
         if  (cptcovn>0) {  {
           for (z1=1; z1<=cptcoveff; z1++)    /* Computes the transition matrix starting at age 'age' over 
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])       'nhstepm*hstepm*stepm' months (i.e. until
               bool=0;       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
         }       nhstepm*hstepm matrices. 
         if (bool==1) {       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
           for(m=firstpass; m<=lastpass; m++){       (typically every 2 years instead of every month which is too big 
             k2=anint[m][i]+(mint[m][i]/12.);       for the memory).
             if ((k2>=dateprev1) && (k2<=dateprev2)) {       Model is determined by parameters x and covariates have to be 
               if(agev[m][i]==0) agev[m][i]=agemax+1;       included manually here. 
               if(agev[m][i]==1) agev[m][i]=agemax+2;  
               if (m<lastpass) freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];       */
               /* freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];  */  
             }    int i, j, d, h, k;
           }    double **out, cov[NCOVMAX+1];
         }    double **newm;
       }  
         for(i=(int)agemin; i <= (int)agemax+3; i++){    /* Hstepm could be zero and should return the unit matrix */
           for(jk=1; jk <=nlstate ; jk++){    for (i=1;i<=nlstate+ndeath;i++)
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)      for (j=1;j<=nlstate+ndeath;j++){
               pp[jk] += freq[jk][m][i];        oldm[i][j]=(i==j ? 1.0 : 0.0);
           }        po[i][j][0]=(i==j ? 1.0 : 0.0);
           for(jk=1; jk <=nlstate ; jk++){      }
             for(m=-1, pos=0; m <=0 ; m++)    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
             pos += freq[jk][m][i];    for(h=1; h <=nhstepm; h++){
         }      for(d=1; d <=hstepm; d++){
                newm=savm;
          for(jk=1; jk <=nlstate ; jk++){        /* Covariates have to be included here again */
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)        cov[1]=1.;
              pp[jk] += freq[jk][m][i];        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
          }        for (k=1; k<=cptcovn;k++) 
                    cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];        for (k=1; k<=cptcovage;k++)
           cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
          for(jk=1; jk <=nlstate ; jk++){                  for (k=1; k<=cptcovprod;k++)
            if( i <= (int) agemax){          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
              if(pos>=1.e-5){  
                probs[i][jk][j1]= pp[jk]/pos;  
              }        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
            }        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
          }        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
                               pmij(pmmij,cov,ncovmodel,x,nlstate));
         }        savm=oldm;
     }        oldm=newm;
   }      }
        for(i=1; i<=nlstate+ndeath; i++)
          for(j=1;j<=nlstate+ndeath;j++) {
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);          po[i][j][h]=newm[i][j];
   free_vector(pp,1,nlstate);          /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
          }
 }  /* End of Freq */      /*printf("h=%d ",h);*/
     } /* end h */
 /************* Waves Concatenation ***************/  /*     printf("\n H=%d \n",h); */
     return po;
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)  }
 {  
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.  
      Death is a valid wave (if date is known).  /*************** log-likelihood *************/
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i  double func( double *x)
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]  {
      and mw[mi+1][i]. dh depends on stepm.    int i, ii, j, k, mi, d, kk;
      */    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
     double **out;
   int i, mi, m;    double sw; /* Sum of weights */
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;    double lli; /* Individual log likelihood */
      double sum=0., jmean=0.;*/    int s1, s2;
     double bbh, survp;
   int j, k=0,jk, ju, jl;    long ipmx;
   double sum=0.;    /*extern weight */
   jmin=1e+5;    /* We are differentiating ll according to initial status */
   jmax=-1;    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   jmean=0.;    /*for(i=1;i<imx;i++) 
   for(i=1; i<=imx; i++){      printf(" %d\n",s[4][i]);
     mi=0;    */
     m=firstpass;    cov[1]=1.;
     while(s[m][i] <= nlstate){  
       if(s[m][i]>=1)    for(k=1; k<=nlstate; k++) ll[k]=0.;
         mw[++mi][i]=m;  
       if(m >=lastpass)    if(mle==1){
         break;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       else        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         m++;        for(mi=1; mi<= wav[i]-1; mi++){
     }/* end while */          for (ii=1;ii<=nlstate+ndeath;ii++)
     if (s[m][i] > nlstate){            for (j=1;j<=nlstate+ndeath;j++){
       mi++;     /* Death is another wave */              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       /* if(mi==0)  never been interviewed correctly before death */              savm[ii][j]=(ii==j ? 1.0 : 0.0);
          /* Only death is a correct wave */            }
       mw[mi][i]=m;          for(d=0; d<dh[mi][i]; d++){
     }            newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     wav[i]=mi;            for (kk=1; kk<=cptcovage;kk++) {
     if(mi==0)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);            }
   }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   for(i=1; i<=imx; i++){            savm=oldm;
     for(mi=1; mi<wav[i];mi++){            oldm=newm;
       if (stepm <=0)          } /* end mult */
         dh[mi][i]=1;        
       else{          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
         if (s[mw[mi+1][i]][i] > nlstate) {          /* But now since version 0.9 we anticipate for bias at large stepm.
           if (agedc[i] < 2*AGESUP) {           * If stepm is larger than one month (smallest stepm) and if the exact delay 
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);           * (in months) between two waves is not a multiple of stepm, we rounded to 
           if(j==0) j=1;  /* Survives at least one month after exam */           * the nearest (and in case of equal distance, to the lowest) interval but now
           k=k+1;           * we keep into memory the bias bh[mi][i] and also the previous matrix product
           if (j >= jmax) jmax=j;           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
           if (j <= jmin) jmin=j;           * probability in order to take into account the bias as a fraction of the way
           sum=sum+j;           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
           /*if (j<0) printf("j=%d num=%d \n",j,i); */           * -stepm/2 to stepm/2 .
           }           * For stepm=1 the results are the same as for previous versions of Imach.
         }           * For stepm > 1 the results are less biased than in previous versions. 
         else{           */
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));          s1=s[mw[mi][i]][i];
           k=k+1;          s2=s[mw[mi+1][i]][i];
           if (j >= jmax) jmax=j;          bbh=(double)bh[mi][i]/(double)stepm; 
           else if (j <= jmin)jmin=j;          /* bias bh is positive if real duration
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */           * is higher than the multiple of stepm and negative otherwise.
           sum=sum+j;           */
         }          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
         jk= j/stepm;          if( s2 > nlstate){ 
         jl= j -jk*stepm;            /* i.e. if s2 is a death state and if the date of death is known 
         ju= j -(jk+1)*stepm;               then the contribution to the likelihood is the probability to 
         if(jl <= -ju)               die between last step unit time and current  step unit time, 
           dh[mi][i]=jk;               which is also equal to probability to die before dh 
         else               minus probability to die before dh-stepm . 
           dh[mi][i]=jk+1;               In version up to 0.92 likelihood was computed
         if(dh[mi][i]==0)          as if date of death was unknown. Death was treated as any other
           dh[mi][i]=1; /* At least one step */          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
     }          to consider that at each interview the state was recorded
   }          (healthy, disable or death) and IMaCh was corrected; but when we
   jmean=sum/k;          introduced the exact date of death then we should have modified
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);          the contribution of an exact death to the likelihood. This new
  }          contribution is smaller and very dependent of the step unit
 /*********** Tricode ****************************/          stepm. It is no more the probability to die between last interview
 void tricode(int *Tvar, int **nbcode, int imx)          and month of death but the probability to survive from last
 {          interview up to one month before death multiplied by the
   int Ndum[20],ij=1, k, j, i;          probability to die within a month. Thanks to Chris
   int cptcode=0;          Jackson for correcting this bug.  Former versions increased
   cptcoveff=0;          mortality artificially. The bad side is that we add another loop
            which slows down the processing. The difference can be up to 10%
   for (k=0; k<19; k++) Ndum[k]=0;          lower mortality.
   for (k=1; k<=7; k++) ncodemax[k]=0;            */
             lli=log(out[s1][s2] - savm[s1][s2]);
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {  
     for (i=1; i<=imx; i++) {  
       ij=(int)(covar[Tvar[j]][i]);          } else if  (s2==-2) {
       Ndum[ij]++;            for (j=1,survp=0. ; j<=nlstate; j++) 
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
       if (ij > cptcode) cptcode=ij;            /*survp += out[s1][j]; */
     }            lli= log(survp);
           }
     for (i=0; i<=cptcode; i++) {          
       if(Ndum[i]!=0) ncodemax[j]++;          else if  (s2==-4) { 
     }            for (j=3,survp=0. ; j<=nlstate; j++)  
     ij=1;              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
             lli= log(survp); 
           } 
     for (i=1; i<=ncodemax[j]; i++) {  
       for (k=0; k<=19; k++) {          else if  (s2==-5) { 
         if (Ndum[k] != 0) {            for (j=1,survp=0. ; j<=2; j++)  
           nbcode[Tvar[j]][ij]=k;              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
                      lli= log(survp); 
           ij++;          } 
         }          
         if (ij > ncodemax[j]) break;          else{
       }              lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
     }            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
   }            } 
           /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
  for (k=0; k<19; k++) Ndum[k]=0;          /*if(lli ==000.0)*/
           /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
  for (i=1; i<=ncovmodel-2; i++) {          ipmx +=1;
       ij=Tvar[i];          sw += weight[i];
       Ndum[ij]++;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     }        } /* end of wave */
       } /* end of individual */
  ij=1;    }  else if(mle==2){
  for (i=1; i<=10; i++) {      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
    if((Ndum[i]!=0) && (i<=ncovcol)){        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
      Tvaraff[ij]=i;        for(mi=1; mi<= wav[i]-1; mi++){
      ij++;          for (ii=1;ii<=nlstate+ndeath;ii++)
    }            for (j=1;j<=nlstate+ndeath;j++){
  }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                savm[ii][j]=(ii==j ? 1.0 : 0.0);
     cptcoveff=ij-1;            }
 }          for(d=0; d<=dh[mi][i]; d++){
             newm=savm;
 /*********** Health Expectancies ****************/            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
 {            }
   /* Health expectancies */            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   int i, j, nhstepm, hstepm, h, nstepm;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   double age, agelim, hf;            savm=oldm;
   double ***p3mat;            oldm=newm;
            } /* end mult */
   fprintf(ficreseij,"# Health expectancies\n");        
   fprintf(ficreseij,"# Age");          s1=s[mw[mi][i]][i];
   for(i=1; i<=nlstate;i++)          s2=s[mw[mi+1][i]][i];
     for(j=1; j<=nlstate;j++)          bbh=(double)bh[mi][i]/(double)stepm; 
       fprintf(ficreseij," %1d-%1d",i,j);          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
   fprintf(ficreseij,"\n");          ipmx +=1;
           sw += weight[i];
   if(estepm < stepm){          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     printf ("Problem %d lower than %d\n",estepm, stepm);        } /* end of wave */
   }      } /* end of individual */
   else  hstepm=estepm;      }  else if(mle==3){  /* exponential inter-extrapolation */
   /* We compute the life expectancy from trapezoids spaced every estepm months      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
    * This is mainly to measure the difference between two models: for example        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
    * if stepm=24 months pijx are given only every 2 years and by summing them        for(mi=1; mi<= wav[i]-1; mi++){
    * we are calculating an estimate of the Life Expectancy assuming a linear          for (ii=1;ii<=nlstate+ndeath;ii++)
    * progression inbetween and thus overestimating or underestimating according            for (j=1;j<=nlstate+ndeath;j++){
    * to the curvature of the survival function. If, for the same date, we              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
    * estimate the model with stepm=1 month, we can keep estepm to 24 months              savm[ii][j]=(ii==j ? 1.0 : 0.0);
    * to compare the new estimate of Life expectancy with the same linear            }
    * hypothesis. A more precise result, taking into account a more precise          for(d=0; d<dh[mi][i]; d++){
    * curvature will be obtained if estepm is as small as stepm. */            newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   /* For example we decided to compute the life expectancy with the smallest unit */            for (kk=1; kk<=cptcovage;kk++) {
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
      nhstepm is the number of hstepm from age to agelim            }
      nstepm is the number of stepm from age to agelin.            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
      Look at hpijx to understand the reason of that which relies in memory size                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
      and note for a fixed period like estepm months */            savm=oldm;
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the            oldm=newm;
      survival function given by stepm (the optimization length). Unfortunately it          } /* end mult */
      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          s1=s[mw[mi][i]][i];
      results. So we changed our mind and took the option of the best precision.          s2=s[mw[mi+1][i]][i];
   */          bbh=(double)bh[mi][i]/(double)stepm; 
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */          lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
           ipmx +=1;
   agelim=AGESUP;          sw += weight[i];
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     /* nhstepm age range expressed in number of stepm */        } /* end of wave */
     nstepm=(int) rint((agelim-age)*YEARM/stepm);      } /* end of individual */
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */    }else if (mle==4){  /* ml=4 no inter-extrapolation */
     /* if (stepm >= YEARM) hstepm=1;*/      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        for(mi=1; mi<= wav[i]-1; mi++){
     /* Computed by stepm unit matrices, product of hstepm matrices, stored          for (ii=1;ii<=nlstate+ndeath;ii++)
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */            for (j=1;j<=nlstate+ndeath;j++){
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);                oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                savm[ii][j]=(ii==j ? 1.0 : 0.0);
     /*for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++) printf("%f %.5f\n", age*12+h, p3mat[1][1][h]);*/            }
           for(d=0; d<dh[mi][i]; d++){
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */            newm=savm;
     for(i=1; i<=nlstate;i++)            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       for(j=1; j<=nlstate;j++)            for (kk=1; kk<=cptcovage;kk++) {
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;            }
           /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/          
         }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     fprintf(ficreseij,"%3.0f",age );                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     for(i=1; i<=nlstate;i++)            savm=oldm;
       for(j=1; j<=nlstate;j++){            oldm=newm;
         fprintf(ficreseij," %9.4f", eij[i][j][(int)age]);          } /* end mult */
       }        
     fprintf(ficreseij,"\n");          s1=s[mw[mi][i]][i];
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          s2=s[mw[mi+1][i]][i];
   }          if( s2 > nlstate){ 
 }            lli=log(out[s1][s2] - savm[s1][s2]);
           }else{
 /************ Variance ******************/            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
 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, int estepm)          }
 {          ipmx +=1;
   /* Variance of health expectancies */          sw += weight[i];
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   double **newm;  /*      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]); */
   double **dnewm,**doldm;        } /* end of wave */
   int i, j, nhstepm, hstepm, h, nstepm ;      } /* end of individual */
   int k, cptcode;    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
   double *xp;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   double **gp, **gm;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   double ***gradg, ***trgradg;        for(mi=1; mi<= wav[i]-1; mi++){
   double ***p3mat;          for (ii=1;ii<=nlstate+ndeath;ii++)
   double age,agelim, hf;            for (j=1;j<=nlstate+ndeath;j++){
   int theta;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               savm[ii][j]=(ii==j ? 1.0 : 0.0);
    fprintf(ficresvij,"# Covariances of life expectancies\n");            }
   fprintf(ficresvij,"# Age");          for(d=0; d<dh[mi][i]; d++){
   for(i=1; i<=nlstate;i++)            newm=savm;
     for(j=1; j<=nlstate;j++)            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);            for (kk=1; kk<=cptcovage;kk++) {
   fprintf(ficresvij,"\n");              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             }
   xp=vector(1,npar);          
   dnewm=matrix(1,nlstate,1,npar);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   doldm=matrix(1,nlstate,1,nlstate);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
              savm=oldm;
   if(estepm < stepm){            oldm=newm;
     printf ("Problem %d lower than %d\n",estepm, stepm);          } /* end mult */
   }        
   else  hstepm=estepm;            s1=s[mw[mi][i]][i];
   /* For example we decided to compute the life expectancy with the smallest unit */          s2=s[mw[mi+1][i]][i];
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
      nhstepm is the number of hstepm from age to agelim          ipmx +=1;
      nstepm is the number of stepm from age to agelin.          sw += weight[i];
      Look at hpijx to understand the reason of that which relies in memory size          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
      and note for a fixed period like k years */          /*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]);*/
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the        } /* end of wave */
      survival function given by stepm (the optimization length). Unfortunately it      } /* end of individual */
      means that if the survival funtion is printed only each two years of age and if    } /* End of if */
      you sum them up and add 1 year (area under the trapezoids) you won't get the same    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
      results. So we changed our mind and took the option of the best precision.    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   */    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */    return -l;
   agelim = AGESUP;  }
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */  
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */  /*************** log-likelihood *************/
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */  double funcone( double *x)
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  {
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);    /* Same as likeli but slower because of a lot of printf and if */
     gp=matrix(0,nhstepm,1,nlstate);    int i, ii, j, k, mi, d, kk;
     gm=matrix(0,nhstepm,1,nlstate);    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
     double **out;
     for(theta=1; theta <=npar; theta++){    double lli; /* Individual log likelihood */
       for(i=1; i<=npar; i++){ /* Computes gradient */    double llt;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    int s1, s2;
       }    double bbh, survp;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      /*extern weight */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    /* We are differentiating ll according to initial status */
     /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
       if (popbased==1) {    /*for(i=1;i<imx;i++) 
         for(i=1; i<=nlstate;i++)      printf(" %d\n",s[4][i]);
           prlim[i][i]=probs[(int)age][i][ij];    */
       }    cov[1]=1.;
    
       for(j=1; j<= nlstate; j++){    for(k=1; k<=nlstate; k++) ll[k]=0.;
         for(h=0; h<=nhstepm; h++){  
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         }      for(mi=1; mi<= wav[i]-1; mi++){
       }        for (ii=1;ii<=nlstate+ndeath;ii++)
              for (j=1;j<=nlstate+ndeath;j++){
       for(i=1; i<=npar; i++) /* Computes gradient */            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         xp[i] = x[i] - (i==theta ?delti[theta]:0);            savm[ii][j]=(ii==j ? 1.0 : 0.0);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        for(d=0; d<dh[mi][i]; d++){
            newm=savm;
       if (popbased==1) {          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         for(i=1; i<=nlstate;i++)          for (kk=1; kk<=cptcovage;kk++) {
           prlim[i][i]=probs[(int)age][i][ij];            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;
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)          oldm=newm;
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];        } /* end mult */
         }        
       }        s1=s[mw[mi][i]][i];
         s2=s[mw[mi+1][i]][i];
       for(j=1; j<= nlstate; j++)        bbh=(double)bh[mi][i]/(double)stepm; 
         for(h=0; h<=nhstepm; h++){        /* bias is positive if real duration
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];         * is higher than the multiple of stepm and negative otherwise.
         }         */
     } /* End theta */        if( s2 > nlstate && (mle <5) ){  /* Jackson */
           lli=log(out[s1][s2] - savm[s1][s2]);
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);        } else if  (s2==-2) {
           for (j=1,survp=0. ; j<=nlstate; j++) 
     for(h=0; h<=nhstepm; h++)            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
       for(j=1; j<=nlstate;j++)          lli= log(survp);
         for(theta=1; theta <=npar; theta++)        }else if (mle==1){
           trgradg[h][j][theta]=gradg[h][theta][j];          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
         } else if(mle==2){
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */          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(i=1;i<=nlstate;i++)        } else if(mle==3){  /* exponential inter-extrapolation */
       for(j=1;j<=nlstate;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 */
         vareij[i][j][(int)age] =0.;        } else if (mle==4){  /* mle=4 no inter-extrapolation */
           lli=log(out[s1][s2]); /* Original formula */
     for(h=0;h<=nhstepm;h++){        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
       for(k=0;k<=nhstepm;k++){          lli=log(out[s1][s2]); /* Original formula */
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);        } /* End of if */
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);        ipmx +=1;
         for(i=1;i<=nlstate;i++)        sw += weight[i];
           for(j=1;j<=nlstate;j++)        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;        /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
       }        if(globpr){
     }          fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
    %11.6f %11.6f %11.6f ", \
     fprintf(ficresvij,"%.0f ",age );                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
     for(i=1; i<=nlstate;i++)                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
       for(j=1; j<=nlstate;j++){          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);            llt +=ll[k]*gipmx/gsw;
       }            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
     fprintf(ficresvij,"\n");          }
     free_matrix(gp,0,nhstepm,1,nlstate);          fprintf(ficresilk," %10.6f\n", -llt);
     free_matrix(gm,0,nhstepm,1,nlstate);        }
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);      } /* end of wave */
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);    } /* end of individual */
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   } /* End age */    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
      l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
   free_vector(xp,1,npar);    if(globpr==0){ /* First time we count the contributions and weights */
   free_matrix(doldm,1,nlstate,1,npar);      gipmx=ipmx;
   free_matrix(dnewm,1,nlstate,1,nlstate);      gsw=sw;
     }
 }    return -l;
   }
 /************ Variance of prevlim ******************/  
 void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)  
 {  /*************** function likelione ***********/
   /* Variance of prevalence limit */  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/  {
   double **newm;    /* This routine should help understanding what is done with 
   double **dnewm,**doldm;       the selection of individuals/waves and
   int i, j, nhstepm, hstepm;       to check the exact contribution to the likelihood.
   int k, cptcode;       Plotting could be done.
   double *xp;     */
   double *gp, *gm;    int k;
   double **gradg, **trgradg;  
   double age,agelim;    if(*globpri !=0){ /* Just counts and sums, no printings */
   int theta;      strcpy(fileresilk,"ilk"); 
          strcat(fileresilk,fileres);
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
   fprintf(ficresvpl,"# Age");        printf("Problem with resultfile: %s\n", fileresilk);
   for(i=1; i<=nlstate;i++)        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
       fprintf(ficresvpl," %1d-%1d",i,i);      }
   fprintf(ficresvpl,"\n");      fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
       fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
   xp=vector(1,npar);      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
   dnewm=matrix(1,nlstate,1,npar);      for(k=1; k<=nlstate; k++) 
   doldm=matrix(1,nlstate,1,nlstate);        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
        fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
   hstepm=1*YEARM; /* Every year of age */    }
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */  
   agelim = AGESUP;    *fretone=(*funcone)(p);
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    if(*globpri !=0){
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      fclose(ficresilk);
     if (stepm >= YEARM) hstepm=1;      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      fflush(fichtm); 
     gradg=matrix(1,npar,1,nlstate);    } 
     gp=vector(1,nlstate);    return;
     gm=vector(1,nlstate);  }
   
     for(theta=1; theta <=npar; theta++){  
       for(i=1; i<=npar; i++){ /* Computes gradient */  /*********** Maximum Likelihood Estimation ***************/
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  
       }  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  {
       for(i=1;i<=nlstate;i++)    int i,j, iter;
         gp[i] = prlim[i][i];    double **xi;
        double fret;
       for(i=1; i<=npar; i++) /* Computes gradient */    double fretone; /* Only one call to likelihood */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    /*  char filerespow[FILENAMELENGTH];*/
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    xi=matrix(1,npar,1,npar);
       for(i=1;i<=nlstate;i++)    for (i=1;i<=npar;i++)
         gm[i] = prlim[i][i];      for (j=1;j<=npar;j++)
         xi[i][j]=(i==j ? 1.0 : 0.0);
       for(i=1;i<=nlstate;i++)    printf("Powell\n");  fprintf(ficlog,"Powell\n");
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];    strcpy(filerespow,"pow"); 
     } /* End theta */    strcat(filerespow,fileres);
     if((ficrespow=fopen(filerespow,"w"))==NULL) {
     trgradg =matrix(1,nlstate,1,npar);      printf("Problem with resultfile: %s\n", filerespow);
       fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
     for(j=1; j<=nlstate;j++)    }
       for(theta=1; theta <=npar; theta++)    fprintf(ficrespow,"# Powell\n# iter -2*LL");
         trgradg[j][theta]=gradg[theta][j];    for (i=1;i<=nlstate;i++)
       for(j=1;j<=nlstate+ndeath;j++)
     for(i=1;i<=nlstate;i++)        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       varpl[i][(int)age] =0.;    fprintf(ficrespow,"\n");
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);  
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);    powell(p,xi,npar,ftol,&iter,&fret,func);
     for(i=1;i<=nlstate;i++)  
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */    free_matrix(xi,1,npar,1,npar);
     fclose(ficrespow);
     fprintf(ficresvpl,"%.0f ",age );    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
     for(i=1; i<=nlstate;i++)    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     fprintf(ficresvpl,"\n");  
     free_vector(gp,1,nlstate);  }
     free_vector(gm,1,nlstate);  
     free_matrix(gradg,1,npar,1,nlstate);  /**** Computes Hessian and covariance matrix ***/
     free_matrix(trgradg,1,nlstate,1,npar);  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
   } /* End age */  {
     double  **a,**y,*x,pd;
   free_vector(xp,1,npar);    double **hess;
   free_matrix(doldm,1,nlstate,1,npar);    int i, j,jk;
   free_matrix(dnewm,1,nlstate,1,nlstate);    int *indx;
   
 }    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
     double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
 /************ Variance of one-step probabilities  ******************/    void lubksb(double **a, int npar, int *indx, double b[]) ;
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)    void ludcmp(double **a, int npar, int *indx, double *d) ;
 {    double gompertz(double p[]);
   int i, j, i1, k1, j1, z1;    hess=matrix(1,npar,1,npar);
   int k=0, cptcode;  
   double **dnewm,**doldm;    printf("\nCalculation of the hessian matrix. Wait...\n");
   double *xp;    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
   double *gp, *gm;    for (i=1;i<=npar;i++){
   double **gradg, **trgradg;      printf("%d",i);fflush(stdout);
   double age,agelim, cov[NCOVMAX];      fprintf(ficlog,"%d",i);fflush(ficlog);
   int theta;     
   char fileresprob[FILENAMELENGTH];       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
       
   strcpy(fileresprob,"prob");      /*  printf(" %f ",p[i]);
   strcat(fileresprob,fileres);          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {    }
     printf("Problem with resultfile: %s\n", fileresprob);    
   }    for (i=1;i<=npar;i++) {
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);      for (j=1;j<=npar;j++)  {
          if (j>i) { 
           printf(".%d%d",i,j);fflush(stdout);
   xp=vector(1,npar);          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);          hess[i][j]=hessij(p,delti,i,j,func,npar);
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));          
            hess[j][i]=hess[i][j];    
   cov[1]=1;          /*printf(" %lf ",hess[i][j]);*/
   j=cptcoveff;        }
   if (cptcovn<1) {j=1;ncodemax[1]=1;}      }
   j1=0;    }
   for(k1=1; k1<=1;k1++){    printf("\n");
     for(i1=1; i1<=ncodemax[k1];i1++){    fprintf(ficlog,"\n");
     j1++;  
     printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
     if  (cptcovn>0) {    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
       fprintf(ficresprob, "\n#********** Variable ");    
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    a=matrix(1,npar,1,npar);
       fprintf(ficresprob, "**********\n#");    y=matrix(1,npar,1,npar);
     }    x=vector(1,npar);
        indx=ivector(1,npar);
       for (age=bage; age<=fage; age ++){    for (i=1;i<=npar;i++)
         cov[2]=age;      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
         for (k=1; k<=cptcovn;k++) {    ludcmp(a,npar,indx,&pd);
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];  
              for (j=1;j<=npar;j++) {
         }      for (i=1;i<=npar;i++) x[i]=0;
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];      x[j]=1;
         for (k=1; k<=cptcovprod;k++)      lubksb(a,npar,indx,x);
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];      for (i=1;i<=npar;i++){ 
                matcov[i][j]=x[i];
         gradg=matrix(1,npar,1,9);      }
         trgradg=matrix(1,9,1,npar);    }
         gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));  
         gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));    printf("\n#Hessian matrix#\n");
        fprintf(ficlog,"\n#Hessian matrix#\n");
         for(theta=1; theta <=npar; theta++){    for (i=1;i<=npar;i++) { 
           for(i=1; i<=npar; i++)      for (j=1;j<=npar;j++) { 
             xp[i] = x[i] + (i==theta ?delti[theta]:0);        printf("%.3e ",hess[i][j]);
                  fprintf(ficlog,"%.3e ",hess[i][j]);
           pmij(pmmij,cov,ncovmodel,xp,nlstate);      }
                printf("\n");
           k=0;      fprintf(ficlog,"\n");
           for(i=1; i<= (nlstate+ndeath); i++){    }
             for(j=1; j<=(nlstate+ndeath);j++){  
               k=k+1;    /* Recompute Inverse */
               gp[k]=pmmij[i][j];    for (i=1;i<=npar;i++)
             }      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
           }    ludcmp(a,npar,indx,&pd);
            
           for(i=1; i<=npar; i++)    /*  printf("\n#Hessian matrix recomputed#\n");
             xp[i] = x[i] - (i==theta ?delti[theta]:0);  
        for (j=1;j<=npar;j++) {
           pmij(pmmij,cov,ncovmodel,xp,nlstate);      for (i=1;i<=npar;i++) x[i]=0;
           k=0;      x[j]=1;
           for(i=1; i<=(nlstate+ndeath); i++){      lubksb(a,npar,indx,x);
             for(j=1; j<=(nlstate+ndeath);j++){      for (i=1;i<=npar;i++){ 
               k=k+1;        y[i][j]=x[i];
               gm[k]=pmmij[i][j];        printf("%.3e ",y[i][j]);
             }        fprintf(ficlog,"%.3e ",y[i][j]);
           }      }
            printf("\n");
           for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)      fprintf(ficlog,"\n");
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];      }
         }    */
   
         for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)    free_matrix(a,1,npar,1,npar);
           for(theta=1; theta <=npar; theta++)    free_matrix(y,1,npar,1,npar);
             trgradg[j][theta]=gradg[theta][j];    free_vector(x,1,npar);
            free_ivector(indx,1,npar);
         matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);    free_matrix(hess,1,npar,1,npar);
         matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);  
          
         pmij(pmmij,cov,ncovmodel,x,nlstate);  }
          
         k=0;  /*************** hessian matrix ****************/
         for(i=1; i<=(nlstate+ndeath); i++){  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
           for(j=1; j<=(nlstate+ndeath);j++){  {
             k=k+1;    int i;
             gm[k]=pmmij[i][j];    int l=1, lmax=20;
           }    double k1,k2;
         }    double p2[MAXPARM+1]; /* identical to x */
          double res;
      /*printf("\n%d ",(int)age);    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){    double fx;
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));    int k=0,kmax=10;
      }*/    double l1;
   
         fprintf(ficresprob,"\n%d ",(int)age);    fx=func(x);
     for (i=1;i<=npar;i++) p2[i]=x[i];
         for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++)    for(l=0 ; l <=lmax; l++){
           fprintf(ficresprob,"%.3e (%.3e) ",gm[i],doldm[i][i]);      l1=pow(10,l);
        delts=delt;
       }      for(k=1 ; k <kmax; k=k+1){
     }        delt = delta*(l1*k);
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));        p2[theta]=x[theta] +delt;
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));        k1=func(p2)-fx;
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);        p2[theta]=x[theta]-delt;
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);        k2=func(p2)-fx;
   }        /*res= (k1-2.0*fx+k2)/delt/delt; */
   free_vector(xp,1,npar);        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
   fclose(ficresprob);        
    #ifdef DEBUGHESS
 }        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
         fprintf(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);
 /******************* Printing html file ***********/  #endif
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
  int lastpass, int stepm, int weightopt, char model[],\        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
  int imx,int jmin, int jmax, double jmeanint,char optionfile[], \          k=kmax;
  char optionfilehtm[],char rfileres[], char optionfilegnuplot[],\        }
  char version[], int popforecast, int estepm ){        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
   int jj1, k1, i1, cpt;          k=kmax; l=lmax*10.;
   FILE *fichtm;        }
   /*char optionfilehtm[FILENAMELENGTH];*/        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
           delts=delt;
   strcpy(optionfilehtm,optionfile);        }
   strcat(optionfilehtm,".htm");      }
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {    }
     printf("Problem with %s \n",optionfilehtm), exit(0);    delti[theta]=delts;
   }    return res; 
     
  fprintf(fichtm,"<body> <font size=\"2\">%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  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
 Total number of observations=%d <br>\n  {
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n    int i;
 <hr  size=\"2\" color=\"#EC5E5E\">    int l=1, l1, lmax=20;
  <ul><li>Outputs files<br>\n    double k1,k2,k3,k4,res,fx;
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n    double p2[MAXPARM+1];
  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n    int k;
  - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n  
  - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>\n    fx=func(x);
  - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>\n    for (k=1; k<=2; k++) {
  - Life expectancies by age and initial health status (estepm=%2d months): <a href=\"e%s\">e%s</a> <br>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot,fileres,fileres,fileres,fileres,fileres,fileres,estepm,fileres,fileres);      for (i=1;i<=npar;i++) p2[i]=x[i];
       p2[thetai]=x[thetai]+delti[thetai]/k;
  fprintf(fichtm,"\n      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
  - Parameter file with estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>\n      k1=func(p2)-fx;
  - Variances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n    
  - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>\n      p2[thetai]=x[thetai]+delti[thetai]/k;
  - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       k2=func(p2)-fx;
  if(popforecast==1) fprintf(fichtm,"\n    
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n      p2[thetai]=x[thetai]-delti[thetai]/k;
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
         <br>",fileres,fileres,fileres,fileres);      k3=func(p2)-fx;
  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);      p2[thetai]=x[thetai]-delti[thetai]/k;
 fprintf(fichtm," <li>Graphs</li><p>");      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       k4=func(p2)-fx;
  m=cptcoveff;      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}  #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);
  jj1=0;      fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
  for(k1=1; k1<=m;k1++){  #endif
    for(i1=1; i1<=ncodemax[k1];i1++){    }
        jj1++;    return res;
        if (cptcovn > 0) {  }
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");  
          for (cpt=1; cpt<=cptcoveff;cpt++)  /************** Inverse of matrix **************/
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);  void ludcmp(double **a, int n, int *indx, double *d) 
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");  { 
        }    int i,imax,j,k; 
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>    double big,dum,sum,temp; 
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);        double *vv; 
        for(cpt=1; cpt<nlstate;cpt++){   
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>    vv=vector(1,n); 
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    *d=1.0; 
        }    for (i=1;i<=n;i++) { 
     for(cpt=1; cpt<=nlstate;cpt++) {      big=0.0; 
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident      for (j=1;j<=n;j++) 
 interval) in state (%d): v%s%d%d.gif <br>        if ((temp=fabs(a[i][j])) > big) big=temp; 
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);        if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
      }      vv[i]=1.0/big; 
      for(cpt=1; cpt<=nlstate;cpt++) {    } 
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>    for (j=1;j<=n;j++) { 
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);      for (i=1;i<j;i++) { 
      }        sum=a[i][j]; 
      fprintf(fichtm,"\n<br>- Total life expectancy by age and        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
 health expectancies in states (1) and (2): e%s%d.gif<br>        a[i][j]=sum; 
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);      } 
 fprintf(fichtm,"\n</body>");      big=0.0; 
    }      for (i=j;i<=n;i++) { 
    }        sum=a[i][j]; 
 fclose(fichtm);        for (k=1;k<j;k++) 
 }          sum -= a[i][k]*a[k][j]; 
         a[i][j]=sum; 
 /******************* Gnuplot file **************/        if ( (dum=vv[i]*fabs(sum)) >= big) { 
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){          big=dum; 
           imax=i; 
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;        } 
       } 
   strcpy(optionfilegnuplot,optionfilefiname);      if (j != imax) { 
   strcat(optionfilegnuplot,".gp.txt");        for (k=1;k<=n;k++) { 
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {          dum=a[imax][k]; 
     printf("Problem with file %s",optionfilegnuplot);          a[imax][k]=a[j][k]; 
   }          a[j][k]=dum; 
         } 
 #ifdef windows        *d = -(*d); 
     fprintf(ficgp,"cd \"%s\" \n",pathc);        vv[imax]=vv[j]; 
 #endif      } 
 m=pow(2,cptcoveff);      indx[j]=imax; 
        if (a[j][j] == 0.0) a[j][j]=TINY; 
  /* 1eme*/      if (j != n) { 
   for (cpt=1; cpt<= nlstate ; cpt ++) {        dum=1.0/(a[j][j]); 
    for (k1=1; k1<= m ; k1 ++) {        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
       } 
 #ifdef windows    } 
     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);    free_vector(vv,1,n);  /* Doesn't work */
 #endif  ;
 #ifdef unix  } 
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);  
 #endif  void lubksb(double **a, int n, int *indx, double b[]) 
   { 
 for (i=1; i<= nlstate ; i ++) {    int i,ii=0,ip,j; 
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    double sum; 
   else fprintf(ficgp," \%%*lf (\%%*lf)");   
 }    for (i=1;i<=n;i++) { 
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);      ip=indx[i]; 
     for (i=1; i<= nlstate ; i ++) {      sum=b[ip]; 
   if (i==cpt) 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]; 
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);      else if (sum) ii=i; 
      for (i=1; i<= nlstate ; i ++) {      b[i]=sum; 
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    } 
   else fprintf(ficgp," \%%*lf (\%%*lf)");    for (i=n;i>=1;i--) { 
 }        sum=b[i]; 
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
 #ifdef unix      b[i]=sum/a[i][i]; 
 fprintf(ficgp,"\nset ter gif small size 400,300");    } 
 #endif  } 
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);  
    }  void pstamp(FILE *fichier)
   }  {
   /*2 eme*/    fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
   }
   for (k1=1; k1<= m ; k1 ++) {  
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",ageminpar,fage);  /************ 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[])
     for (i=1; i<= nlstate+1 ; i ++) {  {  /* Some frequencies */
       k=2*i;    
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);    int i, m, jk, k1,i1, j1, bool, z1,j;
       for (j=1; j<= nlstate+1 ; j ++) {    int first;
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    double ***freq; /* Frequencies */
   else fprintf(ficgp," \%%*lf (\%%*lf)");    double *pp, **prop;
 }      double pos,posprop, k2, dateintsum=0,k2cpt=0;
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");    char fileresp[FILENAMELENGTH];
       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);    pp=vector(1,nlstate);
       for (j=1; j<= nlstate+1 ; j ++) {    prop=matrix(1,nlstate,iagemin,iagemax+3);
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    strcpy(fileresp,"p");
         else fprintf(ficgp," \%%*lf (\%%*lf)");    strcat(fileresp,fileres);
 }      if((ficresp=fopen(fileresp,"w"))==NULL) {
       fprintf(ficgp,"\" t\"\" w l 0,");      printf("Problem with prevalence resultfile: %s\n", fileresp);
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
       for (j=1; j<= nlstate+1 ; j ++) {      exit(0);
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    }
   else fprintf(ficgp," \%%*lf (\%%*lf)");    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
 }      j1=0;
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");    
       else fprintf(ficgp,"\" t\"\" w l 0,");    j=cptcoveff;
     }    if (cptcovn<1) {j=1;ncodemax[1]=1;}
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);  
   }    first=1;
    
   /*3eme*/    for(k1=1; k1<=j;k1++){
       for(i1=1; i1<=ncodemax[k1];i1++){
   for (k1=1; k1<= m ; k1 ++) {        j1++;
     for (cpt=1; cpt<= nlstate ; cpt ++) {        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
       k=2+nlstate*(cpt-1);          scanf("%d", i);*/
       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",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);        for (i=-5; i<=nlstate+ndeath; i++)  
       for (i=1; i< nlstate ; i ++) {          for (jk=-5; jk<=nlstate+ndeath; jk++)  
         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);            for(m=iagemin; m <= iagemax+3; m++)
       }              freq[i][jk][m]=0;
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);  
     }      for (i=1; i<=nlstate; i++)  
     }        for(m=iagemin; m <= iagemax+3; m++)
            prop[i][m]=0;
   /* CV preval stat */        
     for (k1=1; k1<= m ; k1 ++) {        dateintsum=0;
     for (cpt=1; cpt<nlstate ; cpt ++) {        k2cpt=0;
       k=3;        for (i=1; i<=imx; i++) {
       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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);          bool=1;
           if  (cptcovn>0) {
       for (i=1; i< nlstate ; i ++)            for (z1=1; z1<=cptcoveff; z1++) 
         fprintf(ficgp,"+$%d",k+i+1);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);                bool=0;
                }
       l=3+(nlstate+ndeath)*cpt;          if (bool==1){
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);            for(m=firstpass; m<=lastpass; m++){
       for (i=1; i< nlstate ; i ++) {              k2=anint[m][i]+(mint[m][i]/12.);
         l=3+(nlstate+ndeath)*cpt;              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
         fprintf(ficgp,"+$%d",l+i+1);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
       }                if(agev[m][i]==1) agev[m][i]=iagemax+2;
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);                  if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);                if (m<lastpass) {
     }                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
   }                    freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
                  }
   /* proba elementaires */                
    for(i=1,jk=1; i <=nlstate; i++){                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
     for(k=1; k <=(nlstate+ndeath); k++){                  dateintsum=dateintsum+k2;
       if (k != i) {                  k2cpt++;
         for(j=1; j <=ncovmodel; j++){                }
                        /*}*/
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);            }
           jk++;          }
           fprintf(ficgp,"\n");        }
         }         
       }        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
     }        pstamp(ficresp);
     }        if  (cptcovn>0) {
           fprintf(ficresp, "\n#********** Variable "); 
     for(jk=1; jk <=m; jk++) {          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);          fprintf(ficresp, "**********\n#");
    i=1;        }
    for(k2=1; k2<=nlstate; k2++) {        for(i=1; i<=nlstate;i++) 
      k3=i;          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
      for(k=1; k<=(nlstate+ndeath); k++) {        fprintf(ficresp, "\n");
        if (k != k2){        
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);        for(i=iagemin; i <= iagemax+3; i++){
 ij=1;          if(i==iagemax+3){
         for(j=3; j <=ncovmodel; j++) {            fprintf(ficlog,"Total");
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {          }else{
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);            if(first==1){
             ij++;              first=0;
           }              printf("See log file for details...\n");
           else            }
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);            fprintf(ficlog,"Age %d", i);
         }          }
           fprintf(ficgp,")/(1");          for(jk=1; jk <=nlstate ; jk++){
                    for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
         for(k1=1; k1 <=nlstate; k1++){                pp[jk] += freq[jk][m][i]; 
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);          }
 ij=1;          for(jk=1; jk <=nlstate ; jk++){
           for(j=3; j <=ncovmodel; j++){            for(m=-1, pos=0; m <=0 ; m++)
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {              pos += freq[jk][m][i];
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);            if(pp[jk]>=1.e-10){
             ij++;              if(first==1){
           }                printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
           else              }
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
           }            }else{
           fprintf(ficgp,")");              if(first==1)
         }                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");            }
         i=i+ncovmodel;          }
        }  
      }          for(jk=1; jk <=nlstate ; jk++){
    }            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);              pp[jk] += freq[jk][m][i];
    }          }       
              for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
   fclose(ficgp);            pos += pp[jk];
 }  /* end gnuplot */            posprop += prop[jk][i];
           }
           for(jk=1; jk <=nlstate ; jk++){
 /*************** Moving average **************/            if(pos>=1.e-5){
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){              if(first==1)
                 printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   int i, cpt, cptcod;              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)            }else{
       for (i=1; i<=nlstate;i++)              if(first==1)
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
           mobaverage[(int)agedeb][i][cptcod]=0.;              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
                }
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){            if( i <= iagemax){
       for (i=1; i<=nlstate;i++){              if(pos>=1.e-5){
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
           for (cpt=0;cpt<=4;cpt++){                /*probs[i][jk][j1]= pp[jk]/pos;*/
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
           }              }
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;              else
         }                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
       }            }
     }          }
              
 }          for(jk=-1; jk <=nlstate+ndeath; jk++)
             for(m=-1; m <=nlstate+ndeath; m++)
               if(freq[jk][m][i] !=0 ) {
 /************** Forecasting ******************/              if(first==1)
 prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
                  fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;              }
   int *popage;          if(i <= iagemax)
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;            fprintf(ficresp,"\n");
   double *popeffectif,*popcount;          if(first==1)
   double ***p3mat;            printf("Others in log...\n");
   char fileresf[FILENAMELENGTH];          fprintf(ficlog,"\n");
         }
  agelim=AGESUP;      }
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;    }
     dateintmean=dateintsum/k2cpt; 
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);   
      fclose(ficresp);
      free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
   strcpy(fileresf,"f");    free_vector(pp,1,nlstate);
   strcat(fileresf,fileres);    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
   if((ficresf=fopen(fileresf,"w"))==NULL) {    /* End of Freq */
     printf("Problem with forecast resultfile: %s\n", fileresf);  }
   }  
   printf("Computing forecasting: result on file '%s' \n", fileresf);  /************ Prevalence ********************/
   void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
   if (cptcoveff==0) ncodemax[cptcoveff]=1;  {  
     /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
   if (mobilav==1) {       in each health status at the date of interview (if between dateprev1 and dateprev2).
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);       We still use firstpass and lastpass as another selection.
     movingaverage(agedeb, fage, ageminpar, mobaverage);    */
   }   
     int i, m, jk, k1, i1, j1, bool, z1,j;
   stepsize=(int) (stepm+YEARM-1)/YEARM;    double ***freq; /* Frequencies */
   if (stepm<=12) stepsize=1;    double *pp, **prop;
      double pos,posprop; 
   agelim=AGESUP;    double  y2; /* in fractional years */
      int iagemin, iagemax;
   hstepm=1;  
   hstepm=hstepm/stepm;    iagemin= (int) agemin;
   yp1=modf(dateintmean,&yp);    iagemax= (int) agemax;
   anprojmean=yp;    /*pp=vector(1,nlstate);*/
   yp2=modf((yp1*12),&yp);    prop=matrix(1,nlstate,iagemin,iagemax+3); 
   mprojmean=yp;    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
   yp1=modf((yp2*30.5),&yp);    j1=0;
   jprojmean=yp;    
   if(jprojmean==0) jprojmean=1;    j=cptcoveff;
   if(mprojmean==0) jprojmean=1;    if (cptcovn<1) {j=1;ncodemax[1]=1;}
      
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);    for(k1=1; k1<=j;k1++){
        for(i1=1; i1<=ncodemax[k1];i1++){
   for(cptcov=1;cptcov<=i2;cptcov++){        j1++;
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){        
       k=k+1;        for (i=1; i<=nlstate; i++)  
       fprintf(ficresf,"\n#******");          for(m=iagemin; m <= iagemax+3; m++)
       for(j=1;j<=cptcoveff;j++) {            prop[i][m]=0.0;
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);       
       }        for (i=1; i<=imx; i++) { /* Each individual */
       fprintf(ficresf,"******\n");          bool=1;
       fprintf(ficresf,"# StartingAge FinalAge");          if  (cptcovn>0) {
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);            for (z1=1; z1<=cptcoveff; z1++) 
                    if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
                      bool=0;
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {          } 
         fprintf(ficresf,"\n");          if (bool==1) { 
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);              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 */
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
           nhstepm = nhstepm/hstepm;                if(agev[m][i]==1) agev[m][i]=iagemax+2;
                          if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                if (s[m][i]>0 && s[m][i]<=nlstate) { 
           oldm=oldms;savm=savms;                  /*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]]);*/
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);                    prop[s[m][i]][(int)agev[m][i]] += weight[i];
                          prop[s[m][i]][iagemax+3] += weight[i]; 
           for (h=0; h<=nhstepm; h++){                } 
             if (h==(int) (calagedate+YEARM*cpt)) {              }
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);            } /* end selection of waves */
             }          }
             for(j=1; j<=nlstate+ndeath;j++) {        }
               kk1=0.;kk2=0;        for(i=iagemin; i <= iagemax+3; i++){  
               for(i=1; i<=nlstate;i++) {                        
                 if (mobilav==1)          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];            posprop += prop[jk][i]; 
                 else {          } 
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];  
                 }          for(jk=1; jk <=nlstate ; jk++){     
                            if( i <=  iagemax){ 
               }              if(posprop>=1.e-5){ 
               if (h==(int)(calagedate+12*cpt)){                probs[i][jk][j1]= prop[jk][i]/posprop;
                 fprintf(ficresf," %.3f", kk1);              } else
                                        printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\n",jk,i,j1,probs[i][jk][j1]);
               }            } 
             }          }/* end jk */ 
           }        }/* end i */ 
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      } /* end i1 */
         }    } /* end k1 */
       }    
     }    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
   }    /*free_vector(pp,1,nlstate);*/
            free_matrix(prop,1,nlstate, iagemin,iagemax+3);
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  }  /* End of prevalence */
   
   fclose(ficresf);  /************* Waves Concatenation ***************/
 }  
 /************** Forecasting ******************/  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)
 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){  {
      /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;       Death is a valid wave (if date is known).
   int *popage;       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
   double *popeffectif,*popcount;       and mw[mi+1][i]. dh depends on stepm.
   double ***p3mat,***tabpop,***tabpopprev;       */
   char filerespop[FILENAMELENGTH];  
     int i, mi, m;
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);       double sum=0., jmean=0.;*/
   agelim=AGESUP;    int first;
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;    int j, k=0,jk, ju, jl;
      double sum=0.;
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    first=0;
      jmin=1e+5;
      jmax=-1;
   strcpy(filerespop,"pop");    jmean=0.;
   strcat(filerespop,fileres);    for(i=1; i<=imx; i++){
   if((ficrespop=fopen(filerespop,"w"))==NULL) {      mi=0;
     printf("Problem with forecast resultfile: %s\n", filerespop);      m=firstpass;
   }      while(s[m][i] <= nlstate){
   printf("Computing forecasting: result on file '%s' \n", filerespop);        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
           mw[++mi][i]=m;
   if (cptcoveff==0) ncodemax[cptcoveff]=1;        if(m >=lastpass)
           break;
   if (mobilav==1) {        else
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          m++;
     movingaverage(agedeb, fage, ageminpar, mobaverage);      }/* end while */
   }      if (s[m][i] > nlstate){
         mi++;     /* Death is another wave */
   stepsize=(int) (stepm+YEARM-1)/YEARM;        /* if(mi==0)  never been interviewed correctly before death */
   if (stepm<=12) stepsize=1;           /* Only death is a correct wave */
          mw[mi][i]=m;
   agelim=AGESUP;      }
    
   hstepm=1;      wav[i]=mi;
   hstepm=hstepm/stepm;      if(mi==0){
          nbwarn++;
   if (popforecast==1) {        if(first==0){
     if((ficpop=fopen(popfile,"r"))==NULL) {          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
       printf("Problem with population file : %s\n",popfile);exit(0);          first=1;
     }        }
     popage=ivector(0,AGESUP);        if(first==1){
     popeffectif=vector(0,AGESUP);          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
     popcount=vector(0,AGESUP);        }
          } /* end mi==0 */
     i=1;      } /* End individuals */
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;  
        for(i=1; i<=imx; i++){
     imx=i;      for(mi=1; mi<wav[i];mi++){
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];        if (stepm <=0)
   }          dh[mi][i]=1;
         else{
   for(cptcov=1;cptcov<=i2;cptcov++){          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){            if (agedc[i] < 2*AGESUP) {
       k=k+1;              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
       fprintf(ficrespop,"\n#******");              if(j==0) j=1;  /* Survives at least one month after exam */
       for(j=1;j<=cptcoveff;j++) {              else if(j<0){
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                nberr++;
       }                printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
       fprintf(ficrespop,"******\n");                j=1; /* Temporary Dangerous patch */
       fprintf(ficrespop,"# Age");                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(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);                fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
       if (popforecast==1)  fprintf(ficrespop," [Population]");                fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
                    }
       for (cpt=0; cpt<=0;cpt++) {              k=k+1;
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);                if (j >= jmax){
                        jmax=j;
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){                ijmax=i;
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);              }
           nhstepm = nhstepm/hstepm;              if (j <= jmin){
                          jmin=j;
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                ijmin=i;
           oldm=oldms;savm=savms;              }
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);                sum=sum+j;
                      /*if (j<0) printf("j=%d num=%d \n",j,i);*/
           for (h=0; h<=nhstepm; h++){              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
             if (h==(int) (calagedate+YEARM*cpt)) {            }
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);          }
             }          else{
             for(j=1; j<=nlstate+ndeath;j++) {            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
               kk1=0.;kk2=0;  /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
               for(i=1; i<=nlstate;i++) {                
                 if (mobilav==1)            k=k+1;
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];            if (j >= jmax) {
                 else {              jmax=j;
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];              ijmax=i;
                 }            }
               }            else if (j <= jmin){
               if (h==(int)(calagedate+12*cpt)){              jmin=j;
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;              ijmin=i;
                   /*fprintf(ficrespop," %.3f", kk1);            }
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
               }            /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
             }            if(j<0){
             for(i=1; i<=nlstate;i++){              nberr++;
               kk1=0.;              printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
                 for(j=1; j<=nlstate;j++){              fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];            }
                 }            sum=sum+j;
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];          }
             }          jk= j/stepm;
           jl= j -jk*stepm;
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)          ju= j -(jk+1)*stepm;
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
           }            if(jl==0){
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              dh[mi][i]=jk;
         }              bh[mi][i]=0;
       }            }else{ /* We want a negative bias in order to only have interpolation ie
                      * at the price of an extra matrix product in likelihood */
   /******/              dh[mi][i]=jk+1;
               bh[mi][i]=ju;
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {            }
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);            }else{
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){            if(jl <= -ju){
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);              dh[mi][i]=jk;
           nhstepm = nhstepm/hstepm;              bh[mi][i]=jl;       /* bias is positive if real duration
                                             * is higher than the multiple of stepm and negative otherwise.
           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);              else{
           for (h=0; h<=nhstepm; h++){              dh[mi][i]=jk+1;
             if (h==(int) (calagedate+YEARM*cpt)) {              bh[mi][i]=ju;
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);            }
             }            if(dh[mi][i]==0){
             for(j=1; j<=nlstate+ndeath;j++) {              dh[mi][i]=1; /* At least one step */
               kk1=0.;kk2=0;              bh[mi][i]=ju; /* At least one step */
               for(i=1; i<=nlstate;i++) {                            /*  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);*/
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];                }
               }          } /* end if mle */
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);        }
             }      } /* end wave */
           }    }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    jmean=sum/k;
         }    printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
       }    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);
    }   }
   }  
    /*********** Tricode ****************************/
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  void tricode(int *Tvar, int **nbcode, int imx)
   {
   if (popforecast==1) {    
     free_ivector(popage,0,AGESUP);    /*      Tvar[i]=atoi(stre); /* find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 */
     free_vector(popeffectif,0,AGESUP);  
     free_vector(popcount,0,AGESUP);    int Ndum[20],ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
   }    int cptcode=0;
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    cptcoveff=0; 
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);   
   fclose(ficrespop);    for (k=0; k<maxncov; k++) Ndum[k]=0;
 }    for (k=1; k<=7; k++) ncodemax[k]=0; /* Horrible constant again */
   
 /***********************************************/    for (j=1; j<=(cptcovn+2*cptcovprod); j++) { /* For each covariate */
 /**************** Main Program *****************/      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
 /***********************************************/                                 modality*/ 
         ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual, might be -1*/
 int main(int argc, char *argv[])        Ndum[ij]++; /*counts the occurence of this modality */
 {        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
         if (ij > cptcode) cptcode=ij; /* getting the maximum value of the modality of the covariate  (should be 0 or 1 now) 
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;                                         Tvar[j]. If V=sex and male is 0 and 
   double agedeb, agefin,hf;                                         female is 1, then  cptcode=1.*/
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;      }
   
   double fret;      for (i=0; i<=cptcode; i++) { /* i=-1 ?*/
   double **xi,tmp,delta;        if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j
                                          th covariate. In fact
   double dum; /* Dummy variable */                                         ncodemax[j]=2
   double ***p3mat;                                         (dichotom. variables only) but
   int *indx;                                         it can be more */
   char line[MAXLINE], linepar[MAXLINE];      } /* Ndum[-1] number of undefined modalities */
   char title[MAXLINE];  
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];      ij=1; 
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];      for (i=1; i<=ncodemax[j]; i++) { /* i= 1 to 2 */
          for (k=0; k<= maxncov; k++) { /* k=-1 ?*/
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];          if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
             nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode. 
   char filerest[FILENAMELENGTH];                                       k is a modality. If we have model=V1+V1*sex 
   char fileregp[FILENAMELENGTH];                                       then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
   char popfile[FILENAMELENGTH];            ij++;
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];          }
   int firstobs=1, lastobs=10;          if (ij > ncodemax[j]) break; 
   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,**adl,*tab;   for (k=0; k< maxncov; k++) Ndum[k]=0;
   int mobilav=0,popforecast=0;  
   int hstepm, nhstepm;   for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1;     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
      ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
   double bage, fage, age, agelim, agebase;     Ndum[ij]++;
   double ftolpl=FTOL;   }
   double **prlim;  
   double *severity;   ij=1;
   double ***param; /* Matrix of parameters */   for (i=1; i<= maxncov; i++) {
   double  *p;     if((Ndum[i]!=0) && (i<=ncovcol)){
   double **matcov; /* Matrix of covariance */       Tvaraff[ij]=i; /*For printing */
   double ***delti3; /* Scale */       ij++;
   double *delti; /* Scale */     }
   double ***eij, ***vareij;   }
   double **varpl; /* Variances of prevalence limits by age */   ij--;
   double *epj, vepp;   cptcoveff=ij; /*Number of simple covariates*/
   double kk1, kk2;  }
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;  
    /*********** Health Expectancies ****************/
   
   char version[80]="Imach version 0.8b, March 2002, INED-EUROREVES ";  void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
   char *alph[]={"a","a","b","c","d","e"}, str[4];  
   {
     /* Health expectancies, no variances */
   char z[1]="c", occ;    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
 #include <sys/time.h>    int nhstepma, nstepma; /* Decreasing with age */
 #include <time.h>    double age, agelim, hf;
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];    double ***p3mat;
      double eip;
   /* long total_usecs;  
   struct timeval start_time, end_time;    pstamp(ficreseij);
      fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */    fprintf(ficreseij,"# Age");
   getcwd(pathcd, size);    for(i=1; i<=nlstate;i++){
       for(j=1; j<=nlstate;j++){
   printf("\n%s",version);        fprintf(ficreseij," e%1d%1d ",i,j);
   if(argc <=1){      }
     printf("\nEnter the parameter file name: ");      fprintf(ficreseij," e%1d. ",i);
     scanf("%s",pathtot);    }
   }    fprintf(ficreseij,"\n");
   else{  
     strcpy(pathtot,argv[1]);    
   }    if(estepm < stepm){
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/      printf ("Problem %d lower than %d\n",estepm, stepm);
   /*cygwin_split_path(pathtot,path,optionfile);    }
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/    else  hstepm=estepm;   
   /* cutv(path,optionfile,pathtot,'\\');*/    /* We compute the life expectancy from trapezoids spaced every estepm months
      * This is mainly to measure the difference between two models: for example
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);     * if stepm=24 months pijx are given only every 2 years and by summing them
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);     * we are calculating an estimate of the Life Expectancy assuming a linear 
   chdir(path);     * progression in between and thus overestimating or underestimating according
   replace(pathc,path);     * 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
 /*-------- arguments in the command line --------*/     * to compare the new estimate of Life expectancy with the same linear 
      * hypothesis. A more precise result, taking into account a more precise
   strcpy(fileres,"r");     * curvature will be obtained if estepm is as small as stepm. */
   strcat(fileres, optionfilefiname);  
   strcat(fileres,".txt");    /* Other files have txt extension */    /* 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. 
   /*---------arguments file --------*/       nhstepm is the number of hstepm from age to agelim 
        nstepm is the number of stepm from age to agelin. 
   if((ficpar=fopen(optionfile,"r"))==NULL)    {       Look at hpijx to understand the reason of that which relies in memory size
     printf("Problem with optionfile %s\n",optionfile);       and note for a fixed period like estepm months */
     goto end;    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   }       survival function given by stepm (the optimization length). Unfortunately it
        means that if the survival funtion is printed only each two years of age and if
   strcpy(filereso,"o");       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   strcat(filereso,fileres);       results. So we changed our mind and took the option of the best precision.
   if((ficparo=fopen(filereso,"w"))==NULL) {    */
     printf("Problem with Output resultfile: %s\n", filereso);goto end;    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   }  
     agelim=AGESUP;
   /* Reads comments: lines beginning with '#' */    /* If stepm=6 months */
   while((c=getc(ficpar))=='#' && c!= EOF){      /* Computed by stepm unit matrices, product of hstepm matrices, stored
     ungetc(c,ficpar);         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
     fgets(line, MAXLINE, ficpar);      
     puts(line);  /* nhstepm age range expressed in number of stepm */
     fputs(line,ficparo);    nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
   }    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   ungetc(c,ficpar);    /* if (stepm >= YEARM) hstepm=1;*/
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   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\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   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);    for (age=bage; age<=fage; age ++){ 
 while((c=getc(ficpar))=='#' && c!= EOF){      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
     ungetc(c,ficpar);      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     fgets(line, MAXLINE, ficpar);      /* if (stepm >= YEARM) hstepm=1;*/
     puts(line);      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
     fputs(line,ficparo);  
   }      /* If stepm=6 months */
   ungetc(c,ficpar);      /* Computed by stepm unit matrices, product of hstepma matrices, stored
           in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
          
   covar=matrix(0,NCOVMAX,1,n);      hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
   cptcovn=0;      
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       
   ncovmodel=2+cptcovn;      printf("%d|",(int)age);fflush(stdout);
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
        
   /* Read guess parameters */      /* Computing expectancies */
   /* Reads comments: lines beginning with '#' */      for(i=1; i<=nlstate;i++)
   while((c=getc(ficpar))=='#' && c!= EOF){        for(j=1; j<=nlstate;j++)
     ungetc(c,ficpar);          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
     fgets(line, MAXLINE, ficpar);            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
     puts(line);            
     fputs(line,ficparo);            /* 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]);*/
   }  
   ungetc(c,ficpar);          }
    
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);      fprintf(ficreseij,"%3.0f",age );
     for(i=1; i <=nlstate; i++)      for(i=1; i<=nlstate;i++){
     for(j=1; j <=nlstate+ndeath-1; j++){        eip=0;
       fscanf(ficpar,"%1d%1d",&i1,&j1);        for(j=1; j<=nlstate;j++){
       fprintf(ficparo,"%1d%1d",i1,j1);          eip +=eij[i][j][(int)age];
       printf("%1d%1d",i,j);          fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
       for(k=1; k<=ncovmodel;k++){        }
         fscanf(ficpar," %lf",&param[i][j][k]);        fprintf(ficreseij,"%9.4f", eip );
         printf(" %lf",param[i][j][k]);      }
         fprintf(ficparo," %lf",param[i][j][k]);      fprintf(ficreseij,"\n");
       }      
       fscanf(ficpar,"\n");    }
       printf("\n");    free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       fprintf(ficparo,"\n");    printf("\n");
     }    fprintf(ficlog,"\n");
      
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;  }
   
   p=param[1][1];  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[] )
    
   /* Reads comments: lines beginning with '#' */  {
   while((c=getc(ficpar))=='#' && c!= EOF){    /* Covariances of health expectancies eij and of total life expectancies according
     ungetc(c,ficpar);     to initial status i, ei. .
     fgets(line, MAXLINE, ficpar);    */
     puts(line);    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
     fputs(line,ficparo);    int nhstepma, nstepma; /* Decreasing with age */
   }    double age, agelim, hf;
   ungetc(c,ficpar);    double ***p3matp, ***p3matm, ***varhe;
     double **dnewm,**doldm;
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    double *xp, *xm;
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */    double **gp, **gm;
   for(i=1; i <=nlstate; i++){    double ***gradg, ***trgradg;
     for(j=1; j <=nlstate+ndeath-1; j++){    int theta;
       fscanf(ficpar,"%1d%1d",&i1,&j1);  
       printf("%1d%1d",i,j);    double eip, vip;
       fprintf(ficparo,"%1d%1d",i1,j1);  
       for(k=1; k<=ncovmodel;k++){    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
         fscanf(ficpar,"%le",&delti3[i][j][k]);    xp=vector(1,npar);
         printf(" %le",delti3[i][j][k]);    xm=vector(1,npar);
         fprintf(ficparo," %le",delti3[i][j][k]);    dnewm=matrix(1,nlstate*nlstate,1,npar);
       }    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
       fscanf(ficpar,"\n");    
       printf("\n");    pstamp(ficresstdeij);
       fprintf(ficparo,"\n");    fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
     }    fprintf(ficresstdeij,"# Age");
   }    for(i=1; i<=nlstate;i++){
   delti=delti3[1][1];      for(j=1; j<=nlstate;j++)
          fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
   /* Reads comments: lines beginning with '#' */      fprintf(ficresstdeij," e%1d. ",i);
   while((c=getc(ficpar))=='#' && c!= EOF){    }
     ungetc(c,ficpar);    fprintf(ficresstdeij,"\n");
     fgets(line, MAXLINE, ficpar);  
     puts(line);    pstamp(ficrescveij);
     fputs(line,ficparo);    fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
   }    fprintf(ficrescveij,"# Age");
   ungetc(c,ficpar);    for(i=1; i<=nlstate;i++)
        for(j=1; j<=nlstate;j++){
   matcov=matrix(1,npar,1,npar);        cptj= (j-1)*nlstate+i;
   for(i=1; i <=npar; i++){        for(i2=1; i2<=nlstate;i2++)
     fscanf(ficpar,"%s",&str);          for(j2=1; j2<=nlstate;j2++){
     printf("%s",str);            cptj2= (j2-1)*nlstate+i2;
     fprintf(ficparo,"%s",str);            if(cptj2 <= cptj)
     for(j=1; j <=i; j++){              fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
       fscanf(ficpar," %le",&matcov[i][j]);          }
       printf(" %.5le",matcov[i][j]);      }
       fprintf(ficparo," %.5le",matcov[i][j]);    fprintf(ficrescveij,"\n");
     }    
     fscanf(ficpar,"\n");    if(estepm < stepm){
     printf("\n");      printf ("Problem %d lower than %d\n",estepm, stepm);
     fprintf(ficparo,"\n");    }
   }    else  hstepm=estepm;   
   for(i=1; i <=npar; i++)    /* We compute the life expectancy from trapezoids spaced every estepm months
     for(j=i+1;j<=npar;j++)     * This is mainly to measure the difference between two models: for example
       matcov[i][j]=matcov[j][i];     * if stepm=24 months pijx are given only every 2 years and by summing them
         * we are calculating an estimate of the Life Expectancy assuming a linear 
   printf("\n");     * progression in between and thus overestimating or underestimating according
      * to the curvature of the survival function. If, for the same date, we 
      * estimate the model with stepm=1 month, we can keep estepm to 24 months
     /*-------- Rewriting paramater file ----------*/     * to compare the new estimate of Life expectancy with the same linear 
      strcpy(rfileres,"r");    /* "Rparameterfile */     * hypothesis. A more precise result, taking into account a more precise
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/     * curvature will be obtained if estepm is as small as stepm. */
      strcat(rfileres,".");    /* */  
      strcat(rfileres,optionfilext);    /* Other files have txt extension */    /* For example we decided to compute the life expectancy with the smallest unit */
     if((ficres =fopen(rfileres,"w"))==NULL) {    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
       printf("Problem writing new parameter file: %s\n", fileres);goto end;       nhstepm is the number of hstepm from age to agelim 
     }       nstepm is the number of stepm from age to agelin. 
     fprintf(ficres,"#%s\n",version);       Look at hpijx to understand the reason of that which relies in memory size
           and note for a fixed period like estepm months */
     /*-------- data file ----------*/    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
     if((fic=fopen(datafile,"r"))==NULL)    {       survival function given by stepm (the optimization length). Unfortunately it
       printf("Problem with datafile: %s\n", datafile);goto end;       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.
     n= lastobs;    */
     severity = vector(1,maxwav);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     outcome=imatrix(1,maxwav+1,1,n);  
     num=ivector(1,n);    /* If stepm=6 months */
     moisnais=vector(1,n);    /* nhstepm age range expressed in number of stepm */
     annais=vector(1,n);    agelim=AGESUP;
     moisdc=vector(1,n);    nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
     andc=vector(1,n);    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     agedc=vector(1,n);    /* if (stepm >= YEARM) hstepm=1;*/
     cod=ivector(1,n);    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     weight=vector(1,n);    
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */    p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     mint=matrix(1,maxwav,1,n);    p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     anint=matrix(1,maxwav,1,n);    gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
     s=imatrix(1,maxwav+1,1,n);    trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
     adl=imatrix(1,maxwav+1,1,n);        gp=matrix(0,nhstepm,1,nlstate*nlstate);
     tab=ivector(1,NCOVMAX);    gm=matrix(0,nhstepm,1,nlstate*nlstate);
     ncodemax=ivector(1,8);  
     for (age=bage; age<=fage; age ++){ 
     i=1;      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
     while (fgets(line, MAXLINE, fic) != NULL)    {      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       if ((i >= firstobs) && (i <=lastobs)) {      /* if (stepm >= YEARM) hstepm=1;*/
              nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
         for (j=maxwav;j>=1;j--){  
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);      /* If stepm=6 months */
           strcpy(line,stra);      /* Computed by stepm unit matrices, product of hstepma matrices, stored
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);      
         }      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
          
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);      /* Computing  Variances of health expectancies */
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
          decrease memory allocation */
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);      for(theta=1; theta <=npar; theta++){
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);        for(i=1; i<=npar; i++){ 
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);          xm[i] = x[i] - (i==theta ?delti[theta]:0);
         for (j=ncovcol;j>=1;j--){        }
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);        hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
         }        hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
         num[i]=atol(stra);    
                for(j=1; j<= nlstate; j++){
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){          for(i=1; i<=nlstate; i++){
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/            for(h=0; h<=nhstepm-1; h++){
               gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
         i=i+1;              gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
       }            }
     }          }
     /* printf("ii=%d", ij);        }
        scanf("%d",i);*/       
   imx=i-1; /* Number of individuals */        for(ij=1; ij<= nlstate*nlstate; ij++)
           for(h=0; h<=nhstepm-1; h++){
   /* for (i=1; i<=imx; i++){            gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
     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;      }/* End theta */
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;      
     }*/      
    /*  for (i=1; i<=imx; i++){      for(h=0; h<=nhstepm-1; h++)
      if (s[4][i]==9)  s[4][i]=-1;        for(j=1; j<=nlstate*nlstate;j++)
      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]));}*/          for(theta=1; theta <=npar; theta++)
              trgradg[h][j][theta]=gradg[h][theta][j];
        
   /* Calculation of the number of parameter from char model*/  
   Tvar=ivector(1,15);       for(ij=1;ij<=nlstate*nlstate;ij++)
   Tprod=ivector(1,15);        for(ji=1;ji<=nlstate*nlstate;ji++)
   Tvaraff=ivector(1,15);          varhe[ij][ji][(int)age] =0.;
   Tvard=imatrix(1,15,1,2);  
   Tage=ivector(1,15);             printf("%d|",(int)age);fflush(stdout);
           fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
   if (strlen(model) >1){       for(h=0;h<=nhstepm-1;h++){
     j=0, j1=0, k1=1, k2=1;        for(k=0;k<=nhstepm-1;k++){
     j=nbocc(model,'+');          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
     j1=nbocc(model,'*');          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
     cptcovn=j+1;          for(ij=1;ij<=nlstate*nlstate;ij++)
     cptcovprod=j1;            for(ji=1;ji<=nlstate*nlstate;ji++)
                  varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
     strcpy(modelsav,model);        }
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){      }
       printf("Error. Non available option model=%s ",model);  
       goto end;      /* Computing expectancies */
     }      hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
          for(i=1; i<=nlstate;i++)
     for(i=(j+1); i>=1;i--){        for(j=1; j<=nlstate;j++)
       cutv(stra,strb,modelsav,'+');          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);            eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/            
       /*scanf("%d",i);*/            /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
       if (strchr(strb,'*')) {  
         cutv(strd,strc,strb,'*');          }
         if (strcmp(strc,"age")==0) {  
           cptcovprod--;      fprintf(ficresstdeij,"%3.0f",age );
           cutv(strb,stre,strd,'V');      for(i=1; i<=nlstate;i++){
           Tvar[i]=atoi(stre);        eip=0.;
           cptcovage++;        vip=0.;
             Tage[cptcovage]=i;        for(j=1; j<=nlstate;j++){
             /*printf("stre=%s ", stre);*/          eip += eij[i][j][(int)age];
         }          for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
         else if (strcmp(strd,"age")==0) {            vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
           cptcovprod--;          fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
           cutv(strb,stre,strc,'V');        }
           Tvar[i]=atoi(stre);        fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
           cptcovage++;      }
           Tage[cptcovage]=i;      fprintf(ficresstdeij,"\n");
         }  
         else {      fprintf(ficrescveij,"%3.0f",age );
           cutv(strb,stre,strc,'V');      for(i=1; i<=nlstate;i++)
           Tvar[i]=ncovcol+k1;        for(j=1; j<=nlstate;j++){
           cutv(strb,strc,strd,'V');          cptj= (j-1)*nlstate+i;
           Tprod[k1]=i;          for(i2=1; i2<=nlstate;i2++)
           Tvard[k1][1]=atoi(strc);            for(j2=1; j2<=nlstate;j2++){
           Tvard[k1][2]=atoi(stre);              cptj2= (j2-1)*nlstate+i2;
           Tvar[cptcovn+k2]=Tvard[k1][1];              if(cptj2 <= cptj)
           Tvar[cptcovn+k2+1]=Tvard[k1][2];                fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
           for (k=1; k<=lastobs;k++)            }
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];        }
           k1++;      fprintf(ficrescveij,"\n");
           k2=k2+2;     
         }    }
       }    free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
       else {    free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/    free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
        /*  scanf("%d",i);*/    free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
       cutv(strd,strc,strb,'V');    free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       Tvar[i]=atoi(strc);    free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       }    printf("\n");
       strcpy(modelsav,stra);      fprintf(ficlog,"\n");
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);  
         scanf("%d",i);*/    free_vector(xm,1,npar);
     }    free_vector(xp,1,npar);
 }    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
      free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
   printf("cptcovprod=%d ", cptcovprod);  }
   scanf("%d ",i);*/  
     fclose(fic);  /************ 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[])
     /*  if(mle==1){*/  {
     if (weightopt != 1) { /* Maximisation without weights*/    /* Variance of health expectancies */
       for(i=1;i<=n;i++) weight[i]=1.0;    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
     }    /* double **newm;*/
     /*-calculation of age at interview from date of interview and age at death -*/    double **dnewm,**doldm;
     agev=matrix(1,maxwav,1,imx);    double **dnewmp,**doldmp;
     int i, j, nhstepm, hstepm, h, nstepm ;
     for (i=1; i<=imx; i++) {    int k, cptcode;
       for(m=2; (m<= maxwav); m++) {    double *xp;
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){    double **gp, **gm;  /* for var eij */
          anint[m][i]=9999;    double ***gradg, ***trgradg; /*for var eij */
          s[m][i]=-1;    double **gradgp, **trgradgp; /* for var p point j */
        }    double *gpp, *gmp; /* for var p point j */
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
       }    double ***p3mat;
     }    double age,agelim, hf;
     double ***mobaverage;
     for (i=1; i<=imx; i++)  {    int theta;
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);    char digit[4];
       for(m=1; (m<= maxwav); m++){    char digitp[25];
         if(s[m][i] >0){  
           if (s[m][i] >= nlstate+1) {    char fileresprobmorprev[FILENAMELENGTH];
             if(agedc[i]>0)  
               if(moisdc[i]!=99 && andc[i]!=9999)    if(popbased==1){
                 agev[m][i]=agedc[i];      if(mobilav!=0)
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/        strcpy(digitp,"-populbased-mobilav-");
            else {      else strcpy(digitp,"-populbased-nomobil-");
               if (andc[i]!=9999){    }
               printf("Warning negative age at death: %d line:%d\n",num[i],i);    else 
               agev[m][i]=-1;      strcpy(digitp,"-stablbased-");
               }  
             }    if (mobilav!=0) {
           }      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
           else if(s[m][i] !=9){ /* Should no more exist */      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
             if(mint[m][i]==99 || anint[m][i]==9999)        printf(" Error in movingaverage mobilav=%d\n",mobilav);
               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);*/    strcpy(fileresprobmorprev,"prmorprev"); 
             }    sprintf(digit,"%-d",ij);
             else if(agev[m][i] >agemax){    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
               agemax=agev[m][i];    strcat(fileresprobmorprev,digit); /* Tvar to be done */
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
             }    strcat(fileresprobmorprev,fileres);
             /*agev[m][i]=anint[m][i]-annais[i];*/    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
             /*   agev[m][i] = age[i]+2*m;*/      printf("Problem with resultfile: %s\n", fileresprobmorprev);
           }      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
           else { /* =9 */    }
             agev[m][i]=1;    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
             s[m][i]=-1;   
           }    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
         }    pstamp(ficresprobmorprev);
         else /*= 0 Unknown */    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);
           agev[m][i]=1;    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
       }    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
          fprintf(ficresprobmorprev," p.%-d SE",j);
     }      for(i=1; i<=nlstate;i++)
     for (i=1; i<=imx; i++)  {        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
       for(m=1; (m<= maxwav); m++){    }  
         if (s[m][i] > (nlstate+ndeath)) {    fprintf(ficresprobmorprev,"\n");
           printf("Error: Wrong value in nlstate or ndeath\n");      fprintf(ficgp,"\n# Routine varevsij");
           goto end;    /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
         }    fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
       }    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
     }  /*   } */
     varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);    pstamp(ficresvij);
     fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
     free_vector(severity,1,maxwav);    if(popbased==1)
     free_imatrix(outcome,1,maxwav+1,1,n);      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);
     free_vector(moisnais,1,n);    else
     free_vector(annais,1,n);      fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
     /* free_matrix(mint,1,maxwav,1,n);    fprintf(ficresvij,"# Age");
        free_matrix(anint,1,maxwav,1,n);*/    for(i=1; i<=nlstate;i++)
     free_vector(moisdc,1,n);      for(j=1; j<=nlstate;j++)
     free_vector(andc,1,n);        fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
     fprintf(ficresvij,"\n");
      
     wav=ivector(1,imx);    xp=vector(1,npar);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);    dnewm=matrix(1,nlstate,1,npar);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);    doldm=matrix(1,nlstate,1,nlstate);
        dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
     /* Concatenates waves */    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);  
     gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
     gpp=vector(nlstate+1,nlstate+ndeath);
       Tcode=ivector(1,100);    gmp=vector(nlstate+1,nlstate+ndeath);
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
       ncodemax[1]=1;    
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);    if(estepm < stepm){
            printf ("Problem %d lower than %d\n",estepm, stepm);
    codtab=imatrix(1,100,1,10);    }
    h=0;    else  hstepm=estepm;   
    m=pow(2,cptcoveff);    /* 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. 
    for(k=1;k<=cptcoveff; k++){       nhstepm is the number of hstepm from age to agelim 
      for(i=1; i <=(m/pow(2,k));i++){       nstepm is the number of stepm from age to agelin. 
        for(j=1; j <= ncodemax[k]; j++){       Look at function hpijx to understand why (it is linked to memory size questions) */
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
            h++;       survival function given by stepm (the optimization length). Unfortunately it
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;       means that if the survival funtion is printed every two years of age and if
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
          }       results. So we changed our mind and took the option of the best precision.
        }    */
      }    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
    }    agelim = AGESUP;
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       codtab[1][2]=1;codtab[2][2]=2; */      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
    /* for(i=1; i <=m ;i++){      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       for(k=1; k <=cptcovn; k++){      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
       }      gp=matrix(0,nhstepm,1,nlstate);
       printf("\n");      gm=matrix(0,nhstepm,1,nlstate);
       }  
       scanf("%d",i);*/  
          for(theta=1; theta <=npar; theta++){
    /* Calculates basic frequencies. Computes observed prevalence at single age        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
        and prints on file fileres'p'. */          xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
            hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
            prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        if (popbased==1) {
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          if(mobilav ==0){
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            for(i=1; i<=nlstate;i++)
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */              prlim[i][i]=probs[(int)age][i][ij];
                }else{ /* mobilav */ 
     /* For Powell, parameters are in a vector p[] starting at p[1]            for(i=1; i<=nlstate;i++)
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */              prlim[i][i]=mobaverage[(int)age][i][ij];
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */          }
         }
     if(mle==1){    
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);        for(j=1; j<= nlstate; j++){
     }          for(h=0; h<=nhstepm; h++){
                for(i=1, gp[h][j]=0.;i<=nlstate;i++)
     /*--------- results files --------------*/              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
     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);          }
          }
         /* This for computing probability of death (h=1 means
    jk=1;           computed over hstepm matrices product = hstepm*stepm months) 
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");           as a weighted average of prlim.
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");        */
    for(i=1,jk=1; i <=nlstate; i++){        for(j=nlstate+1;j<=nlstate+ndeath;j++){
      for(k=1; k <=(nlstate+ndeath); k++){          for(i=1,gpp[j]=0.; i<= nlstate; i++)
        if (k != i)            gpp[j] += prlim[i][i]*p3mat[i][j][1];
          {        }    
            printf("%d%d ",i,k);        /* end probability of death */
            fprintf(ficres,"%1d%1d ",i,k);  
            for(j=1; j <=ncovmodel; j++){        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
              printf("%f ",p[jk]);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
              fprintf(ficres,"%f ",p[jk]);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
              jk++;        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
            }   
            printf("\n");        if (popbased==1) {
            fprintf(ficres,"\n");          if(mobilav ==0){
          }            for(i=1; i<=nlstate;i++)
      }              prlim[i][i]=probs[(int)age][i][ij];
    }          }else{ /* mobilav */ 
  if(mle==1){            for(i=1; i<=nlstate;i++)
     /* Computing hessian and covariance matrix */              prlim[i][i]=mobaverage[(int)age][i][ij];
     ftolhess=ftol; /* Usually correct */          }
     hesscov(matcov, p, npar, delti, ftolhess, func);        }
  }  
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");        for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
     printf("# Scales (for hessian or gradient estimation)\n");          for(h=0; h<=nhstepm; h++){
      for(i=1,jk=1; i <=nlstate; i++){            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
       for(j=1; j <=nlstate+ndeath; j++){              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
         if (j!=i) {          }
           fprintf(ficres,"%1d%1d",i,j);        }
           printf("%1d%1d",i,j);        /* This for computing probability of death (h=1 means
           for(k=1; k<=ncovmodel;k++){           computed over hstepm matrices product = hstepm*stepm months) 
             printf(" %.5e",delti[jk]);           as a weighted average of prlim.
             fprintf(ficres," %.5e",delti[jk]);        */
             jk++;        for(j=nlstate+1;j<=nlstate+ndeath;j++){
           }          for(i=1,gmp[j]=0.; i<= nlstate; i++)
           printf("\n");           gmp[j] += prlim[i][i]*p3mat[i][j][1];
           fprintf(ficres,"\n");        }    
         }        /* end probability of death */
       }  
      }        for(j=1; j<= nlstate; j++) /* vareij */
              for(h=0; h<=nhstepm; h++){
     k=1;            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
     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");          }
     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");  
     for(i=1;i<=npar;i++){        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
       /*  if (k>nlstate) k=1;          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
       i1=(i-1)/(ncovmodel*nlstate)+1;        }
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);  
       printf("%s%d%d",alph[k],i1,tab[i]);*/      } /* End theta */
       fprintf(ficres,"%3d",i);  
       printf("%3d",i);      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
       for(j=1; j<=i;j++){  
         fprintf(ficres," %.5e",matcov[i][j]);      for(h=0; h<=nhstepm; h++) /* veij */
         printf(" %.5e",matcov[i][j]);        for(j=1; j<=nlstate;j++)
       }          for(theta=1; theta <=npar; theta++)
       fprintf(ficres,"\n");            trgradg[h][j][theta]=gradg[h][theta][j];
       printf("\n");  
       k++;      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
     }        for(theta=1; theta <=npar; theta++)
              trgradgp[j][theta]=gradgp[theta][j];
     while((c=getc(ficpar))=='#' && c!= EOF){    
       ungetc(c,ficpar);  
       fgets(line, MAXLINE, ficpar);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       puts(line);      for(i=1;i<=nlstate;i++)
       fputs(line,ficparo);        for(j=1;j<=nlstate;j++)
     }          vareij[i][j][(int)age] =0.;
     ungetc(c,ficpar);  
     estepm=0;      for(h=0;h<=nhstepm;h++){
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);        for(k=0;k<=nhstepm;k++){
     if (estepm==0 || estepm < stepm) estepm=stepm;          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
     if (fage <= 2) {          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
       bage = ageminpar;          for(i=1;i<=nlstate;i++)
       fage = agemaxpar;            for(j=1;j<=nlstate;j++)
     }              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
            }
     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);      /* pptj */
        matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
     while((c=getc(ficpar))=='#' && c!= EOF){      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
     ungetc(c,ficpar);      for(j=nlstate+1;j<=nlstate+ndeath;j++)
     fgets(line, MAXLINE, ficpar);        for(i=nlstate+1;i<=nlstate+ndeath;i++)
     puts(line);          varppt[j][i]=doldmp[j][i];
     fputs(line,ficparo);      /* end ppptj */
   }      /*  x centered again */
   ungetc(c,ficpar);      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
        prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);   
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);      if (popbased==1) {
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        if(mobilav ==0){
                for(i=1; i<=nlstate;i++)
   while((c=getc(ficpar))=='#' && c!= EOF){            prlim[i][i]=probs[(int)age][i][ij];
     ungetc(c,ficpar);        }else{ /* mobilav */ 
     fgets(line, MAXLINE, ficpar);          for(i=1; i<=nlstate;i++)
     puts(line);            prlim[i][i]=mobaverage[(int)age][i][ij];
     fputs(line,ficparo);        }
   }      }
   ungetc(c,ficpar);               
        /* This for computing probability of death (h=1 means
          computed over hstepm (estepm) matrices product = hstepm*stepm months) 
    dateprev1=anprev1+mprev1/12.+jprev1/365.;         as a weighted average of prlim.
    dateprev2=anprev2+mprev2/12.+jprev2/365.;      */
       for(j=nlstate+1;j<=nlstate+ndeath;j++){
   fscanf(ficpar,"pop_based=%d\n",&popbased);        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
   fprintf(ficparo,"pop_based=%d\n",popbased);            gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
   fprintf(ficres,"pop_based=%d\n",popbased);        }    
        /* end probability of death */
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
     fgets(line, MAXLINE, ficpar);      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
     puts(line);        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
     fputs(line,ficparo);        for(i=1; i<=nlstate;i++){
   }          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
   ungetc(c,ficpar);        }
       } 
   fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mov_average=%d\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);      fprintf(ficresprobmorprev,"\n");
 fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);  
 fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);      fprintf(ficresvij,"%.0f ",age );
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
 while((c=getc(ficpar))=='#' && c!= EOF){          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
     ungetc(c,ficpar);        }
     fgets(line, MAXLINE, ficpar);      fprintf(ficresvij,"\n");
     puts(line);      free_matrix(gp,0,nhstepm,1,nlstate);
     fputs(line,ficparo);      free_matrix(gm,0,nhstepm,1,nlstate);
   }      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
   ungetc(c,ficpar);      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
       free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);    } /* End age */
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);    free_vector(gpp,nlstate+1,nlstate+ndeath);
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);    free_vector(gmp,nlstate+1,nlstate+ndeath);
     free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     fprintf(ficgp,"\nunset parametric;unset label; set ter png small;set size 0.65, 0.65");
 /*------------ gnuplot -------------*/    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, ageminpar,agemaxpar,fage, pathc,p);    fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
    /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
 /*------------ free_vector  -------------*/  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
  chdir(path);  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
      fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
  free_ivector(wav,1,imx);    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);      fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
  free_ivector(num,1,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);
  free_vector(agedc,1,n);    /*  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);
  /*free_matrix(covar,1,NCOVMAX,1,n);*/  */
  fclose(ficparo);  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
  fclose(ficres);    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
   
 /*--------- index.htm --------*/    free_vector(xp,1,npar);
     free_matrix(doldm,1,nlstate,1,nlstate);
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres,optionfilegnuplot,version,popforecast,estepm);    free_matrix(dnewm,1,nlstate,1,npar);
     free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
      free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
   /*--------------- Prevalence limit --------------*/    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
      if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   strcpy(filerespl,"pl");    fclose(ficresprobmorprev);
   strcat(filerespl,fileres);    fflush(ficgp);
   if((ficrespl=fopen(filerespl,"w"))==NULL) {    fflush(fichtm); 
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;  }  /* end varevsij */
   }  
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);  /************ Variance of prevlim ******************/
   fprintf(ficrespl,"#Prevalence limit\n");  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[])
   fprintf(ficrespl,"#Age ");  {
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);    /* Variance of prevalence limit */
   fprintf(ficrespl,"\n");    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
      double **newm;
   prlim=matrix(1,nlstate,1,nlstate);    double **dnewm,**doldm;
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    int i, j, nhstepm, hstepm;
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    int k, cptcode;
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    double *xp;
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    double *gp, *gm;
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    double **gradg, **trgradg;
   k=0;    double age,agelim;
   agebase=ageminpar;    int theta;
   agelim=agemaxpar;    
   ftolpl=1.e-10;    pstamp(ficresvpl);
   i1=cptcoveff;    fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
   if (cptcovn < 1){i1=1;}    fprintf(ficresvpl,"# Age");
     for(i=1; i<=nlstate;i++)
   for(cptcov=1;cptcov<=i1;cptcov++){        fprintf(ficresvpl," %1d-%1d",i,i);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    fprintf(ficresvpl,"\n");
         k=k+1;  
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/    xp=vector(1,npar);
         fprintf(ficrespl,"\n#******");    dnewm=matrix(1,nlstate,1,npar);
         for(j=1;j<=cptcoveff;j++)    doldm=matrix(1,nlstate,1,nlstate);
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    
         fprintf(ficrespl,"******\n");    hstepm=1*YEARM; /* Every year of age */
            hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
         for (age=agebase; age<=agelim; age++){    agelim = AGESUP;
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
           fprintf(ficrespl,"%.0f",age );      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
           for(i=1; i<=nlstate;i++)      if (stepm >= YEARM) hstepm=1;
           fprintf(ficrespl," %.5f", prlim[i][i]);      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
           fprintf(ficrespl,"\n");      gradg=matrix(1,npar,1,nlstate);
         }      gp=vector(1,nlstate);
       }      gm=vector(1,nlstate);
     }  
   fclose(ficrespl);      for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient */
   /*------------- h Pij x at various ages ------------*/          xp[i] = x[i] + (i==theta ?delti[theta]:0);
          }
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   if((ficrespij=fopen(filerespij,"w"))==NULL) {        for(i=1;i<=nlstate;i++)
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;          gp[i] = prlim[i][i];
   }      
   printf("Computing pij: result on file '%s' \n", filerespij);        for(i=1; i<=npar; i++) /* Computes gradient */
            xp[i] = x[i] - (i==theta ?delti[theta]:0);
   stepsize=(int) (stepm+YEARM-1)/YEARM;        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   /*if (stepm<=24) stepsize=2;*/        for(i=1;i<=nlstate;i++)
           gm[i] = prlim[i][i];
   agelim=AGESUP;  
   hstepm=stepsize*YEARM; /* Every year of age */        for(i=1;i<=nlstate;i++)
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
        } /* End theta */
   k=0;  
   for(cptcov=1;cptcov<=i1;cptcov++){      trgradg =matrix(1,nlstate,1,npar);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  
       k=k+1;      for(j=1; j<=nlstate;j++)
         fprintf(ficrespij,"\n#****** ");        for(theta=1; theta <=npar; theta++)
         for(j=1;j<=cptcoveff;j++)          trgradg[j][theta]=gradg[theta][j];
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
         fprintf(ficrespij,"******\n");      for(i=1;i<=nlstate;i++)
                varpl[i][(int)age] =0.;
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      for(i=1;i<=nlstate;i++)
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
           oldm=oldms;savm=savms;  
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        fprintf(ficresvpl,"%.0f ",age );
           fprintf(ficrespij,"# Age");      for(i=1; i<=nlstate;i++)
           for(i=1; i<=nlstate;i++)        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
             for(j=1; j<=nlstate+ndeath;j++)      fprintf(ficresvpl,"\n");
               fprintf(ficrespij," %1d-%1d",i,j);      free_vector(gp,1,nlstate);
           fprintf(ficrespij,"\n");      free_vector(gm,1,nlstate);
           for (h=0; h<=nhstepm; h++){      free_matrix(gradg,1,npar,1,nlstate);
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );      free_matrix(trgradg,1,nlstate,1,npar);
             for(i=1; i<=nlstate;i++)    } /* End age */
               for(j=1; j<=nlstate+ndeath;j++)  
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);    free_vector(xp,1,npar);
             fprintf(ficrespij,"\n");    free_matrix(doldm,1,nlstate,1,npar);
           }    free_matrix(dnewm,1,nlstate,1,nlstate);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
           fprintf(ficrespij,"\n");  }
         }  
     }  /************ Variance of one-step probabilities  ******************/
   }  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
   {
   varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);    int i, j=0,  i1, k1, l1, t, tj;
     int k2, l2, j1,  z1;
   fclose(ficrespij);    int k=0,l, cptcode;
     int first=1, first1;
     double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
   /*---------- Forecasting ------------------*/    double **dnewm,**doldm;
   if((stepm == 1) && (strcmp(model,".")==0)){    double *xp;
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);    double *gp, *gm;
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);    double **gradg, **trgradg;
     free_matrix(mint,1,maxwav,1,n);    double **mu;
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);    double age,agelim, cov[NCOVMAX];
     free_vector(weight,1,n);}    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
   else{    int theta;
     erreur=108;    char fileresprob[FILENAMELENGTH];
     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);    char fileresprobcov[FILENAMELENGTH];
   }    char fileresprobcor[FILENAMELENGTH];
    
     double ***varpij;
   /*---------- Health expectancies and variances ------------*/  
     strcpy(fileresprob,"prob"); 
   strcpy(filerest,"t");    strcat(fileresprob,fileres);
   strcat(filerest,fileres);    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
   if((ficrest=fopen(filerest,"w"))==NULL) {      printf("Problem with resultfile: %s\n", fileresprob);
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
   }    }
   printf("Computing Total LEs with variances: file '%s' \n", filerest);    strcpy(fileresprobcov,"probcov"); 
     strcat(fileresprobcov,fileres);
     if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
   strcpy(filerese,"e");      printf("Problem with resultfile: %s\n", fileresprobcov);
   strcat(filerese,fileres);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
   if((ficreseij=fopen(filerese,"w"))==NULL) {    }
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);    strcpy(fileresprobcor,"probcor"); 
   }    strcat(fileresprobcor,fileres);
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcor);
  strcpy(fileresv,"v");      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
   strcat(fileresv,fileres);    }
   if((ficresvij=fopen(fileresv,"w"))==NULL) {    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);    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);
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    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);
   k=0;    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   for(cptcov=1;cptcov<=i1;cptcov++){    pstamp(ficresprob);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
       k=k+1;    fprintf(ficresprob,"# Age");
       fprintf(ficrest,"\n#****** ");    pstamp(ficresprobcov);
       for(j=1;j<=cptcoveff;j++)    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    fprintf(ficresprobcov,"# Age");
       fprintf(ficrest,"******\n");    pstamp(ficresprobcor);
     fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
       fprintf(ficreseij,"\n#****** ");    fprintf(ficresprobcor,"# Age");
       for(j=1;j<=cptcoveff;j++)  
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
       fprintf(ficreseij,"******\n");    for(i=1; i<=nlstate;i++)
       for(j=1; j<=(nlstate+ndeath);j++){
       fprintf(ficresvij,"\n#****** ");        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
       for(j=1;j<=cptcoveff;j++)        fprintf(ficresprobcov," p%1d-%1d ",i,j);
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        fprintf(ficresprobcor," p%1d-%1d ",i,j);
       fprintf(ficresvij,"******\n");      }  
    /* fprintf(ficresprob,"\n");
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    fprintf(ficresprobcov,"\n");
       oldm=oldms;savm=savms;    fprintf(ficresprobcor,"\n");
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm);     */
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    xp=vector(1,npar);
       oldm=oldms;savm=savms;    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);    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(ficrest,"#Total LEs with variances: e.. (std) ");    fprintf(ficgp,"\n# Routine varprob");
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
       fprintf(ficrest,"\n");    fprintf(fichtm,"\n");
   
       epj=vector(1,nlstate+1);    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
       for(age=bage; age <=fage ;age++){    fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    file %s<br>\n",optionfilehtmcov);
         if (popbased==1) {    fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
           for(i=1; i<=nlstate;i++)  and drawn. It helps understanding how is the covariance between two incidences.\
             prlim[i][i]=probs[(int)age][i][k];   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 \
         fprintf(ficrest," %4.0f",age);  would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){  standard deviations wide on each axis. <br>\
           for(i=1, epj[j]=0.;i <=nlstate;i++) {   Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
             epj[j] += prlim[i][i]*eij[i][j][(int)age];   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");
           epj[nlstate+1] +=epj[j];  
         }    cov[1]=1;
         for(i=1, vepp=0.;i <=nlstate;i++)    tj=cptcoveff;
           for(j=1;j <=nlstate;j++)    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
             vepp += vareij[i][j][(int)age];    j1=0;
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));    for(t=1; t<=tj;t++){
         for(j=1;j <=nlstate;j++){      for(i1=1; i1<=ncodemax[t];i1++){ 
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));        j1++;
         }        if  (cptcovn>0) {
         fprintf(ficrest,"\n");          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]]);
   fclose(ficreseij);          fprintf(ficresprobcov, "**********\n#\n");
   fclose(ficresvij);          
   fclose(ficrest);          fprintf(ficgp, "\n#********** Variable "); 
   fclose(ficpar);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   free_vector(epj,1,nlstate+1);          fprintf(ficgp, "**********\n#\n");
            
   /*------- Variance limit prevalence------*/            
           fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
   strcpy(fileresvpl,"vpl");          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   strcat(fileresvpl,fileres);          fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {          
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);          fprintf(ficresprobcor, "\n#********** Variable ");    
     exit(0);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   }          fprintf(ficresprobcor, "**********\n#");    
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);        }
         
   k=0;        for (age=bage; age<=fage; age ++){ 
   for(cptcov=1;cptcov<=i1;cptcov++){          cov[2]=age;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          for (k=1; k<=cptcovn;k++) {
       k=k+1;            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
       fprintf(ficresvpl,"\n#****** ");          }
       for(j=1;j<=cptcoveff;j++)          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          for (k=1; k<=cptcovprod;k++)
       fprintf(ficresvpl,"******\n");            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
                
       varpl=matrix(1,nlstate,(int) bage, (int) fage);          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
       oldm=oldms;savm=savms;          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);          gp=vector(1,(nlstate)*(nlstate+ndeath));
     }          gm=vector(1,(nlstate)*(nlstate+ndeath));
  }      
           for(theta=1; theta <=npar; theta++){
   fclose(ficresvpl);            for(i=1; i<=npar; i++)
               xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
   /*---------- End : free ----------------*/            
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);            pmij(pmmij,cov,ncovmodel,xp,nlstate);
              
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);            k=0;
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);            for(i=1; i<= (nlstate); i++){
                for(j=1; j<=(nlstate+ndeath);j++){
                  k=k+1;
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);                gp[k]=pmmij[i][j];
   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);            
              for(i=1; i<=npar; i++)
   free_matrix(matcov,1,npar,1,npar);              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
   free_vector(delti,1,npar);      
   free_matrix(agev,1,maxwav,1,imx);            pmij(pmmij,cov,ncovmodel,xp,nlstate);
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);            k=0;
             for(i=1; i<=(nlstate); i++){
   if(erreur >0)              for(j=1; j<=(nlstate+ndeath);j++){
     printf("End of Imach with error or warning %d\n",erreur);                k=k+1;
   else   printf("End of Imach\n");                gm[k]=pmmij[i][j];
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */              }
              }
   /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/       
   /*printf("Total time was %d uSec.\n", total_usecs);*/            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
   /*------ End -----------*/              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
           }
   
  end:          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
 #ifdef windows            for(theta=1; theta <=npar; theta++)
   /* chdir(pathcd);*/              trgradg[j][theta]=gradg[theta][j];
 #endif          
  /*system("wgnuplot graph.plt");*/          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
  /*system("../gp37mgw/wgnuplot graph.plt");*/          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
  /*system("cd ../gp37mgw");*/          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
  strcpy(plotcmd,GNUPLOTPROGRAM);          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
  strcat(plotcmd," ");          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
  strcat(plotcmd,optionfilegnuplot);  
  system(plotcmd);          pmij(pmmij,cov,ncovmodel,x,nlstate);
           
 #ifdef windows          k=0;
   while (z[0] != 'q') {          for(i=1; i<=(nlstate); i++){
     /* chdir(path); */            for(j=1; j<=(nlstate+ndeath);j++){
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");              k=k+1;
     scanf("%s",z);              mu[k][(int) age]=pmmij[i][j];
     if (z[0] == 'c') system("./imach");            }
     else if (z[0] == 'e') system(optionfilehtm);          }
     else if (z[0] == 'g') system(plotcmd);          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
     else if (z[0] == 'q') exit(0);            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
   }              varpij[i][j][(int)age] = doldm[i][j];
 #endif  
 }          /*printf("\n%d ",(int)age);
             for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             }*/
   
           fprintf(ficresprob,"\n%d ",(int)age);
           fprintf(ficresprobcov,"\n%d ",(int)age);
           fprintf(ficresprobcor,"\n%d ",(int)age);
   
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
             fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
             fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
           }
           i=0;
           for (k=1; k<=(nlstate);k++){
             for (l=1; l<=(nlstate+ndeath);l++){ 
               i=i++;
               fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
               fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
               for (j=1; j<=i;j++){
                 fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
                 fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
               }
             }
           }/* end of loop for state */
         } /* end of loop for age */
   
         /* Confidence intervalle of pij  */
         /*
           fprintf(ficgp,"\nunset parametric;unset label");
           fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
           fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
           fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
           fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
           fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
           fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
         */
   
         /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
         first1=1;
         for (k2=1; k2<=(nlstate);k2++){
           for (l2=1; l2<=(nlstate+ndeath);l2++){ 
             if(l2==k2) continue;
             j=(k2-1)*(nlstate+ndeath)+l2;
             for (k1=1; k1<=(nlstate);k1++){
               for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                 if(l1==k1) continue;
                 i=(k1-1)*(nlstate+ndeath)+l1;
                 if(i<=j) continue;
                 for (age=bage; age<=fage; age ++){ 
                   if ((int)age %5==0){
                     v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                     v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     mu1=mu[i][(int) age]/stepm*YEARM ;
                     mu2=mu[j][(int) age]/stepm*YEARM;
                     c12=cv12/sqrt(v1*v2);
                     /* Computing eigen value of matrix of covariance */
                     lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     if ((lc2 <0) || (lc1 <0) ){
                       printf("Error: One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Continuing by making them positive: WRONG RESULTS.\n", lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);
                       fprintf(ficlog,"Error: One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e\n", lc1, lc2, v1, v2, cv12);fflush(ficlog);
                       lc1=fabs(lc1);
                       lc2=fabs(lc2);
                     }
   
                     /* Eigen vectors */
                     v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                     /*v21=sqrt(1.-v11*v11); *//* error */
                     v21=(lc1-v1)/cv12*v11;
                     v12=-v21;
                     v22=v11;
                     tnalp=v21/v11;
                     if(first1==1){
                       first1=0;
                       printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     }
                     fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     /*printf(fignu*/
                     /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                     /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                     if(first==1){
                       first=0;
                       fprintf(ficgp,"\nset parametric;unset label");
                       fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
                       fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
                       fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
    :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
   %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }else{
                       first=0;
                       fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }/* if first */
                   } /* age mod 5 */
                 } /* end loop age */
                 fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                 first=1;
               } /*l12 */
             } /* k12 */
           } /*l1 */
         }/* k1 */
       } /* loop covariates */
     }
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
     free_vector(xp,1,npar);
     fclose(ficresprob);
     fclose(ficresprobcov);
     fclose(ficresprobcor);
     fflush(ficgp);
     fflush(fichtmcov);
   }
   
   
   /******************* Printing html file ***********/
   void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                     int popforecast, int estepm ,\
                     double jprev1, double mprev1,double anprev1, \
                     double jprev2, double mprev2,double anprev2){
     int jj1, k1, i1, cpt;
   
      fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
      <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
   </ul>");
      fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
    - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
              jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
      fprintf(fichtm,"\
    - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
              stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
      fprintf(fichtm,"\
    - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
              subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
      fprintf(fichtm,"\
    - (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n",
              estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
      fprintf(fichtm,"\
    - Population projections by age and states: \
      <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
   
   fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
    m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        /* Pij */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d1.png\">%s%d1.png</a><br> \
   <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
        /* Quasi-incidences */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
    before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d2.png\">%s%d2.png</a><br> \
   <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
          /* Period (stable) prevalence in each health state */
          for(cpt=1; cpt<nlstate;cpt++){
            fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
   <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
          }
        for(cpt=1; cpt<=nlstate;cpt++) {
           fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
   <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
        }
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
   
   
    fprintf(fichtm,"\
   \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
    - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
   
    fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
    fprintf(fichtm,"\
    - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
   
    fprintf(fichtm,"\
    - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
    fprintf(fichtm,"\
    - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
            estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
    fprintf(fichtm,"\
    - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",
            estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
    fprintf(fichtm,"\
    - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
            subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   
   /*  if(popforecast==1) fprintf(fichtm,"\n */
   /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
   /*      <br>",fileres,fileres,fileres,fileres); */
   /*  else  */
   /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
    fflush(fichtm);
    fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   
    m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        for(cpt=1; cpt<=nlstate;cpt++) {
          fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
   prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
   <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
        }
        fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
   true period expectancies (those weighted with period prevalences are also\
    drawn in addition to the population based expectancies computed using\
    observed and cahotic prevalences: %s%d.png<br>\
   <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
    fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m0,cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
     int ng=0;
   /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   /*     printf("Problem with file %s",optionfilegnuplot); */
   /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   /*   } */
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
     m=pow(2,cptcoveff);
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
    /* 1eme*/
     for (cpt=1; cpt<= nlstate ; cpt ++) {
      for (k1=1; k1<= m ; k1 ++) {
        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
        fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
        fprintf(ficgp,"set xlabel \"Age\" \n\
   set ylabel \"Probability\" \n\
   set ter png small\n\
   set size 0.65,0.65\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else        fprintf(ficgp," \%%*lf (\%%*lf)");
        }
        fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        } 
        fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }  
        fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
      }
     }
     /*2 eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
       fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
       
       for (i=1; i<= nlstate+1 ; i ++) {
         k=2*i;
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         fprintf(ficgp,"\" t\"\" w l 0,");
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
         else fprintf(ficgp,"\" t\"\" w l 0,");
       }
     }
     
     /*3eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<= nlstate ; cpt ++) {
         /*       k=2+nlstate*(2*cpt-2); */
         k=2+(nlstate+1)*(cpt-1);
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
         fprintf(ficgp,"set ter png small\n\
   set size 0.65,0.65\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           
         */
         for (i=1; i< nlstate ; i ++) {
           fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1);
           /*      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
           
         } 
         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
       }
     }
     
     /* CV preval stable (period) */
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<=nlstate ; cpt ++) {
         k=3;
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   set ter png small\nset size 0.65,0.65\n\
   unset log y\n\
   plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
         
         for (i=1; i< nlstate ; i ++)
           fprintf(ficgp,"+$%d",k+i+1);
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
         
         l=3+(nlstate+ndeath)*cpt;
         fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
         for (i=1; i< nlstate ; i ++) {
           l=3+(nlstate+ndeath)*cpt;
           fprintf(ficgp,"+$%d",l+i+1);
         }
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
       } 
     }  
     
     /* proba elementaires */
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             jk++; 
             fprintf(ficgp,"\n");
           }
         }
       }
      }
   
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        for(jk=1; jk <=m; jk++) {
          fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
          if (ng==2)
            fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
          else
            fprintf(ficgp,"\nset title \"Probability\"\n");
          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
          for(k2=1; k2<=nlstate; k2++) {
            k3=i;
            for(k=1; k<=(nlstate+ndeath); k++) {
              if (k != k2){
                if(ng==2)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                else
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;
                for(j=3; j <=ncovmodel; j++) {
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                    fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                    ij++;
                  }
                  else
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
                fprintf(ficgp,")/(1");
                
                for(k1=1; k1 <=nlstate; k1++){   
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
                  for(j=3; j <=ncovmodel; j++){
                    if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                      fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                      ij++;
                    }
                    else
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                  }
                  fprintf(ficgp,")");
                }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
              }
            } /* end k */
          } /* end k2 */
        } /* end jk */
      } /* end ng */
      fflush(ficgp); 
   }  /* end gnuplot */
   
   
   /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
     int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
     double age;
   
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          we use a 5 terms etc. until the borders are no more concerned. 
       */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
           }
         }/* end age */
       }/* end mob */
     }else return -1;
     return 0;
   }/* End movingaverage */
   
   
   /************** Forecasting ******************/
   prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
     int *popage;
     double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   
   
   /**************** function prwizard **********************/
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     /* Wizard to print covariance matrix template */
   
     char ca[32], cb[32], cc[32];
     int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
   } /* end of prwizard */
   /******************* Gompertz Likelihood ******************************/
   double gompertz(double x[])
   { 
     double A,B,L=0.0,sump=0.,num=0.;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
   
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
                +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           L=L+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
    
     return -2*L*num/sump;
   }
   
   /******************* Printing html file ***********/
   void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,  double p[],double **matcov,double agemortsup){
     int i,k;
   
     fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
     fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
     for (i=1;i<=2;i++) 
       fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
     fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
     fprintf(fichtm,"</ul>");
   
   fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
   
    fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
   
    for (k=agegomp;k<(agemortsup-2);k++) 
      fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
   
    
     fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
     fprintf(ficgp,"set out \"graphmort.png\"\n "); 
     fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
     fprintf(ficgp, "set ter png small\n set log y\n"); 
     fprintf(ficgp, "set size 0.65,0.65\n");
     fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
   
   } 
   
   
   
   
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
     int linei, month, year,iout;
     int jj, ll, li, lj, lk, imk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int itimes;
     int NDIM=2;
     int vpopbased=0;
   
     char ca[32], cb[32], cc[32];
     char dummy[]="                         ";
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     struct stat info;
     double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char linetmp[MAXLINE];
       char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE], pathimach[MAXLINE]; 
     char **bp, *tok, *val; /* pathtot */
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     int agemortsup;
     float  sumlpop=0.;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double *severity;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
     double **ximort;
     char *alph[]={"a","a","b","c","d","e"}, str[4];
     int *dcwave;
   
     char z[1]="c", occ;
   
     char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
     char  *strt, strtend[80];
     char *stratrunc;
     int lstra;
   
     long total_usecs;
    
   /*   setlocale (LC_ALL, ""); */
   /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   /*   textdomain (PACKAGE); */
   /*   setlocale (LC_CTYPE, ""); */
   /*   setlocale (LC_MESSAGES, ""); */
   
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     (void) gettimeofday(&start_time,&tzp);
     curr_time=start_time;
     tm = *localtime(&start_time.tv_sec);
     tmg = *gmtime(&start_time.tv_sec);
     strcpy(strstart,asctime(&tm));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tv_sec = tp.tv_sec +86400; */
   /*  tm = *localtime(&start_time.tv_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tv_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     nberr=0; /* Number of errors and warnings */
     nbwarn=0;
     getcwd(pathcd, size);
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       fgets(pathr,FILENAMELENGTH,stdin);
       i=strlen(pathr);
       if(pathr[i-1]=='\n')
         pathr[i-1]='\0';
      for (tok = pathr; tok != NULL; ){
         printf("Pathr |%s|\n",pathr);
         while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
         printf("val= |%s| pathr=%s\n",val,pathr);
         strcpy (pathtot, val);
         if(pathr[0] == '\0') break; /* Dirty */
       }
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     /* Split argv[0], imach program to get pathimach */
     printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
     split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
     printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
    /*   strcpy(pathimach,argv[0]); */
     /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path); /* Can be a relative path */
     if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
       printf("Current directory %s!\n",pathcd);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s\n%s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: \n");
     fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     printf("Local time (at start):%s",strstart);
     fprintf(ficlog,"Local time (at start): %s",strstart);
     fflush(ficlog);
   /*   (void) gettimeofday(&curr_time,&tzp); */
   /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile %s\n",optionfile);
       fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       fflush(ficlog);
       goto end;
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n); 
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
     if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
     /* where is ncovprod ?*/
     ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7*/
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
     npar= nforce*ncovmodel; /* Number of parameters like aij*/
     if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
       printf("Too complex model for current IMaCh: npar=(nlstate+ndeath-1)*nlstate*ncovmodel=%d >= %d(MAXPARM) or nlstate=%d >= %d(NLSTATEMAX) or ndeath=%d >= %d(NDEATHMAX) or ncovmodel=(k+age+#of+signs)=%d(NCOVMAX) >= %d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fprintf(ficlog,"Too complex model for current IMaCh: %d >=%d(MAXPARM) or %d >=%d(NLSTATEMAX) or %d >=%d(NDEATHMAX) or %d(NCOVMAX) >=%d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fflush(stdout);
       fclose (ficlog);
       goto end;
     }
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     delti=delti3[1][1];
     /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
     if(mle==-1){ /* Print a wizard for help writing covariance matrix */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       fclose (ficparo);
       fclose (ficlog);
       goto end;
       exit(0);
     }
     else if(mle==-3) {
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       matcov=matrix(1,npar,1,npar);
     }
     else{
       /* Read guess parameters */
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
       
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       for(i=1; i <=nlstate; i++){
         j=0;
         for(jj=1; jj <=nlstate+ndeath; jj++){
           if(jj==i) continue;
           j++;
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1 != i) && (j1 != j)){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
   It might be a problem of design; if ncovcol and the model are correct\n \
   run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           fprintf(ficparo,"%1d%1d",i1,j1);
           if(mle==1)
             printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar," %lf",&param[i][j][k]);
             if(mle==1){
               printf(" %lf",param[i][j][k]);
               fprintf(ficlog," %lf",param[i][j][k]);
             }
             else
               fprintf(ficlog," %lf",param[i][j][k]);
             fprintf(ficparo," %lf",param[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           if(mle==1)
             printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficparo,"\n");
         }
       }  
       fflush(ficlog);
   
       p=param[1][1];
       
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
   
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath-1; j++){
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1-i)*(j1-j)!=0){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           printf("%1d%1d",i,j);
           fprintf(ficparo,"%1d%1d",i1,j1);
           fprintf(ficlog,"%1d%1d",i1,j1);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar,"%le",&delti3[i][j][k]);
             printf(" %le",delti3[i][j][k]);
             fprintf(ficparo," %le",delti3[i][j][k]);
             fprintf(ficlog," %le",delti3[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           printf("\n");
           fprintf(ficparo,"\n");
           fprintf(ficlog,"\n");
         }
       }
       fflush(ficlog);
   
       delti=delti3[1][1];
   
   
       /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
     
       matcov=matrix(1,npar,1,npar);
       for(i=1; i <=npar; i++)
         for(j=1; j <=npar; j++) matcov[i][j]=0.;
         
       for(i=1; i <=npar; i++){
         fscanf(ficpar,"%s",&str);
         if(mle==1)
           printf("%s",str);
         fprintf(ficlog,"%s",str);
         fprintf(ficparo,"%s",str);
         for(j=1; j <=i; j++){
           fscanf(ficpar," %le",&matcov[i][j]);
           if(mle==1){
             printf(" %.5le",matcov[i][j]);
           }
           fprintf(ficlog," %.5le",matcov[i][j]);
           fprintf(ficparo," %.5le",matcov[i][j]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
       for(i=1; i <=npar; i++)
         for(j=i+1;j<=npar;j++)
           matcov[i][j]=matcov[j][i];
       
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       
       fflush(ficlog);
       
       /*-------- Rewriting parameter file ----------*/
       strcpy(rfileres,"r");    /* "Rparameterfile */
       strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
       strcat(rfileres,".");    /* */
       strcat(rfileres,optionfilext);    /* Other files have txt extension */
       if((ficres =fopen(rfileres,"w"))==NULL) {
         printf("Problem writing new parameter file: %s\n", fileres);goto end;
         fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
       }
       fprintf(ficres,"#%s\n",version);
     }    /* End of mle != -3 */
   
     /*-------- data file ----------*/
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem while opening datafile: %s\n", datafile);goto end;
       fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);goto end;
     }
   
     n= lastobs;
     severity = vector(1,maxwav);
     outcome=imatrix(1,maxwav+1,1,n);
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */ 
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,8);
   
     i=1;
     linei=0;
     while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
       linei=linei+1;
       for(j=strlen(line); j>=0;j--){  /* Untabifies line */
         if(line[j] == '\t')
           line[j] = ' ';
       }
       for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
         ;
       };
       line[j+1]=0;  /* Trims blanks at end of line */
       if(line[0]=='#'){
         fprintf(ficlog,"Comment line\n%s\n",line);
         printf("Comment line\n%s\n",line);
         continue;
       }
       trimbb(linetmp,line); /* Trims multiple blanks in line */
       for (j=0; line[j]!='\0';j++){
         line[j]=linetmp[j];
       }
     
   
       for (j=maxwav;j>=1;j--){
         cutv(stra, strb,line,' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
         /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
             fprintf(ficlog,"Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);
             goto end;
           }
         }
         s[j][i]=lval;
         
         strcpy(line,stra);
         cutv(stra, strb,line,' ');
         if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
         }
         else  if(iout=sscanf(strb,"%s.") != 0){
           month=99;
           year=9999;
         }else{
           printf("Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
           fprintf(ficlog,"Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);fflush(ficlog);
           goto end;
         }
         anint[j][i]= (double) year; 
         mint[j][i]= (double)month; 
         strcpy(line,stra);
       } /* ENd Waves */
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.",dummy) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
           fprintf(ficlog,"Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
           goto end;
       }
       andc[i]=(double) year; 
       moisdc[i]=(double) month; 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.") != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
         fprintf(ficlog,"Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
           goto end;
       }
       if (year==9999) {
         printf("Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given.  Exiting.\n",strb, linei,i,line);
         fprintf(ficlog,"Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog);
           goto end;
   
       }
       annais[i]=(double)(year);
       moisnais[i]=(double)(month); 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       errno=0;
       dval=strtod(strb,&endptr); 
       if( strb[0]=='\0' || (*endptr != '\0')){
         printf("Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fprintf(ficlog,"Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fflush(ficlog);
         goto end;
       }
       weight[i]=dval; 
       strcpy(line,stra);
       
       for (j=ncovcol;j>=1;j--){
         cutv(stra, strb,line,' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);
             fprintf(ficlog,"Error reading data around '%d' at line number %ld for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);fflush(ficlog);
             goto end;
           }
         }
         if(lval <-1 || lval >1){
           printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);
           fprintf(ficlog,"Error reading data around '%d' at line number %ld for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
           goto end;
         }
         covar[j][i]=(double)(lval);
         strcpy(line,stra);
       }  
       lstra=strlen(stra);
        
       if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
         stratrunc = &(stra[lstra-9]);
         num[i]=atol(stratrunc);
       }
       else
         num[i]=atol(stra);
       /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
         printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
       
       i=i+1;
     } /* End loop reading  data */
     fclose(fic);
     /* printf("ii=%d", ij);
        scanf("%d",i);*/
     imx=i-1; /* Number of individuals */
   
     /* for (i=1; i<=imx; i++){
       if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
       if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
       if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
       }*/
      /*  for (i=1; i<=imx; i++){
        if (s[4][i]==9)  s[4][i]=-1; 
        printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
     
     /* for (i=1; i<=imx; i++) */
    
      /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
        else weight[i]=1;*/
   
     /* Calculation of the number of parameters from char model */
     Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. Stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
     Tprod=ivector(1,15); 
     Tvaraff=ivector(1,15); 
     Tvard=imatrix(1,15,1,2);
     Tage=ivector(1,15);      
      
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=1, k2=1;
       j=nbocc(model,'+'); /* j=Number of '+' */
       j1=nbocc(model,'*'); /* j1=Number of '*' */
       cptcovn=j+1; /* Number of covariates V1+V2+V3 =>2+1=3 */
       cptcovprod=j1; /*Number of products  V1*V2 =1 */
       
       strcpy(modelsav,model); 
       if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
         printf("Error. Non available option model=%s ",model);
         fprintf(ficlog,"Error. Non available option model=%s ",model);fflush(ficlog);
         goto end;
       }
       
       /* This loop fills the array Tvar from the string 'model'.*/
       /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
       for(i=(j+1); i>=1;i--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' 
                                        modelsav=V2+V3*age+V1+V4 strb=V3*age+V1+V4 
                                        stra=V2
                                       */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /* Model includes a product V1+V3*age+V2 strb=V3*age*/
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn: V3*age strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
           if (strcmp(strc,"age")==0) { /* Vn*age */
             cptcovprod--;
             cutv(strb,stre,strd,'V');
             Tvar[i]=atoi(stre);  /* V1+V3*age+V2 Tvar[2]=3 */
             cptcovage++; /* Sums the number of covariates including age as a product */
             Tage[cptcovage]=i;  /* Tage[1] =2 */
             /*printf("stre=%s ", stre);*/
           }
           else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutv(strb,stre,strc,'V');
             Tvar[i]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=i;
           }
           else {  /* Age is not in the model V1+V3*V2+V2  strb=V3*V2*/
             cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
             Tvar[i]=ncovcol+k1;  /* find 'n' in Vn and stores in Tvar. 
                                     If already ncovcol=2 and model=V2*V1 Tvar[1]=2+1 and Tvar[2]=2+2 etc */
             cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=i;  /* Tprod[1]  */
             Tvard[k1][1]=atoi(strc); /* m*/
             Tvard[k1][2]=atoi(stre); /* n */
             Tvar[cptcovn+k2]=Tvard[k1][1];
             Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
             for (k=1; k<=lastobs;k++) 
               covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
             k1++;
             k2=k2+2;
           }
         }
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
         cutv(strd,strc,strb,'V');
         Tvar[i]=atoi(strc);
         }
         strcpy(modelsav,stra);  /* modelsav=V2+V3*age+V1+V4 strb=V3*age+V1+V4 */ 
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);*/
   
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights*/
       for(i=1;i<=n;i++) weight[i]=1.0;
     }
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           nberr++;
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           nberr++;
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if ((int)andc[i]!=9999){
                   nbwarn++;
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] <agemin){ 
               agemin=agev[m][i];
               printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);
             }
             else if(agev[m][i] >agemax){
               agemax=agev[m][i];
               /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           nberr++;
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           goto end;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
   
     agegomp=(int)agemin;
     free_vector(severity,1,maxwav);
     free_imatrix(outcome,1,maxwav+1,1,n);
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
   
      
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     if (cptcovn > 0) tricode(Tvar,nbcode,imx);
         
     codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
                                    the estimations*/
     h=0;
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
       for(i=1; i <=(m/pow(2,k));i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */ 
         for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate */
           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){  /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */ 
             h++;
             if (h>m) 
               h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
             printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]);
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
          printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
       
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     if(mle==-3)
       strcat(optionfilegnuplot,"-mort");
     strcat(optionfilegnuplot,".gp");
   
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       fprintf(ficgp,"set missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname); /* Main html file */
     if(mle==-3)
       strcat(optionfilehtm,"-mort");
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm);
       exit(0);
     }
   
     strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
     strcat(optionfilehtmcov,"-cov.htm");
     if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtmcov), exit(0);
     }
     else{
     fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
             optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
    - Log file of the run: <a href=\"%s\">%s</a><br>\n\
    - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
    - Date and time at start: %s</ul>\n",\
             optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
             optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
             fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
     chdir(optionfilefiname); /* Move to directory named optionfile */
     
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
   
     fprintf(fichtm,"\n");
     fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
             imx,agemin,agemax,jmin,jmax,jmean);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
   
     if (mle==-3){
       ximort=matrix(1,NDIM,1,NDIM);
       cens=ivector(1,n);
       ageexmed=vector(1,n);
       agecens=vector(1,n);
       dcwave=ivector(1,n);
    
       for (i=1; i<=imx; i++){
         dcwave[i]=-1;
         for (m=firstpass; m<=lastpass; m++)
           if (s[m][i]>nlstate) {
             dcwave[i]=m;
             /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
             break;
           }
       }
   
       for (i=1; i<=imx; i++) {
         if (wav[i]>0){
           ageexmed[i]=agev[mw[1][i]][i];
           j=wav[i];
           agecens[i]=1.; 
   
           if (ageexmed[i]> 1 && wav[i] > 0){
             agecens[i]=agev[mw[j][i]][i];
             cens[i]= 1;
           }else if (ageexmed[i]< 1) 
             cens[i]= -1;
           if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
             cens[i]=0 ;
         }
         else cens[i]=-1;
       }
       
       for (i=1;i<=NDIM;i++) {
         for (j=1;j<=NDIM;j++)
           ximort[i][j]=(i == j ? 1.0 : 0.0);
       }
       
       p[1]=0.0268; p[NDIM]=0.083;
       /*printf("%lf %lf", p[1], p[2]);*/
       
       
       printf("Powell\n");  fprintf(ficlog,"Powell\n");
       strcpy(filerespow,"pow-mort"); 
       strcat(filerespow,fileres);
       if((ficrespow=fopen(filerespow,"w"))==NULL) {
         printf("Problem with resultfile: %s\n", filerespow);
         fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
       }
       fprintf(ficrespow,"# Powell\n# iter -2*LL");
       /*  for (i=1;i<=nlstate;i++)
           for(j=1;j<=nlstate+ndeath;j++)
           if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       */
       fprintf(ficrespow,"\n");
       
       powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
       fclose(ficrespow);
       
       hesscov(matcov, p, NDIM, delti, 1e-4, gompertz); 
   
       for(i=1; i <=NDIM; i++)
         for(j=i+1;j<=NDIM;j++)
           matcov[i][j]=matcov[j][i];
       
       printf("\nCovariance matrix\n ");
       for(i=1; i <=NDIM; i++) {
         for(j=1;j<=NDIM;j++){ 
           printf("%f ",matcov[i][j]);
         }
         printf("\n ");
       }
       
       printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
       for (i=1;i<=NDIM;i++) 
         printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
   
       lsurv=vector(1,AGESUP);
       lpop=vector(1,AGESUP);
       tpop=vector(1,AGESUP);
       lsurv[agegomp]=100000;
       
       for (k=agegomp;k<=AGESUP;k++) {
         agemortsup=k;
         if (p[1]*exp(p[2]*(k-agegomp))>1) break;
       }
       
       for (k=agegomp;k<agemortsup;k++)
         lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
       
       for (k=agegomp;k<agemortsup;k++){
         lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
         sumlpop=sumlpop+lpop[k];
       }
       
       tpop[agegomp]=sumlpop;
       for (k=agegomp;k<(agemortsup-3);k++){
         /*  tpop[k+1]=2;*/
         tpop[k+1]=tpop[k]-lpop[k];
       }
       
       
       printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
       for (k=agegomp;k<(agemortsup-2);k++) 
         printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
       
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
                        stepm, weightopt,\
                        model,imx,p,matcov,agemortsup);
       
       free_vector(lsurv,1,AGESUP);
       free_vector(lpop,1,AGESUP);
       free_vector(tpop,1,AGESUP);
     } /* Endof if mle==-3 */
     
     else{ /* For mle >=1 */
       globpr=0;/* debug */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       globpr=1; /* to print the contributions */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       if(mle>=1){ /* Could be 1 or 2 */
         mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
       }
       
       /*--------- results files --------------*/
       fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
       
       
       fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(k=1; k <=(nlstate+ndeath); k++){
           if (k != i) {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%lf ",p[jk]);
               fprintf(ficlog,"%lf ",p[jk]);
               fprintf(ficres,"%lf ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       if(mle!=0){
         /* Computing hessian and covariance matrix */
         ftolhess=ftol; /* Usually correct */
         hesscov(matcov, p, npar, delti, ftolhess, func);
       }
       fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
       printf("# Scales (for hessian or gradient estimation)\n");
       fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if (j!=i) {
             fprintf(ficres,"%1d%1d",i,j);
             printf("%1d%1d",i,j);
             fprintf(ficlog,"%1d%1d",i,j);
             for(k=1; k<=ncovmodel;k++){
               printf(" %.5e",delti[jk]);
               fprintf(ficlog," %.5e",delti[jk]);
               fprintf(ficres," %.5e",delti[jk]);
               jk++;
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       
       fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       if(mle>=1)
         printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       /* # 121 Var(a12)\n\ */
       /* # 122 Cov(b12,a12) Var(b12)\n\ */
       /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
       /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
       /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
       /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
       /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
       /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
       
       
       /* Just to have a covariance matrix which will be more understandable
          even is we still don't want to manage dictionary of variables
       */
       for(itimes=1;itimes<=2;itimes++){
         jj=0;
         for(i=1; i <=nlstate; i++){
           for(j=1; j <=nlstate+ndeath; j++){
             if(j==i) continue;
             for(k=1; k<=ncovmodel;k++){
               jj++;
               ca[0]= k+'a'-1;ca[1]='\0';
               if(itimes==1){
                 if(mle>=1)
                   printf("#%1d%1d%d",i,j,k);
                 fprintf(ficlog,"#%1d%1d%d",i,j,k);
                 fprintf(ficres,"#%1d%1d%d",i,j,k);
               }else{
                 if(mle>=1)
                   printf("%1d%1d%d",i,j,k);
                 fprintf(ficlog,"%1d%1d%d",i,j,k);
                 fprintf(ficres,"%1d%1d%d",i,j,k);
               }
               ll=0;
               for(li=1;li <=nlstate; li++){
                 for(lj=1;lj <=nlstate+ndeath; lj++){
                   if(lj==li) continue;
                   for(lk=1;lk<=ncovmodel;lk++){
                     ll++;
                     if(ll<=jj){
                       cb[0]= lk +'a'-1;cb[1]='\0';
                       if(ll<jj){
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }else{
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }
                     }
                   } /* end lk */
                 } /* end lj */
               } /* end li */
               if(mle>=1)
                 printf("\n");
               fprintf(ficlog,"\n");
               fprintf(ficres,"\n");
               numlinepar++;
             } /* end k*/
           } /*end j */
         } /* end i */
       } /* end itimes */
       
       fflush(ficlog);
       fflush(ficres);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       estepm=0;
       fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
       if (estepm==0 || estepm < stepm) estepm=stepm;
       if (fage <= 2) {
         bage = ageminpar;
         fage = agemaxpar;
       }
       
       fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
       fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
       fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       
       dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
       dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
       
       fscanf(ficpar,"pop_based=%d\n",&popbased);
       fprintf(ficparo,"pop_based=%d\n",popbased);   
       fprintf(ficres,"pop_based=%d\n",popbased);   
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
       fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       /* day and month of proj2 are not used but only year anproj2.*/
       
       
       
       /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
       /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                    model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                    jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
         
      /*------------ free_vector  -------------*/
      /*  chdir(path); */
    
       free_ivector(wav,1,imx);
       free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
       free_lvector(num,1,n);
       free_vector(agedc,1,n);
       /*free_matrix(covar,0,NCOVMAX,1,n);*/
       /*free_matrix(covar,1,NCOVMAX,1,n);*/
       fclose(ficparo);
       fclose(ficres);
   
   
       /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
     
       strcpy(filerespl,"pl");
       strcat(filerespl,fileres);
       if((ficrespl=fopen(filerespl,"w"))==NULL) {
         printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
         fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
       }
       printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
       fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
       pstamp(ficrespl);
       fprintf(ficrespl,"# Period (stable) prevalence \n");
       fprintf(ficrespl,"#Age ");
       for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
       fprintf(ficrespl,"\n");
     
       prlim=matrix(1,nlstate,1,nlstate);
   
       agebase=ageminpar;
       agelim=agemaxpar;
       ftolpl=1.e-10;
       i1=cptcoveff;
       if (cptcovn < 1){i1=1;}
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           /* to clean */
           printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,codtab[cptcod][cptcov],nbcode);
           fprintf(ficrespl,"\n#******");
           printf("\n#******");
           fprintf(ficlog,"\n#******");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficrespl,"******\n");
           printf("******\n");
           fprintf(ficlog,"******\n");
           
           for (age=agebase; age<=agelim; age++){
             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
             fprintf(ficrespl,"%.0f ",age );
             for(j=1;j<=cptcoveff;j++)
               fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             for(i=1; i<=nlstate;i++)
               fprintf(ficrespl," %.5f", prlim[i][i]);
             fprintf(ficrespl,"\n");
           }
         }
       }
       fclose(ficrespl);
   
       /*------------- h Pij x at various ages ------------*/
     
       strcpy(filerespij,"pij");  strcat(filerespij,fileres);
       if((ficrespij=fopen(filerespij,"w"))==NULL) {
         printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
         fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
       }
       printf("Computing pij: result on file '%s' \n", filerespij);
       fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
       stepsize=(int) (stepm+YEARM-1)/YEARM;
       /*if (stepm<=24) stepsize=2;*/
   
       agelim=AGESUP;
       hstepm=stepsize*YEARM; /* Every year of age */
       hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
       /* hstepm=1;   aff par mois*/
       pstamp(ficrespij);
       fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           fprintf(ficrespij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrespij,"******\n");
           
           for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
             nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   
             /*      nhstepm=nhstepm*YEARM; aff par mois*/
   
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %1d-%1d",i,j);
             fprintf(ficrespij,"\n");
             for (h=0; h<=nhstepm; h++){
               fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
               for(i=1; i<=nlstate;i++)
                 for(j=1; j<=nlstate+ndeath;j++)
                   fprintf(ficrespij," %.5f", p3mat[i][j][h]);
               fprintf(ficrespij,"\n");
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             fprintf(ficrespij,"\n");
           }
         }
       }
   
       varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
   
       fclose(ficrespij);
   
       probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for(i=1;i<=AGESUP;i++)
         for(j=1;j<=NCOVMAX;j++)
           for(k=1;k<=NCOVMAX;k++)
             probs[i][j][k]=0.;
   
       /*---------- Forecasting ------------------*/
       /*if((stepm == 1) && (strcmp(model,".")==0)){*/
       if(prevfcast==1){
         /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
         /*      }  */
         /*      else{ */
         /*        erreur=108; */
         /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*      } */
       }
     
   
       /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
   
       prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
       /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
           ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
       */
   
       if (mobilav!=0) {
         mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
           fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
           printf(" Error in movingaverage mobilav=%d\n",mobilav);
         }
       }
   
   
       /*---------- Health expectancies, no variances ------------*/
   
       strcpy(filerese,"e");
       strcat(filerese,fileres);
       if((ficreseij=fopen(filerese,"w"))==NULL) {
         printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
         fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       }
       printf("Computing Health Expectancies: result on file '%s' \n", filerese);
       fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1; 
           fprintf(ficreseij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficreseij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);  
         
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         }
       }
       fclose(ficreseij);
   
   
       /*---------- Health expectancies and variances ------------*/
   
   
       strcpy(filerest,"t");
       strcat(filerest,fileres);
       if((ficrest=fopen(filerest,"w"))==NULL) {
         printf("Problem with total LE resultfile: %s\n", filerest);goto end;
         fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
       }
       printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
       fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
   
   
       strcpy(fileresstde,"stde");
       strcat(fileresstde,fileres);
       if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
         printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
         fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
       }
       printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
       fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
   
       strcpy(filerescve,"cve");
       strcat(filerescve,fileres);
       if((ficrescveij=fopen(filerescve,"w"))==NULL) {
         printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
         fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
       }
       printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
       fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
   
       strcpy(fileresv,"v");
       strcat(fileresv,fileres);
       if((ficresvij=fopen(fileresv,"w"))==NULL) {
         printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
         fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
       }
       printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
       fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1; 
           fprintf(ficrest,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrest,"******\n");
   
           fprintf(ficresstdeij,"\n#****** ");
           fprintf(ficrescveij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficresstdeij,"******\n");
           fprintf(ficrescveij,"******\n");
   
           fprintf(ficresvij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);  
    
           vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           pstamp(ficrest);
           for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
             oldm=oldms;savm=savms;
             varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart);   fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");
             if(vpopbased==1)
               fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
             else
               fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
             fprintf(ficrest,"# Age e.. (std) ");
             for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
             fprintf(ficrest,"\n");
   
             epj=vector(1,nlstate+1);
             for(age=bage; age <=fage ;age++){
               prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
               if (vpopbased==1) {
                 if(mobilav ==0){
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=probs[(int)age][i][k];
                 }else{ /* mobilav */ 
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=mobaverage[(int)age][i][k];
                 }
               }
           
               fprintf(ficrest," %4.0f",age);
               for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
                 for(i=1, epj[j]=0.;i <=nlstate;i++) {
                   epj[j] += prlim[i][i]*eij[i][j][(int)age];
                   /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
                 }
                 epj[nlstate+1] +=epj[j];
               }
   
               for(i=1, vepp=0.;i <=nlstate;i++)
                 for(j=1;j <=nlstate;j++)
                   vepp += vareij[i][j][(int)age];
               fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
               for(j=1;j <=nlstate;j++){
                 fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
               }
               fprintf(ficrest,"\n");
             }
           }
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_vector(epj,1,nlstate+1);
         }
       }
       free_vector(weight,1,n);
       free_imatrix(Tvard,1,15,1,2);
       free_imatrix(s,1,maxwav+1,1,n);
       free_matrix(anint,1,maxwav,1,n); 
       free_matrix(mint,1,maxwav,1,n);
       free_ivector(cod,1,n);
       free_ivector(tab,1,NCOVMAX);
       fclose(ficresstdeij);
       fclose(ficrescveij);
       fclose(ficresvij);
       fclose(ficrest);
       fclose(ficpar);
     
       /*------- Variance of period (stable) prevalence------*/   
   
       strcpy(fileresvpl,"vpl");
       strcat(fileresvpl,fileres);
       if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
         printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
         exit(0);
       }
       printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           fprintf(ficresvpl,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvpl,"******\n");
         
           varpl=matrix(1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
           free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
         }
       }
   
       fclose(ficresvpl);
   
       /*---------- End : free ----------------*/
       if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     }  /* mle==-3 arrives here for freeing */
    endfree:
     free_matrix(prlim,1,nlstate,1,nlstate);
       free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(covar,0,NCOVMAX,1,n);
       free_matrix(matcov,1,npar,1,npar);
       /*free_vector(delti,1,npar);*/
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       free_matrix(agev,1,maxwav,1,imx);
       free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   
       free_ivector(ncodemax,1,8);
       free_ivector(Tvar,1,15);
       free_ivector(Tprod,1,15);
       free_ivector(Tvaraff,1,15);
       free_ivector(Tage,1,15);
   
       free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
       free_imatrix(codtab,1,100,1,10);
     fflush(fichtm);
     fflush(ficgp);
     
   
     if((nberr >0) || (nbwarn>0)){
       printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
       fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
     }else{
       printf("End of Imach\n");
       fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     (void) gettimeofday(&end_time,&tzp);
     tm = *localtime(&end_time.tv_sec);
     tmg = *gmtime(&end_time.tv_sec);
     strcpy(strtend,asctime(&tm));
     printf("Local time at start %s\nLocal time at end   %s",strstart, strtend); 
     fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
     printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
   
     printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
     fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
     fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
     /*  printf("Total time was %d uSec.\n", total_usecs);*/
   /*   if(fileappend(fichtm,optionfilehtm)){ */
     fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtm);
     fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtmcov);
     fclose(ficgp);
     fclose(ficlog);
     /*------ End -----------*/
   
   
      printf("Before Current directory %s!\n",pathcd);
      if(chdir(pathcd) != 0)
       printf("Can't move to directory %s!\n",path);
     if(getcwd(pathcd,MAXLINE) > 0)
       printf("Current directory %s!\n",pathcd);
     /*strcat(plotcmd,CHARSEPARATOR);*/
     sprintf(plotcmd,"gnuplot");
   #ifndef UNIX
     sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
   #endif
     if(!stat(plotcmd,&info)){
       printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
       if(!stat(getenv("GNUPLOTBIN"),&info)){
         printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #ifdef UNIX
       strcpy(plotcmd,GNUPLOTPROGRAM);
       if(!stat(plotcmd,&info)){
         printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #endif
     }else
       strcpy(pplotcmd,plotcmd);
     
     sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
     printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
   
     if((outcmd=system(plotcmd)) != 0){
       printf("\n Problem with gnuplot\n");
     }
     printf(" Wait...");
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again and q for exiting: ");
       scanf("%s",z);
   /*     if (z[0] == 'c') system("./imach"); */
       if (z[0] == 'e') {
         printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
         system(optionfilehtm);
       }
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     end:
     while (z[0] != 'q') {
       printf("\nType  q for exiting: ");
       scanf("%s",z);
     }
   }
   
   
   

Removed from v.1.39  
changed lines
  Added in v.1.135


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