Diff for /imach/src/imach.c between versions 1.26 and 1.135

version 1.26, 2002/02/27 15:42:00 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
   probabibility 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 "..\\gp37mgw\\wgnuplot"  
 #define FILENAMELENGTH 80    * imach.c (Module): Weights can have a decimal point as for
 /*#define DEBUG*/    English (a comma might work with a correct LC_NUMERIC environment,
 #define windows    otherwise the weight is truncated).
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    Modification of warning when the covariates values are not 0 or
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    1.
     Version 0.98g
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */  
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    Revision 1.122  2006/03/20 09:45:41  brouard
     (Module): Weights can have a decimal point as for
 #define NINTERVMAX 8    English (a comma might work with a correct LC_NUMERIC environment,
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    otherwise the weight is truncated).
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    Modification of warning when the covariates values are not 0 or
 #define NCOVMAX 8 /* Maximum number of covariates */    1.
 #define MAXN 20000    Version 0.98g
 #define YEARM 12. /* Number of months per year */  
 #define AGESUP 130    Revision 1.121  2006/03/16 17:45:01  lievre
 #define AGEBASE 40    * imach.c (Module): Comments concerning covariates added
   
     * imach.c (Module): refinements in the computation of lli if
 int erreur; /* Error number */    status=-2 in order to have more reliable computation if stepm is
 int nvar;    not 1 month. Version 0.98f
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;  
 int npar=NPARMAX;    Revision 1.120  2006/03/16 15:10:38  lievre
 int nlstate=2; /* Number of live states */    (Module): refinements in the computation of lli if
 int ndeath=1; /* Number of dead states */    status=-2 in order to have more reliable computation if stepm is
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    not 1 month. Version 0.98f
 int popbased=0;  
     Revision 1.119  2006/03/15 17:42:26  brouard
 int *wav; /* Number of waves for this individuual 0 is possible */    (Module): Bug if status = -2, the loglikelihood was
 int maxwav; /* Maxim number of waves */    computed as likelihood omitting the logarithm. Version O.98e
 int jmin, jmax; /* min, max spacing between 2 waves */  
 int mle, weightopt;    Revision 1.118  2006/03/14 18:20:07  brouard
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    (Module): varevsij Comments added explaining the second
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    table of variances if popbased=1 .
 double jmean; /* Mean space between 2 waves */    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 double **oldm, **newm, **savm; /* Working pointers to matrices */    (Module): Function pstamp added
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    (Module): Version 0.98d
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf;  
 FILE *ficgp,*ficresprob,*ficpop;    Revision 1.117  2006/03/14 17:16:22  brouard
 FILE *ficreseij;    (Module): varevsij Comments added explaining the second
   char filerese[FILENAMELENGTH];    table of variances if popbased=1 .
  FILE  *ficresvij;    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
   char fileresv[FILENAMELENGTH];    (Module): Function pstamp added
  FILE  *ficresvpl;    (Module): Version 0.98d
   char fileresvpl[FILENAMELENGTH];  
     Revision 1.116  2006/03/06 10:29:27  brouard
 #define NR_END 1    (Module): Variance-covariance wrong links and
 #define FREE_ARG char*    varian-covariance of ej. is needed (Saito).
 #define FTOL 1.0e-10  
     Revision 1.115  2006/02/27 12:17:45  brouard
 #define NRANSI    (Module): One freematrix added in mlikeli! 0.98c
 #define ITMAX 200  
     Revision 1.114  2006/02/26 12:57:58  brouard
 #define TOL 2.0e-4    (Module): Some improvements in processing parameter
     filename with strsep.
 #define CGOLD 0.3819660  
 #define ZEPS 1.0e-10    Revision 1.113  2006/02/24 14:20:24  brouard
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    (Module): Memory leaks checks with valgrind and:
     datafile was not closed, some imatrix were not freed and on matrix
 #define GOLD 1.618034    allocation too.
 #define GLIMIT 100.0  
 #define TINY 1.0e-20    Revision 1.112  2006/01/30 09:55:26  brouard
     (Module): Back to gnuplot.exe instead of wgnuplot.exe
 static double maxarg1,maxarg2;  
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    Revision 1.111  2006/01/25 20:38:18  brouard
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    (Module): Lots of cleaning and bugs added (Gompertz)
      (Module): Comments can be added in data file. Missing date values
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    can be a simple dot '.'.
 #define rint(a) floor(a+0.5)  
     Revision 1.110  2006/01/25 00:51:50  brouard
 static double sqrarg;    (Module): Lots of cleaning and bugs added (Gompertz)
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    Revision 1.109  2006/01/24 19:37:15  brouard
     (Module): Comments (lines starting with a #) are allowed in data.
 int imx;  
 int stepm;    Revision 1.108  2006/01/19 18:05:42  lievre
 /* Stepm, step in month: minimum step interpolation*/    Gnuplot problem appeared...
     To be fixed
 int m,nb;  
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    Revision 1.107  2006/01/19 16:20:37  brouard
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    Test existence of gnuplot in imach path
 double **pmmij, ***probs, ***mobaverage;  
 double dateintmean=0;    Revision 1.106  2006/01/19 13:24:36  brouard
     Some cleaning and links added in html output
 double *weight;  
 int **s; /* Status */    Revision 1.105  2006/01/05 20:23:19  lievre
 double *agedc, **covar, idx;    *** empty log message ***
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  
     Revision 1.104  2005/09/30 16:11:43  lievre
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    (Module): sump fixed, loop imx fixed, and simplifications.
 double ftolhess; /* Tolerance for computing hessian */    (Module): If the status is missing at the last wave but we know
     that the person is alive, then we can code his/her status as -2
 /**************** split *************************/    (instead of missing=-1 in earlier versions) and his/her
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    contributions to the likelihood is 1 - Prob of dying from last
 {    health status (= 1-p13= p11+p12 in the easiest case of somebody in
    char *s;                             /* pointer */    the healthy state at last known wave). Version is 0.98
    int  l1, l2;                         /* length counters */  
     Revision 1.103  2005/09/30 15:54:49  lievre
    l1 = strlen( path );                 /* length of path */    (Module): sump fixed, loop imx fixed, and simplifications.
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  
 #ifdef windows    Revision 1.102  2004/09/15 17:31:30  brouard
    s = strrchr( path, '\\' );           /* find last / */    Add the possibility to read data file including tab characters.
 #else  
    s = strrchr( path, '/' );            /* find last / */    Revision 1.101  2004/09/15 10:38:38  brouard
 #endif    Fix on curr_time
    if ( s == NULL ) {                   /* no directory, so use current */  
 #if     defined(__bsd__)                /* get current working directory */    Revision 1.100  2004/07/12 18:29:06  brouard
       extern char       *getwd( );    Add version for Mac OS X. Just define UNIX in Makefile
   
       if ( getwd( dirc ) == NULL ) {    Revision 1.99  2004/06/05 08:57:40  brouard
 #else    *** empty log message ***
       extern char       *getcwd( );  
     Revision 1.98  2004/05/16 15:05:56  brouard
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    New version 0.97 . First attempt to estimate force of mortality
 #endif    directly from the data i.e. without the need of knowing the health
          return( GLOCK_ERROR_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
       strcpy( name, path );             /* we've got it */    other analysis, in order to test if the mortality estimated from the
    } else {                             /* strip direcotry from path */    cross-longitudinal survey is different from the mortality estimated
       s++;                              /* after this, the filename */    from other sources like vital statistic data.
       l2 = strlen( s );                 /* length of filename */  
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    The same imach parameter file can be used but the option for mle should be -3.
       strcpy( name, s );                /* save file name */  
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    Agnès, who wrote this part of the code, tried to keep most of the
       dirc[l1-l2] = 0;                  /* add zero */    former routines in order to include the new code within the former code.
    }  
    l1 = strlen( dirc );                 /* length of directory */    The output is very simple: only an estimate of the intercept and of
 #ifdef windows    the slope with 95% confident intervals.
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  
 #else    Current limitations:
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }    A) Even if you enter covariates, i.e. with the
 #endif    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
    s = strrchr( name, '.' );            /* find last / */    B) There is no computation of Life Expectancy nor Life Table.
    s++;  
    strcpy(ext,s);                       /* save extension */    Revision 1.97  2004/02/20 13:25:42  lievre
    l1= strlen( name);    Version 0.96d. Population forecasting command line is (temporarily)
    l2= strlen( s)+1;    suppressed.
    strncpy( finame, name, l1-l2);  
    finame[l1-l2]= 0;    Revision 1.96  2003/07/15 15:38:55  brouard
    return( 0 );                         /* we're done */    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
 }    rewritten within the same printf. Workaround: many printfs.
   
     Revision 1.95  2003/07/08 07:54:34  brouard
 /******************************************/    * imach.c (Repository):
     (Repository): Using imachwizard code to output a more meaningful covariance
 void replace(char *s, char*t)    matrix (cov(a12,c31) instead of numbers.
 {  
   int i;    Revision 1.94  2003/06/27 13:00:02  brouard
   int lg=20;    Just cleaning
   i=0;  
   lg=strlen(t);    Revision 1.93  2003/06/25 16:33:55  brouard
   for(i=0; i<= lg; i++) {    (Module): On windows (cygwin) function asctime_r doesn't
     (s[i] = t[i]);    exist so I changed back to asctime which exists.
     if (t[i]== '\\') s[i]='/';    (Module): Version 0.96b
   }  
 }    Revision 1.92  2003/06/25 16:30:45  brouard
     (Module): On windows (cygwin) function asctime_r doesn't
 int nbocc(char *s, char occ)    exist so I changed back to asctime which exists.
 {  
   int i,j=0;    Revision 1.91  2003/06/25 15:30:29  brouard
   int lg=20;    * imach.c (Repository): Duplicated warning errors corrected.
   i=0;    (Repository): Elapsed time after each iteration is now output. It
   lg=strlen(s);    helps to forecast when convergence will be reached. Elapsed time
   for(i=0; i<= lg; i++) {    is stamped in powell.  We created a new html file for the graphs
   if  (s[i] == occ ) j++;    concerning matrix of covariance. It has extension -cov.htm.
   }  
   return j;    Revision 1.90  2003/06/24 12:34:15  brouard
 }    (Module): Some bugs corrected for windows. Also, when
     mle=-1 a template is output in file "or"mypar.txt with the design
 void cutv(char *u,char *v, char*t, char occ)    of the covariance matrix to be input.
 {  
   int i,lg,j,p=0;    Revision 1.89  2003/06/24 12:30:52  brouard
   i=0;    (Module): Some bugs corrected for windows. Also, when
   for(j=0; j<=strlen(t)-1; j++) {    mle=-1 a template is output in file "or"mypar.txt with the design
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    of the covariance matrix to be input.
   }  
     Revision 1.88  2003/06/23 17:54:56  brouard
   lg=strlen(t);    * 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.
   for(j=0; j<p; j++) {  
     (u[j] = t[j]);    Revision 1.87  2003/06/18 12:26:01  brouard
   }    Version 0.96
      u[p]='\0';  
     Revision 1.86  2003/06/17 20:04:08  brouard
    for(j=0; j<= lg; j++) {    (Module): Change position of html and gnuplot routines and added
     if (j>=(p+1))(v[j-p-1] = t[j]);    routine fileappend.
   }  
 }    Revision 1.85  2003/06/17 13:12:43  brouard
     * imach.c (Repository): Check when date of death was earlier that
 /********************** nrerror ********************/    current date of interview. It may happen when the death was just
     prior to the death. In this case, dh was negative and likelihood
 void nrerror(char error_text[])    was wrong (infinity). We still send an "Error" but patch by
 {    assuming that the date of death was just one stepm after the
   fprintf(stderr,"ERREUR ...\n");    interview.
   fprintf(stderr,"%s\n",error_text);    (Repository): Because some people have very long ID (first column)
   exit(1);    we changed int to long in num[] and we added a new lvector for
 }    memory allocation. But we also truncated to 8 characters (left
 /*********************** vector *******************/    truncation)
 double *vector(int nl, int nh)    (Repository): No more line truncation errors.
 {  
   double *v;    Revision 1.84  2003/06/13 21:44:43  brouard
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    * imach.c (Repository): Replace "freqsummary" at a correct
   if (!v) nrerror("allocation failure in vector");    place. It differs from routine "prevalence" which may be called
   return v-nl+NR_END;    many times. Probs is memory consuming and must be used with
 }    parcimony.
     Version 0.95a3 (should output exactly the same maximization than 0.8a2)
 /************************ free vector ******************/  
 void free_vector(double*v, int nl, int nh)    Revision 1.83  2003/06/10 13:39:11  lievre
 {    *** empty log message ***
   free((FREE_ARG)(v+nl-NR_END));  
 }    Revision 1.82  2003/06/05 15:57:20  brouard
     Add log in  imach.c and  fullversion number is now printed.
 /************************ivector *******************************/  
 int *ivector(long nl,long nh)  */
 {  /*
   int *v;     Interpolated Markov Chain
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  
   if (!v) nrerror("allocation failure in ivector");    Short summary of the programme:
   return v-nl+NR_END;    
 }    This program computes Healthy Life Expectancies from
     cross-longitudinal data. Cross-longitudinal data consist in: -1- a
 /******************free ivector **************************/    first survey ("cross") where individuals from different ages are
 void free_ivector(int *v, long nl, long nh)    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
   free((FREE_ARG)(v+nl-NR_END));    second wave of interviews ("longitudinal") which measure each change
 }    (if any) in individual health status.  Health expectancies are
     computed from the time spent in each health state according to a
 /******************* imatrix *******************************/    model. More health states you consider, more time is necessary to reach the
 int **imatrix(long nrl, long nrh, long ncl, long nch)    Maximum Likelihood of the parameters involved in the model.  The
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    simplest model is the multinomial logistic model where pij is the
 {    probability to be observed in state j at the second wave
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    conditional to be observed in state i at the first wave. Therefore
   int **m;    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
      'age' is age and 'sex' is a covariate. If you want to have a more
   /* allocate pointers to rows */    complex model than "constant and age", you should modify the program
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    where the markup *Covariates have to be included here again* invites
   if (!m) nrerror("allocation failure 1 in matrix()");    you to do it.  More covariates you add, slower the
   m += NR_END;    convergence.
   m -= nrl;  
      The advantage of this computer programme, compared to a simple
      multinomial logistic model, is clear when the delay between waves is not
   /* allocate rows and set pointers to them */    identical for each individual. Also, if a individual missed an
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    intermediate interview, the information is lost, but taken into
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    account using an interpolation or extrapolation.  
   m[nrl] += NR_END;  
   m[nrl] -= ncl;    hPijx is the probability to be observed in state i at age x+h
      conditional to the observed state i at age x. The delay 'h' can be
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    split into an exact number (nh*stepm) of unobserved intermediate
      states. This elementary transition (by month, quarter,
   /* return pointer to array of pointers to rows */    semester or year) is modelled as a multinomial logistic.  The hPx
   return m;    matrix is simply the matrix product of nh*stepm elementary matrices
 }    and the contribution of each individual to the likelihood is simply
     hPijx.
 /****************** free_imatrix *************************/  
 void free_imatrix(m,nrl,nrh,ncl,nch)    Also this programme outputs the covariance matrix of the parameters but also
       int **m;    of the life expectancies. It also computes the period (stable) prevalence. 
       long nch,ncl,nrh,nrl;    
      /* free an int matrix allocated by imatrix() */    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
 {             Institut national d'études démographiques, Paris.
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    This software have been partly granted by Euro-REVES, a concerted action
   free((FREE_ARG) (m+nrl-NR_END));    from the European Union.
 }    It is copyrighted identically to a GNU software product, ie programme and
     software can be distributed freely for non commercial use. Latest version
 /******************* matrix *******************************/    can be accessed at http://euroreves.ined.fr/imach .
 double **matrix(long nrl, long nrh, long ncl, long nch)  
 {    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
   double **m;    
     **********************************************************************/
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  /*
   if (!m) nrerror("allocation failure 1 in matrix()");    main
   m += NR_END;    read parameterfile
   m -= nrl;    read datafile
     concatwav
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    freqsummary
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    if (mle >= 1)
   m[nrl] += NR_END;      mlikeli
   m[nrl] -= ncl;    print results files
     if mle==1 
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;       computes hessian
   return m;    read end of parameter file: agemin, agemax, bage, fage, estepm
 }        begin-prev-date,...
     open gnuplot file
 /*************************free matrix ************************/    open html file
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    period (stable) prevalence
 {     for age prevalim()
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    h Pij x
   free((FREE_ARG)(m+nrl-NR_END));    variance of p varprob
 }    forecasting if prevfcast==1 prevforecast call prevalence()
     health expectancies
 /******************* ma3x *******************************/    Variance-covariance of DFLE
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    prevalence()
 {     movingaverage()
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    varevsij() 
   double ***m;    if popbased==1 varevsij(,popbased)
     total life expectancies
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    Variance of period (stable) prevalence
   if (!m) nrerror("allocation failure 1 in matrix()");   end
   m += NR_END;  */
   m -= nrl;  
   
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");   
   m[nrl] += NR_END;  #include <math.h>
   m[nrl] -= ncl;  #include <stdio.h>
   #include <stdlib.h>
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  #include <string.h>
   #include <unistd.h>
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  #include <limits.h>
   m[nrl][ncl] += NR_END;  #include <sys/types.h>
   m[nrl][ncl] -= nll;  #include <sys/stat.h>
   for (j=ncl+1; j<=nch; j++)  #include <errno.h>
     m[nrl][j]=m[nrl][j-1]+nlay;  extern int errno;
    
   for (i=nrl+1; i<=nrh; i++) {  /* #include <sys/time.h> */
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  #include <time.h>
     for (j=ncl+1; j<=nch; j++)  #include "timeval.h"
       m[i][j]=m[i][j-1]+nlay;  
   }  /* #include <libintl.h> */
   return m;  /* #define _(String) gettext (String) */
 }  
   #define MAXLINE 256
 /*************************free ma3x ************************/  
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  #define GNUPLOTPROGRAM "gnuplot"
 {  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  #define FILENAMELENGTH 132
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  
   free((FREE_ARG)(m+nrl-NR_END));  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 }  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   
 /***************** f1dim *************************/  #define MAXPARM 128 /* Maximum number of parameters for the optimization */
 extern int ncom;  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
 extern double *pcom,*xicom;  
 extern double (*nrfunc)(double []);  #define NINTERVMAX 8
    #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 double f1dim(double x)  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
 {  #define NCOVMAX 20 /* Maximum number of covariates */
   int j;  #define MAXN 20000
   double f;  #define YEARM 12. /* Number of months per year */
   double *xt;  #define AGESUP 130
    #define AGEBASE 40
   xt=vector(1,ncom);  #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  #ifdef UNIX
   f=(*nrfunc)(xt);  #define DIRSEPARATOR '/'
   free_vector(xt,1,ncom);  #define CHARSEPARATOR "/"
   return f;  #define ODIRSEPARATOR '\\'
 }  #else
   #define DIRSEPARATOR '\\'
 /*****************brent *************************/  #define CHARSEPARATOR "\\"
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  #define ODIRSEPARATOR '/'
 {  #endif
   int iter;  
   double a,b,d,etemp;  /* $Id$ */
   double fu,fv,fw,fx;  /* $State$ */
   double ftemp;  
   double p,q,r,tol1,tol2,u,v,w,x,xm;  char version[]="Imach version 0.98l, October 2009, INED-EUROREVES-Institut de longevite ";
   double e=0.0;  char fullversion[]="$Revision$ $Date$"; 
    char strstart[80];
   a=(ax < cx ? ax : cx);  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
   b=(ax > cx ? ax : cx);  int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
   x=w=v=bx;  int nvar=0, nforce=0; /* Number of variables, number of forces */
   fw=fv=fx=(*f)(x);  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov=0; /* Number of covariates, of covariates with '*age' */
   for (iter=1;iter<=ITMAX;iter++) {  int npar=NPARMAX;
     xm=0.5*(a+b);  int nlstate=2; /* Number of live states */
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  int ndeath=1; /* Number of dead states */
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
     printf(".");fflush(stdout);  int popbased=0;
 #ifdef DEBUG  
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);  int *wav; /* Number of waves for this individuual 0 is possible */
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  int maxwav=0; /* Maxim number of waves */
 #endif  int jmin=0, jmax=0; /* min, max spacing between 2 waves */
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
       *xmin=x;  int gipmx=0, gsw=0; /* Global variables on the number of contributions 
       return fx;                     to the likelihood and the sum of weights (done by funcone)*/
     }  int mle=1, weightopt=0;
     ftemp=fu;  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
     if (fabs(e) > tol1) {  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
       r=(x-w)*(fx-fv);  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
       q=(x-v)*(fx-fw);             * wave mi and wave mi+1 is not an exact multiple of stepm. */
       p=(x-v)*q-(x-w)*r;  double jmean=1; /* Mean space between 2 waves */
       q=2.0*(q-r);  double **oldm, **newm, **savm; /* Working pointers to matrices */
       if (q > 0.0) p = -p;  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
       q=fabs(q);  FILE *fic,*ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
       etemp=e;  FILE *ficlog, *ficrespow;
       e=d;  int globpr=0; /* Global variable for printing or not */
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  double fretone; /* Only one call to likelihood */
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  long ipmx=0; /* Number of contributions */
       else {  double sw; /* Sum of weights */
         d=p/q;  char filerespow[FILENAMELENGTH];
         u=x+d;  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
         if (u-a < tol2 || b-u < tol2)  FILE *ficresilk;
           d=SIGN(tol1,xm-x);  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
       }  FILE *ficresprobmorprev;
     } else {  FILE *fichtm, *fichtmcov; /* Html File */
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  FILE *ficreseij;
     }  char filerese[FILENAMELENGTH];
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  FILE *ficresstdeij;
     fu=(*f)(u);  char fileresstde[FILENAMELENGTH];
     if (fu <= fx) {  FILE *ficrescveij;
       if (u >= x) a=x; else b=x;  char filerescve[FILENAMELENGTH];
       SHFT(v,w,x,u)  FILE  *ficresvij;
         SHFT(fv,fw,fx,fu)  char fileresv[FILENAMELENGTH];
         } else {  FILE  *ficresvpl;
           if (u < x) a=u; else b=u;  char fileresvpl[FILENAMELENGTH];
           if (fu <= fw || w == x) {  char title[MAXLINE];
             v=w;  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
             w=u;  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
             fv=fw;  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
             fw=fu;  char command[FILENAMELENGTH];
           } else if (fu <= fv || v == x || v == w) {  int  outcmd=0;
             v=u;  
             fv=fu;  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
           }  
         }  char filelog[FILENAMELENGTH]; /* Log file */
   }  char filerest[FILENAMELENGTH];
   nrerror("Too many iterations in brent");  char fileregp[FILENAMELENGTH];
   *xmin=x;  char popfile[FILENAMELENGTH];
   return fx;  
 }  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
   
 /****************** mnbrak ***********************/  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
   struct timezone tzp;
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  extern int gettimeofday();
             double (*func)(double))  struct tm tmg, tm, tmf, *gmtime(), *localtime();
 {  long time_value;
   double ulim,u,r,q, dum;  extern long time();
   double fu;  char strcurr[80], strfor[80];
    
   *fa=(*func)(*ax);  char *endptr;
   *fb=(*func)(*bx);  long lval;
   if (*fb > *fa) {  double dval;
     SHFT(dum,*ax,*bx,dum)  
       SHFT(dum,*fb,*fa,dum)  #define NR_END 1
       }  #define FREE_ARG char*
   *cx=(*bx)+GOLD*(*bx-*ax);  #define FTOL 1.0e-10
   *fc=(*func)(*cx);  
   while (*fb > *fc) {  #define NRANSI 
     r=(*bx-*ax)*(*fb-*fc);  #define ITMAX 200 
     q=(*bx-*cx)*(*fb-*fa);  
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  #define TOL 2.0e-4 
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  
     ulim=(*bx)+GLIMIT*(*cx-*bx);  #define CGOLD 0.3819660 
     if ((*bx-u)*(u-*cx) > 0.0) {  #define ZEPS 1.0e-10 
       fu=(*func)(u);  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
     } else if ((*cx-u)*(u-ulim) > 0.0) {  
       fu=(*func)(u);  #define GOLD 1.618034 
       if (fu < *fc) {  #define GLIMIT 100.0 
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  #define TINY 1.0e-20 
           SHFT(*fb,*fc,fu,(*func)(u))  
           }  static double maxarg1,maxarg2;
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
       u=ulim;  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
       fu=(*func)(u);    
     } else {  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
       u=(*cx)+GOLD*(*cx-*bx);  #define rint(a) floor(a+0.5)
       fu=(*func)(u);  
     }  static double sqrarg;
     SHFT(*ax,*bx,*cx,u)  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
       SHFT(*fa,*fb,*fc,fu)  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
       }  int agegomp= AGEGOMP;
 }  
   int imx; 
 /*************** linmin ************************/  int stepm=1;
   /* Stepm, step in month: minimum step interpolation*/
 int ncom;  
 double *pcom,*xicom;  int estepm;
 double (*nrfunc)(double []);  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
    
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  int m,nb;
 {  long *num;
   double brent(double ax, double bx, double cx,  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
                double (*f)(double), double tol, double *xmin);  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
   double f1dim(double x);  double **pmmij, ***probs;
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  double *ageexmed,*agecens;
               double *fc, double (*func)(double));  double dateintmean=0;
   int j;  
   double xx,xmin,bx,ax;  double *weight;
   double fx,fb,fa;  int **s; /* Status */
    double *agedc, **covar, idx;
   ncom=n;  int **nbcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
   pcom=vector(1,n);  double *lsurv, *lpop, *tpop;
   xicom=vector(1,n);  
   nrfunc=func;  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
   for (j=1;j<=n;j++) {  double ftolhess; /* Tolerance for computing hessian */
     pcom[j]=p[j];  
     xicom[j]=xi[j];  /**************** split *************************/
   }  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   ax=0.0;  {
   xx=1.0;    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);       the name of the file (name), its extension only (ext) and its first part of the name (finame)
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    */ 
 #ifdef DEBUG    char  *ss;                            /* pointer */
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    int   l1, l2;                         /* length counters */
 #endif  
   for (j=1;j<=n;j++) {    l1 = strlen(path );                   /* length of path */
     xi[j] *= xmin;    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
     p[j] += xi[j];    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
   }    if ( ss == NULL ) {                   /* no directory, so determine current directory */
   free_vector(xicom,1,n);      strcpy( name, path );               /* we got the fullname name because no directory */
   free_vector(pcom,1,n);      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
 }        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
       /* get current working directory */
 /*************** powell ************************/      /*    extern  char* getcwd ( char *buf , int len);*/
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
             double (*func)(double []))        return( GLOCK_ERROR_GETCWD );
 {      }
   void linmin(double p[], double xi[], int n, double *fret,      /* got dirc from getcwd*/
               double (*func)(double []));      printf(" DIRC = %s \n",dirc);
   int i,ibig,j;    } else {                              /* strip direcotry from path */
   double del,t,*pt,*ptt,*xit;      ss++;                               /* after this, the filename */
   double fp,fptt;      l2 = strlen( ss );                  /* length of filename */
   double *xits;      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
   pt=vector(1,n);      strcpy( name, ss );         /* save file name */
   ptt=vector(1,n);      strncpy( dirc, path, l1 - l2 );     /* now the directory */
   xit=vector(1,n);      dirc[l1-l2] = 0;                    /* add zero */
   xits=vector(1,n);      printf(" DIRC2 = %s \n",dirc);
   *fret=(*func)(p);    }
   for (j=1;j<=n;j++) pt[j]=p[j];    /* We add a separator at the end of dirc if not exists */
   for (*iter=1;;++(*iter)) {    l1 = strlen( dirc );                  /* length of directory */
     fp=(*fret);    if( dirc[l1-1] != DIRSEPARATOR ){
     ibig=0;      dirc[l1] =  DIRSEPARATOR;
     del=0.0;      dirc[l1+1] = 0; 
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);      printf(" DIRC3 = %s \n",dirc);
     for (i=1;i<=n;i++)    }
       printf(" %d %.12f",i, p[i]);    ss = strrchr( name, '.' );            /* find last / */
     printf("\n");    if (ss >0){
     for (i=1;i<=n;i++) {      ss++;
       for (j=1;j<=n;j++) xit[j]=xi[j][i];      strcpy(ext,ss);                     /* save extension */
       fptt=(*fret);      l1= strlen( name);
 #ifdef DEBUG      l2= strlen(ss)+1;
       printf("fret=%lf \n",*fret);      strncpy( finame, name, l1-l2);
 #endif      finame[l1-l2]= 0;
       printf("%d",i);fflush(stdout);    }
       linmin(p,xit,n,fret,func);  
       if (fabs(fptt-(*fret)) > del) {    return( 0 );                          /* we're done */
         del=fabs(fptt-(*fret));  }
         ibig=i;  
       }  
 #ifdef DEBUG  /******************************************/
       printf("%d %.12e",i,(*fret));  
       for (j=1;j<=n;j++) {  void replace_back_to_slash(char *s, char*t)
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  {
         printf(" x(%d)=%.12e",j,xit[j]);    int i;
       }    int lg=0;
       for(j=1;j<=n;j++)    i=0;
         printf(" p=%.12e",p[j]);    lg=strlen(t);
       printf("\n");    for(i=0; i<= lg; i++) {
 #endif      (s[i] = t[i]);
     }      if (t[i]== '\\') s[i]='/';
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {    }
 #ifdef DEBUG  }
       int k[2],l;  
       k[0]=1;  char *trimbb(char *out, char *in)
       k[1]=-1;  { /* Trim multiple blanks in line */
       printf("Max: %.12e",(*func)(p));    char *s;
       for (j=1;j<=n;j++)    s=out;
         printf(" %.12e",p[j]);    while (*in != '\0'){
       printf("\n");      while( *in == ' ' && *(in+1) == ' ' && *(in+1) != '\0'){
       for(l=0;l<=1;l++) {        in++;
         for (j=1;j<=n;j++) {      }
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];      *out++ = *in++;
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);    }
         }    *out='\0';
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    return s;
       }  }
 #endif  
   int nbocc(char *s, char occ)
   {
       free_vector(xit,1,n);    int i,j=0;
       free_vector(xits,1,n);    int lg=20;
       free_vector(ptt,1,n);    i=0;
       free_vector(pt,1,n);    lg=strlen(s);
       return;    for(i=0; i<= lg; i++) {
     }    if  (s[i] == occ ) j++;
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    }
     for (j=1;j<=n;j++) {    return j;
       ptt[j]=2.0*p[j]-pt[j];  }
       xit[j]=p[j]-pt[j];  
       pt[j]=p[j];  void cutv(char *u,char *v, char*t, char occ)
     }  {
     fptt=(*func)(ptt);    /* cuts string t into u and v where u ends before first occurence of char 'occ' 
     if (fptt < fp) {       and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);       gives u="abcedf" and v="ghi2j" */
       if (t < 0.0) {    int i,lg,j,p=0;
         linmin(p,xit,n,fret,func);    i=0;
         for (j=1;j<=n;j++) {    for(j=0; j<=strlen(t)-1; j++) {
           xi[j][ibig]=xi[j][n];      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
           xi[j][n]=xit[j];    }
         }  
 #ifdef DEBUG    lg=strlen(t);
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);    for(j=0; j<p; j++) {
         for(j=1;j<=n;j++)      (u[j] = t[j]);
           printf(" %.12e",xit[j]);    }
         printf("\n");       u[p]='\0';
 #endif  
       }     for(j=0; j<= lg; j++) {
     }      if (j>=(p+1))(v[j-p-1] = t[j]);
   }    }
 }  }
   
 /**** Prevalence limit ****************/  /********************** nrerror ********************/
   
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  void nrerror(char error_text[])
 {  {
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit    fprintf(stderr,"ERREUR ...\n");
      matrix by transitions matrix until convergence is reached */    fprintf(stderr,"%s\n",error_text);
     exit(EXIT_FAILURE);
   int i, ii,j,k;  }
   double min, max, maxmin, maxmax,sumnew=0.;  /*********************** vector *******************/
   double **matprod2();  double *vector(int nl, int nh)
   double **out, cov[NCOVMAX], **pmij();  {
   double **newm;    double *v;
   double agefin, delaymax=50 ; /* Max number of years to converge */    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
     if (!v) nrerror("allocation failure in vector");
   for (ii=1;ii<=nlstate+ndeath;ii++)    return v-nl+NR_END;
     for (j=1;j<=nlstate+ndeath;j++){  }
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);  
     }  /************************ free vector ******************/
   void free_vector(double*v, int nl, int nh)
    cov[1]=1.;  {
      free((FREE_ARG)(v+nl-NR_END));
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */  }
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){  
     newm=savm;  /************************ivector *******************************/
     /* Covariates have to be included here again */  int *ivector(long nl,long nh)
      cov[2]=agefin;  {
      int *v;
       for (k=1; k<=cptcovn;k++) {    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    if (!v) nrerror("allocation failure in ivector");
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/    return v-nl+NR_END;
       }  }
       for (k=1; k<=cptcovage;k++)  
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  /******************free ivector **************************/
       for (k=1; k<=cptcovprod;k++)  void free_ivector(int *v, long nl, long nh)
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  {
     free((FREE_ARG)(v+nl-NR_END));
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/  }
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/  
   /************************lvector *******************************/
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  long *lvector(long nl,long nh)
   {
     savm=oldm;    long *v;
     oldm=newm;    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
     maxmax=0.;    if (!v) nrerror("allocation failure in ivector");
     for(j=1;j<=nlstate;j++){    return v-nl+NR_END;
       min=1.;  }
       max=0.;  
       for(i=1; i<=nlstate; i++) {  /******************free lvector **************************/
         sumnew=0;  void free_lvector(long *v, long nl, long nh)
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  {
         prlim[i][j]= newm[i][j]/(1-sumnew);    free((FREE_ARG)(v+nl-NR_END));
         max=FMAX(max,prlim[i][j]);  }
         min=FMIN(min,prlim[i][j]);  
       }  /******************* imatrix *******************************/
       maxmin=max-min;  int **imatrix(long nrl, long nrh, long ncl, long nch) 
       maxmax=FMAX(maxmax,maxmin);       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
     }  { 
     if(maxmax < ftolpl){    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
       return prlim;    int **m; 
     }    
   }    /* allocate pointers to rows */ 
 }    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
     if (!m) nrerror("allocation failure 1 in matrix()"); 
 /*************** transition probabilities ***************/    m += NR_END; 
     m -= nrl; 
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )    
 {    
   double s1, s2;    /* allocate rows and set pointers to them */ 
   /*double t34;*/    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
   int i,j,j1, nc, ii, jj;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
     m[nrl] += NR_END; 
     for(i=1; i<= nlstate; i++){    m[nrl] -= ncl; 
     for(j=1; j<i;j++){    
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
         /*s2 += param[i][j][nc]*cov[nc];*/    
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    /* return pointer to array of pointers to rows */ 
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/    return m; 
       }  } 
       ps[i][j]=s2;  
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/  /****************** free_imatrix *************************/
     }  void free_imatrix(m,nrl,nrh,ncl,nch)
     for(j=i+1; j<=nlstate+ndeath;j++){        int **m;
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){        long nch,ncl,nrh,nrl; 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];       /* free an int matrix allocated by imatrix() */ 
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/  { 
       }    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
       ps[i][j]=s2;    free((FREE_ARG) (m+nrl-NR_END)); 
     }  } 
   }  
     /*ps[3][2]=1;*/  /******************* matrix *******************************/
   double **matrix(long nrl, long nrh, long ncl, long nch)
   for(i=1; i<= nlstate; i++){  {
      s1=0;    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
     for(j=1; j<i; j++)    double **m;
       s1+=exp(ps[i][j]);  
     for(j=i+1; j<=nlstate+ndeath; j++)    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       s1+=exp(ps[i][j]);    if (!m) nrerror("allocation failure 1 in matrix()");
     ps[i][i]=1./(s1+1.);    m += NR_END;
     for(j=1; j<i; j++)    m -= nrl;
       ps[i][j]= exp(ps[i][j])*ps[i][i];  
     for(j=i+1; j<=nlstate+ndeath; j++)    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       ps[i][j]= exp(ps[i][j])*ps[i][i];    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */    m[nrl] += NR_END;
   } /* end i */    m[nrl] -= ncl;
   
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     for(jj=1; jj<= nlstate+ndeath; jj++){    return m;
       ps[ii][jj]=0;    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
       ps[ii][ii]=1;     */
     }  }
   }  
   /*************************free matrix ************************/
   void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){  {
     for(jj=1; jj<= nlstate+ndeath; jj++){    free((FREE_ARG)(m[nrl]+ncl-NR_END));
      printf("%lf ",ps[ii][jj]);    free((FREE_ARG)(m+nrl-NR_END));
    }  }
     printf("\n ");  
     }  /******************* ma3x *******************************/
     printf("\n ");printf("%lf ",cov[2]);*/  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
 /*  {
   for(i=1; i<= npar; i++) printf("%f ",x[i]);    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
   goto end;*/    double ***m;
     return ps;  
 }    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     if (!m) nrerror("allocation failure 1 in matrix()");
 /**************** Product of 2 matrices ******************/    m += NR_END;
     m -= nrl;
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)  
 {    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */    m[nrl] += NR_END;
   /* in, b, out are matrice of pointers which should have been initialized    m[nrl] -= ncl;
      before: only the contents of out is modified. The function returns  
      a pointer to pointers identical to out */    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   long i, j, k;  
   for(i=nrl; i<= nrh; i++)    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
     for(k=ncolol; k<=ncoloh; k++)    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
       for(j=ncl,out[i][k]=0.; j<=nch; j++)    m[nrl][ncl] += NR_END;
         out[i][k] +=in[i][j]*b[j][k];    m[nrl][ncl] -= nll;
     for (j=ncl+1; j<=nch; j++) 
   return out;      m[nrl][j]=m[nrl][j-1]+nlay;
 }    
     for (i=nrl+1; i<=nrh; i++) {
       m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
 /************* Higher Matrix Product ***************/      for (j=ncl+1; j<=nch; j++) 
         m[i][j]=m[i][j-1]+nlay;
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )    }
 {    return m; 
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
      duration (i.e. until             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.    */
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step  }
      (typically every 2 years instead of every month which is too big).  
      Model is determined by parameters x and covariates have to be  /*************************free ma3x ************************/
      included manually here.  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
   {
      */    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
     free((FREE_ARG)(m[nrl]+ncl-NR_END));
   int i, j, d, h, k;    free((FREE_ARG)(m+nrl-NR_END));
   double **out, cov[NCOVMAX];  }
   double **newm;  
   /*************** function subdirf ***********/
   /* Hstepm could be zero and should return the unit matrix */  char *subdirf(char fileres[])
   for (i=1;i<=nlstate+ndeath;i++)  {
     for (j=1;j<=nlstate+ndeath;j++){    /* Caution optionfilefiname is hidden */
       oldm[i][j]=(i==j ? 1.0 : 0.0);    strcpy(tmpout,optionfilefiname);
       po[i][j][0]=(i==j ? 1.0 : 0.0);    strcat(tmpout,"/"); /* Add to the right */
     }    strcat(tmpout,fileres);
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    return tmpout;
   for(h=1; h <=nhstepm; h++){  }
     for(d=1; d <=hstepm; d++){  
       newm=savm;  /*************** function subdirf2 ***********/
       /* Covariates have to be included here again */  char *subdirf2(char fileres[], char *preop)
       cov[1]=1.;  {
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;    
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    /* Caution optionfilefiname is hidden */
       for (k=1; k<=cptcovage;k++)    strcpy(tmpout,optionfilefiname);
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    strcat(tmpout,"/");
       for (k=1; k<=cptcovprod;k++)    strcat(tmpout,preop);
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    strcat(tmpout,fileres);
     return tmpout;
   }
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/  
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/  /*************** function subdirf3 ***********/
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,  char *subdirf3(char fileres[], char *preop, char *preop2)
                    pmij(pmmij,cov,ncovmodel,x,nlstate));  {
       savm=oldm;    
       oldm=newm;    /* Caution optionfilefiname is hidden */
     }    strcpy(tmpout,optionfilefiname);
     for(i=1; i<=nlstate+ndeath; i++)    strcat(tmpout,"/");
       for(j=1;j<=nlstate+ndeath;j++) {    strcat(tmpout,preop);
         po[i][j][h]=newm[i][j];    strcat(tmpout,preop2);
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);    strcat(tmpout,fileres);
          */    return tmpout;
       }  }
   } /* end h */  
   return po;  /***************** f1dim *************************/
 }  extern int ncom; 
   extern double *pcom,*xicom;
   extern double (*nrfunc)(double []); 
 /*************** log-likelihood *************/   
 double func( double *x)  double f1dim(double x) 
 {  { 
   int i, ii, j, k, mi, d, kk;    int j; 
   double l, ll[NLSTATEMAX], cov[NCOVMAX];    double f;
   double **out;    double *xt; 
   double sw; /* Sum of weights */   
   double lli; /* Individual log likelihood */    xt=vector(1,ncom); 
   long ipmx;    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
   /*extern weight */    f=(*nrfunc)(xt); 
   /* We are differentiating ll according to initial status */    free_vector(xt,1,ncom); 
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    return f; 
   /*for(i=1;i<imx;i++)  } 
     printf(" %d\n",s[4][i]);  
   */  /*****************brent *************************/
   cov[1]=1.;  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
   { 
   for(k=1; k<=nlstate; k++) ll[k]=0.;    int iter; 
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){    double a,b,d,etemp;
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];    double fu,fv,fw,fx;
     for(mi=1; mi<= wav[i]-1; mi++){    double ftemp;
       for (ii=1;ii<=nlstate+ndeath;ii++)    double p,q,r,tol1,tol2,u,v,w,x,xm; 
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);    double e=0.0; 
       for(d=0; d<dh[mi][i]; d++){   
         newm=savm;    a=(ax < cx ? ax : cx); 
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;    b=(ax > cx ? ax : cx); 
         for (kk=1; kk<=cptcovage;kk++) {    x=w=v=bx; 
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];    fw=fv=fx=(*f)(x); 
         }    for (iter=1;iter<=ITMAX;iter++) { 
              xm=0.5*(a+b); 
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
         savm=oldm;      printf(".");fflush(stdout);
         oldm=newm;      fprintf(ficlog,".");fflush(ficlog);
          #ifdef DEBUG
              printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
       } /* end mult */      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)))) { */
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);  #endif
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
       ipmx +=1;        *xmin=x; 
       sw += weight[i];        return fx; 
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;      } 
     } /* end of wave */      ftemp=fu;
   } /* end of individual */      if (fabs(e) > tol1) { 
         r=(x-w)*(fx-fv); 
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];        q=(x-v)*(fx-fw); 
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */        p=(x-v)*q-(x-w)*r; 
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */        q=2.0*(q-r); 
   return -l;        if (q > 0.0) p = -p; 
 }        q=fabs(q); 
         etemp=e; 
         e=d; 
 /*********** Maximum Likelihood Estimation ***************/        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)); 
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))        else { 
 {          d=p/q; 
   int i,j, iter;          u=x+d; 
   double **xi,*delti;          if (u-a < tol2 || b-u < tol2) 
   double fret;            d=SIGN(tol1,xm-x); 
   xi=matrix(1,npar,1,npar);        } 
   for (i=1;i<=npar;i++)      } else { 
     for (j=1;j<=npar;j++)        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       xi[i][j]=(i==j ? 1.0 : 0.0);      } 
   printf("Powell\n");      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
   powell(p,xi,npar,ftol,&iter,&fret,func);      fu=(*f)(u); 
       if (fu <= fx) { 
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));        if (u >= x) a=x; else b=x; 
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));        SHFT(v,w,x,u) 
           SHFT(fv,fw,fx,fu) 
 }          } else { 
             if (u < x) a=u; else b=u; 
 /**** Computes Hessian and covariance matrix ***/            if (fu <= fw || w == x) { 
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))              v=w; 
 {              w=u; 
   double  **a,**y,*x,pd;              fv=fw; 
   double **hess;              fw=fu; 
   int i, j,jk;            } else if (fu <= fv || v == x || v == w) { 
   int *indx;              v=u; 
               fv=fu; 
   double hessii(double p[], double delta, int theta, double delti[]);            } 
   double hessij(double p[], double delti[], int i, int j);          } 
   void lubksb(double **a, int npar, int *indx, double b[]) ;    } 
   void ludcmp(double **a, int npar, int *indx, double *d) ;    nrerror("Too many iterations in brent"); 
     *xmin=x; 
   hess=matrix(1,npar,1,npar);    return fx; 
   } 
   printf("\nCalculation of the hessian matrix. Wait...\n");  
   for (i=1;i<=npar;i++){  /****************** mnbrak ***********************/
     printf("%d",i);fflush(stdout);  
     hess[i][i]=hessii(p,ftolhess,i,delti);  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
     /*printf(" %f ",p[i]);*/              double (*func)(double)) 
     /*printf(" %lf ",hess[i][i]);*/  { 
   }    double ulim,u,r,q, dum;
      double fu; 
   for (i=1;i<=npar;i++) {   
     for (j=1;j<=npar;j++)  {    *fa=(*func)(*ax); 
       if (j>i) {    *fb=(*func)(*bx); 
         printf(".%d%d",i,j);fflush(stdout);    if (*fb > *fa) { 
         hess[i][j]=hessij(p,delti,i,j);      SHFT(dum,*ax,*bx,dum) 
         hess[j][i]=hess[i][j];            SHFT(dum,*fb,*fa,dum) 
         /*printf(" %lf ",hess[i][j]);*/        } 
       }    *cx=(*bx)+GOLD*(*bx-*ax); 
     }    *fc=(*func)(*cx); 
   }    while (*fb > *fc) { 
   printf("\n");      r=(*bx-*ax)*(*fb-*fc); 
       q=(*bx-*cx)*(*fb-*fa); 
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
          (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
   a=matrix(1,npar,1,npar);      ulim=(*bx)+GLIMIT*(*cx-*bx); 
   y=matrix(1,npar,1,npar);      if ((*bx-u)*(u-*cx) > 0.0) { 
   x=vector(1,npar);        fu=(*func)(u); 
   indx=ivector(1,npar);      } else if ((*cx-u)*(u-ulim) > 0.0) { 
   for (i=1;i<=npar;i++)        fu=(*func)(u); 
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];        if (fu < *fc) { 
   ludcmp(a,npar,indx,&pd);          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
             SHFT(*fb,*fc,fu,(*func)(u)) 
   for (j=1;j<=npar;j++) {            } 
     for (i=1;i<=npar;i++) x[i]=0;      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
     x[j]=1;        u=ulim; 
     lubksb(a,npar,indx,x);        fu=(*func)(u); 
     for (i=1;i<=npar;i++){      } else { 
       matcov[i][j]=x[i];        u=(*cx)+GOLD*(*cx-*bx); 
     }        fu=(*func)(u); 
   }      } 
       SHFT(*ax,*bx,*cx,u) 
   printf("\n#Hessian matrix#\n");        SHFT(*fa,*fb,*fc,fu) 
   for (i=1;i<=npar;i++) {        } 
     for (j=1;j<=npar;j++) {  } 
       printf("%.3e ",hess[i][j]);  
     }  /*************** linmin ************************/
     printf("\n");  
   }  int ncom; 
   double *pcom,*xicom;
   /* Recompute Inverse */  double (*nrfunc)(double []); 
   for (i=1;i<=npar;i++)   
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
   ludcmp(a,npar,indx,&pd);  { 
     double brent(double ax, double bx, double cx, 
   /*  printf("\n#Hessian matrix recomputed#\n");                 double (*f)(double), double tol, double *xmin); 
     double f1dim(double x); 
   for (j=1;j<=npar;j++) {    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
     for (i=1;i<=npar;i++) x[i]=0;                double *fc, double (*func)(double)); 
     x[j]=1;    int j; 
     lubksb(a,npar,indx,x);    double xx,xmin,bx,ax; 
     for (i=1;i<=npar;i++){    double fx,fb,fa;
       y[i][j]=x[i];   
       printf("%.3e ",y[i][j]);    ncom=n; 
     }    pcom=vector(1,n); 
     printf("\n");    xicom=vector(1,n); 
   }    nrfunc=func; 
   */    for (j=1;j<=n;j++) { 
       pcom[j]=p[j]; 
   free_matrix(a,1,npar,1,npar);      xicom[j]=xi[j]; 
   free_matrix(y,1,npar,1,npar);    } 
   free_vector(x,1,npar);    ax=0.0; 
   free_ivector(indx,1,npar);    xx=1.0; 
   free_matrix(hess,1,npar,1,npar);    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
     *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
   #ifdef DEBUG
 }    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
 /*************** hessian matrix ****************/  #endif
 double hessii( double x[], double delta, int theta, double delti[])    for (j=1;j<=n;j++) { 
 {      xi[j] *= xmin; 
   int i;      p[j] += xi[j]; 
   int l=1, lmax=20;    } 
   double k1,k2;    free_vector(xicom,1,n); 
   double p2[NPARMAX+1];    free_vector(pcom,1,n); 
   double res;  } 
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;  
   double fx;  char *asc_diff_time(long time_sec, char ascdiff[])
   int k=0,kmax=10;  {
   double l1;    long sec_left, days, hours, minutes;
     days = (time_sec) / (60*60*24);
   fx=func(x);    sec_left = (time_sec) % (60*60*24);
   for (i=1;i<=npar;i++) p2[i]=x[i];    hours = (sec_left) / (60*60) ;
   for(l=0 ; l <=lmax; l++){    sec_left = (sec_left) %(60*60);
     l1=pow(10,l);    minutes = (sec_left) /60;
     delts=delt;    sec_left = (sec_left) % (60);
     for(k=1 ; k <kmax; k=k+1){    sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
       delt = delta*(l1*k);    return ascdiff;
       p2[theta]=x[theta] +delt;  }
       k1=func(p2)-fx;  
       p2[theta]=x[theta]-delt;  /*************** powell ************************/
       k2=func(p2)-fx;  void powell(double p[], double **xi, int n, double ftol, int *iter, 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 */  { 
          void linmin(double p[], double xi[], int n, double *fret, 
 #ifdef DEBUG                double (*func)(double [])); 
       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);    int i,ibig,j; 
 #endif    double del,t,*pt,*ptt,*xit;
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */    double fp,fptt;
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){    double *xits;
         k=kmax;    int niterf, itmp;
       }  
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */    pt=vector(1,n); 
         k=kmax; l=lmax*10.;    ptt=vector(1,n); 
       }    xit=vector(1,n); 
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){    xits=vector(1,n); 
         delts=delt;    *fret=(*func)(p); 
       }    for (j=1;j<=n;j++) pt[j]=p[j]; 
     }    for (*iter=1;;++(*iter)) { 
   }      fp=(*fret); 
   delti[theta]=delts;      ibig=0; 
   return res;      del=0.0; 
        last_time=curr_time;
 }      (void) gettimeofday(&curr_time,&tzp);
       printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);
 double hessij( double x[], double delti[], int thetai,int thetaj)      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); */
   int i;     for (i=1;i<=n;i++) {
   int l=1, l1, lmax=20;        printf(" %d %.12f",i, p[i]);
   double k1,k2,k3,k4,res,fx;        fprintf(ficlog," %d %.12lf",i, p[i]);
   double p2[NPARMAX+1];        fprintf(ficrespow," %.12lf", p[i]);
   int k;      }
       printf("\n");
   fx=func(x);      fprintf(ficlog,"\n");
   for (k=1; k<=2; k++) {      fprintf(ficrespow,"\n");fflush(ficrespow);
     for (i=1;i<=npar;i++) p2[i]=x[i];      if(*iter <=3){
     p2[thetai]=x[thetai]+delti[thetai]/k;        tm = *localtime(&curr_time.tv_sec);
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;        strcpy(strcurr,asctime(&tm));
     k1=func(p2)-fx;  /*       asctime_r(&tm,strcurr); */
          forecast_time=curr_time; 
     p2[thetai]=x[thetai]+delti[thetai]/k;        itmp = strlen(strcurr);
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
     k2=func(p2)-fx;          strcurr[itmp-1]='\0';
          printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
     p2[thetai]=x[thetai]-delti[thetai]/k;        fprintf(ficlog,"\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;        for(niterf=10;niterf<=30;niterf+=10){
     k3=func(p2)-fx;          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
            tmf = *localtime(&forecast_time.tv_sec);
     p2[thetai]=x[thetai]-delti[thetai]/k;  /*      asctime_r(&tmf,strfor); */
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          strcpy(strfor,asctime(&tmf));
     k4=func(p2)-fx;          itmp = strlen(strfor);
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */          if(strfor[itmp-1]=='\n')
 #ifdef DEBUG          strfor[itmp-1]='\0';
     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);          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);
 #endif          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);
   }        }
   return res;      }
 }      for (i=1;i<=n;i++) { 
         for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
 /************** Inverse of matrix **************/        fptt=(*fret); 
 void ludcmp(double **a, int n, int *indx, double *d)  #ifdef DEBUG
 {        printf("fret=%lf \n",*fret);
   int i,imax,j,k;        fprintf(ficlog,"fret=%lf \n",*fret);
   double big,dum,sum,temp;  #endif
   double *vv;        printf("%d",i);fflush(stdout);
          fprintf(ficlog,"%d",i);fflush(ficlog);
   vv=vector(1,n);        linmin(p,xit,n,fret,func); 
   *d=1.0;        if (fabs(fptt-(*fret)) > del) { 
   for (i=1;i<=n;i++) {          del=fabs(fptt-(*fret)); 
     big=0.0;          ibig=i; 
     for (j=1;j<=n;j++)        } 
       if ((temp=fabs(a[i][j])) > big) big=temp;  #ifdef DEBUG
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");        printf("%d %.12e",i,(*fret));
     vv[i]=1.0/big;        fprintf(ficlog,"%d %.12e",i,(*fret));
   }        for (j=1;j<=n;j++) {
   for (j=1;j<=n;j++) {          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
     for (i=1;i<j;i++) {          printf(" x(%d)=%.12e",j,xit[j]);
       sum=a[i][j];          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];        }
       a[i][j]=sum;        for(j=1;j<=n;j++) {
     }          printf(" p=%.12e",p[j]);
     big=0.0;          fprintf(ficlog," p=%.12e",p[j]);
     for (i=j;i<=n;i++) {        }
       sum=a[i][j];        printf("\n");
       for (k=1;k<j;k++)        fprintf(ficlog,"\n");
         sum -= a[i][k]*a[k][j];  #endif
       a[i][j]=sum;      } 
       if ( (dum=vv[i]*fabs(sum)) >= big) {      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
         big=dum;  #ifdef DEBUG
         imax=i;        int k[2],l;
       }        k[0]=1;
     }        k[1]=-1;
     if (j != imax) {        printf("Max: %.12e",(*func)(p));
       for (k=1;k<=n;k++) {        fprintf(ficlog,"Max: %.12e",(*func)(p));
         dum=a[imax][k];        for (j=1;j<=n;j++) {
         a[imax][k]=a[j][k];          printf(" %.12e",p[j]);
         a[j][k]=dum;          fprintf(ficlog," %.12e",p[j]);
       }        }
       *d = -(*d);        printf("\n");
       vv[imax]=vv[j];        fprintf(ficlog,"\n");
     }        for(l=0;l<=1;l++) {
     indx[j]=imax;          for (j=1;j<=n;j++) {
     if (a[j][j] == 0.0) a[j][j]=TINY;            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
     if (j != n) {            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
       dum=1.0/(a[j][j]);            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
       for (i=j+1;i<=n;i++) a[i][j] *= dum;          }
     }          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   }          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   free_vector(vv,1,n);  /* Doesn't work */        }
 ;  #endif
 }  
   
 void lubksb(double **a, int n, int *indx, double b[])        free_vector(xit,1,n); 
 {        free_vector(xits,1,n); 
   int i,ii=0,ip,j;        free_vector(ptt,1,n); 
   double sum;        free_vector(pt,1,n); 
          return; 
   for (i=1;i<=n;i++) {      } 
     ip=indx[i];      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
     sum=b[ip];      for (j=1;j<=n;j++) { 
     b[ip]=b[i];        ptt[j]=2.0*p[j]-pt[j]; 
     if (ii)        xit[j]=p[j]-pt[j]; 
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];        pt[j]=p[j]; 
     else if (sum) ii=i;      } 
     b[i]=sum;      fptt=(*func)(ptt); 
   }      if (fptt < fp) { 
   for (i=n;i>=1;i--) {        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
     sum=b[i];        if (t < 0.0) { 
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];          linmin(p,xit,n,fret,func); 
     b[i]=sum/a[i][i];          for (j=1;j<=n;j++) { 
   }            xi[j][ibig]=xi[j][n]; 
 }            xi[j][n]=xit[j]; 
           }
 /************ Frequencies ********************/  #ifdef DEBUG
 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("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
 {  /* Some frequencies */          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
            for(j=1;j<=n;j++){
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;            printf(" %.12e",xit[j]);
   double ***freq; /* Frequencies */            fprintf(ficlog," %.12e",xit[j]);
   double *pp;          }
   double pos, k2, dateintsum=0,k2cpt=0;          printf("\n");
   FILE *ficresp;          fprintf(ficlog,"\n");
   char fileresp[FILENAMELENGTH];  #endif
         }
   pp=vector(1,nlstate);      } 
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    } 
   strcpy(fileresp,"p");  } 
   strcat(fileresp,fileres);  
   if((ficresp=fopen(fileresp,"w"))==NULL) {  /**** Prevalence limit (stable or period prevalence)  ****************/
     printf("Problem with prevalence resultfile: %s\n", fileresp);  
     exit(0);  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
   }  {
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
   j1=0;       matrix by transitions matrix until convergence is reached */
   
   j=cptcoveff;    int i, ii,j,k;
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    double min, max, maxmin, maxmax,sumnew=0.;
     double **matprod2();
   for(k1=1; k1<=j;k1++){    double **out, cov[NCOVMAX+1], **pmij();
    for(i1=1; i1<=ncodemax[k1];i1++){    double **newm;
        j1++;    double agefin, delaymax=50 ; /* Max number of years to converge */
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);  
          scanf("%d", i);*/    for (ii=1;ii<=nlstate+ndeath;ii++)
         for (i=-1; i<=nlstate+ndeath; i++)        for (j=1;j<=nlstate+ndeath;j++){
          for (jk=-1; jk<=nlstate+ndeath; jk++)          oldm[ii][j]=(ii==j ? 1.0 : 0.0);
            for(m=agemin; m <= agemax+3; m++)      }
              freq[i][jk][m]=0;  
      cov[1]=1.;
         dateintsum=0;   
         k2cpt=0;   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
        for (i=1; i<=imx; i++) {    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
          bool=1;      newm=savm;
          if  (cptcovn>0) {      /* Covariates have to be included here again */
            for (z1=1; z1<=cptcoveff; z1++)       cov[2]=agefin;
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])    
                bool=0;        for (k=1; k<=cptcovn;k++) {
          }          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
          if (bool==1) {          /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
            for(m=firstpass; m<=lastpass; m++){        }
              k2=anint[m][i]+(mint[m][i]/12.);        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
              if ((k2>=dateprev1) && (k2<=dateprev2)) {        for (k=1; k<=cptcovprod;k++)
                if(agev[m][i]==0) agev[m][i]=agemax+1;          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
                if(agev[m][i]==1) agev[m][i]=agemax+2;  
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
                freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
                  dateintsum=dateintsum+k2;      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
                  k2cpt++;  
                }      savm=oldm;
       oldm=newm;
              }      maxmax=0.;
            }      for(j=1;j<=nlstate;j++){
          }        min=1.;
        }        max=0.;
                for(i=1; i<=nlstate; i++) {
        fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);          sumnew=0;
           for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
         if  (cptcovn>0) {          prlim[i][j]= newm[i][j]/(1-sumnew);
          fprintf(ficresp, "\n#********** Variable ");          max=FMAX(max,prlim[i][j]);
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          min=FMIN(min,prlim[i][j]);
        fprintf(ficresp, "**********\n#");        }
         }        maxmin=max-min;
        for(i=1; i<=nlstate;i++)        maxmax=FMAX(maxmax,maxmin);
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);      }
        fprintf(ficresp, "\n");      if(maxmax < ftolpl){
                return prlim;
   for(i=(int)agemin; i <= (int)agemax+3; i++){      }
     if(i==(int)agemax+3)    }
       printf("Total");  }
     else  
       printf("Age %d", i);  /*************** transition probabilities ***************/ 
     for(jk=1; jk <=nlstate ; jk++){  
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
         pp[jk] += freq[jk][m][i];  {
     }    double s1, s2;
     for(jk=1; jk <=nlstate ; jk++){    /*double t34;*/
       for(m=-1, pos=0; m <=0 ; m++)    int i,j,j1, nc, ii, jj;
         pos += freq[jk][m][i];  
       if(pp[jk]>=1.e-10)      for(i=1; i<= nlstate; i++){
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);        for(j=1; j<i;j++){
       else          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);            /*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); */
      for(jk=1; jk <=nlstate ; jk++){          }
       for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)          ps[i][j]=s2;
         pp[jk] += freq[jk][m][i];  /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
      }        }
         for(j=i+1; j<=nlstate+ndeath;j++){
     for(jk=1,pos=0; jk <=nlstate ; jk++)          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
       pos += pp[jk];            s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
     for(jk=1; jk <=nlstate ; jk++){  /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
       if(pos>=1.e-5)          }
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);          ps[i][j]=s2;
       else        }
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);      }
       if( i <= (int) agemax){      /*ps[3][2]=1;*/
         if(pos>=1.e-5){      
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);      for(i=1; i<= nlstate; i++){
           probs[i][jk][j1]= pp[jk]/pos;        s1=0;
           /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/        for(j=1; j<i; j++){
         }          s1+=exp(ps[i][j]);
       else          /*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 NaNq %.0f %.0f",i,pp[jk],pos);        }
       }        for(j=i+1; j<=nlstate+ndeath; j++){
     }          s1+=exp(ps[i][j]);
     for(jk=-1; jk <=nlstate+ndeath; jk++)          /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
       for(m=-1; m <=nlstate+ndeath; m++)        }
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);        ps[i][i]=1./(s1+1.);
     if(i <= (int) agemax)        for(j=1; j<i; j++)
       fprintf(ficresp,"\n");          ps[i][j]= exp(ps[i][j])*ps[i][i];
     printf("\n");        for(j=i+1; j<=nlstate+ndeath; j++)
     }          ps[i][j]= exp(ps[i][j])*ps[i][i];
     }        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
  }      } /* end i */
   dateintmean=dateintsum/k2cpt;      
        for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
   fclose(ficresp);        for(jj=1; jj<= nlstate+ndeath; jj++){
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);          ps[ii][jj]=0;
   free_vector(pp,1,nlstate);          ps[ii][ii]=1;
         }
   /* End of Freq */      }
 }      
   
 /************ Prevalence ********************/  /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
 void prevalence(int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
 {  /* Some frequencies */  /*         printf("ddd %lf ",ps[ii][jj]); */
    /*       } */
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;  /*       printf("\n "); */
   double ***freq; /* Frequencies */  /*        } */
   double *pp;  /*        printf("\n ");printf("%lf ",cov[2]); */
   double pos, k2;         /*
         for(i=1; i<= npar; i++) printf("%f ",x[i]);
   pp=vector(1,nlstate);        goto end;*/
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);      return ps;
    }
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);  
   j1=0;  /**************** Product of 2 matrices ******************/
    
   j=cptcoveff;  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  {
      /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
  for(k1=1; k1<=j;k1++){       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
     for(i1=1; i1<=ncodemax[k1];i1++){    /* in, b, out are matrice of pointers which should have been initialized 
       j1++;       before: only the contents of out is modified. The function returns
         a pointer to pointers identical to out */
       for (i=-1; i<=nlstate+ndeath; i++)      long i, j, k;
         for (jk=-1; jk<=nlstate+ndeath; jk++)      for(i=nrl; i<= nrh; i++)
           for(m=agemin; m <= agemax+3; m++)      for(k=ncolol; k<=ncoloh; k++)
             freq[i][jk][m]=0;        for(j=ncl,out[i][k]=0.; j<=nch; j++)
                out[i][k] +=in[i][j]*b[j][k];
       for (i=1; i<=imx; i++) {  
         bool=1;    return out;
         if  (cptcovn>0) {  }
           for (z1=1; z1<=cptcoveff; z1++)  
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])  
               bool=0;  /************* Higher Matrix Product ***************/
         }  
         if (bool==1) {  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
           for(m=firstpass; m<=lastpass; m++){  {
             k2=anint[m][i]+(mint[m][i]/12.);    /* Computes the transition matrix starting at age 'age' over 
             if ((k2>=dateprev1) && (k2<=dateprev2)) {       'nhstepm*hstepm*stepm' months (i.e. until
               if(agev[m][i]==0) agev[m][i]=agemax+1;       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
               if(agev[m][i]==1) agev[m][i]=agemax+2;       nhstepm*hstepm matrices. 
               freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
               freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];         (typically every 2 years instead of every month which is too big 
             }       for the memory).
           }       Model is determined by parameters x and covariates have to be 
         }       included manually here. 
       }  
             */
         for(i=(int)agemin; i <= (int)agemax+3; i++){  
           for(jk=1; jk <=nlstate ; jk++){    int i, j, d, h, k;
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    double **out, cov[NCOVMAX+1];
               pp[jk] += freq[jk][m][i];    double **newm;
           }  
           for(jk=1; jk <=nlstate ; jk++){    /* Hstepm could be zero and should return the unit matrix */
             for(m=-1, pos=0; m <=0 ; m++)    for (i=1;i<=nlstate+ndeath;i++)
             pos += freq[jk][m][i];      for (j=1;j<=nlstate+ndeath;j++){
         }        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=0, pp[jk]=0; m <=nlstate+ndeath; m++)    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
              pp[jk] += freq[jk][m][i];    for(h=1; h <=nhstepm; h++){
          }      for(d=1; d <=hstepm; d++){
                  newm=savm;
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];        /* Covariates have to be included here again */
         cov[1]=1.;
          for(jk=1; jk <=nlstate ; jk++){                  cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
            if( i <= (int) agemax){        for (k=1; k<=cptcovn;k++) 
              if(pos>=1.e-5){          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
                probs[i][jk][j1]= pp[jk]/pos;        for (k=1; k<=cptcovage;k++)
              }          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
            }        for (k=1; k<=cptcovprod;k++)
          }          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
            
         }  
     }        /*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));
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);        savm=oldm;
   free_vector(pp,1,nlstate);        oldm=newm;
        }
 }  /* End of Freq */      for(i=1; i<=nlstate+ndeath; i++)
         for(j=1;j<=nlstate+ndeath;j++) {
 /************* Waves Concatenation ***************/          po[i][j][h]=newm[i][j];
           /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)        }
 {      /*printf("h=%d ",h);*/
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.    } /* end h */
      Death is a valid wave (if date is known).  /*     printf("\n H=%d \n",h); */
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i    return po;
      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.  
      */  
   /*************** log-likelihood *************/
   int i, mi, m;  double func( double *x)
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;  {
      double sum=0., jmean=0.;*/    int i, ii, j, k, mi, d, kk;
     double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
   int j, k=0,jk, ju, jl;    double **out;
   double sum=0.;    double sw; /* Sum of weights */
   jmin=1e+5;    double lli; /* Individual log likelihood */
   jmax=-1;    int s1, s2;
   jmean=0.;    double bbh, survp;
   for(i=1; i<=imx; i++){    long ipmx;
     mi=0;    /*extern weight */
     m=firstpass;    /* We are differentiating ll according to initial status */
     while(s[m][i] <= nlstate){    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
       if(s[m][i]>=1)    /*for(i=1;i<imx;i++) 
         mw[++mi][i]=m;      printf(" %d\n",s[4][i]);
       if(m >=lastpass)    */
         break;    cov[1]=1.;
       else  
         m++;    for(k=1; k<=nlstate; k++) ll[k]=0.;
     }/* end while */  
     if (s[m][i] > nlstate){    if(mle==1){
       mi++;     /* Death is another wave */      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       /* if(mi==0)  never been interviewed correctly before death */        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
          /* Only death is a correct wave */        for(mi=1; mi<= wav[i]-1; mi++){
       mw[mi][i]=m;          for (ii=1;ii<=nlstate+ndeath;ii++)
     }            for (j=1;j<=nlstate+ndeath;j++){
               oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     wav[i]=mi;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     if(mi==0)            }
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);          for(d=0; d<dh[mi][i]; d++){
   }            newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   for(i=1; i<=imx; i++){            for (kk=1; kk<=cptcovage;kk++) {
     for(mi=1; mi<wav[i];mi++){              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       if (stepm <=0)            }
         dh[mi][i]=1;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       else{                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         if (s[mw[mi+1][i]][i] > nlstate) {            savm=oldm;
           if (agedc[i] < 2*AGESUP) {            oldm=newm;
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);          } /* end mult */
           if(j==0) j=1;  /* Survives at least one month after exam */        
           k=k+1;          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
           if (j >= jmax) jmax=j;          /* But now since version 0.9 we anticipate for bias at large stepm.
           if (j <= jmin) jmin=j;           * If stepm is larger than one month (smallest stepm) and if the exact delay 
           sum=sum+j;           * (in months) between two waves is not a multiple of stepm, we rounded to 
           /* if (j<10) printf("j=%d num=%d ",j,i); */           * the nearest (and in case of equal distance, to the lowest) interval but now
           }           * we keep into memory the bias bh[mi][i] and also the previous matrix product
         }           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
         else{           * probability in order to take into account the bias as a fraction of the way
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
           k=k+1;           * -stepm/2 to stepm/2 .
           if (j >= jmax) jmax=j;           * For stepm=1 the results are the same as for previous versions of Imach.
           else if (j <= jmin)jmin=j;           * For stepm > 1 the results are less biased than in previous versions. 
           /*   if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */           */
           sum=sum+j;          s1=s[mw[mi][i]][i];
         }          s2=s[mw[mi+1][i]][i];
         jk= j/stepm;          bbh=(double)bh[mi][i]/(double)stepm; 
         jl= j -jk*stepm;          /* bias bh is positive if real duration
         ju= j -(jk+1)*stepm;           * is higher than the multiple of stepm and negative otherwise.
         if(jl <= -ju)           */
           dh[mi][i]=jk;          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
         else          if( s2 > nlstate){ 
           dh[mi][i]=jk+1;            /* i.e. if s2 is a death state and if the date of death is known 
         if(dh[mi][i]==0)               then the contribution to the likelihood is the probability to 
           dh[mi][i]=1; /* At least one step */               die between last step unit time and current  step unit time, 
       }               which is also equal to probability to die before dh 
     }               minus probability to die before dh-stepm . 
   }               In version up to 0.92 likelihood was computed
   jmean=sum/k;          as if date of death was unknown. Death was treated as any other
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);          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
 /*********** Tricode ****************************/          to consider that at each interview the state was recorded
 void tricode(int *Tvar, int **nbcode, int imx)          (healthy, disable or death) and IMaCh was corrected; but when we
 {          introduced the exact date of death then we should have modified
   int Ndum[20],ij=1, k, j, i;          the contribution of an exact death to the likelihood. This new
   int cptcode=0;          contribution is smaller and very dependent of the step unit
   cptcoveff=0;          stepm. It is no more the probability to die between last interview
            and month of death but the probability to survive from last
   for (k=0; k<19; k++) Ndum[k]=0;          interview up to one month before death multiplied by the
   for (k=1; k<=7; k++) ncodemax[k]=0;          probability to die within a month. Thanks to Chris
           Jackson for correcting this bug.  Former versions increased
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {          mortality artificially. The bad side is that we add another loop
     for (i=1; i<=imx; i++) {          which slows down the processing. The difference can be up to 10%
       ij=(int)(covar[Tvar[j]][i]);          lower mortality.
       Ndum[ij]++;            */
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/            lli=log(out[s1][s2] - savm[s1][s2]);
       if (ij > cptcode) cptcode=ij;  
     }  
           } else if  (s2==-2) {
     for (i=0; i<=cptcode; i++) {            for (j=1,survp=0. ; j<=nlstate; j++) 
       if(Ndum[i]!=0) ncodemax[j]++;              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
     }            /*survp += out[s1][j]; */
     ij=1;            lli= log(survp);
           }
           
     for (i=1; i<=ncodemax[j]; i++) {          else if  (s2==-4) { 
       for (k=0; k<=19; k++) {            for (j=3,survp=0. ; j<=nlstate; j++)  
         if (Ndum[k] != 0) {              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
           nbcode[Tvar[j]][ij]=k;            lli= log(survp); 
           ij++;          } 
         }  
         if (ij > ncodemax[j]) break;          else if  (s2==-5) { 
       }              for (j=1,survp=0. ; j<=2; j++)  
     }              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   }              lli= log(survp); 
           } 
  for (k=0; k<19; k++) Ndum[k]=0;          
           else{
  for (i=1; i<=ncovmodel-2; i++) {            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
       ij=Tvar[i];            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
       Ndum[ij]++;          } 
     }          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
           /*if(lli ==000.0)*/
  ij=1;          /*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<=10; i++) {          ipmx +=1;
    if((Ndum[i]!=0) && (i<=ncov)){          sw += weight[i];
      Tvaraff[ij]=i;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
      ij++;        } /* end of wave */
    }      } /* end of individual */
  }    }  else if(mle==2){
        for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     cptcoveff=ij-1;        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++)
 /*********** Health Expectancies ****************/            for (j=1;j<=nlstate+ndeath;j++){
               oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)              savm[ii][j]=(ii==j ? 1.0 : 0.0);
 {            }
   /* Health expectancies */          for(d=0; d<=dh[mi][i]; d++){
   int i, j, nhstepm, hstepm, h;            newm=savm;
   double age, agelim,hf;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   double ***p3mat;            for (kk=1; kk<=cptcovage;kk++) {
                cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   fprintf(ficreseij,"# Health expectancies\n");            }
   fprintf(ficreseij,"# Age");            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   for(i=1; i<=nlstate;i++)                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     for(j=1; j<=nlstate;j++)            savm=oldm;
       fprintf(ficreseij," %1d-%1d",i,j);            oldm=newm;
   fprintf(ficreseij,"\n");          } /* end mult */
         
   hstepm=1*YEARM; /*  Every j years of age (in month) */          s1=s[mw[mi][i]][i];
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */          s2=s[mw[mi+1][i]][i];
           bbh=(double)bh[mi][i]/(double)stepm; 
   agelim=AGESUP;          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 (age=bage; age<=fage; age ++){ /* If stepm=6 months */          ipmx +=1;
     /* nhstepm age range expressed in number of stepm */          sw += weight[i];
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     /* Typically if 20 years = 20*12/6=40 stepm */        } /* end of wave */
     if (stepm >= YEARM) hstepm=1;      } /* end of individual */
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */    }  else if(mle==3){  /* exponential inter-extrapolation */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     /* Computed by stepm unit matrices, product of hstepm matrices, stored        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */        for(mi=1; mi<= wav[i]-1; mi++){
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);            for (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
               oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     for(i=1; i<=nlstate;i++)              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       for(j=1; j<=nlstate;j++)            }
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){          for(d=0; d<dh[mi][i]; d++){
           eij[i][j][(int)age] +=p3mat[i][j][h];            newm=savm;
         }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
                for (kk=1; kk<=cptcovage;kk++) {
     hf=1;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     if (stepm >= YEARM) hf=stepm/YEARM;            }
     fprintf(ficreseij,"%.0f",age );            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     for(i=1; i<=nlstate;i++)                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       for(j=1; j<=nlstate;j++){            savm=oldm;
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);            oldm=newm;
       }          } /* end mult */
     fprintf(ficreseij,"\n");        
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          s1=s[mw[mi][i]][i];
   }          s2=s[mw[mi+1][i]][i];
 }          bbh=(double)bh[mi][i]/(double)stepm; 
           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 */
 /************ Variance ******************/          ipmx +=1;
 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)          sw += weight[i];
 {          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   /* Variance of health expectancies */        } /* end of wave */
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/      } /* end of individual */
   double **newm;    }else if (mle==4){  /* ml=4 no inter-extrapolation */
   double **dnewm,**doldm;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   int i, j, nhstepm, hstepm, h;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   int k, cptcode;        for(mi=1; mi<= wav[i]-1; mi++){
   double *xp;          for (ii=1;ii<=nlstate+ndeath;ii++)
   double **gp, **gm;            for (j=1;j<=nlstate+ndeath;j++){
   double ***gradg, ***trgradg;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   double ***p3mat;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   double age,agelim;            }
   int theta;          for(d=0; d<dh[mi][i]; d++){
             newm=savm;
    fprintf(ficresvij,"# Covariances of life expectancies\n");            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   fprintf(ficresvij,"# Age");            for (kk=1; kk<=cptcovage;kk++) {
   for(i=1; i<=nlstate;i++)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     for(j=1; j<=nlstate;j++)            }
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);          
   fprintf(ficresvij,"\n");            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   xp=vector(1,npar);            savm=oldm;
   dnewm=matrix(1,nlstate,1,npar);            oldm=newm;
   doldm=matrix(1,nlstate,1,nlstate);          } /* end mult */
          
   hstepm=1*YEARM; /* Every year of age */          s1=s[mw[mi][i]][i];
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */          s2=s[mw[mi+1][i]][i];
   agelim = AGESUP;          if( s2 > nlstate){ 
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */            lli=log(out[s1][s2] - savm[s1][s2]);
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          }else{
     if (stepm >= YEARM) hstepm=1;            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */          }
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          ipmx +=1;
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);          sw += weight[i];
     gp=matrix(0,nhstepm,1,nlstate);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     gm=matrix(0,nhstepm,1,nlstate);  /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
         } /* end of wave */
     for(theta=1; theta <=npar; theta++){      } /* end of individual */
       for(i=1; i<=npar; i++){ /* Computes gradient */    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          for(mi=1; mi<= wav[i]-1; mi++){
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          for (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
       if (popbased==1) {              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         for(i=1; i<=nlstate;i++)              savm[ii][j]=(ii==j ? 1.0 : 0.0);
           prlim[i][i]=probs[(int)age][i][ij];            }
       }          for(d=0; d<dh[mi][i]; d++){
              newm=savm;
       for(j=1; j<= nlstate; j++){            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         for(h=0; h<=nhstepm; h++){            for (kk=1; kk<=cptcovage;kk++) {
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];            }
         }          
       }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                             1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       for(i=1; i<=npar; i++) /* Computes gradient */            savm=oldm;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);            oldm=newm;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            } /* end mult */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        
            s1=s[mw[mi][i]][i];
       if (popbased==1) {          s2=s[mw[mi+1][i]][i];
         for(i=1; i<=nlstate;i++)          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
           prlim[i][i]=probs[(int)age][i][ij];          ipmx +=1;
       }          sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       for(j=1; j<= nlstate; j++){          /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
         for(h=0; h<=nhstepm; h++){        } /* end of wave */
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)      } /* end of individual */
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];    } /* End of if */
         }    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
       }    /* 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 */
       for(j=1; j<= nlstate; j++)    return -l;
         for(h=0; h<=nhstepm; h++){  }
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];  
         }  /*************** log-likelihood *************/
     } /* End theta */  double funcone( double *x)
   {
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);    /* Same as likeli but slower because of a lot of printf and if */
     int i, ii, j, k, mi, d, kk;
     for(h=0; h<=nhstepm; h++)    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
       for(j=1; j<=nlstate;j++)    double **out;
         for(theta=1; theta <=npar; theta++)    double lli; /* Individual log likelihood */
           trgradg[h][j][theta]=gradg[h][theta][j];    double llt;
     int s1, s2;
     for(i=1;i<=nlstate;i++)    double bbh, survp;
       for(j=1;j<=nlstate;j++)    /*extern weight */
         vareij[i][j][(int)age] =0.;    /* We are differentiating ll according to initial status */
     for(h=0;h<=nhstepm;h++){    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
       for(k=0;k<=nhstepm;k++){    /*for(i=1;i<imx;i++) 
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);      printf(" %d\n",s[4][i]);
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);    */
         for(i=1;i<=nlstate;i++)    cov[1]=1.;
           for(j=1;j<=nlstate;j++)  
             vareij[i][j][(int)age] += doldm[i][j];    for(k=1; k<=nlstate; k++) ll[k]=0.;
       }  
     }    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     h=1;      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     if (stepm >= YEARM) h=stepm/YEARM;      for(mi=1; mi<= wav[i]-1; mi++){
     fprintf(ficresvij,"%.0f ",age );        for (ii=1;ii<=nlstate+ndeath;ii++)
     for(i=1; i<=nlstate;i++)          for (j=1;j<=nlstate+ndeath;j++){
       for(j=1; j<=nlstate;j++){            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);            savm[ii][j]=(ii==j ? 1.0 : 0.0);
       }          }
     fprintf(ficresvij,"\n");        for(d=0; d<dh[mi][i]; d++){
     free_matrix(gp,0,nhstepm,1,nlstate);          newm=savm;
     free_matrix(gm,0,nhstepm,1,nlstate);          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);          for (kk=1; kk<=cptcovage;kk++) {
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          }
   } /* End age */          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   free_vector(xp,1,npar);          savm=oldm;
   free_matrix(doldm,1,nlstate,1,npar);          oldm=newm;
   free_matrix(dnewm,1,nlstate,1,nlstate);        } /* end mult */
         
 }        s1=s[mw[mi][i]][i];
         s2=s[mw[mi+1][i]][i];
 /************ Variance of prevlim ******************/        bbh=(double)bh[mi][i]/(double)stepm; 
 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)        /* bias is positive if real duration
 {         * is higher than the multiple of stepm and negative otherwise.
   /* Variance of prevalence limit */         */
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/        if( s2 > nlstate && (mle <5) ){  /* Jackson */
   double **newm;          lli=log(out[s1][s2] - savm[s1][s2]);
   double **dnewm,**doldm;        } else if  (s2==-2) {
   int i, j, nhstepm, hstepm;          for (j=1,survp=0. ; j<=nlstate; j++) 
   int k, cptcode;            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   double *xp;          lli= log(survp);
   double *gp, *gm;        }else if (mle==1){
   double **gradg, **trgradg;          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   double age,agelim;        } else if(mle==2){
   int theta;          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
            } else if(mle==3){  /* exponential inter-extrapolation */
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");          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 */
   fprintf(ficresvpl,"# Age");        } else if (mle==4){  /* mle=4 no inter-extrapolation */
   for(i=1; i<=nlstate;i++)          lli=log(out[s1][s2]); /* Original formula */
       fprintf(ficresvpl," %1d-%1d",i,i);        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
   fprintf(ficresvpl,"\n");          lli=log(out[s1][s2]); /* Original formula */
         } /* End of if */
   xp=vector(1,npar);        ipmx +=1;
   dnewm=matrix(1,nlstate,1,npar);        sw += weight[i];
   doldm=matrix(1,nlstate,1,nlstate);        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
          /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
   hstepm=1*YEARM; /* Every year of age */        if(globpr){
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */          fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
   agelim = AGESUP;   %11.6f %11.6f %11.6f ", \
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
     if (stepm >= YEARM) hstepm=1;          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */            llt +=ll[k]*gipmx/gsw;
     gradg=matrix(1,npar,1,nlstate);            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
     gp=vector(1,nlstate);          }
     gm=vector(1,nlstate);          fprintf(ficresilk," %10.6f\n", -llt);
         }
     for(theta=1; theta <=npar; theta++){      } /* end of wave */
       for(i=1; i<=npar; i++){ /* Computes gradient */    } /* end of individual */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
       }    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
       for(i=1;i<=nlstate;i++)    if(globpr==0){ /* First time we count the contributions and weights */
         gp[i] = prlim[i][i];      gipmx=ipmx;
          gsw=sw;
       for(i=1; i<=npar; i++) /* Computes gradient */    }
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    return -l;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  }
       for(i=1;i<=nlstate;i++)  
         gm[i] = prlim[i][i];  
   /*************** function likelione ***********/
       for(i=1;i<=nlstate;i++)  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];  {
     } /* End theta */    /* This routine should help understanding what is done with 
        the selection of individuals/waves and
     trgradg =matrix(1,nlstate,1,npar);       to check the exact contribution to the likelihood.
        Plotting could be done.
     for(j=1; j<=nlstate;j++)     */
       for(theta=1; theta <=npar; theta++)    int k;
         trgradg[j][theta]=gradg[theta][j];  
     if(*globpri !=0){ /* Just counts and sums, no printings */
     for(i=1;i<=nlstate;i++)      strcpy(fileresilk,"ilk"); 
       varpl[i][(int)age] =0.;      strcat(fileresilk,fileres);
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);        printf("Problem with resultfile: %s\n", fileresilk);
     for(i=1;i<=nlstate;i++)        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */      }
       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(ficresvpl,"%.0f ",age );      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
     for(i=1; i<=nlstate;i++)      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));      for(k=1; k<=nlstate; k++) 
     fprintf(ficresvpl,"\n");        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
     free_vector(gp,1,nlstate);      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
     free_vector(gm,1,nlstate);    }
     free_matrix(gradg,1,npar,1,nlstate);  
     free_matrix(trgradg,1,nlstate,1,npar);    *fretone=(*funcone)(p);
   } /* End age */    if(*globpri !=0){
       fclose(ficresilk);
   free_vector(xp,1,npar);      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
   free_matrix(doldm,1,nlstate,1,npar);      fflush(fichtm); 
   free_matrix(dnewm,1,nlstate,1,nlstate);    } 
     return;
 }  }
   
 /************ Variance of one-step probabilities  ******************/  
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)  /*********** Maximum Likelihood Estimation ***************/
 {  
   int i, j;  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   int k=0, cptcode;  {
   double **dnewm,**doldm;    int i,j, iter;
   double *xp;    double **xi;
   double *gp, *gm;    double fret;
   double **gradg, **trgradg;    double fretone; /* Only one call to likelihood */
   double age,agelim, cov[NCOVMAX];    /*  char filerespow[FILENAMELENGTH];*/
   int theta;    xi=matrix(1,npar,1,npar);
   char fileresprob[FILENAMELENGTH];    for (i=1;i<=npar;i++)
       for (j=1;j<=npar;j++)
   strcpy(fileresprob,"prob");        xi[i][j]=(i==j ? 1.0 : 0.0);
   strcat(fileresprob,fileres);    printf("Powell\n");  fprintf(ficlog,"Powell\n");
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {    strcpy(filerespow,"pow"); 
     printf("Problem with resultfile: %s\n", fileresprob);    strcat(filerespow,fileres);
   }    if((ficrespow=fopen(filerespow,"w"))==NULL) {
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);      printf("Problem with resultfile: %s\n", filerespow);
        fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
     }
   xp=vector(1,npar);    fprintf(ficrespow,"# Powell\n# iter -2*LL");
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    for (i=1;i<=nlstate;i++)
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));      for(j=1;j<=nlstate+ndeath;j++)
          if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
   cov[1]=1;    fprintf(ficrespow,"\n");
   for (age=bage; age<=fage; age ++){  
     cov[2]=age;    powell(p,xi,npar,ftol,&iter,&fret,func);
     gradg=matrix(1,npar,1,9);  
     trgradg=matrix(1,9,1,npar);    free_matrix(xi,1,npar,1,npar);
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));    fclose(ficrespow);
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
        fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     for(theta=1; theta <=npar; theta++){    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
       for(i=1; i<=npar; i++)  
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  }
        
       pmij(pmmij,cov,ncovmodel,xp,nlstate);  /**** Computes Hessian and covariance matrix ***/
      void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
       k=0;  {
       for(i=1; i<= (nlstate+ndeath); i++){    double  **a,**y,*x,pd;
         for(j=1; j<=(nlstate+ndeath);j++){    double **hess;
            k=k+1;    int i, j,jk;
           gp[k]=pmmij[i][j];    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);
       for(i=1; i<=npar; i++)    void lubksb(double **a, int npar, int *indx, double b[]) ;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    void ludcmp(double **a, int npar, int *indx, double *d) ;
        double gompertz(double p[]);
     hess=matrix(1,npar,1,npar);
       pmij(pmmij,cov,ncovmodel,xp,nlstate);  
       k=0;    printf("\nCalculation of the hessian matrix. Wait...\n");
       for(i=1; i<=(nlstate+ndeath); i++){    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
         for(j=1; j<=(nlstate+ndeath);j++){    for (i=1;i<=npar;i++){
           k=k+1;      printf("%d",i);fflush(stdout);
           gm[k]=pmmij[i][j];      fprintf(ficlog,"%d",i);fflush(ficlog);
         }     
       }       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
            
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)      /*  printf(" %f ",p[i]);
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];            printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
     }    }
     
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)    for (i=1;i<=npar;i++) {
       for(theta=1; theta <=npar; theta++)      for (j=1;j<=npar;j++)  {
       trgradg[j][theta]=gradg[theta][j];        if (j>i) { 
            printf(".%d%d",i,j);fflush(stdout);
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);          hess[i][j]=hessij(p,delti,i,j,func,npar);
           
      pmij(pmmij,cov,ncovmodel,x,nlstate);          hess[j][i]=hess[i][j];    
           /*printf(" %lf ",hess[i][j]);*/
      k=0;        }
      for(i=1; i<=(nlstate+ndeath); i++){      }
        for(j=1; j<=(nlstate+ndeath);j++){    }
          k=k+1;    printf("\n");
          gm[k]=pmmij[i][j];    fprintf(ficlog,"\n");
         }  
      }    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
          fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
      /*printf("\n%d ",(int)age);    
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){    a=matrix(1,npar,1,npar);
            y=matrix(1,npar,1,npar);
     x=vector(1,npar);
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));    indx=ivector(1,npar);
      }*/    for (i=1;i<=npar;i++)
       for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
   fprintf(ficresprob,"\n%d ",(int)age);    ludcmp(a,npar,indx,&pd);
   
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){    for (j=1;j<=npar;j++) {
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);      for (i=1;i<=npar;i++) x[i]=0;
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);      x[j]=1;
   }      lubksb(a,npar,indx,x);
       for (i=1;i<=npar;i++){ 
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));        matcov[i][j]=x[i];
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));      }
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    }
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);  
 }    printf("\n#Hessian matrix#\n");
  free_vector(xp,1,npar);    fprintf(ficlog,"\n#Hessian matrix#\n");
 fclose(ficresprob);    for (i=1;i<=npar;i++) { 
       for (j=1;j<=npar;j++) { 
 }        printf("%.3e ",hess[i][j]);
         fprintf(ficlog,"%.3e ",hess[i][j]);
 /******************* 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 optionfile[],char optionfilehtm[] ){      printf("\n");
   int jj1, k1, i1, cpt;      fprintf(ficlog,"\n");
   FILE *fichtm;    }
   /*char optionfilehtm[FILENAMELENGTH];*/  
     /* Recompute Inverse */
   strcpy(optionfilehtm,optionfile);    for (i=1;i<=npar;i++)
   strcat(optionfilehtm,".htm");      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {    ludcmp(a,npar,indx,&pd);
     printf("Problem with %s \n",optionfilehtm), exit(0);  
   }    /*  printf("\n#Hessian matrix recomputed#\n");
   
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.7 </font> <hr size=\"2\" color=\"#EC5E5E\">    for (j=1;j<=npar;j++) {
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>      for (i=1;i<=npar;i++) x[i]=0;
       x[j]=1;
 Total number of observations=%d <br>      lubksb(a,npar,indx,x);
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>      for (i=1;i<=npar;i++){ 
 <hr  size=\"2\" color=\"#EC5E5E\">        y[i][j]=x[i];
 <li>Outputs files<br><br>\n        printf("%.3e ",y[i][j]);
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n        fprintf(ficlog,"%.3e ",y[i][j]);
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>      }
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>      printf("\n");
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>      fprintf(ficlog,"\n");
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>    }
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>    */
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>  
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>    free_matrix(a,1,npar,1,npar);
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>    free_matrix(y,1,npar,1,npar);
         - Prevalences and population forecasting: <a href=\"f%s\">f%s</a> <br>    free_vector(x,1,npar);
         <br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);    free_ivector(indx,1,npar);
      free_matrix(hess,1,npar,1,npar);
 fprintf(fichtm," <li>Graphs</li><p>");  
   
  m=cptcoveff;  }
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}  
   /*************** hessian matrix ****************/
  jj1=0;  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
  for(k1=1; k1<=m;k1++){  {
    for(i1=1; i1<=ncodemax[k1];i1++){    int i;
        jj1++;    int l=1, lmax=20;
        if (cptcovn > 0) {    double k1,k2;
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");    double p2[MAXPARM+1]; /* identical to x */
          for (cpt=1; cpt<=cptcoveff;cpt++)    double res;
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");    double fx;
        }    int k=0,kmax=10;
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>    double l1;
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);      
        for(cpt=1; cpt<nlstate;cpt++){    fx=func(x);
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>    for (i=1;i<=npar;i++) p2[i]=x[i];
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    for(l=0 ; l <=lmax; l++){
        }      l1=pow(10,l);
     for(cpt=1; cpt<=nlstate;cpt++) {      delts=delt;
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident      for(k=1 ; k <kmax; k=k+1){
 interval) in state (%d): v%s%d%d.gif <br>        delt = delta*(l1*k);
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);          p2[theta]=x[theta] +delt;
      }        k1=func(p2)-fx;
      for(cpt=1; cpt<=nlstate;cpt++) {        p2[theta]=x[theta]-delt;
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>        k2=func(p2)-fx;
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);        /*res= (k1-2.0*fx+k2)/delt/delt; */
      }        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
      fprintf(fichtm,"\n<br>- Total life expectancy by age and        
 health expectancies in states (1) and (2): e%s%d.gif<br>  #ifdef DEBUGHESS
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
 fprintf(fichtm,"\n</body>");        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);
    }  #endif
    }        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
 fclose(fichtm);        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
 }          k=kmax;
         }
 /******************* Gnuplot file **************/        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double agemin, double agemax, double fage , char pathc[], double p[]){          k=kmax; l=lmax*10.;
         }
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
           delts=delt;
   strcpy(optionfilegnuplot,optionfilefiname);        }
   strcat(optionfilegnuplot,".plt");      }
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {    }
     printf("Problem with file %s",optionfilegnuplot);    delti[theta]=delts;
   }    return res; 
     
 #ifdef windows  }
     fprintf(ficgp,"cd \"%s\" \n",pathc);  
 #endif  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
 m=pow(2,cptcoveff);  {
      int i;
  /* 1eme*/    int l=1, l1, lmax=20;
   for (cpt=1; cpt<= nlstate ; cpt ++) {    double k1,k2,k3,k4,res,fx;
    for (k1=1; k1<= m ; k1 ++) {    double p2[MAXPARM+1];
     int k;
 #ifdef windows  
     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",agemin,fage,fileres,k1-1,k1-1);    fx=func(x);
 #endif    for (k=1; k<=2; k++) {
 #ifdef unix      for (i=1;i<=npar;i++) p2[i]=x[i];
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);      p2[thetai]=x[thetai]+delti[thetai]/k;
 #endif      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       k1=func(p2)-fx;
 for (i=1; i<= nlstate ; i ++) {    
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      p2[thetai]=x[thetai]+delti[thetai]/k;
   else fprintf(ficgp," \%%*lf (\%%*lf)");      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
 }      k2=func(p2)-fx;
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);    
     for (i=1; i<= nlstate ; i ++) {      p2[thetai]=x[thetai]-delti[thetai]/k;
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   else fprintf(ficgp," \%%*lf (\%%*lf)");      k3=func(p2)-fx;
 }    
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);      p2[thetai]=x[thetai]-delti[thetai]/k;
      for (i=1; i<= nlstate ; i ++) {      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      k4=func(p2)-fx;
   else fprintf(ficgp," \%%*lf (\%%*lf)");      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
 }    #ifdef DEBUG
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));      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);
 #ifdef unix      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);
 fprintf(ficgp,"\nset ter gif small size 400,300");  #endif
 #endif    }
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    return res;
    }  }
   }  
   /*2 eme*/  /************** Inverse of matrix **************/
   void ludcmp(double **a, int n, int *indx, double *d) 
   for (k1=1; k1<= m ; k1 ++) {  { 
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);    int i,imax,j,k; 
        double big,dum,sum,temp; 
     for (i=1; i<= nlstate+1 ; i ++) {    double *vv; 
       k=2*i;   
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);    vv=vector(1,n); 
       for (j=1; j<= nlstate+1 ; j ++) {    *d=1.0; 
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    for (i=1;i<=n;i++) { 
   else fprintf(ficgp," \%%*lf (\%%*lf)");      big=0.0; 
 }        for (j=1;j<=n;j++) 
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");        if ((temp=fabs(a[i][j])) > big) big=temp; 
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);      vv[i]=1.0/big; 
       for (j=1; j<= nlstate+1 ; j ++) {    } 
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    for (j=1;j<=n;j++) { 
         else fprintf(ficgp," \%%*lf (\%%*lf)");      for (i=1;i<j;i++) { 
 }          sum=a[i][j]; 
       fprintf(ficgp,"\" t\"\" w l 0,");        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);        a[i][j]=sum; 
       for (j=1; j<= nlstate+1 ; j ++) {      } 
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      big=0.0; 
   else fprintf(ficgp," \%%*lf (\%%*lf)");      for (i=j;i<=n;i++) { 
 }          sum=a[i][j]; 
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");        for (k=1;k<j;k++) 
       else fprintf(ficgp,"\" t\"\" w l 0,");          sum -= a[i][k]*a[k][j]; 
     }        a[i][j]=sum; 
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);        if ( (dum=vv[i]*fabs(sum)) >= big) { 
   }          big=dum; 
            imax=i; 
   /*3eme*/        } 
       } 
   for (k1=1; k1<= m ; k1 ++) {      if (j != imax) { 
     for (cpt=1; cpt<= nlstate ; cpt ++) {        for (k=1;k<=n;k++) { 
       k=2+nlstate*(cpt-1);          dum=a[imax][k]; 
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k1-1,k1-1,k,cpt);          a[imax][k]=a[j][k]; 
       for (i=1; i< nlstate ; i ++) {          a[j][k]=dum; 
         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);        } 
       }        *d = -(*d); 
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);        vv[imax]=vv[j]; 
     }      } 
     }      indx[j]=imax; 
        if (a[j][j] == 0.0) a[j][j]=TINY; 
   /* CV preval stat */      if (j != n) { 
     for (k1=1; k1<= m ; k1 ++) {        dum=1.0/(a[j][j]); 
     for (cpt=1; cpt<nlstate ; cpt ++) {        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
       k=3;      } 
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);    } 
     free_vector(vv,1,n);  /* Doesn't work */
       for (i=1; i< nlstate ; i ++)  ;
         fprintf(ficgp,"+$%d",k+i+1);  } 
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);  
        void lubksb(double **a, int n, int *indx, double b[]) 
       l=3+(nlstate+ndeath)*cpt;  { 
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);    int i,ii=0,ip,j; 
       for (i=1; i< nlstate ; i ++) {    double sum; 
         l=3+(nlstate+ndeath)*cpt;   
         fprintf(ficgp,"+$%d",l+i+1);    for (i=1;i<=n;i++) { 
       }      ip=indx[i]; 
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);        sum=b[ip]; 
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);      b[ip]=b[i]; 
     }      if (ii) 
   }          for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
        else if (sum) ii=i; 
   /* proba elementaires */      b[i]=sum; 
    for(i=1,jk=1; i <=nlstate; i++){    } 
     for(k=1; k <=(nlstate+ndeath); k++){    for (i=n;i>=1;i--) { 
       if (k != i) {      sum=b[i]; 
         for(j=1; j <=ncovmodel; j++){      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
              b[i]=sum/a[i][i]; 
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);    } 
           jk++;  } 
           fprintf(ficgp,"\n");  
         }  void pstamp(FILE *fichier)
       }  {
     }    fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
     }  }
   
     for(jk=1; jk <=m; jk++) {  /************ Frequencies ********************/
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);  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[])
    i=1;  {  /* Some frequencies */
    for(k2=1; k2<=nlstate; k2++) {    
      k3=i;    int i, m, jk, k1,i1, j1, bool, z1,j;
      for(k=1; k<=(nlstate+ndeath); k++) {    int first;
        if (k != k2){    double ***freq; /* Frequencies */
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);    double *pp, **prop;
 ij=1;    double pos,posprop, k2, dateintsum=0,k2cpt=0;
         for(j=3; j <=ncovmodel; j++) {    char fileresp[FILENAMELENGTH];
           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]]]);    pp=vector(1,nlstate);
             ij++;    prop=matrix(1,nlstate,iagemin,iagemax+3);
           }    strcpy(fileresp,"p");
           else    strcat(fileresp,fileres);
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    if((ficresp=fopen(fileresp,"w"))==NULL) {
         }      printf("Problem with prevalence resultfile: %s\n", fileresp);
           fprintf(ficgp,")/(1");      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
              exit(0);
         for(k1=1; k1 <=nlstate; k1++){      }
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
 ij=1;    j1=0;
           for(j=3; j <=ncovmodel; j++){    
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    j=cptcoveff;
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
             ij++;  
           }    first=1;
           else  
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    for(k1=1; k1<=j;k1++){
           }      for(i1=1; i1<=ncodemax[k1];i1++){
           fprintf(ficgp,")");        j1++;
         }        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);          scanf("%d", i);*/
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");        for (i=-5; i<=nlstate+ndeath; i++)  
         i=i+ncovmodel;          for (jk=-5; jk<=nlstate+ndeath; jk++)  
        }            for(m=iagemin; m <= iagemax+3; m++)
      }              freq[i][jk][m]=0;
    }  
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);      for (i=1; i<=nlstate; i++)  
    }        for(m=iagemin; m <= iagemax+3; m++)
              prop[i][m]=0;
   fclose(ficgp);        
 }  /* end gnuplot */        dateintsum=0;
         k2cpt=0;
         for (i=1; i<=imx; i++) {
 /*************** Moving average **************/          bool=1;
 void movingaverage(double agedeb, double fage,double agemin, double ***mobaverage){          if  (cptcovn>0) {
             for (z1=1; z1<=cptcoveff; z1++) 
   int i, cpt, cptcod;              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
     for (agedeb=agemin; agedeb<=fage; agedeb++)                bool=0;
       for (i=1; i<=nlstate;i++)          }
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)          if (bool==1){
           mobaverage[(int)agedeb][i][cptcod]=0.;            for(m=firstpass; m<=lastpass; m++){
                  k2=anint[m][i]+(mint[m][i]/12.);
     for (agedeb=agemin+4; agedeb<=fage; agedeb++){              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
       for (i=1; i<=nlstate;i++){                if(agev[m][i]==0) agev[m][i]=iagemax+1;
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){                if(agev[m][i]==1) agev[m][i]=iagemax+2;
           for (cpt=0;cpt<=4;cpt++){                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];                if (m<lastpass) {
           }                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
         }                }
       }                
     }                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
                      dateintsum=dateintsum+k2;
 }                  k2cpt++;
                 }
 /***********************************************/                /*}*/
 /**************** Main Program *****************/            }
 /***********************************************/          }
         }
 int main(int argc, char *argv[])         
 {        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
         pstamp(ficresp);
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;        if  (cptcovn>0) {
   double agedeb, agefin,hf;          fprintf(ficresp, "\n#********** Variable "); 
   double agemin=1.e20, agemax=-1.e20;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresp, "**********\n#");
   double fret;        }
   double **xi,tmp,delta;        for(i=1; i<=nlstate;i++) 
           fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
   double dum; /* Dummy variable */        fprintf(ficresp, "\n");
   double ***p3mat;        
   int *indx;        for(i=iagemin; i <= iagemax+3; i++){
   char line[MAXLINE], linepar[MAXLINE];          if(i==iagemax+3){
   char title[MAXLINE];            fprintf(ficlog,"Total");
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];          }else{
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];            if(first==1){
                first=0;
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], fileresf[FILENAMELENGTH];              printf("See log file for details...\n");
             }
   char filerest[FILENAMELENGTH];            fprintf(ficlog,"Age %d", i);
   char fileregp[FILENAMELENGTH];          }
   char popfile[FILENAMELENGTH];          for(jk=1; jk <=nlstate ; jk++){
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
   int firstobs=1, lastobs=10;              pp[jk] += freq[jk][m][i]; 
   int sdeb, sfin; /* Status at beginning and end */          }
   int c,  h , cpt,l;          for(jk=1; jk <=nlstate ; jk++){
   int ju,jl, mi;            for(m=-1, pos=0; m <=0 ; m++)
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;              pos += freq[jk][m][i];
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;            if(pp[jk]>=1.e-10){
   int mobilav=0,popforecast=0;              if(first==1){
   int hstepm, nhstepm;                printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   int *popage;/*boolprev=0 if date and zero if wave*/              }
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2;              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
             }else{
   double bage, fage, age, agelim, agebase;              if(first==1)
   double ftolpl=FTOL;                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   double **prlim;              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   double *severity;            }
   double ***param; /* Matrix of parameters */          }
   double  *p;  
   double **matcov; /* Matrix of covariance */          for(jk=1; jk <=nlstate ; jk++){
   double ***delti3; /* Scale */            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
   double *delti; /* Scale */              pp[jk] += freq[jk][m][i];
   double ***eij, ***vareij;          }       
   double **varpl; /* Variances of prevalence limits by age */          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
   double *epj, vepp;            pos += pp[jk];
   double kk1, kk2;            posprop += prop[jk][i];
   double *popeffectif,*popcount;          }
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,jprojmean,mprojmean,anprojmean, calagedate;          for(jk=1; jk <=nlstate ; jk++){
   double yp,yp1,yp2;            if(pos>=1.e-5){
               if(first==1)
   char version[80]="Imach version 0.7, February 2002, INED-EUROREVES ";                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   char *alph[]={"a","a","b","c","d","e"}, str[4];              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
             }else{
               if(first==1)
   char z[1]="c", occ;                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
 #include <sys/time.h>              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
 #include <time.h>            }
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];            if( i <= iagemax){
                if(pos>=1.e-5){
   /* long total_usecs;                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
   struct timeval start_time, end_time;                /*probs[i][jk][j1]= pp[jk]/pos;*/
                  /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */              }
               else
                 fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
   printf("\n%s",version);            }
   if(argc <=1){          }
     printf("\nEnter the parameter file name: ");          
     scanf("%s",pathtot);          for(jk=-1; jk <=nlstate+ndeath; jk++)
   }            for(m=-1; m <=nlstate+ndeath; m++)
   else{              if(freq[jk][m][i] !=0 ) {
     strcpy(pathtot,argv[1]);              if(first==1)
   }                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
   /*cygwin_split_path(pathtot,path,optionfile);              }
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/          if(i <= iagemax)
   /* cutv(path,optionfile,pathtot,'\\');*/            fprintf(ficresp,"\n");
           if(first==1)
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);            printf("Others in log...\n");
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);          fprintf(ficlog,"\n");
   chdir(path);        }
   replace(pathc,path);      }
     }
 /*-------- arguments in the command line --------*/    dateintmean=dateintsum/k2cpt; 
    
   strcpy(fileres,"r");    fclose(ficresp);
   strcat(fileres, optionfilefiname);    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
   strcat(fileres,".txt");    /* Other files have txt extension */    free_vector(pp,1,nlstate);
     free_matrix(prop,1,nlstate,iagemin, iagemax+3);
   /*---------arguments file --------*/    /* End of Freq */
   }
   if((ficpar=fopen(optionfile,"r"))==NULL)    {  
     printf("Problem with optionfile %s\n",optionfile);  /************ Prevalence ********************/
     goto end;  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)
   }  {  
     /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
   strcpy(filereso,"o");       in each health status at the date of interview (if between dateprev1 and dateprev2).
   strcat(filereso,fileres);       We still use firstpass and lastpass as another selection.
   if((ficparo=fopen(filereso,"w"))==NULL) {    */
     printf("Problem with Output resultfile: %s\n", filereso);goto end;   
   }    int i, m, jk, k1, i1, j1, bool, z1,j;
     double ***freq; /* Frequencies */
   /* Reads comments: lines beginning with '#' */    double *pp, **prop;
   while((c=getc(ficpar))=='#' && c!= EOF){    double pos,posprop; 
     ungetc(c,ficpar);    double  y2; /* in fractional years */
     fgets(line, MAXLINE, ficpar);    int iagemin, iagemax;
     puts(line);  
     fputs(line,ficparo);    iagemin= (int) agemin;
   }    iagemax= (int) agemax;
   ungetc(c,ficpar);    /*pp=vector(1,nlstate);*/
     prop=matrix(1,nlstate,iagemin,iagemax+3); 
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncov, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate,ndeath, maxwav, mle, weightopt,model);    j1=0;
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncov,nlstate,ndeath,maxwav, mle, weightopt,model);    
 while((c=getc(ficpar))=='#' && c!= EOF){    j=cptcoveff;
     ungetc(c,ficpar);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
     fgets(line, MAXLINE, ficpar);    
     puts(line);    for(k1=1; k1<=j;k1++){
     fputs(line,ficparo);      for(i1=1; i1<=ncodemax[k1];i1++){
   }        j1++;
   ungetc(c,ficpar);        
          for (i=1; i<=nlstate; i++)  
              for(m=iagemin; m <= iagemax+3; m++)
   covar=matrix(0,NCOVMAX,1,n);            prop[i][m]=0.0;
   cptcovn=0;       
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;        for (i=1; i<=imx; i++) { /* Each individual */
           bool=1;
   ncovmodel=2+cptcovn;          if  (cptcovn>0) {
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */            for (z1=1; z1<=cptcoveff; z1++) 
                if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   /* Read guess parameters */                bool=0;
   /* Reads comments: lines beginning with '#' */          } 
   while((c=getc(ficpar))=='#' && c!= EOF){          if (bool==1) { 
     ungetc(c,ficpar);            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
     fgets(line, MAXLINE, ficpar);              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
     puts(line);              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
     fputs(line,ficparo);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
   }                if(agev[m][i]==1) agev[m][i]=iagemax+2;
   ungetc(c,ficpar);                if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
                  if (s[m][i]>0 && s[m][i]<=nlstate) { 
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);                  /*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]]);*/
     for(i=1; i <=nlstate; i++)                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
     for(j=1; j <=nlstate+ndeath-1; j++){                  prop[s[m][i]][iagemax+3] += weight[i]; 
       fscanf(ficpar,"%1d%1d",&i1,&j1);                } 
       fprintf(ficparo,"%1d%1d",i1,j1);              }
       printf("%1d%1d",i,j);            } /* end selection of waves */
       for(k=1; k<=ncovmodel;k++){          }
         fscanf(ficpar," %lf",&param[i][j][k]);        }
         printf(" %lf",param[i][j][k]);        for(i=iagemin; i <= iagemax+3; i++){  
         fprintf(ficparo," %lf",param[i][j][k]);          
       }          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
       fscanf(ficpar,"\n");            posprop += prop[jk][i]; 
       printf("\n");          } 
       fprintf(ficparo,"\n");  
     }          for(jk=1; jk <=nlstate ; jk++){     
              if( i <=  iagemax){ 
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;              if(posprop>=1.e-5){ 
                 probs[i][jk][j1]= prop[jk][i]/posprop;
   p=param[1][1];              } else
                  printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\n",jk,i,j1,probs[i][jk][j1]);
   /* Reads comments: lines beginning with '#' */            } 
   while((c=getc(ficpar))=='#' && c!= EOF){          }/* end jk */ 
     ungetc(c,ficpar);        }/* end i */ 
     fgets(line, MAXLINE, ficpar);      } /* end i1 */
     puts(line);    } /* end k1 */
     fputs(line,ficparo);    
   }    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
   ungetc(c,ficpar);    /*free_vector(pp,1,nlstate);*/
     free_matrix(prop,1,nlstate, iagemin,iagemax+3);
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);  }  /* End of prevalence */
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */  
   for(i=1; i <=nlstate; i++){  /************* Waves Concatenation ***************/
     for(j=1; j <=nlstate+ndeath-1; j++){  
       fscanf(ficpar,"%1d%1d",&i1,&j1);  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)
       printf("%1d%1d",i,j);  {
       fprintf(ficparo,"%1d%1d",i1,j1);    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
       for(k=1; k<=ncovmodel;k++){       Death is a valid wave (if date is known).
         fscanf(ficpar,"%le",&delti3[i][j][k]);       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
         printf(" %le",delti3[i][j][k]);       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
         fprintf(ficparo," %le",delti3[i][j][k]);       and mw[mi+1][i]. dh depends on stepm.
       }       */
       fscanf(ficpar,"\n");  
       printf("\n");    int i, mi, m;
       fprintf(ficparo,"\n");    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
     }       double sum=0., jmean=0.;*/
   }    int first;
   delti=delti3[1][1];    int j, k=0,jk, ju, jl;
      double sum=0.;
   /* Reads comments: lines beginning with '#' */    first=0;
   while((c=getc(ficpar))=='#' && c!= EOF){    jmin=1e+5;
     ungetc(c,ficpar);    jmax=-1;
     fgets(line, MAXLINE, ficpar);    jmean=0.;
     puts(line);    for(i=1; i<=imx; i++){
     fputs(line,ficparo);      mi=0;
   }      m=firstpass;
   ungetc(c,ficpar);      while(s[m][i] <= nlstate){
          if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
   matcov=matrix(1,npar,1,npar);          mw[++mi][i]=m;
   for(i=1; i <=npar; i++){        if(m >=lastpass)
     fscanf(ficpar,"%s",&str);          break;
     printf("%s",str);        else
     fprintf(ficparo,"%s",str);          m++;
     for(j=1; j <=i; j++){      }/* end while */
       fscanf(ficpar," %le",&matcov[i][j]);      if (s[m][i] > nlstate){
       printf(" %.5le",matcov[i][j]);        mi++;     /* Death is another wave */
       fprintf(ficparo," %.5le",matcov[i][j]);        /* if(mi==0)  never been interviewed correctly before death */
     }           /* Only death is a correct wave */
     fscanf(ficpar,"\n");        mw[mi][i]=m;
     printf("\n");      }
     fprintf(ficparo,"\n");  
   }      wav[i]=mi;
   for(i=1; i <=npar; i++)      if(mi==0){
     for(j=i+1;j<=npar;j++)        nbwarn++;
       matcov[i][j]=matcov[j][i];        if(first==0){
              printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
   printf("\n");          first=1;
         }
         if(first==1){
     /*-------- data file ----------*/          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
     if((ficres =fopen(fileres,"w"))==NULL) {        }
       printf("Problem with resultfile: %s\n", fileres);goto end;      } /* end mi==0 */
     }    } /* End individuals */
     fprintf(ficres,"#%s\n",version);  
        for(i=1; i<=imx; i++){
     if((fic=fopen(datafile,"r"))==NULL)    {      for(mi=1; mi<wav[i];mi++){
       printf("Problem with datafile: %s\n", datafile);goto end;        if (stepm <=0)
     }          dh[mi][i]=1;
         else{
     n= lastobs;          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
     severity = vector(1,maxwav);            if (agedc[i] < 2*AGESUP) {
     outcome=imatrix(1,maxwav+1,1,n);              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
     num=ivector(1,n);              if(j==0) j=1;  /* Survives at least one month after exam */
     moisnais=vector(1,n);              else if(j<0){
     annais=vector(1,n);                nberr++;
     moisdc=vector(1,n);                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]);
     andc=vector(1,n);                j=1; /* Temporary Dangerous patch */
     agedc=vector(1,n);                printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
     cod=ivector(1,n);                fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
     weight=vector(1,n);                fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */              }
     mint=matrix(1,maxwav,1,n);              k=k+1;
     anint=matrix(1,maxwav,1,n);              if (j >= jmax){
     s=imatrix(1,maxwav+1,1,n);                jmax=j;
     adl=imatrix(1,maxwav+1,1,n);                    ijmax=i;
     tab=ivector(1,NCOVMAX);              }
     ncodemax=ivector(1,8);              if (j <= jmin){
                 jmin=j;
     i=1;                ijmin=i;
     while (fgets(line, MAXLINE, fic) != NULL)    {              }
       if ((i >= firstobs) && (i <=lastobs)) {              sum=sum+j;
                      /*if (j<0) printf("j=%d num=%d \n",j,i);*/
         for (j=maxwav;j>=1;j--){              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);            }
           strcpy(line,stra);          }
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);          else{
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
         }  /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
          
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);            k=k+1;
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);            if (j >= jmax) {
               jmax=j;
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);              ijmax=i;
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);            }
             else if (j <= jmin){
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);              jmin=j;
         for (j=ncov;j>=1;j--){              ijmin=i;
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);            }
         }            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
         num[i]=atol(stra);            /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
                    if(j<0){
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){              nberr++;
           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;}*/              printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
               fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
         i=i+1;            }
       }            sum=sum+j;
     }          }
     /* printf("ii=%d", ij);          jk= j/stepm;
        scanf("%d",i);*/          jl= j -jk*stepm;
   imx=i-1; /* Number of individuals */          ju= j -(jk+1)*stepm;
           if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
   /* for (i=1; i<=imx; i++){            if(jl==0){
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;              dh[mi][i]=jk;
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;              bh[mi][i]=0;
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;            }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;
     for (i=1; i<=imx; i++)              bh[mi][i]=ju;
     if (covar[1][i]==0) printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));*/            }
           }else{
   /* Calculation of the number of parameter from char model*/            if(jl <= -ju){
   Tvar=ivector(1,15);              dh[mi][i]=jk;
   Tprod=ivector(1,15);              bh[mi][i]=jl;       /* bias is positive if real duration
   Tvaraff=ivector(1,15);                                   * is higher than the multiple of stepm and negative otherwise.
   Tvard=imatrix(1,15,1,2);                                   */
   Tage=ivector(1,15);                  }
                else{
   if (strlen(model) >1){              dh[mi][i]=jk+1;
     j=0, j1=0, k1=1, k2=1;              bh[mi][i]=ju;
     j=nbocc(model,'+');            }
     j1=nbocc(model,'*');            if(dh[mi][i]==0){
     cptcovn=j+1;              dh[mi][i]=1; /* At least one step */
     cptcovprod=j1;              bh[mi][i]=ju; /* At least one step */
                  /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
                }
     strcpy(modelsav,model);          } /* end if mle */
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){        }
       printf("Error. Non available option model=%s ",model);      } /* end wave */
       goto end;    }
     }    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);
     for(i=(j+1); i>=1;i--){    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);
       cutv(stra,strb,modelsav,'+');   }
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);  
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/  /*********** Tricode ****************************/
       /*scanf("%d",i);*/  void tricode(int *Tvar, int **nbcode, int imx)
       if (strchr(strb,'*')) {  {
         cutv(strd,strc,strb,'*');    
         if (strcmp(strc,"age")==0) {    /*      Tvar[i]=atoi(stre); /* find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 */
           cptcovprod--;  
           cutv(strb,stre,strd,'V');    int Ndum[20],ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
           Tvar[i]=atoi(stre);    int cptcode=0;
           cptcovage++;    cptcoveff=0; 
             Tage[cptcovage]=i;   
             /*printf("stre=%s ", stre);*/    for (k=0; k<maxncov; k++) Ndum[k]=0;
         }    for (k=1; k<=7; k++) ncodemax[k]=0; /* Horrible constant again */
         else if (strcmp(strd,"age")==0) {  
           cptcovprod--;    for (j=1; j<=(cptcovn+2*cptcovprod); j++) { /* For each covariate */
           cutv(strb,stre,strc,'V');      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
           Tvar[i]=atoi(stre);                                 modality*/ 
           cptcovage++;        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual, might be -1*/
           Tage[cptcovage]=i;        Ndum[ij]++; /*counts the occurence of this modality */
         }        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
         else {        if (ij > cptcode) cptcode=ij; /* getting the maximum value of the modality of the covariate  (should be 0 or 1 now) 
           cutv(strb,stre,strc,'V');                                         Tvar[j]. If V=sex and male is 0 and 
           Tvar[i]=ncov+k1;                                         female is 1, then  cptcode=1.*/
           cutv(strb,strc,strd,'V');      }
           Tprod[k1]=i;  
           Tvard[k1][1]=atoi(strc);      for (i=0; i<=cptcode; i++) { /* i=-1 ?*/
           Tvard[k1][2]=atoi(stre);        if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j
           Tvar[cptcovn+k2]=Tvard[k1][1];                                         th covariate. In fact
           Tvar[cptcovn+k2+1]=Tvard[k1][2];                                         ncodemax[j]=2
           for (k=1; k<=lastobs;k++)                                         (dichotom. variables only) but
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];                                         it can be more */
           k1++;      } /* Ndum[-1] number of undefined modalities */
           k2=k2+2;  
         }      ij=1; 
       }      for (i=1; i<=ncodemax[j]; i++) { /* i= 1 to 2 */
       else {        for (k=0; k<= maxncov; k++) { /* k=-1 ?*/
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/          if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
        /*  scanf("%d",i);*/            nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode. 
       cutv(strd,strc,strb,'V');                                       k is a modality. If we have model=V1+V1*sex 
       Tvar[i]=atoi(strc);                                       then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
       }            ij++;
       strcpy(modelsav,stra);            }
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);          if (ij > ncodemax[j]) break; 
         scanf("%d",i);*/        }  
     }      } 
 }    }  
    
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);   for (k=0; k< maxncov; k++) Ndum[k]=0;
   printf("cptcovprod=%d ", cptcovprod);  
   scanf("%d ",i);*/   for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */
     fclose(fic);     /* 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 */
     /*  if(mle==1){*/     Ndum[ij]++;
     if (weightopt != 1) { /* Maximisation without weights*/   }
       for(i=1;i<=n;i++) weight[i]=1.0;  
     }   ij=1;
     /*-calculation of age at interview from date of interview and age at death -*/   for (i=1; i<= maxncov; i++) {
     agev=matrix(1,maxwav,1,imx);     if((Ndum[i]!=0) && (i<=ncovcol)){
        Tvaraff[ij]=i; /*For printing */
    for (i=1; i<=imx; i++)       ij++;
      for(m=2; (m<= maxwav); m++)     }
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){   }
          anint[m][i]=9999;   ij--;
          s[m][i]=-1;   cptcoveff=ij; /*Number of simple covariates*/
        }  }
      
     for (i=1; i<=imx; i++)  {  /*********** Health Expectancies ****************/
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);  
       for(m=1; (m<= maxwav); m++){  void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
         if(s[m][i] >0){  
           if (s[m][i] == nlstate+1) {  {
             if(agedc[i]>0)    /* Health expectancies, no variances */
               if(moisdc[i]!=99 && andc[i]!=9999)    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
               agev[m][i]=agedc[i];    int nhstepma, nstepma; /* Decreasing with age */
             else {    double age, agelim, hf;
               if (andc[i]!=9999){    double ***p3mat;
               printf("Warning negative age at death: %d line:%d\n",num[i],i);    double eip;
               agev[m][i]=-1;  
               }    pstamp(ficreseij);
             }    fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
           }    fprintf(ficreseij,"# Age");
           else if(s[m][i] !=9){ /* Should no more exist */    for(i=1; i<=nlstate;i++){
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);      for(j=1; j<=nlstate;j++){
             if(mint[m][i]==99 || anint[m][i]==9999)        fprintf(ficreseij," e%1d%1d ",i,j);
               agev[m][i]=1;      }
             else if(agev[m][i] <agemin){      fprintf(ficreseij," e%1d. ",i);
               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);*/    fprintf(ficreseij,"\n");
             }  
             else if(agev[m][i] >agemax){    
               agemax=agev[m][i];    if(estepm < stepm){
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/      printf ("Problem %d lower than %d\n",estepm, stepm);
             }    }
             /*agev[m][i]=anint[m][i]-annais[i];*/    else  hstepm=estepm;   
             /*   agev[m][i] = age[i]+2*m;*/    /* We compute the life expectancy from trapezoids spaced every estepm months
           }     * This is mainly to measure the difference between two models: for example
           else { /* =9 */     * if stepm=24 months pijx are given only every 2 years and by summing them
             agev[m][i]=1;     * we are calculating an estimate of the Life Expectancy assuming a linear 
             s[m][i]=-1;     * 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
         else /*= 0 Unknown */     * to compare the new estimate of Life expectancy with the same linear 
           agev[m][i]=1;     * hypothesis. A more precise result, taking into account a more precise
       }     * curvature will be obtained if estepm is as small as stepm. */
      
     }    /* For example we decided to compute the life expectancy with the smallest unit */
     for (i=1; i<=imx; i++)  {    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
       for(m=1; (m<= maxwav); m++){       nhstepm is the number of hstepm from age to agelim 
         if (s[m][i] > (nlstate+ndeath)) {       nstepm is the number of stepm from age to agelin. 
           printf("Error: Wrong value in nlstate or ndeath\n");         Look at hpijx to understand the reason of that which relies in memory size
           goto end;       and note for a fixed period like estepm months */
         }    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
       }       survival function given by stepm (the optimization length). Unfortunately it
     }       means that if the survival funtion is printed only each two years of age and if
        you sum them up and add 1 year (area under the trapezoids) you won't get the same 
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);       results. So we changed our mind and took the option of the best precision.
     */
     free_vector(severity,1,maxwav);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     free_imatrix(outcome,1,maxwav+1,1,n);  
     free_vector(moisnais,1,n);    agelim=AGESUP;
     free_vector(annais,1,n);    /* If stepm=6 months */
     /* free_matrix(mint,1,maxwav,1,n);      /* Computed by stepm unit matrices, product of hstepm matrices, stored
        free_matrix(anint,1,maxwav,1,n);*/         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
     free_vector(moisdc,1,n);      
     free_vector(andc,1,n);  /* nhstepm age range expressed in number of stepm */
     nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
        /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     wav=ivector(1,imx);    /* if (stepm >= YEARM) hstepm=1;*/
     dh=imatrix(1,lastpass-firstpass+1,1,imx);    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     mw=imatrix(1,lastpass-firstpass+1,1,imx);    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
      
     /* Concatenates waves */    for (age=bage; age<=fage; age ++){ 
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
       /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       /* if (stepm >= YEARM) hstepm=1;*/
       Tcode=ivector(1,100);      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);  
       ncodemax[1]=1;      /* If stepm=6 months */
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);      /* Computed by stepm unit matrices, product of hstepma matrices, stored
               in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
    codtab=imatrix(1,100,1,10);      
    h=0;      hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
    m=pow(2,cptcoveff);      
        hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
    for(k=1;k<=cptcoveff; k++){      
      for(i=1; i <=(m/pow(2,k));i++){      printf("%d|",(int)age);fflush(stdout);
        for(j=1; j <= ncodemax[k]; j++){      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){      
            h++;      /* Computing expectancies */
            if (h>m) h=1;codtab[h][k]=j;      for(i=1; i<=nlstate;i++)
          }        for(j=1; j<=nlstate;j++)
        }          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
      }            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
    }            
             /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
   
    /*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);      fprintf(ficreseij,"%3.0f",age );
      }      for(i=1; i<=nlstate;i++){
      printf("\n");        eip=0;
    }        for(j=1; j<=nlstate;j++){
    scanf("%d",i);*/          eip +=eij[i][j][(int)age];
              fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
    /* Calculates basic frequencies. Computes observed prevalence at single age        }
        and prints on file fileres'p'. */        fprintf(ficreseij,"%9.4f", eip );
       }
          fprintf(ficreseij,"\n");
          
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    }
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    printf("\n");
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    fprintf(ficlog,"\n");
     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] */  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[] )
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */  
   {
     if(mle==1){    /* Covariances of health expectancies eij and of total life expectancies according
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);     to initial status i, ei. .
     }    */
        int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
     /*--------- results files --------------*/    int nhstepma, nstepma; /* Decreasing with age */
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, mle,weightopt,model);    double age, agelim, hf;
      double ***p3matp, ***p3matm, ***varhe;
     double **dnewm,**doldm;
    jk=1;    double *xp, *xm;
    fprintf(ficres,"# Parameters\n");    double **gp, **gm;
    printf("# Parameters\n");    double ***gradg, ***trgradg;
    for(i=1,jk=1; i <=nlstate; i++){    int theta;
      for(k=1; k <=(nlstate+ndeath); k++){  
        if (k != i)    double eip, vip;
          {  
            printf("%d%d ",i,k);    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
            fprintf(ficres,"%1d%1d ",i,k);    xp=vector(1,npar);
            for(j=1; j <=ncovmodel; j++){    xm=vector(1,npar);
              printf("%f ",p[jk]);    dnewm=matrix(1,nlstate*nlstate,1,npar);
              fprintf(ficres,"%f ",p[jk]);    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
              jk++;    
            }    pstamp(ficresstdeij);
            printf("\n");    fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
            fprintf(ficres,"\n");    fprintf(ficresstdeij,"# Age");
          }    for(i=1; i<=nlstate;i++){
      }      for(j=1; j<=nlstate;j++)
    }        fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
  if(mle==1){      fprintf(ficresstdeij," e%1d. ",i);
     /* Computing hessian and covariance matrix */    }
     ftolhess=ftol; /* Usually correct */    fprintf(ficresstdeij,"\n");
     hesscov(matcov, p, npar, delti, ftolhess, func);  
  }    pstamp(ficrescveij);
     fprintf(ficres,"# Scales\n");    fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
     printf("# Scales\n");    fprintf(ficrescveij,"# Age");
      for(i=1,jk=1; i <=nlstate; i++){    for(i=1; i<=nlstate;i++)
       for(j=1; j <=nlstate+ndeath; j++){      for(j=1; j<=nlstate;j++){
         if (j!=i) {        cptj= (j-1)*nlstate+i;
           fprintf(ficres,"%1d%1d",i,j);        for(i2=1; i2<=nlstate;i2++)
           printf("%1d%1d",i,j);          for(j2=1; j2<=nlstate;j2++){
           for(k=1; k<=ncovmodel;k++){            cptj2= (j2-1)*nlstate+i2;
             printf(" %.5e",delti[jk]);            if(cptj2 <= cptj)
             fprintf(ficres," %.5e",delti[jk]);              fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
             jk++;          }
           }      }
           printf("\n");    fprintf(ficrescveij,"\n");
           fprintf(ficres,"\n");    
         }    if(estepm < stepm){
       }      printf ("Problem %d lower than %d\n",estepm, stepm);
      }    }
        else  hstepm=estepm;   
     k=1;    /* We compute the life expectancy from trapezoids spaced every estepm months
     fprintf(ficres,"# Covariance\n");     * This is mainly to measure the difference between two models: for example
     printf("# Covariance\n");     * if stepm=24 months pijx are given only every 2 years and by summing them
     for(i=1;i<=npar;i++){     * we are calculating an estimate of the Life Expectancy assuming a linear 
       /*  if (k>nlstate) k=1;     * progression in between and thus overestimating or underestimating according
       i1=(i-1)/(ncovmodel*nlstate)+1;     * to the curvature of the survival function. If, for the same date, we 
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);     * estimate the model with stepm=1 month, we can keep estepm to 24 months
       printf("%s%d%d",alph[k],i1,tab[i]);*/     * to compare the new estimate of Life expectancy with the same linear 
       fprintf(ficres,"%3d",i);     * hypothesis. A more precise result, taking into account a more precise
       printf("%3d",i);     * curvature will be obtained if estepm is as small as stepm. */
       for(j=1; j<=i;j++){  
         fprintf(ficres," %.5e",matcov[i][j]);    /* For example we decided to compute the life expectancy with the smallest unit */
         printf(" %.5e",matcov[i][j]);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
       }       nhstepm is the number of hstepm from age to agelim 
       fprintf(ficres,"\n");       nstepm is the number of stepm from age to agelin. 
       printf("\n");       Look at hpijx to understand the reason of that which relies in memory size
       k++;       and note for a fixed period like estepm months */
     }    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
           survival function given by stepm (the optimization length). Unfortunately it
     while((c=getc(ficpar))=='#' && c!= EOF){       means that if the survival funtion is printed only each two years of age and if
       ungetc(c,ficpar);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
       fgets(line, MAXLINE, ficpar);       results. So we changed our mind and took the option of the best precision.
       puts(line);    */
       fputs(line,ficparo);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     }  
     ungetc(c,ficpar);    /* If stepm=6 months */
      /* nhstepm age range expressed in number of stepm */
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);    agelim=AGESUP;
        nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
     if (fage <= 2) {    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       bage = agemin;    /* if (stepm >= YEARM) hstepm=1;*/
       fage = agemax;    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     }    
        p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");    p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);    gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);    trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
      gp=matrix(0,nhstepm,1,nlstate*nlstate);
     while((c=getc(ficpar))=='#' && c!= EOF){    gm=matrix(0,nhstepm,1,nlstate*nlstate);
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);    for (age=bage; age<=fage; age ++){ 
     puts(line);      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
     fputs(line,ficparo);      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   }      /* if (stepm >= YEARM) hstepm=1;*/
   ungetc(c,ficpar);      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
    
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);      /* If stepm=6 months */
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);      /* Computed by stepm unit matrices, product of hstepma matrices, stored
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
            
   while((c=getc(ficpar))=='#' && c!= EOF){      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);      /* Computing  Variances of health expectancies */
     puts(line);      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
     fputs(line,ficparo);         decrease memory allocation */
   }      for(theta=1; theta <=npar; theta++){
   ungetc(c,ficpar);        for(i=1; i<=npar; i++){ 
            xp[i] = x[i] + (i==theta ?delti[theta]:0);
           xm[i] = x[i] - (i==theta ?delti[theta]:0);
    dateprev1=anprev1+mprev1/12.+jprev1/365.;        }
    dateprev2=anprev2+mprev2/12.+jprev2/365.;        hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
         hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
   fscanf(ficpar,"pop_based=%d\n",&popbased);    
    fprintf(ficparo,"pop_based=%d\n",popbased);          for(j=1; j<= nlstate; j++){
    fprintf(ficres,"pop_based=%d\n",popbased);            for(i=1; i<=nlstate; i++){
             for(h=0; h<=nhstepm-1; h++){
   while((c=getc(ficpar))=='#' && c!= EOF){              gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
     ungetc(c,ficpar);              gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
     fgets(line, MAXLINE, ficpar);            }
     puts(line);          }
     fputs(line,ficparo);        }
   }       
   ungetc(c,ficpar);        for(ij=1; ij<= nlstate*nlstate; ij++)
   fscanf(ficpar,"popforecast=%d popfile=%s starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mov_average=%d\n",&popforecast,popfile,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);          for(h=0; h<=nhstepm-1; h++){
 fprintf(ficparo,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);            gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
 fprintf(ficres,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);          }
       }/* End theta */
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);      
       
 /*------------ gnuplot -------------*/      for(h=0; h<=nhstepm-1; h++)
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, agemin,agemax,fage, pathc,p);        for(j=1; j<=nlstate*nlstate;j++)
            for(theta=1; theta <=npar; theta++)
 /*------------ free_vector  -------------*/            trgradg[h][j][theta]=gradg[h][theta][j];
  chdir(path);      
    
  free_ivector(wav,1,imx);       for(ij=1;ij<=nlstate*nlstate;ij++)
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);        for(ji=1;ji<=nlstate*nlstate;ji++)
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);            varhe[ij][ji][(int)age] =0.;
  free_ivector(num,1,n);  
  free_vector(agedc,1,n);       printf("%d|",(int)age);fflush(stdout);
  /*free_matrix(covar,1,NCOVMAX,1,n);*/       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
  fclose(ficparo);       for(h=0;h<=nhstepm-1;h++){
  fclose(ficres);        for(k=0;k<=nhstepm-1;k++){
            matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
   /* Reads comments: lines beginning with '#' */          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
   while((c=getc(ficpar))=='#' && c!= EOF){          for(ij=1;ij<=nlstate*nlstate;ij++)
     ungetc(c,ficpar);            for(ji=1;ji<=nlstate*nlstate;ji++)
     fgets(line, MAXLINE, ficpar);              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
     puts(line);        }
     fputs(line,ficparo);      }
   }  
   ungetc(c,ficpar);      /* Computing expectancies */
        hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);      for(i=1; i<=nlstate;i++)
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);        for(j=1; j<=nlstate;j++)
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
 /*--------- index.htm --------*/            eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
             
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm);            /* 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]);*/
   
            }
   /*--------------- Prevalence limit --------------*/  
        fprintf(ficresstdeij,"%3.0f",age );
   strcpy(filerespl,"pl");      for(i=1; i<=nlstate;i++){
   strcat(filerespl,fileres);        eip=0.;
   if((ficrespl=fopen(filerespl,"w"))==NULL) {        vip=0.;
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;        for(j=1; j<=nlstate;j++){
   }          eip += eij[i][j][(int)age];
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);          for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
   fprintf(ficrespl,"#Prevalence limit\n");            vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
   fprintf(ficrespl,"#Age ");          fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);        }
   fprintf(ficrespl,"\n");        fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
        }
   prlim=matrix(1,nlstate,1,nlstate);      fprintf(ficresstdeij,"\n");
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      fprintf(ficrescveij,"%3.0f",age );
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      for(i=1; i<=nlstate;i++)
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        for(j=1; j<=nlstate;j++){
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */          cptj= (j-1)*nlstate+i;
   k=0;          for(i2=1; i2<=nlstate;i2++)
   agebase=agemin;            for(j2=1; j2<=nlstate;j2++){
   agelim=agemax;              cptj2= (j2-1)*nlstate+i2;
   ftolpl=1.e-10;              if(cptj2 <= cptj)
   i1=cptcoveff;                fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
   if (cptcovn < 1){i1=1;}            }
         }
   for(cptcov=1;cptcov<=i1;cptcov++){      fprintf(ficrescveij,"\n");
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){     
         k=k+1;    }
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/    free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
         fprintf(ficrespl,"\n#******");    free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
         for(j=1;j<=cptcoveff;j++)    free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
         fprintf(ficrespl,"******\n");    free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
            free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         for (age=agebase; age<=agelim; age++){    printf("\n");
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    fprintf(ficlog,"\n");
           fprintf(ficrespl,"%.0f",age );  
           for(i=1; i<=nlstate;i++)    free_vector(xm,1,npar);
           fprintf(ficrespl," %.5f", prlim[i][i]);    free_vector(xp,1,npar);
           fprintf(ficrespl,"\n");    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
         }    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
       }    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
     }  }
   fclose(ficrespl);  
   /************ Variance ******************/
   /*------------- h Pij x at various ages ------------*/  void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
    {
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);    /* Variance of health expectancies */
   if((ficrespij=fopen(filerespij,"w"))==NULL) {    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;    /* double **newm;*/
   }    double **dnewm,**doldm;
   printf("Computing pij: result on file '%s' \n", filerespij);    double **dnewmp,**doldmp;
      int i, j, nhstepm, hstepm, h, nstepm ;
   stepsize=(int) (stepm+YEARM-1)/YEARM;    int k, cptcode;
   /*if (stepm<=24) stepsize=2;*/    double *xp;
     double **gp, **gm;  /* for var eij */
   agelim=AGESUP;    double ***gradg, ***trgradg; /*for var eij */
   hstepm=stepsize*YEARM; /* Every year of age */    double **gradgp, **trgradgp; /* for var p point j */
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */    double *gpp, *gmp; /* for var p point j */
      double **varppt; /* for var p point j nlstate to nlstate+ndeath */
   k=0;    double ***p3mat;
   for(cptcov=1;cptcov<=i1;cptcov++){    double age,agelim, hf;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    double ***mobaverage;
       k=k+1;    int theta;
         fprintf(ficrespij,"\n#****** ");    char digit[4];
         for(j=1;j<=cptcoveff;j++)    char digitp[25];
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
         fprintf(ficrespij,"******\n");    char fileresprobmorprev[FILENAMELENGTH];
          
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */    if(popbased==1){
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      if(mobilav!=0)
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */        strcpy(digitp,"-populbased-mobilav-");
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      else strcpy(digitp,"-populbased-nomobil-");
           oldm=oldms;savm=savms;    }
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      else 
           fprintf(ficrespij,"# Age");      strcpy(digitp,"-stablbased-");
           for(i=1; i<=nlstate;i++)  
             for(j=1; j<=nlstate+ndeath;j++)    if (mobilav!=0) {
               fprintf(ficrespij," %1d-%1d",i,j);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
           fprintf(ficrespij,"\n");      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
           for (h=0; h<=nhstepm; h++){        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );        printf(" Error in movingaverage mobilav=%d\n",mobilav);
             for(i=1; i<=nlstate;i++)      }
               for(j=1; j<=nlstate+ndeath;j++)    }
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);  
             fprintf(ficrespij,"\n");    strcpy(fileresprobmorprev,"prmorprev"); 
           }    sprintf(digit,"%-d",ij);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
           fprintf(ficrespij,"\n");    strcat(fileresprobmorprev,digit); /* Tvar to be done */
         }    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
     }    strcat(fileresprobmorprev,fileres);
   }    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobmorprev);
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
     }
   fclose(ficrespij);    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
    
   if(stepm == 1) {    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   /*---------- Forecasting ------------------*/    pstamp(ficresprobmorprev);
   calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;    fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
     fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
        fprintf(ficresprobmorprev," p.%-d SE",j);
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);      for(i=1; i<=nlstate;i++)
         fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
      }  
   strcpy(fileresf,"f");    fprintf(ficresprobmorprev,"\n");
   strcat(fileresf,fileres);    fprintf(ficgp,"\n# Routine varevsij");
   if((ficresf=fopen(fileresf,"w"))==NULL) {    /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
     printf("Problem with forecast resultfile: %s\n", fileresf);goto end;    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);
   printf("Computing forecasting: result on file '%s' \n", fileresf);  /*   } */
      varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   free_matrix(mint,1,maxwav,1,n);    pstamp(ficresvij);
   free_matrix(anint,1,maxwav,1,n);    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
     if(popbased==1)
   if (cptcoveff==0) ncodemax[cptcoveff]=1;      fprintf(ficresvij,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d\n",mobilav);
     else
   if (mobilav==1) {      fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    fprintf(ficresvij,"# Age");
     movingaverage(agedeb, fage, agemin, mobaverage);    for(i=1; i<=nlstate;i++)
   }      for(j=1; j<=nlstate;j++)
         fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
   stepsize=(int) (stepm+YEARM-1)/YEARM;    fprintf(ficresvij,"\n");
   if (stepm<=12) stepsize=1;  
      xp=vector(1,npar);
   agelim=AGESUP;    dnewm=matrix(1,nlstate,1,npar);
      doldm=matrix(1,nlstate,1,nlstate);
   hstepm=1;    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
   hstepm=hstepm/stepm;    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   yp1=modf(dateintmean,&yp);  
   anprojmean=yp;    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
   yp2=modf((yp1*12),&yp);    gpp=vector(nlstate+1,nlstate+ndeath);
   mprojmean=yp;    gmp=vector(nlstate+1,nlstate+ndeath);
   yp1=modf((yp2*30.5),&yp);    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
   jprojmean=yp;    
   if(jprojmean==0) jprojmean=1;    if(estepm < stepm){
   if(mprojmean==0) jprojmean=1;      printf ("Problem %d lower than %d\n",estepm, stepm);
      }
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);    else  hstepm=estepm;   
      /* For example we decided to compute the life expectancy with the smallest unit */
   if (popforecast==1) {    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
     if((ficpop=fopen(popfile,"r"))==NULL)    {       nhstepm is the number of hstepm from age to agelim 
       printf("Problem with population file : %s\n",popfile);goto end;       nstepm is the number of stepm from age to agelin. 
     }       Look at function hpijx to understand why (it is linked to memory size questions) */
     popage=ivector(0,AGESUP);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
     popeffectif=vector(0,AGESUP);       survival function given by stepm (the optimization length). Unfortunately it
     popcount=vector(0,AGESUP);       means that if the survival funtion is printed every two years of age and if
           you sum them up and add 1 year (area under the trapezoids) you won't get the same 
     i=1;         results. So we changed our mind and took the option of the best precision.
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF)    */
       {    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
         i=i+1;    agelim = AGESUP;
       }    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
     imx=i;      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
          nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   }      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
        gp=matrix(0,nhstepm,1,nlstate);
   for(cptcov=1;cptcov<=i1;cptcov++){      gm=matrix(0,nhstepm,1,nlstate);
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){  
       k=k+1;  
       fprintf(ficresf,"\n#******");      for(theta=1; theta <=npar; theta++){
       for(j=1;j<=cptcoveff;j++) {        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
       }        }
       fprintf(ficresf,"******\n");        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
       fprintf(ficresf,"# StartingAge FinalAge");        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);  
       if (popforecast==1)  fprintf(ficresf," [Population]");        if (popbased==1) {
                if(mobilav ==0){
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {            for(i=1; i<=nlstate;i++)
         fprintf(ficresf,"\n");              prlim[i][i]=probs[(int)age][i][ij];
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);            }else{ /* mobilav */ 
                    for(i=1; i<=nlstate;i++)
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){              prlim[i][i]=mobaverage[(int)age][i][ij];
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);          }
           nhstepm = nhstepm/hstepm;        }
              
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        for(j=1; j<= nlstate; j++){
           oldm=oldms;savm=savms;          for(h=0; h<=nhstepm; h++){
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);              for(i=1, gp[h][j]=0.;i<=nlstate;i++)
                      gp[h][j] += prlim[i][i]*p3mat[i][j][h];
           for (h=0; h<=nhstepm; h++){          }
             if (h==(int) (calagedate+YEARM*cpt)) {        }
               fprintf(ficresf,"\n %.f ",agedeb+h*hstepm/YEARM*stepm);        /* This for computing probability of death (h=1 means
             }           computed over hstepm matrices product = hstepm*stepm months) 
             for(j=1; j<=nlstate+ndeath;j++) {           as a weighted average of prlim.
               kk1=0.;kk2=0;        */
               for(i=1; i<=nlstate;i++) {                      for(j=nlstate+1;j<=nlstate+ndeath;j++){
                 if (mobilav==1)          for(i=1,gpp[j]=0.; i<= nlstate; i++)
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];            gpp[j] += prlim[i][i]*p3mat[i][j][1];
                 else {        }    
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];        /* end probability of death */
                 }  
                 if (popforecast==1) kk2=kk1*popeffectif[(int)agedeb];        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
               }          xp[i] = x[i] - (i==theta ?delti[theta]:0);
               if (h==(int)(calagedate+12*cpt)){        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
                 fprintf(ficresf," %.3f", kk1);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
                 
                 if (popforecast==1) fprintf(ficresf," [%.f]", kk2);        if (popbased==1) {
               }          if(mobilav ==0){
             }            for(i=1; i<=nlstate;i++)
           }              prlim[i][i]=probs[(int)age][i][ij];
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          }else{ /* mobilav */ 
         }            for(i=1; i<=nlstate;i++)
       }              prlim[i][i]=mobaverage[(int)age][i][ij];
     }          }
   }        }
          
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
           for(h=0; h<=nhstepm; h++){
   if (popforecast==1) {            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
     free_ivector(popage,0,AGESUP);              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
     free_vector(popeffectif,0,AGESUP);          }
     free_vector(popcount,0,AGESUP);        }
   }        /* This for computing probability of death (h=1 means
             computed over hstepm matrices product = hstepm*stepm months) 
   free_imatrix(s,1,maxwav+1,1,n);           as a weighted average of prlim.
   free_vector(weight,1,n);        */
   fclose(ficresf);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
   }          for(i=1,gmp[j]=0.; i<= nlstate; i++)
            gmp[j] += prlim[i][i]*p3mat[i][j][1];
   /* End forecasting */        }    
   else{        /* end probability of death */
     erreur=108;  
     printf("Error %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d\n", erreur, stepm);        for(j=1; j<= nlstate; j++) /* vareij */
   }          for(h=0; h<=nhstepm; h++){
              gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
            }
   /*---------- Health expectancies and variances ------------*/  
         for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
   strcpy(filerest,"t");          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
   strcat(filerest,fileres);        }
   if((ficrest=fopen(filerest,"w"))==NULL) {  
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;      } /* End theta */
   }  
   printf("Computing Total LEs with variances: file '%s' \n", filerest);      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   
       for(h=0; h<=nhstepm; h++) /* veij */
   strcpy(filerese,"e");        for(j=1; j<=nlstate;j++)
   strcat(filerese,fileres);          for(theta=1; theta <=npar; theta++)
   if((ficreseij=fopen(filerese,"w"))==NULL) {            trgradg[h][j][theta]=gradg[h][theta][j];
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);  
   }      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);        for(theta=1; theta <=npar; theta++)
           trgradgp[j][theta]=gradgp[theta][j];
  strcpy(fileresv,"v");    
   strcat(fileresv,fileres);  
   if((ficresvij=fopen(fileresv,"w"))==NULL) {      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);      for(i=1;i<=nlstate;i++)
   }        for(j=1;j<=nlstate;j++)
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);          vareij[i][j][(int)age] =0.;
   
   k=0;      for(h=0;h<=nhstepm;h++){
   for(cptcov=1;cptcov<=i1;cptcov++){        for(k=0;k<=nhstepm;k++){
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
       k=k+1;          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
       fprintf(ficrest,"\n#****** ");          for(i=1;i<=nlstate;i++)
       for(j=1;j<=cptcoveff;j++)            for(j=1;j<=nlstate;j++)
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
       fprintf(ficrest,"******\n");        }
       }
       fprintf(ficreseij,"\n#****** ");    
       for(j=1;j<=cptcoveff;j++)      /* pptj */
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
       fprintf(ficreseij,"******\n");      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
       for(j=nlstate+1;j<=nlstate+ndeath;j++)
       fprintf(ficresvij,"\n#****** ");        for(i=nlstate+1;i<=nlstate+ndeath;i++)
       for(j=1;j<=cptcoveff;j++)          varppt[j][i]=doldmp[j][i];
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);      /* end ppptj */
       fprintf(ficresvij,"******\n");      /*  x centered again */
       hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
       oldm=oldms;savm=savms;   
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);        if (popbased==1) {
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);        if(mobilav ==0){
       oldm=oldms;savm=savms;          for(i=1; i<=nlstate;i++)
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);            prlim[i][i]=probs[(int)age][i][ij];
            }else{ /* mobilav */ 
           for(i=1; i<=nlstate;i++)
              prlim[i][i]=mobaverage[(int)age][i][ij];
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");        }
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);      }
       fprintf(ficrest,"\n");               
       /* This for computing probability of death (h=1 means
       hf=1;         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
       if (stepm >= YEARM) hf=stepm/YEARM;         as a weighted average of prlim.
       epj=vector(1,nlstate+1);      */
       for(age=bage; age <=fage ;age++){      for(j=nlstate+1;j<=nlstate+ndeath;j++){
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
         if (popbased==1) {          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
           for(i=1; i<=nlstate;i++)      }    
             prlim[i][i]=probs[(int)age][i][k];      /* end probability of death */
         }  
              fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
         fprintf(ficrest," %.0f",age);      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
           for(i=1, epj[j]=0.;i <=nlstate;i++) {        for(i=1; i<=nlstate;i++){
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
           }        }
           epj[nlstate+1] +=epj[j];      } 
         }      fprintf(ficresprobmorprev,"\n");
         for(i=1, vepp=0.;i <=nlstate;i++)  
           for(j=1;j <=nlstate;j++)      fprintf(ficresvij,"%.0f ",age );
             vepp += vareij[i][j][(int)age];      for(i=1; i<=nlstate;i++)
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));        for(j=1; j<=nlstate;j++){
         for(j=1;j <=nlstate;j++){          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));        }
         }      fprintf(ficresvij,"\n");
         fprintf(ficrest,"\n");      free_matrix(gp,0,nhstepm,1,nlstate);
       }      free_matrix(gm,0,nhstepm,1,nlstate);
     }      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
   }      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
              free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
            } /* End age */
     free_vector(gpp,nlstate+1,nlstate+ndeath);
     free_vector(gmp,nlstate+1,nlstate+ndeath);
  fclose(ficreseij);    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
  fclose(ficresvij);    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
   fclose(ficrest);    fprintf(ficgp,"\nunset parametric;unset label; set ter png small;set size 0.65, 0.65");
   fclose(ficpar);    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
   free_vector(epj,1,nlstate+1);    fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
   /*  scanf("%d ",i); */  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
    /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
   /*------- Variance limit prevalence------*/    /*   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));
 strcpy(fileresvpl,"vpl");    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
   strcat(fileresvpl,fileres);    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);    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);
     exit(0);    /*  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);
   }  */
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
     fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
  k=0;  
  for(cptcov=1;cptcov<=i1;cptcov++){    free_vector(xp,1,npar);
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    free_matrix(doldm,1,nlstate,1,nlstate);
      k=k+1;    free_matrix(dnewm,1,nlstate,1,npar);
      fprintf(ficresvpl,"\n#****** ");    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
      for(j=1;j<=cptcoveff;j++)    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
        fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
      fprintf(ficresvpl,"******\n");    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
          fclose(ficresprobmorprev);
      varpl=matrix(1,nlstate,(int) bage, (int) fage);    fflush(ficgp);
      oldm=oldms;savm=savms;    fflush(fichtm); 
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);  }  /* end varevsij */
    }  
  }  /************ Variance of prevlim ******************/
   void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, char strstart[])
   fclose(ficresvpl);  {
     /* Variance of prevalence limit */
   /*---------- End : free ----------------*/    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);    double **newm;
      double **dnewm,**doldm;
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);    int i, j, nhstepm, hstepm;
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);    int k, cptcode;
      double *xp;
      double *gp, *gm;
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);    double **gradg, **trgradg;
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);    double age,agelim;
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);    int theta;
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);    
      pstamp(ficresvpl);
   free_matrix(matcov,1,npar,1,npar);    fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
   free_vector(delti,1,npar);    fprintf(ficresvpl,"# Age");
   free_matrix(agev,1,maxwav,1,imx);    for(i=1; i<=nlstate;i++)
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);        fprintf(ficresvpl," %1d-%1d",i,i);
     fprintf(ficresvpl,"\n");
   if(erreur >0)  
     printf("End of Imach with error %d\n",erreur);    xp=vector(1,npar);
   else   printf("End of Imach\n");    dnewm=matrix(1,nlstate,1,npar);
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */    doldm=matrix(1,nlstate,1,nlstate);
      
   /* 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);*/    hstepm=1*YEARM; /* Every year of age */
   /*printf("Total time was %d uSec.\n", total_usecs);*/    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
   /*------ End -----------*/    agelim = AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
  end:      if (stepm >= YEARM) hstepm=1;
 #ifdef windows      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   /* chdir(pathcd);*/      gradg=matrix(1,npar,1,nlstate);
 #endif      gp=vector(1,nlstate);
  /*system("wgnuplot graph.plt");*/      gm=vector(1,nlstate);
  /*system("../gp37mgw/wgnuplot graph.plt");*/  
  /*system("cd ../gp37mgw");*/      for(theta=1; theta <=npar; theta++){
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/        for(i=1; i<=npar; i++){ /* Computes gradient */
  strcpy(plotcmd,GNUPLOTPROGRAM);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
  strcat(plotcmd," ");        }
  strcat(plotcmd,optionfilegnuplot);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
  system(plotcmd);        for(i=1;i<=nlstate;i++)
           gp[i] = prlim[i][i];
 #ifdef windows      
   while (z[0] != 'q') {        for(i=1; i<=npar; i++) /* Computes gradient */
     chdir(path);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
     printf("\nType e to edit output files, c to start again, and q for exiting: ");        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     scanf("%s",z);        for(i=1;i<=nlstate;i++)
     if (z[0] == 'c') system("./imach");          gm[i] = prlim[i][i];
     else if (z[0] == 'e') {  
       chdir(path);        for(i=1;i<=nlstate;i++)
       system(optionfilehtm);          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
     }      } /* End theta */
     else if (z[0] == 'q') exit(0);  
   }      trgradg =matrix(1,nlstate,1,npar);
 #endif  
 }      for(j=1; j<=nlstate;j++)
         for(theta=1; theta <=npar; theta++)
           trgradg[j][theta]=gradg[theta][j];
   
       for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] =0.;
       matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
       matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
       for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   
       fprintf(ficresvpl,"%.0f ",age );
       for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
       fprintf(ficresvpl,"\n");
       free_vector(gp,1,nlstate);
       free_vector(gm,1,nlstate);
       free_matrix(gradg,1,npar,1,nlstate);
       free_matrix(trgradg,1,nlstate,1,npar);
     } /* End age */
   
     free_vector(xp,1,npar);
     free_matrix(doldm,1,nlstate,1,npar);
     free_matrix(dnewm,1,nlstate,1,nlstate);
   
   }
   
   /************ Variance of one-step probabilities  ******************/
   void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
   {
     int i, j=0,  i1, k1, l1, t, tj;
     int k2, l2, j1,  z1;
     int k=0,l, cptcode;
     int first=1, first1;
     double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
     double **dnewm,**doldm;
     double *xp;
     double *gp, *gm;
     double **gradg, **trgradg;
     double **mu;
     double age,agelim, cov[NCOVMAX];
     double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
     int theta;
     char fileresprob[FILENAMELENGTH];
     char fileresprobcov[FILENAMELENGTH];
     char fileresprobcor[FILENAMELENGTH];
   
     double ***varpij;
   
     strcpy(fileresprob,"prob"); 
     strcat(fileresprob,fileres);
     if((ficresprob=fopen(fileresprob,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprob);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
     }
     strcpy(fileresprobcov,"probcov"); 
     strcat(fileresprobcov,fileres);
     if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcov);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
     }
     strcpy(fileresprobcor,"probcor"); 
     strcat(fileresprobcor,fileres);
     if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcor);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
     }
     printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     pstamp(ficresprob);
     fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
     fprintf(ficresprob,"# Age");
     pstamp(ficresprobcov);
     fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
     fprintf(ficresprobcov,"# Age");
     pstamp(ficresprobcor);
     fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
     fprintf(ficresprobcor,"# Age");
   
   
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprob," p%1d-%1d (SE)",i,j);
         fprintf(ficresprobcov," p%1d-%1d ",i,j);
         fprintf(ficresprobcor," p%1d-%1d ",i,j);
       }  
    /* fprintf(ficresprob,"\n");
     fprintf(ficresprobcov,"\n");
     fprintf(ficresprobcor,"\n");
    */
     xp=vector(1,npar);
     dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
     varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
     first=1;
     fprintf(ficgp,"\n# Routine varprob");
     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
     fprintf(fichtm,"\n");
   
     fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
     fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
     file %s<br>\n",optionfilehtmcov);
     fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
   and drawn. It helps understanding how is the covariance between two incidences.\
    They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
     fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
   It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
   would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
   standard deviations wide on each axis. <br>\
    Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
    and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
   To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
   
     cov[1]=1;
     tj=cptcoveff;
     if (cptcovn<1) {tj=1;ncodemax[1]=1;}
     j1=0;
     for(t=1; t<=tj;t++){
       for(i1=1; i1<=ncodemax[t];i1++){ 
         j1++;
         if  (cptcovn>0) {
           fprintf(ficresprob, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprob, "**********\n#\n");
           fprintf(ficresprobcov, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcov, "**********\n#\n");
           
           fprintf(ficgp, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficgp, "**********\n#\n");
           
           
           fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
           
           fprintf(ficresprobcor, "\n#********** Variable ");    
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcor, "**********\n#");    
         }
         
         for (age=bage; age<=fage; age ++){ 
           cov[2]=age;
           for (k=1; k<=cptcovn;k++) {
             cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
           }
           for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
           for (k=1; k<=cptcovprod;k++)
             cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
           
           gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
           trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
           gp=vector(1,(nlstate)*(nlstate+ndeath));
           gm=vector(1,(nlstate)*(nlstate+ndeath));
       
           for(theta=1; theta <=npar; theta++){
             for(i=1; i<=npar; i++)
               xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
             
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             
             k=0;
             for(i=1; i<= (nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gp[k]=pmmij[i][j];
               }
             }
             
             for(i=1; i<=npar; i++)
               xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
       
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             k=0;
             for(i=1; i<=(nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gm[k]=pmmij[i][j];
               }
             }
        
             for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
               gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
           }
   
           for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
             for(theta=1; theta <=npar; theta++)
               trgradg[j][theta]=gradg[theta][j];
           
           matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
           matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
           free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
           free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
           free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
           free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   
           pmij(pmmij,cov,ncovmodel,x,nlstate);
           
           k=0;
           for(i=1; i<=(nlstate); i++){
             for(j=1; j<=(nlstate+ndeath);j++){
               k=k+1;
               mu[k][(int) age]=pmmij[i][j];
             }
           }
           for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
             for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
               varpij[i][j][(int)age] = doldm[i][j];
   
           /*printf("\n%d ",(int)age);
             for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             }*/
   
           fprintf(ficresprob,"\n%d ",(int)age);
           fprintf(ficresprobcov,"\n%d ",(int)age);
           fprintf(ficresprobcor,"\n%d ",(int)age);
   
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
             fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
             fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
           }
           i=0;
           for (k=1; k<=(nlstate);k++){
             for (l=1; l<=(nlstate+ndeath);l++){ 
               i=i++;
               fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
               fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
               for (j=1; j<=i;j++){
                 fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
                 fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
               }
             }
           }/* end of loop for state */
         } /* end of loop for age */
   
         /* Confidence intervalle of pij  */
         /*
           fprintf(ficgp,"\nunset parametric;unset label");
           fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
           fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
           fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
           fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
           fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
           fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
         */
   
         /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
         first1=1;
         for (k2=1; k2<=(nlstate);k2++){
           for (l2=1; l2<=(nlstate+ndeath);l2++){ 
             if(l2==k2) continue;
             j=(k2-1)*(nlstate+ndeath)+l2;
             for (k1=1; k1<=(nlstate);k1++){
               for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                 if(l1==k1) continue;
                 i=(k1-1)*(nlstate+ndeath)+l1;
                 if(i<=j) continue;
                 for (age=bage; age<=fage; age ++){ 
                   if ((int)age %5==0){
                     v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                     v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     mu1=mu[i][(int) age]/stepm*YEARM ;
                     mu2=mu[j][(int) age]/stepm*YEARM;
                     c12=cv12/sqrt(v1*v2);
                     /* Computing eigen value of matrix of covariance */
                     lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     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);
     }
   }
   
   
   

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changed lines
  Added in v.1.135


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