[BACK]Return to imach.c CVS log [TXT] [DIR] Up to [Local Repository] / imach / src

Diff for /imach/src/imach.c between versions 1.15 and 1.131

version 1.15, 2002/02/20 17:08:52 version 1.131, 2009/06/20 16:22:47
Line 1 Line 1
      /* $Id$
 /*********************** Imach **************************************            $State$
   This program computes Healthy Life Expectancies from cross-longitudinal    $Log$
   data. Cross-longitudinal consist in a first survey ("cross") where    Revision 1.131  2009/06/20 16:22:47  brouard
   individuals from different ages are interviewed on their health status    Some dimensions resccaled
   or degree of  disability. At least a second wave of interviews  
   ("longitudinal") should  measure each new individual health status.    Revision 1.130  2009/05/26 06:44:34  brouard
   Health expectancies are computed from the transistions observed between    (Module): Max Covariate is now set to 20 instead of 8. A
   waves and are computed for each degree of severity of disability (number    lot of cleaning with variables initialized to 0. Trying to make
   of life states). More degrees you consider, more time is necessary to    V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
   reach the Maximum Likelihood of the parameters involved in the model.  
   The simplest model is the multinomial logistic model where pij is    Revision 1.129  2007/08/31 13:49:27  lievre
   the probabibility to be observed in state j at the second wave conditional    Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
   to be observed in state i at the first wave. Therefore the model is:  
   log(pij/pii)= aij + bij*age+ cij*sex + etc , where 'age' is age and 'sex'    Revision 1.128  2006/06/30 13:02:05  brouard
   is a covariate. If you want to have a more complex model than "constant and    (Module): Clarifications on computing e.j
   age", you should modify the program where the markup  
     *Covariates have to be included here again* invites you to do it.    Revision 1.127  2006/04/28 18:11:50  brouard
   More covariates you add, less is the speed of the convergence.    (Module): Yes the sum of survivors was wrong since
     imach-114 because nhstepm was no more computed in the age
   The advantage that this computer programme claims, comes from that if the    loop. Now we define nhstepma in the age loop.
   delay between waves is not identical for each individual, or if some    (Module): In order to speed up (in case of numerous covariates) we
   individual missed an interview, the information is not rounded or lost, but    compute health expectancies (without variances) in a first step
   taken into account using an interpolation or extrapolation.    and then all the health expectancies with variances or standard
   hPijx is the probability to be    deviation (needs data from the Hessian matrices) which slows the
   observed in state i at age x+h conditional to the observed state i at age    computation.
   x. The delay 'h' can be split into an exact number (nh*stepm) of    In the future we should be able to stop the program is only health
   unobserved intermediate  states. This elementary transition (by month or    expectancies and graph are needed without standard deviations.
   quarter trimester, semester or year) is model as a multinomial logistic.  
   The hPx matrix is simply the matrix product of nh*stepm elementary matrices    Revision 1.126  2006/04/28 17:23:28  brouard
   and the contribution of each individual to the likelihood is simply hPijx.    (Module): Yes the sum of survivors was wrong since
     imach-114 because nhstepm was no more computed in the age
   Also this programme outputs the covariance matrix of the parameters but also    loop. Now we define nhstepma in the age loop.
   of the life expectancies. It also computes the prevalence limits.    Version 0.98h
    
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    Revision 1.125  2006/04/04 15:20:31  lievre
            Institut national d'études démographiques, Paris.    Errors in calculation of health expectancies. Age was not initialized.
   This software have been partly granted by Euro-REVES, a concerted action    Forecasting file added.
   from the European Union.  
   It is copyrighted identically to a GNU software product, ie programme and    Revision 1.124  2006/03/22 17:13:53  lievre
   software can be distributed freely for non commercial use. Latest version    Parameters are printed with %lf instead of %f (more numbers after the comma).
   can be accessed at http://euroreves.ined.fr/imach .    The log-likelihood is printed in the log file
   **********************************************************************/  
      Revision 1.123  2006/03/20 10:52:43  brouard
 #include <math.h>    * imach.c (Module): <title> changed, corresponds to .htm file
 #include <stdio.h>    name. <head> headers where missing.
 #include <stdlib.h>  
 #include <unistd.h>    * imach.c (Module): Weights can have a decimal point as for
     English (a comma might work with a correct LC_NUMERIC environment,
 #define MAXLINE 256    otherwise the weight is truncated).
 #define FILENAMELENGTH 80    Modification of warning when the covariates values are not 0 or
 /*#define DEBUG*/    1.
 #define windows    Version 0.98g
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */  
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    Revision 1.122  2006/03/20 09:45:41  brouard
     (Module): Weights can have a decimal point as for
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    English (a comma might work with a correct LC_NUMERIC environment,
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    otherwise the weight is truncated).
     Modification of warning when the covariates values are not 0 or
 #define NINTERVMAX 8    1.
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    Version 0.98g
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */  
 #define NCOVMAX 8 /* Maximum number of covariates */    Revision 1.121  2006/03/16 17:45:01  lievre
 #define MAXN 20000    * imach.c (Module): Comments concerning covariates added
 #define YEARM 12. /* Number of months per year */  
 #define AGESUP 130    * imach.c (Module): refinements in the computation of lli if
 #define AGEBASE 40    status=-2 in order to have more reliable computation if stepm is
     not 1 month. Version 0.98f
   
 int nvar;    Revision 1.120  2006/03/16 15:10:38  lievre
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    (Module): refinements in the computation of lli if
 int npar=NPARMAX;    status=-2 in order to have more reliable computation if stepm is
 int nlstate=2; /* Number of live states */    not 1 month. Version 0.98f
 int ndeath=1; /* Number of dead states */  
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    Revision 1.119  2006/03/15 17:42:26  brouard
 int popbased=0;    (Module): Bug if status = -2, the loglikelihood was
     computed as likelihood omitting the logarithm. Version O.98e
 int *wav; /* Number of waves for this individuual 0 is possible */  
 int maxwav; /* Maxim number of waves */    Revision 1.118  2006/03/14 18:20:07  brouard
 int jmin, jmax; /* min, max spacing between 2 waves */    (Module): varevsij Comments added explaining the second
 int mle, weightopt;    table of variances if popbased=1 .
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    (Module): Function pstamp added
 double jmean; /* Mean space between 2 waves */    (Module): Version 0.98d
 double **oldm, **newm, **savm; /* Working pointers to matrices */  
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    Revision 1.117  2006/03/14 17:16:22  brouard
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf;    (Module): varevsij Comments added explaining the second
 FILE *ficgp, *fichtm,*ficresprob;    table of variances if popbased=1 .
 FILE *ficreseij;    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
   char filerese[FILENAMELENGTH];    (Module): Function pstamp added
  FILE  *ficresvij;    (Module): Version 0.98d
   char fileresv[FILENAMELENGTH];  
  FILE  *ficresvpl;    Revision 1.116  2006/03/06 10:29:27  brouard
   char fileresvpl[FILENAMELENGTH];    (Module): Variance-covariance wrong links and
     varian-covariance of ej. is needed (Saito).
 #define NR_END 1  
 #define FREE_ARG char*    Revision 1.115  2006/02/27 12:17:45  brouard
 #define FTOL 1.0e-10    (Module): One freematrix added in mlikeli! 0.98c
   
 #define NRANSI    Revision 1.114  2006/02/26 12:57:58  brouard
 #define ITMAX 200    (Module): Some improvements in processing parameter
     filename with strsep.
 #define TOL 2.0e-4  
     Revision 1.113  2006/02/24 14:20:24  brouard
 #define CGOLD 0.3819660    (Module): Memory leaks checks with valgrind and:
 #define ZEPS 1.0e-10    datafile was not closed, some imatrix were not freed and on matrix
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    allocation too.
   
 #define GOLD 1.618034    Revision 1.112  2006/01/30 09:55:26  brouard
 #define GLIMIT 100.0    (Module): Back to gnuplot.exe instead of wgnuplot.exe
 #define TINY 1.0e-20  
     Revision 1.111  2006/01/25 20:38:18  brouard
 static double maxarg1,maxarg2;    (Module): Lots of cleaning and bugs added (Gompertz)
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    (Module): Comments can be added in data file. Missing date values
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    can be a simple dot '.'.
    
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    Revision 1.110  2006/01/25 00:51:50  brouard
 #define rint(a) floor(a+0.5)    (Module): Lots of cleaning and bugs added (Gompertz)
   
 static double sqrarg;    Revision 1.109  2006/01/24 19:37:15  brouard
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    (Module): Comments (lines starting with a #) are allowed in data.
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  
     Revision 1.108  2006/01/19 18:05:42  lievre
 int imx;    Gnuplot problem appeared...
 int stepm;    To be fixed
 /* Stepm, step in month: minimum step interpolation*/  
     Revision 1.107  2006/01/19 16:20:37  brouard
 int m,nb;    Test existence of gnuplot in imach path
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    Revision 1.106  2006/01/19 13:24:36  brouard
 double **pmmij, ***probs, ***mobaverage;    Some cleaning and links added in html output
   
 double *weight;    Revision 1.105  2006/01/05 20:23:19  lievre
 int **s; /* Status */    *** empty log message ***
 double *agedc, **covar, idx;  
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    Revision 1.104  2005/09/30 16:11:43  lievre
     (Module): sump fixed, loop imx fixed, and simplifications.
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    (Module): If the status is missing at the last wave but we know
 double ftolhess; /* Tolerance for computing hessian */    that the person is alive, then we can code his/her status as -2
     (instead of missing=-1 in earlier versions) and his/her
 /**************** split *************************/    contributions to the likelihood is 1 - Prob of dying from last
 static  int split( char *path, char *dirc, char *name )    health status (= 1-p13= p11+p12 in the easiest case of somebody in
 {    the healthy state at last known wave). Version is 0.98
    char *s;                             /* pointer */  
    int  l1, l2;                         /* length counters */    Revision 1.103  2005/09/30 15:54:49  lievre
     (Module): sump fixed, loop imx fixed, and simplifications.
    l1 = strlen( path );                 /* length of path */  
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    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.
    if ( s == NULL ) {                   /* no directory, so use current */  
 #if     defined(__bsd__)                /* get current working directory */    Revision 1.101  2004/09/15 10:38:38  brouard
       extern char       *getwd( );    Fix on curr_time
   
       if ( getwd( dirc ) == NULL ) {    Revision 1.100  2004/07/12 18:29:06  brouard
 #else    Add version for Mac OS X. Just define UNIX in Makefile
       extern char       *getcwd( );  
     Revision 1.99  2004/06/05 08:57:40  brouard
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    *** empty log message ***
 #endif  
          return( GLOCK_ERROR_GETCWD );    Revision 1.98  2004/05/16 15:05:56  brouard
       }    New version 0.97 . First attempt to estimate force of mortality
       strcpy( name, path );             /* we've got it */    directly from the data i.e. without the need of knowing the health
    } else {                             /* strip direcotry from path */    state at each age, but using a Gompertz model: log u =a + b*age .
       s++;                              /* after this, the filename */    This is the basic analysis of mortality and should be done before any
       l2 = strlen( s );                 /* length of filename */    other analysis, in order to test if the mortality estimated from the
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    cross-longitudinal survey is different from the mortality estimated
       strcpy( name, s );                /* save file name */    from other sources like vital statistic data.
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  
       dirc[l1-l2] = 0;                  /* add zero */    The same imach parameter file can be used but the option for mle should be -3.
    }  
    l1 = strlen( dirc );                 /* length of directory */    Agnès, who wrote this part of the code, tried to keep most of the
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    former routines in order to include the new code within the former code.
    return( 0 );                         /* we're done */  
 }    The output is very simple: only an estimate of the intercept and of
     the slope with 95% confident intervals.
   
 /******************************************/    Current limitations:
     A) Even if you enter covariates, i.e. with the
 void replace(char *s, char*t)    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
 {    B) There is no computation of Life Expectancy nor Life Table.
   int i;  
   int lg=20;    Revision 1.97  2004/02/20 13:25:42  lievre
   i=0;    Version 0.96d. Population forecasting command line is (temporarily)
   lg=strlen(t);    suppressed.
   for(i=0; i<= lg; i++) {  
     (s[i] = t[i]);    Revision 1.96  2003/07/15 15:38:55  brouard
     if (t[i]== '\\') s[i]='/';    * 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
 int nbocc(char *s, char occ)    * imach.c (Repository):
 {    (Repository): Using imachwizard code to output a more meaningful covariance
   int i,j=0;    matrix (cov(a12,c31) instead of numbers.
   int lg=20;  
   i=0;    Revision 1.94  2003/06/27 13:00:02  brouard
   lg=strlen(s);    Just cleaning
   for(i=0; i<= lg; i++) {  
   if  (s[i] == occ ) j++;    Revision 1.93  2003/06/25 16:33:55  brouard
   }    (Module): On windows (cygwin) function asctime_r doesn't
   return j;    exist so I changed back to asctime which exists.
 }    (Module): Version 0.96b
   
 void cutv(char *u,char *v, char*t, char occ)    Revision 1.92  2003/06/25 16:30:45  brouard
 {    (Module): On windows (cygwin) function asctime_r doesn't
   int i,lg,j,p=0;    exist so I changed back to asctime which exists.
   i=0;  
   for(j=0; j<=strlen(t)-1; j++) {    Revision 1.91  2003/06/25 15:30:29  brouard
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    * imach.c (Repository): Duplicated warning errors corrected.
   }    (Repository): Elapsed time after each iteration is now output. It
     helps to forecast when convergence will be reached. Elapsed time
   lg=strlen(t);    is stamped in powell.  We created a new html file for the graphs
   for(j=0; j<p; j++) {    concerning matrix of covariance. It has extension -cov.htm.
     (u[j] = t[j]);  
   }    Revision 1.90  2003/06/24 12:34:15  brouard
      u[p]='\0';    (Module): Some bugs corrected for windows. Also, when
     mle=-1 a template is output in file "or"mypar.txt with the design
    for(j=0; j<= lg; j++) {    of the covariance matrix to be input.
     if (j>=(p+1))(v[j-p-1] = t[j]);  
   }    Revision 1.89  2003/06/24 12:30:52  brouard
 }    (Module): Some bugs corrected for windows. Also, when
     mle=-1 a template is output in file "or"mypar.txt with the design
 /********************** nrerror ********************/    of the covariance matrix to be input.
   
 void nrerror(char error_text[])    Revision 1.88  2003/06/23 17:54:56  brouard
 {    * imach.c (Repository): Create a sub-directory where all the secondary files are. Only imach, htm, gp and r(imach) are on the main directory. Correct time and other things.
   fprintf(stderr,"ERREUR ...\n");  
   fprintf(stderr,"%s\n",error_text);    Revision 1.87  2003/06/18 12:26:01  brouard
   exit(1);    Version 0.96
 }  
 /*********************** vector *******************/    Revision 1.86  2003/06/17 20:04:08  brouard
 double *vector(int nl, int nh)    (Module): Change position of html and gnuplot routines and added
 {    routine fileappend.
   double *v;  
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    Revision 1.85  2003/06/17 13:12:43  brouard
   if (!v) nrerror("allocation failure in vector");    * imach.c (Repository): Check when date of death was earlier that
   return v-nl+NR_END;    current date of interview. It may happen when the death was just
 }    prior to the death. In this case, dh was negative and likelihood
     was wrong (infinity). We still send an "Error" but patch by
 /************************ free vector ******************/    assuming that the date of death was just one stepm after the
 void free_vector(double*v, int nl, int nh)    interview.
 {    (Repository): Because some people have very long ID (first column)
   free((FREE_ARG)(v+nl-NR_END));    we changed int to long in num[] and we added a new lvector for
 }    memory allocation. But we also truncated to 8 characters (left
     truncation)
 /************************ivector *******************************/    (Repository): No more line truncation errors.
 int *ivector(long nl,long nh)  
 {    Revision 1.84  2003/06/13 21:44:43  brouard
   int *v;    * imach.c (Repository): Replace "freqsummary" at a correct
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    place. It differs from routine "prevalence" which may be called
   if (!v) nrerror("allocation failure in ivector");    many times. Probs is memory consuming and must be used with
   return v-nl+NR_END;    parcimony.
 }    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
   
 /******************free ivector **************************/    Revision 1.83  2003/06/10 13:39:11  lievre
 void free_ivector(int *v, long nl, long nh)    *** 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.
   
 /******************* imatrix *******************************/  */
 int **imatrix(long nrl, long nrh, long ncl, long nch)  /*
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */     Interpolated Markov Chain
 {  
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    Short summary of the programme:
   int **m;    
      This program computes Healthy Life Expectancies from
   /* allocate pointers to rows */    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    first survey ("cross") where individuals from different ages are
   if (!m) nrerror("allocation failure 1 in matrix()");    interviewed on their health status or degree of disability (in the
   m += NR_END;    case of a health survey which is our main interest) -2- at least a
   m -= nrl;    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
   /* allocate rows and set pointers to them */    model. More health states you consider, more time is necessary to reach the
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    Maximum Likelihood of the parameters involved in the model.  The
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    simplest model is the multinomial logistic model where pij is the
   m[nrl] += NR_END;    probability to be observed in state j at the second wave
   m[nrl] -= ncl;    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
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    'age' is age and 'sex' is a covariate. If you want to have a more
      complex model than "constant and age", you should modify the program
   /* return pointer to array of pointers to rows */    where the markup *Covariates have to be included here again* invites
   return m;    you to do it.  More covariates you add, slower the
 }    convergence.
   
 /****************** free_imatrix *************************/    The advantage of this computer programme, compared to a simple
 void free_imatrix(m,nrl,nrh,ncl,nch)    multinomial logistic model, is clear when the delay between waves is not
       int **m;    identical for each individual. Also, if a individual missed an
       long nch,ncl,nrh,nrl;    intermediate interview, the information is lost, but taken into
      /* free an int matrix allocated by imatrix() */    account using an interpolation or extrapolation.  
 {  
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    hPijx is the probability to be observed in state i at age x+h
   free((FREE_ARG) (m+nrl-NR_END));    conditional to the observed state i at age x. The delay 'h' can be
 }    split into an exact number (nh*stepm) of unobserved intermediate
     states. This elementary transition (by month, quarter,
 /******************* matrix *******************************/    semester or year) is modelled as a multinomial logistic.  The hPx
 double **matrix(long nrl, long nrh, long ncl, long nch)    matrix is simply the matrix product of nh*stepm elementary matrices
 {    and the contribution of each individual to the likelihood is simply
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    hPijx.
   double **m;  
     Also this programme outputs the covariance matrix of the parameters but also
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    of the life expectancies. It also computes the period (stable) prevalence. 
   if (!m) nrerror("allocation failure 1 in matrix()");    
   m += NR_END;    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
   m -= nrl;             Institut national d'études démographiques, Paris.
     This software have been partly granted by Euro-REVES, a concerted action
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    from the European Union.
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    It is copyrighted identically to a GNU software product, ie programme and
   m[nrl] += NR_END;    software can be distributed freely for non commercial use. Latest version
   m[nrl] -= ncl;    can be accessed at http://euroreves.ined.fr/imach .
   
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
   return m;    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
 }    
     **********************************************************************/
 /*************************free matrix ************************/  /*
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    main
 {    read parameterfile
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    read datafile
   free((FREE_ARG)(m+nrl-NR_END));    concatwav
 }    freqsummary
     if (mle >= 1)
 /******************* ma3x *******************************/      mlikeli
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    print results files
 {    if mle==1 
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;       computes hessian
   double ***m;    read end of parameter file: agemin, agemax, bage, fage, estepm
         begin-prev-date,...
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    open gnuplot file
   if (!m) nrerror("allocation failure 1 in matrix()");    open html file
   m += NR_END;    period (stable) prevalence
   m -= nrl;     for age prevalim()
     h Pij x
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    variance of p varprob
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    forecasting if prevfcast==1 prevforecast call prevalence()
   m[nrl] += NR_END;    health expectancies
   m[nrl] -= ncl;    Variance-covariance of DFLE
     prevalence()
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;     movingaverage()
     varevsij() 
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    if popbased==1 varevsij(,popbased)
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    total life expectancies
   m[nrl][ncl] += NR_END;    Variance of period (stable) prevalence
   m[nrl][ncl] -= nll;   end
   for (j=ncl+1; j<=nch; j++)  */
     m[nrl][j]=m[nrl][j-1]+nlay;  
    
   for (i=nrl+1; i<=nrh; i++) {  
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;   
     for (j=ncl+1; j<=nch; j++)  #include <math.h>
       m[i][j]=m[i][j-1]+nlay;  #include <stdio.h>
   }  #include <stdlib.h>
   return m;  #include <string.h>
 }  #include <unistd.h>
   
 /*************************free ma3x ************************/  #include <limits.h>
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  #include <sys/types.h>
 {  #include <sys/stat.h>
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  #include <errno.h>
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  extern int errno;
   free((FREE_ARG)(m+nrl-NR_END));  
 }  /* #include <sys/time.h> */
   #include <time.h>
 /***************** f1dim *************************/  #include "timeval.h"
 extern int ncom;  
 extern double *pcom,*xicom;  /* #include <libintl.h> */
 extern double (*nrfunc)(double []);  /* #define _(String) gettext (String) */
    
 double f1dim(double x)  #define MAXLINE 256
 {  
   int j;  #define GNUPLOTPROGRAM "gnuplot"
   double f;  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
   double *xt;  #define FILENAMELENGTH 132
    
   xt=vector(1,ncom);  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   f=(*nrfunc)(xt);  
   free_vector(xt,1,ncom);  #define MAXPARM 128 /* Maximum number of parameters for the optimization */
   return f;  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
 }  
   #define NINTERVMAX 8
 /*****************brent *************************/  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
 {  #define NCOVMAX 20 /* Maximum number of covariates */
   int iter;  #define MAXN 20000
   double a,b,d,etemp;  #define YEARM 12. /* Number of months per year */
   double fu,fv,fw,fx;  #define AGESUP 130
   double ftemp;  #define AGEBASE 40
   double p,q,r,tol1,tol2,u,v,w,x,xm;  #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
   double e=0.0;  #ifdef UNIX
    #define DIRSEPARATOR '/'
   a=(ax < cx ? ax : cx);  #define CHARSEPARATOR "/"
   b=(ax > cx ? ax : cx);  #define ODIRSEPARATOR '\\'
   x=w=v=bx;  #else
   fw=fv=fx=(*f)(x);  #define DIRSEPARATOR '\\'
   for (iter=1;iter<=ITMAX;iter++) {  #define CHARSEPARATOR "\\"
     xm=0.5*(a+b);  #define ODIRSEPARATOR '/'
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  #endif
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  
     printf(".");fflush(stdout);  /* $Id$ */
 #ifdef DEBUG  /* $State$ */
     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);  
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  char version[]="Imach version 0.98k, June 2006, INED-EUROREVES-Institut de longevite ";
 #endif  char fullversion[]="$Revision$ $Date$"; 
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  char strstart[80];
       *xmin=x;  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
       return fx;  int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
     }  int nvar=0;
     ftemp=fu;  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov=0; /* Number of covariates, of covariates with '*age' */
     if (fabs(e) > tol1) {  int npar=NPARMAX;
       r=(x-w)*(fx-fv);  int nlstate=2; /* Number of live states */
       q=(x-v)*(fx-fw);  int ndeath=1; /* Number of dead states */
       p=(x-v)*q-(x-w)*r;  int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
       q=2.0*(q-r);  int popbased=0;
       if (q > 0.0) p = -p;  
       q=fabs(q);  int *wav; /* Number of waves for this individuual 0 is possible */
       etemp=e;  int maxwav=0; /* Maxim number of waves */
       e=d;  int jmin=0, jmax=0; /* min, max spacing between 2 waves */
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  int gipmx=0, gsw=0; /* Global variables on the number of contributions 
       else {                     to the likelihood and the sum of weights (done by funcone)*/
         d=p/q;  int mle=1, weightopt=0;
         u=x+d;  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
         if (u-a < tol2 || b-u < tol2)  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
           d=SIGN(tol1,xm-x);  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
       }             * wave mi and wave mi+1 is not an exact multiple of stepm. */
     } else {  double jmean=1; /* Mean space between 2 waves */
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  double **oldm, **newm, **savm; /* Working pointers to matrices */
     }  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  FILE *fic,*ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
     fu=(*f)(u);  FILE *ficlog, *ficrespow;
     if (fu <= fx) {  int globpr=0; /* Global variable for printing or not */
       if (u >= x) a=x; else b=x;  double fretone; /* Only one call to likelihood */
       SHFT(v,w,x,u)  long ipmx=0; /* Number of contributions */
         SHFT(fv,fw,fx,fu)  double sw; /* Sum of weights */
         } else {  char filerespow[FILENAMELENGTH];
           if (u < x) a=u; else b=u;  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
           if (fu <= fw || w == x) {  FILE *ficresilk;
             v=w;  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
             w=u;  FILE *ficresprobmorprev;
             fv=fw;  FILE *fichtm, *fichtmcov; /* Html File */
             fw=fu;  FILE *ficreseij;
           } else if (fu <= fv || v == x || v == w) {  char filerese[FILENAMELENGTH];
             v=u;  FILE *ficresstdeij;
             fv=fu;  char fileresstde[FILENAMELENGTH];
           }  FILE *ficrescveij;
         }  char filerescve[FILENAMELENGTH];
   }  FILE  *ficresvij;
   nrerror("Too many iterations in brent");  char fileresv[FILENAMELENGTH];
   *xmin=x;  FILE  *ficresvpl;
   return fx;  char fileresvpl[FILENAMELENGTH];
 }  char title[MAXLINE];
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
 /****************** mnbrak ***********************/  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
   char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  char command[FILENAMELENGTH];
             double (*func)(double))  int  outcmd=0;
 {  
   double ulim,u,r,q, dum;  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   double fu;  
    char filelog[FILENAMELENGTH]; /* Log file */
   *fa=(*func)(*ax);  char filerest[FILENAMELENGTH];
   *fb=(*func)(*bx);  char fileregp[FILENAMELENGTH];
   if (*fb > *fa) {  char popfile[FILENAMELENGTH];
     SHFT(dum,*ax,*bx,dum)  
       SHFT(dum,*fb,*fa,dum)  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
       }  
   *cx=(*bx)+GOLD*(*bx-*ax);  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
   *fc=(*func)(*cx);  struct timezone tzp;
   while (*fb > *fc) {  extern int gettimeofday();
     r=(*bx-*ax)*(*fb-*fc);  struct tm tmg, tm, tmf, *gmtime(), *localtime();
     q=(*bx-*cx)*(*fb-*fa);  long time_value;
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  extern long time();
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  char strcurr[80], strfor[80];
     ulim=(*bx)+GLIMIT*(*cx-*bx);  
     if ((*bx-u)*(u-*cx) > 0.0) {  char *endptr;
       fu=(*func)(u);  long lval;
     } else if ((*cx-u)*(u-ulim) > 0.0) {  double dval;
       fu=(*func)(u);  
       if (fu < *fc) {  #define NR_END 1
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  #define FREE_ARG char*
           SHFT(*fb,*fc,fu,(*func)(u))  #define FTOL 1.0e-10
           }  
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  #define NRANSI 
       u=ulim;  #define ITMAX 200 
       fu=(*func)(u);  
     } else {  #define TOL 2.0e-4 
       u=(*cx)+GOLD*(*cx-*bx);  
       fu=(*func)(u);  #define CGOLD 0.3819660 
     }  #define ZEPS 1.0e-10 
     SHFT(*ax,*bx,*cx,u)  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
       SHFT(*fa,*fb,*fc,fu)  
       }  #define GOLD 1.618034 
 }  #define GLIMIT 100.0 
   #define TINY 1.0e-20 
 /*************** linmin ************************/  
   static double maxarg1,maxarg2;
 int ncom;  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
 double *pcom,*xicom;  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
 double (*nrfunc)(double []);    
    #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  #define rint(a) floor(a+0.5)
 {  
   double brent(double ax, double bx, double cx,  static double sqrarg;
                double (*f)(double), double tol, double *xmin);  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
   double f1dim(double x);  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  int agegomp= AGEGOMP;
               double *fc, double (*func)(double));  
   int j;  int imx; 
   double xx,xmin,bx,ax;  int stepm=1;
   double fx,fb,fa;  /* Stepm, step in month: minimum step interpolation*/
    
   ncom=n;  int estepm;
   pcom=vector(1,n);  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
   xicom=vector(1,n);  
   nrfunc=func;  int m,nb;
   for (j=1;j<=n;j++) {  long *num;
     pcom[j]=p[j];  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
     xicom[j]=xi[j];  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
   }  double **pmmij, ***probs;
   ax=0.0;  double *ageexmed,*agecens;
   xx=1.0;  double dateintmean=0;
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  double *weight;
 #ifdef DEBUG  int **s; /* Status */
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  double *agedc, **covar, idx;
 #endif  int **nbcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
   for (j=1;j<=n;j++) {  double *lsurv, *lpop, *tpop;
     xi[j] *= xmin;  
     p[j] += xi[j];  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
   }  double ftolhess; /* Tolerance for computing hessian */
   free_vector(xicom,1,n);  
   free_vector(pcom,1,n);  /**************** split *************************/
 }  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   {
 /*************** powell ************************/    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,       the name of the file (name), its extension only (ext) and its first part of the name (finame)
             double (*func)(double []))    */ 
 {    char  *ss;                            /* pointer */
   void linmin(double p[], double xi[], int n, double *fret,    int   l1, l2;                         /* length counters */
               double (*func)(double []));  
   int i,ibig,j;    l1 = strlen(path );                   /* length of path */
   double del,t,*pt,*ptt,*xit;    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   double fp,fptt;    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
   double *xits;    if ( ss == NULL ) {                   /* no directory, so determine current directory */
   pt=vector(1,n);      strcpy( name, path );               /* we got the fullname name because no directory */
   ptt=vector(1,n);      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
   xit=vector(1,n);        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
   xits=vector(1,n);      /* get current working directory */
   *fret=(*func)(p);      /*    extern  char* getcwd ( char *buf , int len);*/
   for (j=1;j<=n;j++) pt[j]=p[j];      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
   for (*iter=1;;++(*iter)) {        return( GLOCK_ERROR_GETCWD );
     fp=(*fret);      }
     ibig=0;      /* got dirc from getcwd*/
     del=0.0;      printf(" DIRC = %s \n",dirc);
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);    } else {                              /* strip direcotry from path */
     for (i=1;i<=n;i++)      ss++;                               /* after this, the filename */
       printf(" %d %.12f",i, p[i]);      l2 = strlen( ss );                  /* length of filename */
     printf("\n");      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
     for (i=1;i<=n;i++) {      strcpy( name, ss );         /* save file name */
       for (j=1;j<=n;j++) xit[j]=xi[j][i];      strncpy( dirc, path, l1 - l2 );     /* now the directory */
       fptt=(*fret);      dirc[l1-l2] = 0;                    /* add zero */
 #ifdef DEBUG      printf(" DIRC2 = %s \n",dirc);
       printf("fret=%lf \n",*fret);    }
 #endif    /* We add a separator at the end of dirc if not exists */
       printf("%d",i);fflush(stdout);    l1 = strlen( dirc );                  /* length of directory */
       linmin(p,xit,n,fret,func);    if( dirc[l1-1] != DIRSEPARATOR ){
       if (fabs(fptt-(*fret)) > del) {      dirc[l1] =  DIRSEPARATOR;
         del=fabs(fptt-(*fret));      dirc[l1+1] = 0; 
         ibig=i;      printf(" DIRC3 = %s \n",dirc);
       }    }
 #ifdef DEBUG    ss = strrchr( name, '.' );            /* find last / */
       printf("%d %.12e",i,(*fret));    if (ss >0){
       for (j=1;j<=n;j++) {      ss++;
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);      strcpy(ext,ss);                     /* save extension */
         printf(" x(%d)=%.12e",j,xit[j]);      l1= strlen( name);
       }      l2= strlen(ss)+1;
       for(j=1;j<=n;j++)      strncpy( finame, name, l1-l2);
         printf(" p=%.12e",p[j]);      finame[l1-l2]= 0;
       printf("\n");    }
 #endif  
     }    return( 0 );                          /* we're done */
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  }
 #ifdef DEBUG  
       int k[2],l;  
       k[0]=1;  /******************************************/
       k[1]=-1;  
       printf("Max: %.12e",(*func)(p));  void replace_back_to_slash(char *s, char*t)
       for (j=1;j<=n;j++)  {
         printf(" %.12e",p[j]);    int i;
       printf("\n");    int lg=0;
       for(l=0;l<=1;l++) {    i=0;
         for (j=1;j<=n;j++) {    lg=strlen(t);
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];    for(i=0; i<= lg; i++) {
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);      (s[i] = t[i]);
         }      if (t[i]== '\\') s[i]='/';
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    }
       }  }
 #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 ",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, int fprev1,int lprev1)          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;          printf("\n");
   FILE *ficresp;          fprintf(ficlog,"\n");
   char fileresp[FILENAMELENGTH];  #endif
         }
   pp=vector(1,nlstate);      } 
  probs= ma3x(1,130 ,1,8, 1,8);    } 
   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.;
        for (i=1; i<=imx; i++) {   
          bool=1;   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
          if  (cptcovn>0) {    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
            for (z1=1; z1<=cptcoveff; z1++)      newm=savm;
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])      /* Covariates have to be included here again */
                bool=0;       cov[2]=agefin;
          }    
           if (bool==1) {        for (k=1; k<=cptcovn;k++) {
            for(m=fprev1; m<=lprev1; m++){          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
              if(agev[m][i]==0) agev[m][i]=agemax+1;          /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
              if(agev[m][i]==1) agev[m][i]=agemax+2;        }
              freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
              freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];        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("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
         if  (cptcovn>0) {        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
          fprintf(ficresp, "\n#********** Variable ");        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
        fprintf(ficresp, "**********\n#");  
         }      savm=oldm;
        for(i=1; i<=nlstate;i++)      oldm=newm;
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);      maxmax=0.;
        fprintf(ficresp, "\n");      for(j=1;j<=nlstate;j++){
                min=1.;
   for(i=(int)agemin; i <= (int)agemax+3; i++){        max=0.;
     if(i==(int)agemax+3)        for(i=1; i<=nlstate; i++) {
       printf("Total");          sumnew=0;
     else          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
       printf("Age %d", i);          prlim[i][j]= newm[i][j]/(1-sumnew);
     for(jk=1; jk <=nlstate ; jk++){          max=FMAX(max,prlim[i][j]);
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)          min=FMIN(min,prlim[i][j]);
         pp[jk] += freq[jk][m][i];        }
     }        maxmin=max-min;
     for(jk=1; jk <=nlstate ; jk++){        maxmax=FMAX(maxmax,maxmin);
       for(m=-1, pos=0; m <=0 ; m++)      }
         pos += freq[jk][m][i];      if(maxmax < ftolpl){
       if(pp[jk]>=1.e-10)        return prlim;
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);      }
       else    }
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);  }
     }  
   /*************** transition probabilities ***************/ 
      for(jk=1; jk <=nlstate ; jk++){  
       for(m=0, 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;
     /*double t34;*/
     for(jk=1,pos=0; jk <=nlstate ; jk++)    int i,j,j1, nc, ii, jj;
       pos += pp[jk];  
     for(jk=1; jk <=nlstate ; jk++){      for(i=1; i<= nlstate; i++){
       if(pos>=1.e-5)        for(j=1; j<i;j++){
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
       else            /*s2 += param[i][j][nc]*cov[nc];*/
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);            s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
       if( i <= (int) agemax){  /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
         if(pos>=1.e-5){          }
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);          ps[i][j]=s2;
           probs[i][jk][j1]= pp[jk]/pos;  /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
           /*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=i+1; j<=nlstate+ndeath;j++){
       else          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);            s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
       }  /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
     }          }
     for(jk=-1; jk <=nlstate+ndeath; jk++)          ps[i][j]=s2;
       for(m=-1; m <=nlstate+ndeath; m++)        }
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);      }
     if(i <= (int) agemax)      /*ps[3][2]=1;*/
       fprintf(ficresp,"\n");      
     printf("\n");      for(i=1; i<= nlstate; i++){
     }        s1=0;
     }        for(j=1; j<i; j++){
  }          s1+=exp(ps[i][j]);
            /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
   fclose(ficresp);        }
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);        for(j=i+1; j<=nlstate+ndeath; j++){
   free_vector(pp,1,nlstate);          s1+=exp(ps[i][j]);
           /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
 }  /* End of Freq */        }
         ps[i][i]=1./(s1+1.);
 /************ Prevalence ********************/        for(j=1; j<i; j++)
 void prevalence(int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax, int fprev1,int lprev1)          ps[i][j]= exp(ps[i][j])*ps[i][i];
 {  /* Some frequencies */        for(j=i+1; j<=nlstate+ndeath; j++)
            ps[i][j]= exp(ps[i][j])*ps[i][i];
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
   double ***freq; /* Frequencies */      } /* end i */
   double *pp;      
   double pos;      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
         for(jj=1; jj<= nlstate+ndeath; jj++){
   pp=vector(1,nlstate);          ps[ii][jj]=0;
   probs= ma3x(1,130 ,1,8, 1,8);          ps[ii][ii]=1;
          }
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);      }
   j1=0;      
    
   j=cptcoveff;  /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
    /*         printf("ddd %lf ",ps[ii][jj]); */
  for(k1=1; k1<=j;k1++){  /*       } */
     for(i1=1; i1<=ncodemax[k1];i1++){  /*       printf("\n "); */
       j1++;  /*        } */
    /*        printf("\n ");printf("%lf ",cov[2]); */
       for (i=-1; i<=nlstate+ndeath; i++)           /*
         for (jk=-1; jk<=nlstate+ndeath; jk++)          for(i=1; i<= npar; i++) printf("%f ",x[i]);
           for(m=agemin; m <= agemax+3; m++)        goto end;*/
           freq[i][jk][m]=0;      return ps;
        }
       for (i=1; i<=imx; i++) {  
         bool=1;  /**************** Product of 2 matrices ******************/
         if  (cptcovn>0) {  
           for (z1=1; z1<=cptcoveff; z1++)  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])  {
               bool=0;    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
               }       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
         if (bool==1) {    /* in, b, out are matrice of pointers which should have been initialized 
           for(m=fprev1; m<=lprev1; m++){       before: only the contents of out is modified. The function returns
             if(agev[m][i]==0) agev[m][i]=agemax+1;       a pointer to pointers identical to out */
             if(agev[m][i]==1) agev[m][i]=agemax+2;    long i, j, k;
             freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    for(i=nrl; i<= nrh; i++)
             freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];      for(k=ncolol; k<=ncoloh; k++)
           }        for(j=ncl,out[i][k]=0.; j<=nch; j++)
         }          out[i][k] +=in[i][j]*b[j][k];
       }  
        for(i=(int)agemin; i <= (int)agemax+3; i++){    return out;
         for(jk=1; jk <=nlstate ; jk++){  }
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)  
             pp[jk] += freq[jk][m][i];  
         }  /************* Higher Matrix Product ***************/
         for(jk=1; jk <=nlstate ; jk++){  
           for(m=-1, pos=0; m <=0 ; m++)  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
             pos += freq[jk][m][i];  {
         }    /* Computes the transition matrix starting at age 'age' over 
               'nhstepm*hstepm*stepm' months (i.e. until
          for(jk=1; jk <=nlstate ; jk++){       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)       nhstepm*hstepm matrices. 
              pp[jk] += freq[jk][m][i];       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 
                 for the memory).
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];       Model is determined by parameters x and covariates have to be 
        included manually here. 
          for(jk=1; jk <=nlstate ; jk++){            
            if( i <= (int) agemax){       */
              if(pos>=1.e-5){  
                probs[i][jk][j1]= pp[jk]/pos;    int i, j, d, h, k;
              }    double **out, cov[NCOVMAX+1];
            }    double **newm;
          }  
              /* Hstepm could be zero and should return the unit matrix */
          }    for (i=1;i<=nlstate+ndeath;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);
        }
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   free_vector(pp,1,nlstate);    for(h=1; h <=nhstepm; h++){
        for(d=1; d <=hstepm; d++){
 }  /* End of Freq */        newm=savm;
 /************* Waves Concatenation ***************/        /* Covariates have to be included here again */
         cov[1]=1.;
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
 {        for (k=1; k<=cptcovn;k++) 
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
      Death is a valid wave (if date is known).        for (k=1; k<=cptcovage;k++)
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]        for (k=1; k<=cptcovprod;k++)
      and mw[mi+1][i]. dh depends on stepm.          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
      */  
   
   int i, mi, m;        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
      double sum=0., jmean=0.;*/        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
                      pmij(pmmij,cov,ncovmodel,x,nlstate));
   int j, k=0,jk, ju, jl;        savm=oldm;
   double sum=0.;        oldm=newm;
   jmin=1e+5;      }
   jmax=-1;      for(i=1; i<=nlstate+ndeath; i++)
   jmean=0.;        for(j=1;j<=nlstate+ndeath;j++) {
   for(i=1; i<=imx; i++){          po[i][j][h]=newm[i][j];
     mi=0;          /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
     m=firstpass;        }
     while(s[m][i] <= nlstate){      /*printf("h=%d ",h);*/
       if(s[m][i]>=1)    } /* end h */
         mw[++mi][i]=m;  /*     printf("\n H=%d \n",h); */
       if(m >=lastpass)    return po;
         break;  }
       else  
         m++;  
     }/* end while */  /*************** log-likelihood *************/
     if (s[m][i] > nlstate){  double func( double *x)
       mi++;     /* Death is another wave */  {
       /* if(mi==0)  never been interviewed correctly before death */    int i, ii, j, k, mi, d, kk;
          /* Only death is a correct wave */    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
       mw[mi][i]=m;    double **out;
     }    double sw; /* Sum of weights */
     double lli; /* Individual log likelihood */
     wav[i]=mi;    int s1, s2;
     if(mi==0)    double bbh, survp;
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);    long ipmx;
   }    /*extern weight */
     /* We are differentiating ll according to initial status */
   for(i=1; i<=imx; i++){    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     for(mi=1; mi<wav[i];mi++){    /*for(i=1;i<imx;i++) 
       if (stepm <=0)      printf(" %d\n",s[4][i]);
         dh[mi][i]=1;    */
       else{    cov[1]=1.;
         if (s[mw[mi+1][i]][i] > nlstate) {  
           if (agedc[i] < 2*AGESUP) {    for(k=1; k<=nlstate; k++) ll[k]=0.;
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);  
           if(j==0) j=1;  /* Survives at least one month after exam */    if(mle==1){
           k=k+1;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
           if (j >= jmax) jmax=j;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
           if (j <= jmin) jmin=j;        for(mi=1; mi<= wav[i]-1; mi++){
           sum=sum+j;          for (ii=1;ii<=nlstate+ndeath;ii++)
           /* if (j<10) printf("j=%d num=%d ",j,i); */            for (j=1;j<=nlstate+ndeath;j++){
           }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         else{            }
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));          for(d=0; d<dh[mi][i]; d++){
           k=k+1;            newm=savm;
           if (j >= jmax) jmax=j;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           else if (j <= jmin)jmin=j;            for (kk=1; kk<=cptcovage;kk++) {
           /*   if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
           sum=sum+j;            }
         }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         jk= j/stepm;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         jl= j -jk*stepm;            savm=oldm;
         ju= j -(jk+1)*stepm;            oldm=newm;
         if(jl <= -ju)          } /* end mult */
           dh[mi][i]=jk;        
         else          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
           dh[mi][i]=jk+1;          /* But now since version 0.9 we anticipate for bias at large stepm.
         if(dh[mi][i]==0)           * If stepm is larger than one month (smallest stepm) and if the exact delay 
           dh[mi][i]=1; /* At least one step */           * (in months) between two waves is not a multiple of stepm, we rounded to 
       }           * 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
   jmean=sum/k;           * probability in order to take into account the bias as a fraction of the way
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
  }           * -stepm/2 to stepm/2 .
 /*********** Tricode ****************************/           * For stepm=1 the results are the same as for previous versions of Imach.
 void tricode(int *Tvar, int **nbcode, int imx)           * For stepm > 1 the results are less biased than in previous versions. 
 {           */
   int Ndum[20],ij=1, k, j, i;          s1=s[mw[mi][i]][i];
   int cptcode=0;          s2=s[mw[mi+1][i]][i];
   cptcoveff=0;          bbh=(double)bh[mi][i]/(double)stepm; 
            /* bias bh is positive if real duration
   for (k=0; k<19; k++) Ndum[k]=0;           * is higher than the multiple of stepm and negative otherwise.
   for (k=1; k<=7; k++) ncodemax[k]=0;           */
           /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {          if( s2 > nlstate){ 
     for (i=1; i<=imx; i++) {            /* i.e. if s2 is a death state and if the date of death is known 
       ij=(int)(covar[Tvar[j]][i]);               then the contribution to the likelihood is the probability to 
       Ndum[ij]++;               die between last step unit time and current  step unit time, 
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/               which is also equal to probability to die before dh 
       if (ij > cptcode) cptcode=ij;               minus probability to die before dh-stepm . 
     }               In version up to 0.92 likelihood was computed
           as if date of death was unknown. Death was treated as any other
     for (i=0; i<=cptcode; i++) {          health state: the date of the interview describes the actual state
       if(Ndum[i]!=0) ncodemax[j]++;          and not the date of a change in health state. The former idea was
     }          to consider that at each interview the state was recorded
     ij=1;          (healthy, disable or death) and IMaCh was corrected; but when we
           introduced the exact date of death then we should have modified
           the contribution of an exact death to the likelihood. This new
     for (i=1; i<=ncodemax[j]; i++) {          contribution is smaller and very dependent of the step unit
       for (k=0; k<=19; k++) {          stepm. It is no more the probability to die between last interview
         if (Ndum[k] != 0) {          and month of death but the probability to survive from last
           nbcode[Tvar[j]][ij]=k;          interview up to one month before death multiplied by the
           ij++;          probability to die within a month. Thanks to Chris
         }          Jackson for correcting this bug.  Former versions increased
         if (ij > ncodemax[j]) break;          mortality artificially. The bad side is that we add another loop
       }            which slows down the processing. The difference can be up to 10%
     }          lower mortality.
   }              */
             lli=log(out[s1][s2] - savm[s1][s2]);
  for (k=0; k<19; k++) Ndum[k]=0;  
   
  for (i=1; i<=ncovmodel-2; i++) {          } else if  (s2==-2) {
       ij=Tvar[i];            for (j=1,survp=0. ; j<=nlstate; j++) 
       Ndum[ij]++;              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
     }            /*survp += out[s1][j]; */
             lli= log(survp);
  ij=1;          }
  for (i=1; i<=10; i++) {          
    if((Ndum[i]!=0) && (i<=ncov)){          else if  (s2==-4) { 
      Tvaraff[ij]=i;            for (j=3,survp=0. ; j<=nlstate; j++)  
      ij++;              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
    }            lli= log(survp); 
  }          } 
    
     cptcoveff=ij-1;          else if  (s2==-5) { 
 }            for (j=1,survp=0. ; j<=2; j++)  
               survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
 /*********** Health Expectancies ****************/            lli= log(survp); 
           } 
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)          
 {          else{
   /* Health expectancies */            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   int i, j, nhstepm, hstepm, h;            /*  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 */
   double age, agelim,hf;          } 
   double ***p3mat;          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
            /*if(lli ==000.0)*/
   fprintf(ficreseij,"# Health expectancies\n");          /*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); */
   fprintf(ficreseij,"# Age");          ipmx +=1;
   for(i=1; i<=nlstate;i++)          sw += weight[i];
     for(j=1; j<=nlstate;j++)          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       fprintf(ficreseij," %1d-%1d",i,j);        } /* end of wave */
   fprintf(ficreseij,"\n");      } /* end of individual */
     }  else if(mle==2){
   hstepm=1*YEARM; /*  Every j years of age (in month) */      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for(mi=1; mi<= wav[i]-1; mi++){
   agelim=AGESUP;          for (ii=1;ii<=nlstate+ndeath;ii++)
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */            for (j=1;j<=nlstate+ndeath;j++){
     /* nhstepm age range expressed in number of stepm */              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     /* Typically if 20 years = 20*12/6=40 stepm */            }
     if (stepm >= YEARM) hstepm=1;          for(d=0; d<=dh[mi][i]; d++){
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */            newm=savm;
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     /* Computed by stepm unit matrices, product of hstepm matrices, stored            for (kk=1; kk<=cptcovage;kk++) {
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);              }
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     for(i=1; i<=nlstate;i++)            savm=oldm;
       for(j=1; j<=nlstate;j++)            oldm=newm;
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){          } /* end mult */
           eij[i][j][(int)age] +=p3mat[i][j][h];        
         }          s1=s[mw[mi][i]][i];
              s2=s[mw[mi+1][i]][i];
     hf=1;          bbh=(double)bh[mi][i]/(double)stepm; 
     if (stepm >= YEARM) hf=stepm/YEARM;          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
     fprintf(ficreseij,"%.0f",age );          ipmx +=1;
     for(i=1; i<=nlstate;i++)          sw += weight[i];
       for(j=1; j<=nlstate;j++){          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);        } /* end of wave */
       }      } /* end of individual */
     fprintf(ficreseij,"\n");    }  else if(mle==3){  /* exponential inter-extrapolation */
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   }        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++)
 /************ Variance ******************/            for (j=1;j<=nlstate+ndeath;j++){
 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)              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 {              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   /* Variance of health expectancies */            }
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/          for(d=0; d<dh[mi][i]; d++){
   double **newm;            newm=savm;
   double **dnewm,**doldm;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   int i, j, nhstepm, hstepm, h;            for (kk=1; kk<=cptcovage;kk++) {
   int k, cptcode;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   double *xp;            }
   double **gp, **gm;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   double ***gradg, ***trgradg;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   double ***p3mat;            savm=oldm;
   double age,agelim;            oldm=newm;
   int theta;          } /* end mult */
         
    fprintf(ficresvij,"# Covariances of life expectancies\n");          s1=s[mw[mi][i]][i];
   fprintf(ficresvij,"# Age");          s2=s[mw[mi+1][i]][i];
   for(i=1; i<=nlstate;i++)          bbh=(double)bh[mi][i]/(double)stepm; 
     for(j=1; j<=nlstate;j++)          lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);          ipmx +=1;
   fprintf(ficresvij,"\n");          sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   xp=vector(1,npar);        } /* end of wave */
   dnewm=matrix(1,nlstate,1,npar);      } /* end of individual */
   doldm=matrix(1,nlstate,1,nlstate);    }else if (mle==4){  /* ml=4 no inter-extrapolation */
        for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   hstepm=1*YEARM; /* Every year of age */        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */        for(mi=1; mi<= wav[i]-1; mi++){
   agelim = AGESUP;          for (ii=1;ii<=nlstate+ndeath;ii++)
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */            for (j=1;j<=nlstate+ndeath;j++){
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     if (stepm >= YEARM) hstepm=1;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */            }
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          for(d=0; d<dh[mi][i]; d++){
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);            newm=savm;
     gp=matrix(0,nhstepm,1,nlstate);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     gm=matrix(0,nhstepm,1,nlstate);            for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     for(theta=1; theta <=npar; theta++){            }
       for(i=1; i<=npar; i++){ /* Computes gradient */          
         xp[i] = x[i] + (i==theta ?delti[theta]:0);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);              savm=oldm;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);            oldm=newm;
           } /* end mult */
       if (popbased==1) {        
         for(i=1; i<=nlstate;i++)          s1=s[mw[mi][i]][i];
           prlim[i][i]=probs[(int)age][i][ij];          s2=s[mw[mi+1][i]][i];
       }          if( s2 > nlstate){ 
                  lli=log(out[s1][s2] - savm[s1][s2]);
       for(j=1; j<= nlstate; j++){          }else{
         for(h=0; h<=nhstepm; h++){            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)          }
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];          ipmx +=1;
         }          sw += weight[i];
       }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
      /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
       for(i=1; i<=npar; i++) /* Computes gradient */        } /* end of wave */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      } /* end of individual */
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       if (popbased==1) {        for(mi=1; mi<= wav[i]-1; mi++){
         for(i=1; i<=nlstate;i++)          for (ii=1;ii<=nlstate+ndeath;ii++)
           prlim[i][i]=probs[(int)age][i][ij];            for (j=1;j<=nlstate+ndeath;j++){
       }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               savm[ii][j]=(ii==j ? 1.0 : 0.0);
       for(j=1; j<= nlstate; j++){            }
         for(h=0; h<=nhstepm; h++){          for(d=0; d<dh[mi][i]; d++){
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)            newm=savm;
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         }            for (kk=1; kk<=cptcovage;kk++) {
       }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             }
       for(j=1; j<= nlstate; j++)          
         for(h=0; h<=nhstepm; h++){            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         }            savm=oldm;
     } /* End theta */            oldm=newm;
           } /* end mult */
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);        
           s1=s[mw[mi][i]][i];
     for(h=0; h<=nhstepm; h++)          s2=s[mw[mi+1][i]][i];
       for(j=1; j<=nlstate;j++)          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
         for(theta=1; theta <=npar; theta++)          ipmx +=1;
           trgradg[h][j][theta]=gradg[h][theta][j];          sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     for(i=1;i<=nlstate;i++)          /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
       for(j=1;j<=nlstate;j++)        } /* end of wave */
         vareij[i][j][(int)age] =0.;      } /* end of individual */
     for(h=0;h<=nhstepm;h++){    } /* End of if */
       for(k=0;k<=nhstepm;k++){    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
         for(i=1;i<=nlstate;i++)    return -l;
           for(j=1;j<=nlstate;j++)  }
             vareij[i][j][(int)age] += doldm[i][j];  
       }  /*************** log-likelihood *************/
     }  double funcone( double *x)
     h=1;  {
     if (stepm >= YEARM) h=stepm/YEARM;    /* Same as likeli but slower because of a lot of printf and if */
     fprintf(ficresvij,"%.0f ",age );    int i, ii, j, k, mi, d, kk;
     for(i=1; i<=nlstate;i++)    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
       for(j=1; j<=nlstate;j++){    double **out;
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);    double lli; /* Individual log likelihood */
       }    double llt;
     fprintf(ficresvij,"\n");    int s1, s2;
     free_matrix(gp,0,nhstepm,1,nlstate);    double bbh, survp;
     free_matrix(gm,0,nhstepm,1,nlstate);    /*extern weight */
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);    /* We are differentiating ll according to initial status */
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    /*for(i=1;i<imx;i++) 
   } /* End age */      printf(" %d\n",s[4][i]);
      */
   free_vector(xp,1,npar);    cov[1]=1.;
   free_matrix(doldm,1,nlstate,1,npar);  
   free_matrix(dnewm,1,nlstate,1,nlstate);    for(k=1; k<=nlstate; k++) ll[k]=0.;
   
 }    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
 /************ Variance of prevlim ******************/      for(mi=1; mi<= wav[i]-1; mi++){
 void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)        for (ii=1;ii<=nlstate+ndeath;ii++)
 {          for (j=1;j<=nlstate+ndeath;j++){
   /* Variance of prevalence limit */            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/            savm[ii][j]=(ii==j ? 1.0 : 0.0);
   double **newm;          }
   double **dnewm,**doldm;        for(d=0; d<dh[mi][i]; d++){
   int i, j, nhstepm, hstepm;          newm=savm;
   int k, cptcode;          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   double *xp;          for (kk=1; kk<=cptcovage;kk++) {
   double *gp, *gm;            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   double **gradg, **trgradg;          }
   double age,agelim;          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   int theta;                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
              savm=oldm;
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");          oldm=newm;
   fprintf(ficresvpl,"# Age");        } /* end mult */
   for(i=1; i<=nlstate;i++)        
       fprintf(ficresvpl," %1d-%1d",i,i);        s1=s[mw[mi][i]][i];
   fprintf(ficresvpl,"\n");        s2=s[mw[mi+1][i]][i];
         bbh=(double)bh[mi][i]/(double)stepm; 
   xp=vector(1,npar);        /* bias is positive if real duration
   dnewm=matrix(1,nlstate,1,npar);         * is higher than the multiple of stepm and negative otherwise.
   doldm=matrix(1,nlstate,1,nlstate);         */
          if( s2 > nlstate && (mle <5) ){  /* Jackson */
   hstepm=1*YEARM; /* Every year of age */          lli=log(out[s1][s2] - savm[s1][s2]);
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */        } else if  (s2==-2) {
   agelim = AGESUP;          for (j=1,survp=0. ; j<=nlstate; j++) 
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          lli= log(survp);
     if (stepm >= YEARM) hstepm=1;        }else if (mle==1){
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
     gradg=matrix(1,npar,1,nlstate);        } else if(mle==2){
     gp=vector(1,nlstate);          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 */
     gm=vector(1,nlstate);        } else if(mle==3){  /* exponential inter-extrapolation */
           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 */
     for(theta=1; theta <=npar; theta++){        } else if (mle==4){  /* mle=4 no inter-extrapolation */
       for(i=1; i<=npar; i++){ /* Computes gradient */          lli=log(out[s1][s2]); /* Original formula */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
       }          lli=log(out[s1][s2]); /* Original formula */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        } /* End of if */
       for(i=1;i<=nlstate;i++)        ipmx +=1;
         gp[i] = prlim[i][i];        sw += weight[i];
            ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       for(i=1; i<=npar; i++) /* Computes gradient */        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]); 
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        if(globpr){
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
       for(i=1;i<=nlstate;i++)   %11.6f %11.6f %11.6f ", \
         gm[i] = prlim[i][i];                  num[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]);
       for(i=1;i<=nlstate;i++)          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];            llt +=ll[k]*gipmx/gsw;
     } /* End theta */            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
           }
     trgradg =matrix(1,nlstate,1,npar);          fprintf(ficresilk," %10.6f\n", -llt);
         }
     for(j=1; j<=nlstate;j++)      } /* end of wave */
       for(theta=1; theta <=npar; theta++)    } /* end of individual */
         trgradg[j][theta]=gradg[theta][j];    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     for(i=1;i<=nlstate;i++)    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
       varpl[i][(int)age] =0.;    if(globpr==0){ /* First time we count the contributions and weights */
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);      gipmx=ipmx;
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);      gsw=sw;
     for(i=1;i<=nlstate;i++)    }
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */    return -l;
   }
     fprintf(ficresvpl,"%.0f ",age );  
     for(i=1; i<=nlstate;i++)  
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));  /*************** function likelione ***********/
     fprintf(ficresvpl,"\n");  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
     free_vector(gp,1,nlstate);  {
     free_vector(gm,1,nlstate);    /* This routine should help understanding what is done with 
     free_matrix(gradg,1,npar,1,nlstate);       the selection of individuals/waves and
     free_matrix(trgradg,1,nlstate,1,npar);       to check the exact contribution to the likelihood.
   } /* End age */       Plotting could be done.
      */
   free_vector(xp,1,npar);    int k;
   free_matrix(doldm,1,nlstate,1,npar);  
   free_matrix(dnewm,1,nlstate,1,nlstate);    if(*globpri !=0){ /* Just counts and sums, no printings */
       strcpy(fileresilk,"ilk"); 
 }      strcat(fileresilk,fileres);
       if((ficresilk=fopen(fileresilk,"w"))==NULL) {
 /************ Variance of one-step probabilities  ******************/        printf("Problem with resultfile: %s\n", fileresilk);
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
 {      }
   int i, j;      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");
   int k=0, cptcode;      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
   double **dnewm,**doldm;      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
   double *xp;      for(k=1; k<=nlstate; k++) 
   double *gp, *gm;        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
   double **gradg, **trgradg;      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
   double age,agelim, cov[NCOVMAX];    }
   int theta;  
   char fileresprob[FILENAMELENGTH];    *fretone=(*funcone)(p);
     if(*globpri !=0){
   strcpy(fileresprob,"prob");      fclose(ficresilk);
   strcat(fileresprob,fileres);      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {      fflush(fichtm); 
     printf("Problem with resultfile: %s\n", fileresprob);    } 
   }    return;
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);  }
    
   
   xp=vector(1,npar);  /*********** Maximum Likelihood Estimation ***************/
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);  
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
    {
   cov[1]=1;    int i,j, iter;
   for (age=bage; age<=fage; age ++){    double **xi;
     cov[2]=age;    double fret;
     gradg=matrix(1,npar,1,9);    double fretone; /* Only one call to likelihood */
     trgradg=matrix(1,9,1,npar);    /*  char filerespow[FILENAMELENGTH];*/
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));    xi=matrix(1,npar,1,npar);
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));    for (i=1;i<=npar;i++)
          for (j=1;j<=npar;j++)
     for(theta=1; theta <=npar; theta++){        xi[i][j]=(i==j ? 1.0 : 0.0);
       for(i=1; i<=npar; i++)    printf("Powell\n");  fprintf(ficlog,"Powell\n");
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    strcpy(filerespow,"pow"); 
          strcat(filerespow,fileres);
       pmij(pmmij,cov,ncovmodel,xp,nlstate);    if((ficrespow=fopen(filerespow,"w"))==NULL) {
          printf("Problem with resultfile: %s\n", filerespow);
       k=0;      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
       for(i=1; i<= (nlstate+ndeath); i++){    }
         for(j=1; j<=(nlstate+ndeath);j++){    fprintf(ficrespow,"# Powell\n# iter -2*LL");
            k=k+1;    for (i=1;i<=nlstate;i++)
           gp[k]=pmmij[i][j];      for(j=1;j<=nlstate+ndeath;j++)
         }        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       }    fprintf(ficrespow,"\n");
   
       for(i=1; i<=npar; i++)    powell(p,xi,npar,ftol,&iter,&fret,func);
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  
        free_matrix(xi,1,npar,1,npar);
     fclose(ficrespow);
       pmij(pmmij,cov,ncovmodel,xp,nlstate);    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
       k=0;    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
       for(i=1; i<=(nlstate+ndeath); i++){    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
         for(j=1; j<=(nlstate+ndeath);j++){  
           k=k+1;  }
           gm[k]=pmmij[i][j];  
         }  /**** Computes Hessian and covariance matrix ***/
       }  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
        {
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)    double  **a,**y,*x,pd;
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];      double **hess;
     }    int i, j,jk;
     int *indx;
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)  
       for(theta=1; theta <=npar; theta++)    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
       trgradg[j][theta]=gradg[theta][j];    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
      void lubksb(double **a, int npar, int *indx, double b[]) ;
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);    void ludcmp(double **a, int npar, int *indx, double *d) ;
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);    double gompertz(double p[]);
     hess=matrix(1,npar,1,npar);
      pmij(pmmij,cov,ncovmodel,x,nlstate);  
     printf("\nCalculation of the hessian matrix. Wait...\n");
      k=0;    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
      for(i=1; i<=(nlstate+ndeath); i++){    for (i=1;i<=npar;i++){
        for(j=1; j<=(nlstate+ndeath);j++){      printf("%d",i);fflush(stdout);
          k=k+1;      fprintf(ficlog,"%d",i);fflush(ficlog);
          gm[k]=pmmij[i][j];     
         }       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
      }      
            /*  printf(" %f ",p[i]);
      /*printf("\n%d ",(int)age);          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){    }
            
     for (i=1;i<=npar;i++) {
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));      for (j=1;j<=npar;j++)  {
      }*/        if (j>i) { 
           printf(".%d%d",i,j);fflush(stdout);
   fprintf(ficresprob,"\n%d ",(int)age);          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
           hess[i][j]=hessij(p,delti,i,j,func,npar);
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){          
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);          hess[j][i]=hess[i][j];    
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);          /*printf(" %lf ",hess[i][j]);*/
   }        }
       }
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));    }
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));    printf("\n");
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    fprintf(ficlog,"\n");
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);  
 }    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
  free_vector(xp,1,npar);    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
 fclose(ficresprob);    
  exit(0);    a=matrix(1,npar,1,npar);
 }    y=matrix(1,npar,1,npar);
     x=vector(1,npar);
 /***********************************************/    indx=ivector(1,npar);
 /**************** Main Program *****************/    for (i=1;i<=npar;i++)
 /***********************************************/      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
     ludcmp(a,npar,indx,&pd);
 /*int main(int argc, char *argv[])*/  
 int main()    for (j=1;j<=npar;j++) {
 {      for (i=1;i<=npar;i++) x[i]=0;
       x[j]=1;
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;      lubksb(a,npar,indx,x);
   double agedeb, agefin,hf;      for (i=1;i<=npar;i++){ 
   double agemin=1.e20, agemax=-1.e20;        matcov[i][j]=x[i];
       }
   double fret;    }
   double **xi,tmp,delta;  
     printf("\n#Hessian matrix#\n");
   double dum; /* Dummy variable */    fprintf(ficlog,"\n#Hessian matrix#\n");
   double ***p3mat;    for (i=1;i<=npar;i++) { 
   int *indx;      for (j=1;j<=npar;j++) { 
   char line[MAXLINE], linepar[MAXLINE];        printf("%.3e ",hess[i][j]);
   char title[MAXLINE];        fprintf(ficlog,"%.3e ",hess[i][j]);
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];      }
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], fileresf[FILENAMELENGTH];      printf("\n");
   char filerest[FILENAMELENGTH];      fprintf(ficlog,"\n");
   char fileregp[FILENAMELENGTH];    }
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];  
   int firstobs=1, lastobs=10;    /* Recompute Inverse */
   int sdeb, sfin; /* Status at beginning and end */    for (i=1;i<=npar;i++)
   int c,  h , cpt,l;      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
   int ju,jl, mi;    ludcmp(a,npar,indx,&pd);
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;  
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;    /*  printf("\n#Hessian matrix recomputed#\n");
   int mobilav=0, fprev, lprev ,fprevfore=1, lprevfore=1,nforecast;  
   int hstepm, nhstepm;    for (j=1;j<=npar;j++) {
       for (i=1;i<=npar;i++) x[i]=0;
   double bage, fage, age, agelim, agebase;      x[j]=1;
   double ftolpl=FTOL;      lubksb(a,npar,indx,x);
   double **prlim;      for (i=1;i<=npar;i++){ 
   double *severity;        y[i][j]=x[i];
   double ***param; /* Matrix of parameters */        printf("%.3e ",y[i][j]);
   double  *p;        fprintf(ficlog,"%.3e ",y[i][j]);
   double **matcov; /* Matrix of covariance */      }
   double ***delti3; /* Scale */      printf("\n");
   double *delti; /* Scale */      fprintf(ficlog,"\n");
   double ***eij, ***vareij;    }
   double **varpl; /* Variances of prevalence limits by age */    */
   double *epj, vepp;  
   double kk1;    free_matrix(a,1,npar,1,npar);
     free_matrix(y,1,npar,1,npar);
   char version[80]="Imach version 64b, May 2001, INED-EUROREVES ";    free_vector(x,1,npar);
   char *alph[]={"a","a","b","c","d","e"}, str[4];    free_ivector(indx,1,npar);
     free_matrix(hess,1,npar,1,npar);
   
   char z[1]="c", occ;  
 #include <sys/time.h>  }
 #include <time.h>  
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];  /*************** hessian matrix ****************/
   /* long total_usecs;  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
   struct timeval start_time, end_time;  {
      int i;
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */    int l=1, lmax=20;
     double k1,k2;
     double p2[NPARMAX+1];
   printf("\nIMACH, Version 0.64b");    double res;
   printf("\nEnter the parameter file name: ");    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
     double fx;
 #ifdef windows    int k=0,kmax=10;
   scanf("%s",pathtot);    double l1;
   getcwd(pathcd, size);  
   /*cygwin_split_path(pathtot,path,optionfile);    fx=func(x);
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/    for (i=1;i<=npar;i++) p2[i]=x[i];
   /* cutv(path,optionfile,pathtot,'\\');*/    for(l=0 ; l <=lmax; l++){
       l1=pow(10,l);
 split(pathtot, path,optionfile);      delts=delt;
   chdir(path);      for(k=1 ; k <kmax; k=k+1){
   replace(pathc,path);        delt = delta*(l1*k);
 #endif        p2[theta]=x[theta] +delt;
 #ifdef unix        k1=func(p2)-fx;
   scanf("%s",optionfile);        p2[theta]=x[theta]-delt;
 #endif        k2=func(p2)-fx;
         /*res= (k1-2.0*fx+k2)/delt/delt; */
 /*-------- arguments in the command line --------*/        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
         
   strcpy(fileres,"r");  #ifdef DEBUG
   strcat(fileres, optionfile);        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
         fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
   /*---------arguments file --------*/  #endif
         /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
   if((ficpar=fopen(optionfile,"r"))==NULL)    {        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
     printf("Problem with optionfile %s\n",optionfile);          k=kmax;
     goto end;        }
   }        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
           k=kmax; l=lmax*10.;
   strcpy(filereso,"o");        }
   strcat(filereso,fileres);        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
   if((ficparo=fopen(filereso,"w"))==NULL) {          delts=delt;
     printf("Problem with Output resultfile: %s\n", filereso);goto end;        }
   }      }
     }
   /* Reads comments: lines beginning with '#' */    delti[theta]=delts;
   while((c=getc(ficpar))=='#' && c!= EOF){    return res; 
     ungetc(c,ficpar);    
     fgets(line, MAXLINE, ficpar);  }
     puts(line);  
     fputs(line,ficparo);  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
   }  {
   ungetc(c,ficpar);    int i;
     int l=1, l1, lmax=20;
   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);    double k1,k2,k3,k4,res,fx;
   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);    double p2[NPARMAX+1];
   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);    int k;
 while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);    fx=func(x);
     fgets(line, MAXLINE, ficpar);    for (k=1; k<=2; k++) {
     puts(line);      for (i=1;i<=npar;i++) p2[i]=x[i];
     fputs(line,ficparo);      p2[thetai]=x[thetai]+delti[thetai]/k;
   }      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   ungetc(c,ficpar);      k1=func(p2)-fx;
      
   fscanf(ficpar,"fprevalence=%d lprevalence=%d pop_based=%d\n",&fprev,&lprev,&popbased);      p2[thetai]=x[thetai]+delti[thetai]/k;
  while((c=getc(ficpar))=='#' && c!= EOF){      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
     ungetc(c,ficpar);      k2=func(p2)-fx;
     fgets(line, MAXLINE, ficpar);    
     puts(line);      p2[thetai]=x[thetai]-delti[thetai]/k;
     fputs(line,ficparo);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   }      k3=func(p2)-fx;
   ungetc(c,ficpar);    
        p2[thetai]=x[thetai]-delti[thetai]/k;
   fscanf(ficpar,"fprevalence=%d lprevalence=%d nforecast=%d mob_average=%d\n",&fprevfore,&lprevfore,&nforecast,&mobilav);      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
        k4=func(p2)-fx;
   covar=matrix(0,NCOVMAX,1,n);      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
   cptcovn=0;  #ifdef DEBUG
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+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);
       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);
   ncovmodel=2+cptcovn;  #endif
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */    }
      return res;
   /* Read guess parameters */  }
   /* Reads comments: lines beginning with '#' */  
   while((c=getc(ficpar))=='#' && c!= EOF){  /************** Inverse of matrix **************/
     ungetc(c,ficpar);  void ludcmp(double **a, int n, int *indx, double *d) 
     fgets(line, MAXLINE, ficpar);  { 
     puts(line);    int i,imax,j,k; 
     fputs(line,ficparo);    double big,dum,sum,temp; 
   }    double *vv; 
   ungetc(c,ficpar);   
      vv=vector(1,n); 
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    *d=1.0; 
     for(i=1; i <=nlstate; i++)    for (i=1;i<=n;i++) { 
     for(j=1; j <=nlstate+ndeath-1; j++){      big=0.0; 
       fscanf(ficpar,"%1d%1d",&i1,&j1);      for (j=1;j<=n;j++) 
       fprintf(ficparo,"%1d%1d",i1,j1);        if ((temp=fabs(a[i][j])) > big) big=temp; 
       printf("%1d%1d",i,j);      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
       for(k=1; k<=ncovmodel;k++){      vv[i]=1.0/big; 
         fscanf(ficpar," %lf",&param[i][j][k]);    } 
         printf(" %lf",param[i][j][k]);    for (j=1;j<=n;j++) { 
         fprintf(ficparo," %lf",param[i][j][k]);      for (i=1;i<j;i++) { 
       }        sum=a[i][j]; 
       fscanf(ficpar,"\n");        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
       printf("\n");        a[i][j]=sum; 
       fprintf(ficparo,"\n");      } 
     }      big=0.0; 
        for (i=j;i<=n;i++) { 
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;        sum=a[i][j]; 
         for (k=1;k<j;k++) 
   p=param[1][1];          sum -= a[i][k]*a[k][j]; 
          a[i][j]=sum; 
   /* Reads comments: lines beginning with '#' */        if ( (dum=vv[i]*fabs(sum)) >= big) { 
   while((c=getc(ficpar))=='#' && c!= EOF){          big=dum; 
     ungetc(c,ficpar);          imax=i; 
     fgets(line, MAXLINE, ficpar);        } 
     puts(line);      } 
     fputs(line,ficparo);      if (j != imax) { 
   }        for (k=1;k<=n;k++) { 
   ungetc(c,ficpar);          dum=a[imax][k]; 
           a[imax][k]=a[j][k]; 
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);          a[j][k]=dum; 
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */        } 
   for(i=1; i <=nlstate; i++){        *d = -(*d); 
     for(j=1; j <=nlstate+ndeath-1; j++){        vv[imax]=vv[j]; 
       fscanf(ficpar,"%1d%1d",&i1,&j1);      } 
       printf("%1d%1d",i,j);      indx[j]=imax; 
       fprintf(ficparo,"%1d%1d",i1,j1);      if (a[j][j] == 0.0) a[j][j]=TINY; 
       for(k=1; k<=ncovmodel;k++){      if (j != n) { 
         fscanf(ficpar,"%le",&delti3[i][j][k]);        dum=1.0/(a[j][j]); 
         printf(" %le",delti3[i][j][k]);        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
         fprintf(ficparo," %le",delti3[i][j][k]);      } 
       }    } 
       fscanf(ficpar,"\n");    free_vector(vv,1,n);  /* Doesn't work */
       printf("\n");  ;
       fprintf(ficparo,"\n");  } 
     }  
   }  void lubksb(double **a, int n, int *indx, double b[]) 
   delti=delti3[1][1];  { 
      int i,ii=0,ip,j; 
   /* Reads comments: lines beginning with '#' */    double sum; 
   while((c=getc(ficpar))=='#' && c!= EOF){   
     ungetc(c,ficpar);    for (i=1;i<=n;i++) { 
     fgets(line, MAXLINE, ficpar);      ip=indx[i]; 
     puts(line);      sum=b[ip]; 
     fputs(line,ficparo);      b[ip]=b[i]; 
   }      if (ii) 
   ungetc(c,ficpar);        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
        else if (sum) ii=i; 
   matcov=matrix(1,npar,1,npar);      b[i]=sum; 
   for(i=1; i <=npar; i++){    } 
     fscanf(ficpar,"%s",&str);    for (i=n;i>=1;i--) { 
     printf("%s",str);      sum=b[i]; 
     fprintf(ficparo,"%s",str);      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
     for(j=1; j <=i; j++){      b[i]=sum/a[i][i]; 
       fscanf(ficpar," %le",&matcov[i][j]);    } 
       printf(" %.5le",matcov[i][j]);  } 
       fprintf(ficparo," %.5le",matcov[i][j]);  
     }  void pstamp(FILE *fichier)
     fscanf(ficpar,"\n");  {
     printf("\n");    fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
     fprintf(ficparo,"\n");  }
   }  
   for(i=1; i <=npar; i++)  /************ Frequencies ********************/
     for(j=i+1;j<=npar;j++)  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[])
       matcov[i][j]=matcov[j][i];  {  /* Some frequencies */
        
   printf("\n");    int i, m, jk, k1,i1, j1, bool, z1,j;
     int first;
     double ***freq; /* Frequencies */
     /*-------- data file ----------*/    double *pp, **prop;
     if((ficres =fopen(fileres,"w"))==NULL) {    double pos,posprop, k2, dateintsum=0,k2cpt=0;
       printf("Problem with resultfile: %s\n", fileres);goto end;    char fileresp[FILENAMELENGTH];
     }    
     fprintf(ficres,"#%s\n",version);    pp=vector(1,nlstate);
        prop=matrix(1,nlstate,iagemin,iagemax+3);
     if((fic=fopen(datafile,"r"))==NULL)    {    strcpy(fileresp,"p");
       printf("Problem with datafile: %s\n", datafile);goto end;    strcat(fileresp,fileres);
     }    if((ficresp=fopen(fileresp,"w"))==NULL) {
       printf("Problem with prevalence resultfile: %s\n", fileresp);
     n= lastobs;      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
     severity = vector(1,maxwav);      exit(0);
     outcome=imatrix(1,maxwav+1,1,n);    }
     num=ivector(1,n);    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
     moisnais=vector(1,n);    j1=0;
     annais=vector(1,n);    
     moisdc=vector(1,n);    j=cptcoveff;
     andc=vector(1,n);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
     agedc=vector(1,n);  
     cod=ivector(1,n);    first=1;
     weight=vector(1,n);  
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */    for(k1=1; k1<=j;k1++){
     mint=matrix(1,maxwav,1,n);      for(i1=1; i1<=ncodemax[k1];i1++){
     anint=matrix(1,maxwav,1,n);        j1++;
     s=imatrix(1,maxwav+1,1,n);        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
     adl=imatrix(1,maxwav+1,1,n);              scanf("%d", i);*/
     tab=ivector(1,NCOVMAX);        for (i=-5; i<=nlstate+ndeath; i++)  
     ncodemax=ivector(1,8);          for (jk=-5; jk<=nlstate+ndeath; jk++)  
             for(m=iagemin; m <= iagemax+3; m++)
     i=1;              freq[i][jk][m]=0;
     while (fgets(line, MAXLINE, fic) != NULL)    {  
       if ((i >= firstobs) && (i <=lastobs)) {      for (i=1; i<=nlstate; i++)  
                for(m=iagemin; m <= iagemax+3; m++)
         for (j=maxwav;j>=1;j--){          prop[i][m]=0;
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);        
           strcpy(line,stra);        dateintsum=0;
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);        k2cpt=0;
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);        for (i=1; i<=imx; i++) {
         }          bool=1;
                  if  (cptcovn>0) {
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);            for (z1=1; z1<=cptcoveff; z1++) 
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
                 bool=0;
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);          }
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);          if (bool==1){
             for(m=firstpass; m<=lastpass; m++){
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);              k2=anint[m][i]+(mint[m][i]/12.);
         for (j=ncov;j>=1;j--){              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
         }                if(agev[m][i]==1) agev[m][i]=iagemax+2;
         num[i]=atol(stra);                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
                        if (m<lastpass) {
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
                 }
         i=i+1;                
       }                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
     }                  dateintsum=dateintsum+k2;
     /* printf("ii=%d", ij);                  k2cpt++;
        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;        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
     }        pstamp(ficresp);
     for (i=1; i<=imx; i++) printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));*/        if  (cptcovn>0) {
           fprintf(ficresp, "\n#********** Variable "); 
   /* Calculation of the number of parameter from char model*/          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   Tvar=ivector(1,15);          fprintf(ficresp, "**********\n#");
   Tprod=ivector(1,15);        }
   Tvaraff=ivector(1,15);        for(i=1; i<=nlstate;i++) 
   Tvard=imatrix(1,15,1,2);          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
   Tage=ivector(1,15);              fprintf(ficresp, "\n");
            
   if (strlen(model) >1){        for(i=iagemin; i <= iagemax+3; i++){
     j=0, j1=0, k1=1, k2=1;          if(i==iagemax+3){
     j=nbocc(model,'+');            fprintf(ficlog,"Total");
     j1=nbocc(model,'*');          }else{
     cptcovn=j+1;            if(first==1){
     cptcovprod=j1;              first=0;
                  printf("See log file for details...\n");
                }
     strcpy(modelsav,model);            fprintf(ficlog,"Age %d", i);
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){          }
       printf("Error. Non available option model=%s ",model);          for(jk=1; jk <=nlstate ; jk++){
       goto end;            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
     }              pp[jk] += freq[jk][m][i]; 
              }
     for(i=(j+1); i>=1;i--){          for(jk=1; jk <=nlstate ; jk++){
       cutv(stra,strb,modelsav,'+');            for(m=-1, pos=0; m <=0 ; m++)
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);              pos += freq[jk][m][i];
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/            if(pp[jk]>=1.e-10){
       /*scanf("%d",i);*/              if(first==1){
       if (strchr(strb,'*')) {              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
         cutv(strd,strc,strb,'*');              }
         if (strcmp(strc,"age")==0) {              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
           cptcovprod--;            }else{
           cutv(strb,stre,strd,'V');              if(first==1)
           Tvar[i]=atoi(stre);                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
           cptcovage++;              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
             Tage[cptcovage]=i;            }
             /*printf("stre=%s ", stre);*/          }
         }  
         else if (strcmp(strd,"age")==0) {          for(jk=1; jk <=nlstate ; jk++){
           cptcovprod--;            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
           cutv(strb,stre,strc,'V');              pp[jk] += freq[jk][m][i];
           Tvar[i]=atoi(stre);          }       
           cptcovage++;          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
           Tage[cptcovage]=i;            pos += pp[jk];
         }            posprop += prop[jk][i];
         else {          }
           cutv(strb,stre,strc,'V');          for(jk=1; jk <=nlstate ; jk++){
           Tvar[i]=ncov+k1;            if(pos>=1.e-5){
           cutv(strb,strc,strd,'V');              if(first==1)
           Tprod[k1]=i;                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
           Tvard[k1][1]=atoi(strc);              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
           Tvard[k1][2]=atoi(stre);            }else{
           Tvar[cptcovn+k2]=Tvard[k1][1];              if(first==1)
           Tvar[cptcovn+k2+1]=Tvard[k1][2];                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
           for (k=1; k<=lastobs;k++)              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];            }
           k1++;            if( i <= iagemax){
           k2=k2+2;              if(pos>=1.e-5){
         }                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
       }                /*probs[i][jk][j1]= pp[jk]/pos;*/
       else {                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/              }
        /*  scanf("%d",i);*/              else
       cutv(strd,strc,strb,'V');                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
       Tvar[i]=atoi(strc);            }
       }          }
       strcpy(modelsav,stra);            
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);          for(jk=-1; jk <=nlstate+ndeath; jk++)
         scanf("%d",i);*/            for(m=-1; m <=nlstate+ndeath; m++)
     }              if(freq[jk][m][i] !=0 ) {
 }              if(first==1)
                  printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
   printf("cptcovprod=%d ", cptcovprod);              }
   scanf("%d ",i);*/          if(i <= iagemax)
     fclose(fic);            fprintf(ficresp,"\n");
           if(first==1)
     /*  if(mle==1){*/            printf("Others in log...\n");
     if (weightopt != 1) { /* Maximisation without weights*/          fprintf(ficlog,"\n");
       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);    dateintmean=dateintsum/k2cpt; 
    
    for (i=1; i<=imx; i++)    fclose(ficresp);
      for(m=2; (m<= maxwav); m++)    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){    free_vector(pp,1,nlstate);
          anint[m][i]=9999;    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
          s[m][i]=-1;    /* End of Freq */
        }  }
      
     for (i=1; i<=imx; i++)  {  /************ Prevalence ********************/
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);  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)
       for(m=1; (m<= maxwav); m++){  {  
         if(s[m][i] >0){    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
           if (s[m][i] == nlstate+1) {       in each health status at the date of interview (if between dateprev1 and dateprev2).
             if(agedc[i]>0)       We still use firstpass and lastpass as another selection.
               if(moisdc[i]!=99 && andc[i]!=9999)    */
               agev[m][i]=agedc[i];   
             else {    int i, m, jk, k1, i1, j1, bool, z1,j;
               if (andc[i]!=9999){    double ***freq; /* Frequencies */
               printf("Warning negative age at death: %d line:%d\n",num[i],i);    double *pp, **prop;
               agev[m][i]=-1;    double pos,posprop; 
               }    double  y2; /* in fractional years */
             }    int iagemin, iagemax;
           }  
           else if(s[m][i] !=9){ /* Should no more exist */    iagemin= (int) agemin;
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);    iagemax= (int) agemax;
             if(mint[m][i]==99 || anint[m][i]==9999)    /*pp=vector(1,nlstate);*/
               agev[m][i]=1;    prop=matrix(1,nlstate,iagemin,iagemax+3); 
             else if(agev[m][i] <agemin){    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
               agemin=agev[m][i];    j1=0;
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/    
             }    j=cptcoveff;
             else if(agev[m][i] >agemax){    if (cptcovn<1) {j=1;ncodemax[1]=1;}
               agemax=agev[m][i];    
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/    for(k1=1; k1<=j;k1++){
             }      for(i1=1; i1<=ncodemax[k1];i1++){
             /*agev[m][i]=anint[m][i]-annais[i];*/        j1++;
             /*   agev[m][i] = age[i]+2*m;*/        
           }        for (i=1; i<=nlstate; i++)  
           else { /* =9 */          for(m=iagemin; m <= iagemax+3; m++)
             agev[m][i]=1;            prop[i][m]=0.0;
             s[m][i]=-1;       
           }        for (i=1; i<=imx; i++) { /* Each individual */
         }          bool=1;
         else /*= 0 Unknown */          if  (cptcovn>0) {
           agev[m][i]=1;            for (z1=1; z1<=cptcoveff; z1++) 
       }              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
                    bool=0;
     }          } 
     for (i=1; i<=imx; i++)  {          if (bool==1) { 
       for(m=1; (m<= maxwav); m++){            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
         if (s[m][i] > (nlstate+ndeath)) {              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
           printf("Error: Wrong value in nlstate or ndeath\n");                if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
           goto end;                if(agev[m][i]==0) agev[m][i]=iagemax+1;
         }                if(agev[m][i]==1) agev[m][i]=iagemax+2;
       }                if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
     }                if (s[m][i]>0 && s[m][i]<=nlstate) { 
                   /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
                   prop[s[m][i]][iagemax+3] += weight[i]; 
     free_vector(severity,1,maxwav);                } 
     free_imatrix(outcome,1,maxwav+1,1,n);              }
     free_vector(moisnais,1,n);            } /* end selection of waves */
     free_vector(annais,1,n);          }
     free_matrix(mint,1,maxwav,1,n);        }
     free_matrix(anint,1,maxwav,1,n);        for(i=iagemin; i <= iagemax+3; i++){  
     free_vector(moisdc,1,n);          
     free_vector(andc,1,n);          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
             posprop += prop[jk][i]; 
              } 
     wav=ivector(1,imx);  
     dh=imatrix(1,lastpass-firstpass+1,1,imx);          for(jk=1; jk <=nlstate ; jk++){     
     mw=imatrix(1,lastpass-firstpass+1,1,imx);            if( i <=  iagemax){ 
                  if(posprop>=1.e-5){ 
     /* Concatenates waves */                probs[i][jk][j1]= prop[jk][i]/posprop;
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);              } else
                 printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\n",jk,i,j1,probs[i][jk][j1]);
             } 
       Tcode=ivector(1,100);          }/* end jk */ 
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);        }/* end i */ 
       ncodemax[1]=1;      } /* end i1 */
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);    } /* end k1 */
          
    codtab=imatrix(1,100,1,10);    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
    h=0;    /*free_vector(pp,1,nlstate);*/
    m=pow(2,cptcoveff);    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
    }  /* End of prevalence */
    for(k=1;k<=cptcoveff; k++){  
      for(i=1; i <=(m/pow(2,k));i++){  /************* Waves Concatenation ***************/
        for(j=1; j <= ncodemax[k]; j++){  
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){  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)
            h++;  {
            if (h>m) h=1;codtab[h][k]=j;    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
          }       Death is a valid wave (if date is known).
        }       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
      }       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
    }       and mw[mi+1][i]. dh depends on stepm.
        */
   
    /*for(i=1; i <=m ;i++){    int i, mi, m;
      for(k=1; k <=cptcovn; k++){    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
        printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);       double sum=0., jmean=0.;*/
      }    int first;
      printf("\n");    int j, k=0,jk, ju, jl;
    }    double sum=0.;
    scanf("%d",i);*/    first=0;
        jmin=1e+5;
    /* Calculates basic frequencies. Computes observed prevalence at single age    jmax=-1;
        and prints on file fileres'p'. */    jmean=0.;
   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax, fprev, lprev);    for(i=1; i<=imx; i++){
       mi=0;
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      m=firstpass;
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      while(s[m][i] <= nlstate){
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          mw[++mi][i]=m;
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */        if(m >=lastpass)
                break;
     /* For Powell, parameters are in a vector p[] starting at p[1]        else
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */          m++;
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */      }/* end while */
       if (s[m][i] > nlstate){
     if(mle==1){        mi++;     /* Death is another wave */
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);        /* if(mi==0)  never been interviewed correctly before death */
     }           /* Only death is a correct wave */
            mw[mi][i]=m;
     /*--------- results files --------------*/      }
     fprintf(ficres,"\ntitle=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, mle,weightopt,model);  
          wav[i]=mi;
    jk=1;      if(mi==0){
    fprintf(ficres,"# Parameters\n");        nbwarn++;
    printf("# Parameters\n");        if(first==0){
    for(i=1,jk=1; i <=nlstate; i++){          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
      for(k=1; k <=(nlstate+ndeath); k++){          first=1;
        if (k != i)        }
          {        if(first==1){
            printf("%d%d ",i,k);          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
            fprintf(ficres,"%1d%1d ",i,k);        }
            for(j=1; j <=ncovmodel; j++){      } /* end mi==0 */
              printf("%f ",p[jk]);    } /* End individuals */
              fprintf(ficres,"%f ",p[jk]);  
              jk++;    for(i=1; i<=imx; i++){
            }      for(mi=1; mi<wav[i];mi++){
            printf("\n");        if (stepm <=0)
            fprintf(ficres,"\n");          dh[mi][i]=1;
          }        else{
      }          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
    }            if (agedc[i] < 2*AGESUP) {
  if(mle==1){              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
     /* Computing hessian and covariance matrix */              if(j==0) j=1;  /* Survives at least one month after exam */
     ftolhess=ftol; /* Usually correct */              else if(j<0){
     hesscov(matcov, p, npar, delti, ftolhess, func);                nberr++;
  }                printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
     fprintf(ficres,"# Scales\n");                j=1; /* Temporary Dangerous patch */
     printf("# Scales\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);
      for(i=1,jk=1; i <=nlstate; i++){                fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
       for(j=1; j <=nlstate+ndeath; j++){                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);
         if (j!=i) {              }
           fprintf(ficres,"%1d%1d",i,j);              k=k+1;
           printf("%1d%1d",i,j);              if (j >= jmax){
           for(k=1; k<=ncovmodel;k++){                jmax=j;
             printf(" %.5e",delti[jk]);                ijmax=i;
             fprintf(ficres," %.5e",delti[jk]);              }
             jk++;              if (j <= jmin){
           }                jmin=j;
           printf("\n");                ijmin=i;
           fprintf(ficres,"\n");              }
         }              sum=sum+j;
       }              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
       }              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
                }
     k=1;          }
     fprintf(ficres,"# Covariance\n");          else{
     printf("# Covariance\n");            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
     for(i=1;i<=npar;i++){  /*        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]); */
       /*  if (k>nlstate) k=1;  
       i1=(i-1)/(ncovmodel*nlstate)+1;            k=k+1;
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);            if (j >= jmax) {
       printf("%s%d%d",alph[k],i1,tab[i]);*/              jmax=j;
       fprintf(ficres,"%3d",i);              ijmax=i;
       printf("%3d",i);            }
       for(j=1; j<=i;j++){            else if (j <= jmin){
         fprintf(ficres," %.5e",matcov[i][j]);              jmin=j;
         printf(" %.5e",matcov[i][j]);              ijmin=i;
       }            }
       fprintf(ficres,"\n");            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
       printf("\n");            /*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]);*/
       k++;            if(j<0){
     }              nberr++;
                  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]);
     while((c=getc(ficpar))=='#' && c!= EOF){              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]);
       ungetc(c,ficpar);            }
       fgets(line, MAXLINE, ficpar);            sum=sum+j;
       puts(line);          }
       fputs(line,ficparo);          jk= j/stepm;
     }          jl= j -jk*stepm;
     ungetc(c,ficpar);          ju= j -(jk+1)*stepm;
            if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);            if(jl==0){
                  dh[mi][i]=jk;
     if (fage <= 2) {              bh[mi][i]=0;
       bage = agemin;            }else{ /* We want a negative bias in order to only have interpolation ie
       fage = agemax;                    * at the price of an extra matrix product in likelihood */
     }              dh[mi][i]=jk+1;
               bh[mi][i]=ju;
     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\n",agemin,agemax,bage,fage);          }else{
             if(jl <= -ju){
                  dh[mi][i]=jk;
 /*------------ gnuplot -------------*/              bh[mi][i]=jl;       /* bias is positive if real duration
 chdir(pathcd);                                   * is higher than the multiple of stepm and negative otherwise.
   if((ficgp=fopen("graph.plt","w"))==NULL) {                                   */
     printf("Problem with file graph.gp");goto end;            }
   }            else{
 #ifdef windows              dh[mi][i]=jk+1;
   fprintf(ficgp,"cd \"%s\" \n",pathc);              bh[mi][i]=ju;
 #endif            }
 m=pow(2,cptcoveff);            if(dh[mi][i]==0){
                dh[mi][i]=1; /* At least one step */
  /* 1eme*/              bh[mi][i]=ju; /* At least one step */
   for (cpt=1; cpt<= nlstate ; cpt ++) {              /*  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);*/
    for (k1=1; k1<= m ; k1 ++) {            }
           } /* end if mle */
 #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);      } /* end wave */
 #endif    }
 #ifdef unix    jmean=sum/k;
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);    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);
 #endif    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);
    }
 for (i=1; i<= nlstate ; i ++) {  
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");  /*********** Tricode ****************************/
   else fprintf(ficgp," \%%*lf (\%%*lf)");  void tricode(int *Tvar, int **nbcode, int imx)
 }  {
     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 ++) {    /*      Tvar[i]=atoi(stre); /* find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 */
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");    int Ndum[20],ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
 }    int cptcode=0;
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);    cptcoveff=0; 
      for (i=1; i<= nlstate ; i ++) {   
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    for (k=0; k<maxncov; k++) Ndum[k]=0;
   else fprintf(ficgp," \%%*lf (\%%*lf)");    for (k=1; k<=7; k++) ncodemax[k]=0; /* Horrible constant again */
 }    
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));    for (j=1; j<=(cptcovn+2*cptcovprod); j++) { /* For each covariate */
 #ifdef unix      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
 fprintf(ficgp,"\nset ter gif small size 400,300");                                 modality*/ 
 #endif        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual, might be -1*/
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);        Ndum[ij]++; /*counts the occurence of this modality */
    }        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
   }        if (ij > cptcode) cptcode=ij; /* getting the maximum value of the modality of the covariate  (should be 0 or 1 now) 
   /*2 eme*/                                         Tvar[j]. If V=sex and male is 0 and 
                                          female is 1, then  cptcode=1.*/
   for (k1=1; k1<= m ; k1 ++) {      }
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);  
          for (i=0; i<=cptcode; i++) { /* i=-1 ?*/
     for (i=1; i<= nlstate+1 ; i ++) {        if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariate. In fact ncodemax[j]=2 (dichotom. variables only) but it can be more */
       k=2*i;      } /* Ndum[-1] number of undefined modalities */
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);  
       for (j=1; j<= nlstate+1 ; j ++) {      ij=1; 
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      for (i=1; i<=ncodemax[j]; i++) { /* i= 1 to 2 */
   else fprintf(ficgp," \%%*lf (\%%*lf)");        for (k=0; k<= maxncov; k++) { /* k=-1 ?*/
 }            if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");            nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode. 
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);                                       k is a modality. If we have model=V1+V1*sex 
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);                                       then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
       for (j=1; j<= nlstate+1 ; j ++) {            ij++;
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          }
         else fprintf(ficgp," \%%*lf (\%%*lf)");          if (ij > ncodemax[j]) break; 
 }          }  
       fprintf(ficgp,"\" t\"\" w l 0,");      } 
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);    }  
       for (j=1; j<= nlstate+1 ; j ++) {  
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");   for (k=0; k< maxncov; k++) Ndum[k]=0;
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }     for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
       else fprintf(ficgp,"\" t\"\" w l 0,");     ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
     }     Ndum[ij]++;
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);   }
   }  
     ij=1;
   /*3eme*/   for (i=1; i<= maxncov; i++) {
      if((Ndum[i]!=0) && (i<=ncovcol)){
   for (k1=1; k1<= m ; k1 ++) {       Tvaraff[ij]=i; /*For printing */
     for (cpt=1; cpt<= nlstate ; cpt ++) {       ij++;
       k=2+nlstate*(cpt-1);     }
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k1-1,k1-1,k,cpt);   }
       for (i=1; i< nlstate ; i ++) {   ij--;
         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);   cptcoveff=ij; /*Number of simple covariates*/
       }  }
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);  
     }  /*********** Health Expectancies ****************/
   }  
    void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
   /* CV preval stat */  
   for (k1=1; k1<= m ; k1 ++) {  {
     for (cpt=1; cpt<nlstate ; cpt ++) {    /* Health expectancies, no variances */
       k=3;    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);    int nhstepma, nstepma; /* Decreasing with age */
       for (i=1; i< nlstate ; i ++)    double age, agelim, hf;
         fprintf(ficgp,"+$%d",k+i+1);    double ***p3mat;
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);    double eip;
        
       l=3+(nlstate+ndeath)*cpt;    pstamp(ficreseij);
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);    fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
       for (i=1; i< nlstate ; i ++) {    fprintf(ficreseij,"# Age");
         l=3+(nlstate+ndeath)*cpt;    for(i=1; i<=nlstate;i++){
         fprintf(ficgp,"+$%d",l+i+1);      for(j=1; j<=nlstate;j++){
       }        fprintf(ficreseij," e%1d%1d ",i,j);
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);        }
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);      fprintf(ficreseij," e%1d. ",i);
     }    }
   }      fprintf(ficreseij,"\n");
   
   /* proba elementaires */    
    for(i=1,jk=1; i <=nlstate; i++){    if(estepm < stepm){
     for(k=1; k <=(nlstate+ndeath); k++){      printf ("Problem %d lower than %d\n",estepm, stepm);
       if (k != i) {    }
         for(j=1; j <=ncovmodel; j++){    else  hstepm=estepm;   
           /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/    /* We compute the life expectancy from trapezoids spaced every estepm months
           /*fprintf(ficgp,"%s",alph[1]);*/     * This is mainly to measure the difference between two models: for example
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);     * if stepm=24 months pijx are given only every 2 years and by summing them
           jk++;     * we are calculating an estimate of the Life Expectancy assuming a linear 
           fprintf(ficgp,"\n");     * progression in between and thus overestimating or underestimating according
         }     * to the curvature of the survival function. If, for the same date, we 
       }     * estimate the model with stepm=1 month, we can keep estepm to 24 months
     }     * to compare the new estimate of Life expectancy with the same linear 
     }     * hypothesis. A more precise result, taking into account a more precise
      * curvature will be obtained if estepm is as small as stepm. */
   for(jk=1; jk <=m; jk++) {  
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);    /* For example we decided to compute the life expectancy with the smallest unit */
    i=1;    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
    for(k2=1; k2<=nlstate; k2++) {       nhstepm is the number of hstepm from age to agelim 
      k3=i;       nstepm is the number of stepm from age to agelin. 
      for(k=1; k<=(nlstate+ndeath); k++) {       Look at hpijx to understand the reason of that which relies in memory size
        if (k != k2){       and note for a fixed period like estepm months */
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
 ij=1;       survival function given by stepm (the optimization length). Unfortunately it
         for(j=3; j <=ncovmodel; j++) {       means that if the survival funtion is printed only each two years of age and if
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);       results. So we changed our mind and took the option of the best precision.
             ij++;    */
           }    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
           else  
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    agelim=AGESUP;
         }    /* If stepm=6 months */
           fprintf(ficgp,")/(1");      /* Computed by stepm unit matrices, product of hstepm matrices, stored
                 in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
         for(k1=1; k1 <=nlstate; k1++){        
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);  /* nhstepm age range expressed in number of stepm */
 ij=1;    nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
           for(j=3; j <=ncovmodel; j++){    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    /* if (stepm >= YEARM) hstepm=1;*/
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
             ij++;    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }  
           else    for (age=bage; age<=fage; age ++){ 
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
           }      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
           fprintf(ficgp,")");      /* if (stepm >= YEARM) hstepm=1;*/
         }      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);  
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");      /* If stepm=6 months */
         i=i+ncovmodel;      /* Computed by stepm unit matrices, product of hstepma matrices, stored
        }         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
      }      
    }      hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);      
   }      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
          
   fclose(ficgp);      printf("%d|",(int)age);fflush(stdout);
          fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
 chdir(path);      
          /* Computing expectancies */
     free_ivector(wav,1,imx);      for(i=1; i<=nlstate;i++)
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);        for(j=1; j<=nlstate;j++)
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);            for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
     free_ivector(num,1,n);            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
     free_vector(agedc,1,n);            
     /*free_matrix(covar,1,NCOVMAX,1,n);*/            /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
     fclose(ficparo);  
     fclose(ficres);          }
     /*  }*/  
          fprintf(ficreseij,"%3.0f",age );
    /*________fin mle=1_________*/      for(i=1; i<=nlstate;i++){
            eip=0;
         for(j=1; j<=nlstate;j++){
            eip +=eij[i][j][(int)age];
     /* No more information from the sample is required now */          fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
   /* Reads comments: lines beginning with '#' */        }
   while((c=getc(ficpar))=='#' && c!= EOF){        fprintf(ficreseij,"%9.4f", eip );
     ungetc(c,ficpar);      }
     fgets(line, MAXLINE, ficpar);      fprintf(ficreseij,"\n");
     puts(line);      
     fputs(line,ficparo);    }
   }    free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   ungetc(c,ficpar);    printf("\n");
      fprintf(ficlog,"\n");
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);    
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);  }
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);  
 /*--------- index.htm --------*/  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[] )
   
   strcpy(optionfilehtm,optionfile);  {
   strcat(optionfilehtm,".htm");    /* Covariances of health expectancies eij and of total life expectancies according
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {     to initial status i, ei. .
     printf("Problem with %s \n",optionfilehtm);goto end;    */
   }    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
     int nhstepma, nstepma; /* Decreasing with age */
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.64b </font> <hr size=\"2\" color=\"#EC5E5E\">    double age, agelim, hf;
 Titre=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>    double ***p3matp, ***p3matm, ***varhe;
 Total number of observations=%d <br>    double **dnewm,**doldm;
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>    double *xp, *xm;
 <hr  size=\"2\" color=\"#EC5E5E\">    double **gp, **gm;
 <li>Outputs files<br><br>\n    double ***gradg, ***trgradg;
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n    int theta;
 - 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>    double eip, vip;
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>  
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>    xp=vector(1,npar);
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>    xm=vector(1,npar);
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>    dnewm=matrix(1,nlstate*nlstate,1,npar);
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
         - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>    
 <br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);    pstamp(ficresstdeij);
     fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
  fprintf(fichtm," <li>Graphs</li><p>");    fprintf(ficresstdeij,"# Age");
     for(i=1; i<=nlstate;i++){
  m=cptcoveff;      for(j=1; j<=nlstate;j++)
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}        fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
       fprintf(ficresstdeij," e%1d. ",i);
  j1=0;    }
  for(k1=1; k1<=m;k1++){    fprintf(ficresstdeij,"\n");
    for(i1=1; i1<=ncodemax[k1];i1++){  
        j1++;    pstamp(ficrescveij);
        if (cptcovn > 0) {    fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");    fprintf(ficrescveij,"# Age");
          for (cpt=1; cpt<=cptcoveff;cpt++)    for(i=1; i<=nlstate;i++)
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[j1][cpt]]);      for(j=1; j<=nlstate;j++){
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");        cptj= (j-1)*nlstate+i;
        }        for(i2=1; i2<=nlstate;i2++)
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>          for(j2=1; j2<=nlstate;j2++){
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);                cptj2= (j2-1)*nlstate+i2;
        for(cpt=1; cpt<nlstate;cpt++){            if(cptj2 <= cptj)
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>              fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);          }
        }      }
     for(cpt=1; cpt<=nlstate;cpt++) {    fprintf(ficrescveij,"\n");
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident    
 interval) in state (%d): v%s%d%d.gif <br>    if(estepm < stepm){
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);        printf ("Problem %d lower than %d\n",estepm, stepm);
      }    }
      for(cpt=1; cpt<=nlstate;cpt++) {    else  hstepm=estepm;   
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>    /* We compute the life expectancy from trapezoids spaced every estepm months
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);     * This is mainly to measure the difference between two models: for example
      }     * if stepm=24 months pijx are given only every 2 years and by summing them
      fprintf(fichtm,"\n<br>- Total life expectancy by age and     * we are calculating an estimate of the Life Expectancy assuming a linear 
 health expectancies in states (1) and (2): e%s%d.gif<br>     * progression in between and thus overestimating or underestimating according
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);     * to the curvature of the survival function. If, for the same date, we 
 fprintf(fichtm,"\n</body>");     * estimate the model with stepm=1 month, we can keep estepm to 24 months
    }     * to compare the new estimate of Life expectancy with the same linear 
  }     * hypothesis. A more precise result, taking into account a more precise
 fclose(fichtm);     * curvature will be obtained if estepm is as small as stepm. */
   
   /*--------------- Prevalence limit --------------*/    /* For example we decided to compute the life expectancy with the smallest unit */
      /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   strcpy(filerespl,"pl");       nhstepm is the number of hstepm from age to agelim 
   strcat(filerespl,fileres);       nstepm is the number of stepm from age to agelin. 
   if((ficrespl=fopen(filerespl,"w"))==NULL) {       Look at hpijx to understand the reason of that which relies in memory size
     printf("Problem with Prev limit resultfile: %s\n", filerespl);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
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);       survival function given by stepm (the optimization length). Unfortunately it
   fprintf(ficrespl,"#Prevalence limit\n");       means that if the survival funtion is printed only each two years of age and if
   fprintf(ficrespl,"#Age ");       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);       results. So we changed our mind and took the option of the best precision.
   fprintf(ficrespl,"\n");    */
      hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   prlim=matrix(1,nlstate,1,nlstate);  
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    /* If stepm=6 months */
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    /* nhstepm age range expressed in number of stepm */
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    agelim=AGESUP;
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   k=0;    /* if (stepm >= YEARM) hstepm=1;*/
   agebase=agemin;    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   agelim=agemax;    
   ftolpl=1.e-10;    p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   i1=cptcoveff;    p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   if (cptcovn < 1){i1=1;}    gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
     trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
   for(cptcov=1;cptcov<=i1;cptcov++){    gp=matrix(0,nhstepm,1,nlstate*nlstate);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    gm=matrix(0,nhstepm,1,nlstate*nlstate);
         k=k+1;  
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/    for (age=bage; age<=fage; age ++){ 
         fprintf(ficrespl,"\n#******");      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
         for(j=1;j<=cptcoveff;j++)      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      /* if (stepm >= YEARM) hstepm=1;*/
         fprintf(ficrespl,"******\n");      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
          
         for (age=agebase; age<=agelim; age++){      /* If stepm=6 months */
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);      /* Computed by stepm unit matrices, product of hstepma matrices, stored
           fprintf(ficrespl,"%.0f",age );         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
           for(i=1; i<=nlstate;i++)      
           fprintf(ficrespl," %.5f", prlim[i][i]);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
           fprintf(ficrespl,"\n");  
         }      /* Computing  Variances of health expectancies */
       }      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
     }         decrease memory allocation */
   fclose(ficrespl);      for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ 
   /*------------- h Pij x at various ages ------------*/          xp[i] = x[i] + (i==theta ?delti[theta]:0);
            xm[i] = x[i] - (i==theta ?delti[theta]:0);
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);        }
   if((ficrespij=fopen(filerespij,"w"))==NULL) {        hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;        hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
   }    
   printf("Computing pij: result on file '%s' \n", filerespij);        for(j=1; j<= nlstate; j++){
            for(i=1; i<=nlstate; i++){
   stepsize=(int) (stepm+YEARM-1)/YEARM;            for(h=0; h<=nhstepm-1; h++){
   /*if (stepm<=24) stepsize=2;*/              gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
               gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
   agelim=AGESUP;            }
   hstepm=stepsize*YEARM; /* Every year of age */          }
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */        }
         
   k=0;        for(ij=1; ij<= nlstate*nlstate; ij++)
   for(cptcov=1;cptcov<=i1;cptcov++){          for(h=0; h<=nhstepm-1; h++){
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){            gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
       k=k+1;          }
         fprintf(ficrespij,"\n#****** ");      }/* End theta */
         for(j=1;j<=cptcoveff;j++)      
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      
         fprintf(ficrespij,"******\n");      for(h=0; h<=nhstepm-1; h++)
                for(j=1; j<=nlstate*nlstate;j++)
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */          for(theta=1; theta <=npar; theta++)
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */            trgradg[h][j][theta]=gradg[h][theta][j];
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
           oldm=oldms;savm=savms;       for(ij=1;ij<=nlstate*nlstate;ij++)
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);          for(ji=1;ji<=nlstate*nlstate;ji++)
           fprintf(ficrespij,"# Age");          varhe[ij][ji][(int)age] =0.;
           for(i=1; i<=nlstate;i++)  
             for(j=1; j<=nlstate+ndeath;j++)       printf("%d|",(int)age);fflush(stdout);
               fprintf(ficrespij," %1d-%1d",i,j);       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
           fprintf(ficrespij,"\n");       for(h=0;h<=nhstepm-1;h++){
           for (h=0; h<=nhstepm; h++){        for(k=0;k<=nhstepm-1;k++){
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
             for(i=1; i<=nlstate;i++)          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
               for(j=1; j<=nlstate+ndeath;j++)          for(ij=1;ij<=nlstate*nlstate;ij++)
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);            for(ji=1;ji<=nlstate*nlstate;ji++)
             fprintf(ficrespij,"\n");              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
           }        }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      }
           fprintf(ficrespij,"\n");  
         }      /* Computing expectancies */
     }      hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
   }      for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++)
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
             eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
   fclose(ficrespij);            
             /* 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]);*/
   /*---------- Forecasting ------------------*/  
           }
   strcpy(fileresf,"f");  
   strcat(fileresf,fileres);      fprintf(ficresstdeij,"%3.0f",age );
   if((ficresf=fopen(fileresf,"w"))==NULL) {      for(i=1; i<=nlstate;i++){
     printf("Problem with forecast resultfile: %s\n", fileresf);goto end;        eip=0.;
   }        vip=0.;
   printf("Computing forecasting: result on file '%s' \n", fileresf);        for(j=1; j<=nlstate;j++){
           eip += eij[i][j][(int)age];
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax, fprevfore, lprevfore);          for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
             vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
  free_matrix(agev,1,maxwav,1,imx);          fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
   /* Mobile average */        }
         fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
   if (cptcoveff==0) ncodemax[cptcoveff]=1;      }
       fprintf(ficresstdeij,"\n");
   if (mobilav==1) {  
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      fprintf(ficrescveij,"%3.0f",age );
     for (agedeb=bage+3; agedeb<=fage-2; agedeb++)      for(i=1; i<=nlstate;i++)
       for (i=1; i<=nlstate;i++)        for(j=1; j<=nlstate;j++){
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)          cptj= (j-1)*nlstate+i;
           mobaverage[(int)agedeb][i][cptcod]=0.;          for(i2=1; i2<=nlstate;i2++)
                for(j2=1; j2<=nlstate;j2++){
     for (agedeb=bage+4; agedeb<=fage; agedeb++){              cptj2= (j2-1)*nlstate+i2;
       for (i=1; i<=nlstate;i++){              if(cptj2 <= cptj)
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){                fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
           for (cpt=0;cpt<=4;cpt++){            }
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];        }
           }      fprintf(ficrescveij,"\n");
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;     
         }    }
       }    free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
     }      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
   }    free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
     free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
   stepsize=(int) (stepm+YEARM-1)/YEARM;    free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   if (stepm<=12) stepsize=1;    free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     printf("\n");
   agelim=AGESUP;    fprintf(ficlog,"\n");
   hstepm=stepsize*YEARM; /* Every year of age */  
   hstepm=hstepm/stepm; /* Typically 2 years, = 2 years/6 months = 4 */    free_vector(xm,1,npar);
     free_vector(xp,1,npar);
    k=0;    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
   for(cptcov=1;cptcov<=i1;cptcov++){    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
       k=k+1;  }
       fprintf(ficresf,"\n#****** ");  
       for(j=1;j<=cptcoveff;j++) {  /************ Variance ******************/
         fprintf(ficresf,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  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[])
       }  {
       fprintf(ficresf,"******\n");    /* Variance of health expectancies */
       fprintf(ficresf,"# StartingAge FinalAge Horizon(in years)");    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);    /* double **newm;*/
     double **dnewm,**doldm;
       for (agedeb=fage; agedeb>=bage; agedeb--){    double **dnewmp,**doldmp;
         fprintf(ficresf,"\n%d %.f %.f 0 ",k,agedeb, agedeb);    int i, j, nhstepm, hstepm, h, nstepm ;
        if (mobilav==1) {    int k, cptcode;
         for(j=1; j<=nlstate;j++)    double *xp;
           fprintf(ficresf," %.5f ",mobaverage[(int)agedeb][j][cptcod]);    double **gp, **gm;  /* for var eij */
         }    double ***gradg, ***trgradg; /*for var eij */
         else {    double **gradgp, **trgradgp; /* for var p point j */
           for(j=1; j<=nlstate;j++)    double *gpp, *gmp; /* for var p point j */
           fprintf(ficresf," %.5f ",probs[(int)agedeb][j][cptcod]);    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
         }      double ***p3mat;
       for(j=1; j<=ndeath;j++) fprintf(ficresf," 0.00000");    double age,agelim, hf;
       }    double ***mobaverage;
       for (cpt=1; cpt<=nforecast;cpt++)      int theta;
       for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */    char digit[4];
            char digitp[25];
         nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);  
         nhstepm = nhstepm/hstepm;    char fileresprobmorprev[FILENAMELENGTH];
         /*printf("agedeb=%.lf stepm=%d hstepm=%d nhstepm=%d \n",agedeb,stepm,hstepm,nhstepm);*/  
     if(popbased==1){
         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      if(mobilav!=0)
         oldm=oldms;savm=savms;        strcpy(digitp,"-populbased-mobilav-");
         hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        else strcpy(digitp,"-populbased-nomobil-");
                    }
         for (h=0; h<=nhstepm; h++){    else 
              strcpy(digitp,"-stablbased-");
          if (h*hstepm/YEARM*stepm==cpt)  
             fprintf(ficresf,"\n%d %.f %.f %.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm, h*hstepm/YEARM*stepm);    if (mobilav!=0) {
                mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
                if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
           for(j=1; j<=nlstate+ndeath;j++) {        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
             kk1=0.;        printf(" Error in movingaverage mobilav=%d\n",mobilav);
             for(i=1; i<=nlstate;i++) {              }
               if (mobilav==1)    }
               kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb][i][cptcod];  
               else kk1=kk1+p3mat[i][j][h]*probs[(int)agedeb][i][cptcod];    strcpy(fileresprobmorprev,"prmorprev"); 
             }        sprintf(digit,"%-d",ij);
           if (h*hstepm/YEARM*stepm==cpt) fprintf(ficresf," %.5f ", kk1);    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
           }    strcat(fileresprobmorprev,digit); /* Tvar to be done */
         }    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    strcat(fileresprobmorprev,fileres);
       }    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
     }      printf("Problem with resultfile: %s\n", fileresprobmorprev);
   }      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    }
   free_imatrix(s,1,maxwav+1,1,n);    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   free_vector(weight,1,n);   
   fclose(ficresf);    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   /*---------- Health expectancies and variances ------------*/    pstamp(ficresprobmorprev);
     fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
   strcpy(filerest,"t");    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
   strcat(filerest,fileres);    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
   if((ficrest=fopen(filerest,"w"))==NULL) {      fprintf(ficresprobmorprev," p.%-d SE",j);
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;      for(i=1; i<=nlstate;i++)
   }        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
   printf("Computing Total LEs with variances: file '%s' \n", filerest);    }  
     fprintf(ficresprobmorprev,"\n");
     fprintf(ficgp,"\n# Routine varevsij");
   strcpy(filerese,"e");    /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
   strcat(filerese,fileres);    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");
   if((ficreseij=fopen(filerese,"w"))==NULL) {    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);  /*   } */
   }    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);    pstamp(ficresvij);
     fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
  strcpy(fileresv,"v");    if(popbased==1)
   strcat(fileresv,fileres);      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);
   if((ficresvij=fopen(fileresv,"w"))==NULL) {    else
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);      fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
   }    fprintf(ficresvij,"# Age");
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++)
   k=0;        fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
   for(cptcov=1;cptcov<=i1;cptcov++){    fprintf(ficresvij,"\n");
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  
       k=k+1;    xp=vector(1,npar);
       fprintf(ficrest,"\n#****** ");    dnewm=matrix(1,nlstate,1,npar);
       for(j=1;j<=cptcoveff;j++)    doldm=matrix(1,nlstate,1,nlstate);
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
       fprintf(ficrest,"******\n");    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   
       fprintf(ficreseij,"\n#****** ");    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
       for(j=1;j<=cptcoveff;j++)    gpp=vector(nlstate+1,nlstate+ndeath);
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);    gmp=vector(nlstate+1,nlstate+ndeath);
       fprintf(ficreseij,"******\n");    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     
       fprintf(ficresvij,"\n#****** ");    if(estepm < stepm){
       for(j=1;j<=cptcoveff;j++)      printf ("Problem %d lower than %d\n",estepm, stepm);
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);    }
       fprintf(ficresvij,"******\n");    else  hstepm=estepm;   
     /* For example we decided to compute the life expectancy with the smallest unit */
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
       oldm=oldms;savm=savms;       nhstepm is the number of hstepm from age to agelim 
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);         nstepm is the number of stepm from age to agelin. 
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);       Look at function hpijx to understand why (it is linked to memory size questions) */
       oldm=oldms;savm=savms;    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);       survival function given by stepm (the optimization length). Unfortunately it
             means that if the survival funtion is printed every two years of age and if
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);       results. So we changed our mind and took the option of the best precision.
       fprintf(ficrest,"\n");    */
            hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
       hf=1;    agelim = AGESUP;
       if (stepm >= YEARM) hf=stepm/YEARM;    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       epj=vector(1,nlstate+1);      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       for(age=bage; age <=fage ;age++){      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         if (popbased==1) {      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
           for(i=1; i<=nlstate;i++)      gp=matrix(0,nhstepm,1,nlstate);
             prlim[i][i]=probs[(int)age][i][k];      gm=matrix(0,nhstepm,1,nlstate);
         }  
          
         fprintf(ficrest," %.0f",age);      for(theta=1; theta <=npar; theta++){
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
           for(i=1, epj[j]=0.;i <=nlstate;i++) {          xp[i] = x[i] + (i==theta ?delti[theta]:0);
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];        }
           }        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
           epj[nlstate+1] +=epj[j];        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         }  
         for(i=1, vepp=0.;i <=nlstate;i++)        if (popbased==1) {
           for(j=1;j <=nlstate;j++)          if(mobilav ==0){
             vepp += vareij[i][j][(int)age];            for(i=1; i<=nlstate;i++)
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));              prlim[i][i]=probs[(int)age][i][ij];
         for(j=1;j <=nlstate;j++){          }else{ /* mobilav */ 
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));            for(i=1; i<=nlstate;i++)
         }              prlim[i][i]=mobaverage[(int)age][i][ij];
         fprintf(ficrest,"\n");          }
       }        }
     }    
   }        for(j=1; j<= nlstate; j++){
                  for(h=0; h<=nhstepm; h++){
                    for(i=1, gp[h][j]=0.;i<=nlstate;i++)
               gp[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
  fclose(ficreseij);        }
  fclose(ficresvij);        /* This for computing probability of death (h=1 means
   fclose(ficrest);           computed over hstepm matrices product = hstepm*stepm months) 
   fclose(ficpar);           as a weighted average of prlim.
   free_vector(epj,1,nlstate+1);        */
   /*  scanf("%d ",i); */        for(j=nlstate+1;j<=nlstate+ndeath;j++){
           for(i=1,gpp[j]=0.; i<= nlstate; i++)
   /*------- Variance limit prevalence------*/              gpp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
 strcpy(fileresvpl,"vpl");        /* end probability of death */
   strcat(fileresvpl,fileres);  
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
     exit(0);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   }        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);   
         if (popbased==1) {
  k=0;          if(mobilav ==0){
  for(cptcov=1;cptcov<=i1;cptcov++){            for(i=1; i<=nlstate;i++)
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){              prlim[i][i]=probs[(int)age][i][ij];
      k=k+1;          }else{ /* mobilav */ 
      fprintf(ficresvpl,"\n#****** ");            for(i=1; i<=nlstate;i++)
      for(j=1;j<=cptcoveff;j++)              prlim[i][i]=mobaverage[(int)age][i][ij];
        fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          }
      fprintf(ficresvpl,"******\n");        }
        
      varpl=matrix(1,nlstate,(int) bage, (int) fage);        for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
      oldm=oldms;savm=savms;          for(h=0; h<=nhstepm; h++){
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
    }              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
  }          }
         }
   fclose(ficresvpl);        /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
   /*---------- End : free ----------------*/           as a weighted average of prlim.
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);        */
          for(j=nlstate+1;j<=nlstate+ndeath;j++){
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);          for(i=1,gmp[j]=0.; i<= nlstate; i++)
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);           gmp[j] += prlim[i][i]*p3mat[i][j][1];
          }    
          /* end probability of death */
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);  
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);        for(j=1; j<= nlstate; j++) /* vareij */
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);          for(h=0; h<=nhstepm; h++){
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
            }
   free_matrix(matcov,1,npar,1,npar);  
   free_vector(delti,1,npar);        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
            gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);        }
   
   printf("End of Imach\n");      } /* End theta */
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */  
        trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/  
   /*printf("Total time was %d uSec.\n", total_usecs);*/      for(h=0; h<=nhstepm; h++) /* veij */
   /*------ End -----------*/        for(j=1; j<=nlstate;j++)
           for(theta=1; theta <=npar; theta++)
             trgradg[h][j][theta]=gradg[h][theta][j];
  end:  
 #ifdef windows      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
  chdir(pathcd);        for(theta=1; theta <=npar; theta++)
 #endif          trgradgp[j][theta]=gradgp[theta][j];
      
  system("..\\gp37mgw\\wgnuplot graph.plt");  
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
 #ifdef windows      for(i=1;i<=nlstate;i++)
   while (z[0] != 'q') {        for(j=1;j<=nlstate;j++)
     chdir(pathcd);          vareij[i][j][(int)age] =0.;
     printf("\nType e to edit output files, c to start again, and q for exiting: ");  
     scanf("%s",z);      for(h=0;h<=nhstepm;h++){
     if (z[0] == 'c') system("./imach");        for(k=0;k<=nhstepm;k++){
     else if (z[0] == 'e') {          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
       chdir(path);          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
       system(optionfilehtm);          for(i=1;i<=nlstate;i++)
     }            for(j=1;j<=nlstate;j++)
     else if (z[0] == 'q') exit(0);              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
   }        }
 #endif      }
 }    
       /* pptj */
       matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
       matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
       for(j=nlstate+1;j<=nlstate+ndeath;j++)
         for(i=nlstate+1;i<=nlstate+ndeath;i++)
           varppt[j][i]=doldmp[j][i];
       /* end ppptj */
       /*  x centered again */
       hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
       prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
    
       if (popbased==1) {
         if(mobilav ==0){
           for(i=1; i<=nlstate;i++)
             prlim[i][i]=probs[(int)age][i][ij];
         }else{ /* mobilav */ 
           for(i=1; i<=nlstate;i++)
             prlim[i][i]=mobaverage[(int)age][i][ij];
         }
       }
                
       /* This for computing probability of death (h=1 means
          computed over hstepm (estepm) matrices product = hstepm*stepm months) 
          as a weighted average of prlim.
       */
       for(j=nlstate+1;j<=nlstate+ndeath;j++){
         for(i=1,gmp[j]=0.;i<= nlstate; i++) 
           gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
       }    
       /* end probability of death */
   
       fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
       for(j=nlstate+1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
         for(i=1; i<=nlstate;i++){
           fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
         }
       } 
       fprintf(ficresprobmorprev,"\n");
   
       fprintf(ficresvij,"%.0f ",age );
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
           fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
         }
       fprintf(ficresvij,"\n");
       free_matrix(gp,0,nhstepm,1,nlstate);
       free_matrix(gm,0,nhstepm,1,nlstate);
       free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
       free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
       free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     } /* End age */
     free_vector(gpp,nlstate+1,nlstate+ndeath);
     free_vector(gmp,nlstate+1,nlstate+ndeath);
     free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
     free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     fprintf(ficgp,"\nunset parametric;unset label; set ter png small;set size 0.65, 0.65");
     /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
     fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
   /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
   /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
   /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
     fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
     fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
     fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
     /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
   */
   /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
     fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
   
     free_vector(xp,1,npar);
     free_matrix(doldm,1,nlstate,1,nlstate);
     free_matrix(dnewm,1,nlstate,1,npar);
     free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
     free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficresprobmorprev);
     fflush(ficgp);
     fflush(fichtm); 
   }  /* end varevsij */
   
   /************ Variance of prevlim ******************/
   void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, char strstart[])
   {
     /* Variance of prevalence limit */
     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
     double **newm;
     double **dnewm,**doldm;
     int i, j, nhstepm, hstepm;
     int k, cptcode;
     double *xp;
     double *gp, *gm;
     double **gradg, **trgradg;
     double age,agelim;
     int theta;
     
     pstamp(ficresvpl);
     fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
     fprintf(ficresvpl,"# Age");
     for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %1d-%1d",i,i);
     fprintf(ficresvpl,"\n");
   
     xp=vector(1,npar);
     dnewm=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
     
     hstepm=1*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
     agelim = AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       if (stepm >= YEARM) hstepm=1;
       nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
       gradg=matrix(1,npar,1,nlstate);
       gp=vector(1,nlstate);
       gm=vector(1,nlstate);
   
       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient */
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=nlstate;i++)
           gp[i] = prlim[i][i];
       
         for(i=1; i<=npar; i++) /* Computes gradient */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=nlstate;i++)
           gm[i] = prlim[i][i];
   
         for(i=1;i<=nlstate;i++)
           gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
       } /* End theta */
   
       trgradg =matrix(1,nlstate,1,npar);
   
       for(j=1; j<=nlstate;j++)
         for(theta=1; theta <=npar; theta++)
           trgradg[j][theta]=gradg[theta][j];
   
       for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] =0.;
       matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
       matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
       for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   
       fprintf(ficresvpl,"%.0f ",age );
       for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
       fprintf(ficresvpl,"\n");
       free_vector(gp,1,nlstate);
       free_vector(gm,1,nlstate);
       free_matrix(gradg,1,npar,1,nlstate);
       free_matrix(trgradg,1,nlstate,1,npar);
     } /* End age */
   
     free_vector(xp,1,npar);
     free_matrix(doldm,1,nlstate,1,npar);
     free_matrix(dnewm,1,nlstate,1,nlstate);
   
   }
   
   /************ Variance of one-step probabilities  ******************/
   void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
   {
     int i, j=0,  i1, k1, l1, t, tj;
     int k2, l2, j1,  z1;
     int k=0,l, cptcode;
     int first=1, first1;
     double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
     double **dnewm,**doldm;
     double *xp;
     double *gp, *gm;
     double **gradg, **trgradg;
     double **mu;
     double age,agelim, cov[NCOVMAX];
     double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
     int theta;
     char fileresprob[FILENAMELENGTH];
     char fileresprobcov[FILENAMELENGTH];
     char fileresprobcor[FILENAMELENGTH];
   
     double ***varpij;
   
     strcpy(fileresprob,"prob"); 
     strcat(fileresprob,fileres);
     if((ficresprob=fopen(fileresprob,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprob);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
     }
     strcpy(fileresprobcov,"probcov"); 
     strcat(fileresprobcov,fileres);
     if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcov);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
     }
     strcpy(fileresprobcor,"probcor"); 
     strcat(fileresprobcor,fileres);
     if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcor);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
     }
     printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     pstamp(ficresprob);
     fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
     fprintf(ficresprob,"# Age");
     pstamp(ficresprobcov);
     fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
     fprintf(ficresprobcov,"# Age");
     pstamp(ficresprobcor);
     fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
     fprintf(ficresprobcor,"# Age");
   
   
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprob," p%1d-%1d (SE)",i,j);
         fprintf(ficresprobcov," p%1d-%1d ",i,j);
         fprintf(ficresprobcor," p%1d-%1d ",i,j);
       }  
    /* fprintf(ficresprob,"\n");
     fprintf(ficresprobcov,"\n");
     fprintf(ficresprobcor,"\n");
    */
     xp=vector(1,npar);
     dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
     varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
     first=1;
     fprintf(ficgp,"\n# Routine varprob");
     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
     fprintf(fichtm,"\n");
   
     fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
     fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
     file %s<br>\n",optionfilehtmcov);
     fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
   and drawn. It helps understanding how is the covariance between two incidences.\
    They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
     fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
   It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
   would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
   standard deviations wide on each axis. <br>\
    Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
    and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
   To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
   
     cov[1]=1;
     tj=cptcoveff;
     if (cptcovn<1) {tj=1;ncodemax[1]=1;}
     j1=0;
     for(t=1; t<=tj;t++){
       for(i1=1; i1<=ncodemax[t];i1++){ 
         j1++;
         if  (cptcovn>0) {
           fprintf(ficresprob, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprob, "**********\n#\n");
           fprintf(ficresprobcov, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcov, "**********\n#\n");
           
           fprintf(ficgp, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficgp, "**********\n#\n");
           
           
           fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
           
           fprintf(ficresprobcor, "\n#********** Variable ");    
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcor, "**********\n#");    
         }
         
         for (age=bage; age<=fage; age ++){ 
           cov[2]=age;
           for (k=1; k<=cptcovn;k++) {
             cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
           }
           for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
           for (k=1; k<=cptcovprod;k++)
             cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
           
           gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
           trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
           gp=vector(1,(nlstate)*(nlstate+ndeath));
           gm=vector(1,(nlstate)*(nlstate+ndeath));
       
           for(theta=1; theta <=npar; theta++){
             for(i=1; i<=npar; i++)
               xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
             
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             
             k=0;
             for(i=1; i<= (nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gp[k]=pmmij[i][j];
               }
             }
             
             for(i=1; i<=npar; i++)
               xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
       
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             k=0;
             for(i=1; i<=(nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gm[k]=pmmij[i][j];
               }
             }
        
             for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
               gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
           }
   
           for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
             for(theta=1; theta <=npar; theta++)
               trgradg[j][theta]=gradg[theta][j];
           
           matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
           matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
           free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
           free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
           free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
           free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   
           pmij(pmmij,cov,ncovmodel,x,nlstate);
           
           k=0;
           for(i=1; i<=(nlstate); i++){
             for(j=1; j<=(nlstate+ndeath);j++){
               k=k+1;
               mu[k][(int) age]=pmmij[i][j];
             }
           }
           for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
             for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
               varpij[i][j][(int)age] = doldm[i][j];
   
           /*printf("\n%d ",(int)age);
             for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             }*/
   
           fprintf(ficresprob,"\n%d ",(int)age);
           fprintf(ficresprobcov,"\n%d ",(int)age);
           fprintf(ficresprobcor,"\n%d ",(int)age);
   
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
             fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
             fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
           }
           i=0;
           for (k=1; k<=(nlstate);k++){
             for (l=1; l<=(nlstate+ndeath);l++){ 
               i=i++;
               fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
               fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
               for (j=1; j<=i;j++){
                 fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
                 fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
               }
             }
           }/* end of loop for state */
         } /* end of loop for age */
   
         /* Confidence intervalle of pij  */
         /*
           fprintf(ficgp,"\nunset parametric;unset label");
           fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
           fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
           fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
           fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
           fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
           fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
         */
   
         /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
         first1=1;
         for (k2=1; k2<=(nlstate);k2++){
           for (l2=1; l2<=(nlstate+ndeath);l2++){ 
             if(l2==k2) continue;
             j=(k2-1)*(nlstate+ndeath)+l2;
             for (k1=1; k1<=(nlstate);k1++){
               for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                 if(l1==k1) continue;
                 i=(k1-1)*(nlstate+ndeath)+l1;
                 if(i<=j) continue;
                 for (age=bage; age<=fage; age ++){ 
                   if ((int)age %5==0){
                     v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                     v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     mu1=mu[i][(int) age]/stepm*YEARM ;
                     mu2=mu[j][(int) age]/stepm*YEARM;
                     c12=cv12/sqrt(v1*v2);
                     /* Computing eigen value of matrix of covariance */
                     lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     /* Eigen vectors */
                     v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                     /*v21=sqrt(1.-v11*v11); *//* error */
                     v21=(lc1-v1)/cv12*v11;
                     v12=-v21;
                     v22=v11;
                     tnalp=v21/v11;
                     if(first1==1){
                       first1=0;
                       printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     }
                     fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     /*printf(fignu*/
                     /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                     /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                     if(first==1){
                       first=0;
                       fprintf(ficgp,"\nset parametric;unset label");
                       fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
                       fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
                       fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
    :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
   %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }else{
                       first=0;
                       fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }/* if first */
                   } /* age mod 5 */
                 } /* end loop age */
                 fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                 first=1;
               } /*l12 */
             } /* k12 */
           } /*l1 */
         }/* k1 */
       } /* loop covariates */
     }
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
     free_vector(xp,1,npar);
     fclose(ficresprob);
     fclose(ficresprobcov);
     fclose(ficresprobcor);
     fflush(ficgp);
     fflush(fichtmcov);
   }
   
   
   /******************* Printing html file ***********/
   void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                     int popforecast, int estepm ,\
                     double jprev1, double mprev1,double anprev1, \
                     double jprev2, double mprev2,double anprev2){
     int jj1, k1, i1, cpt;
   
      fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
      <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
   </ul>");
      fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
    - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
              jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
      fprintf(fichtm,"\
    - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
              stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
      fprintf(fichtm,"\
    - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
              subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
      fprintf(fichtm,"\
    - (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n",
              estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
      fprintf(fichtm,"\
    - Population projections by age and states: \
      <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
   
   fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
    m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        /* Pij */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d1.png\">%s%d1.png</a><br> \
   <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
        /* Quasi-incidences */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
    before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d2.png\">%s%d2.png</a><br> \
   <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
          /* Period (stable) prevalence in each health state */
          for(cpt=1; cpt<nlstate;cpt++){
            fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
   <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
          }
        for(cpt=1; cpt<=nlstate;cpt++) {
           fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
   <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
        }
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
   
   
    fprintf(fichtm,"\
   \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
    - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
   
    fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
    fprintf(fichtm,"\
    - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
   
    fprintf(fichtm,"\
    - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
    fprintf(fichtm,"\
    - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
            estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
    fprintf(fichtm,"\
    - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",
            estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
    fprintf(fichtm,"\
    - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
            subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   
   /*  if(popforecast==1) fprintf(fichtm,"\n */
   /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
   /*      <br>",fileres,fileres,fileres,fileres); */
   /*  else  */
   /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
    fflush(fichtm);
    fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   
    m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        for(cpt=1; cpt<=nlstate;cpt++) {
          fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
   prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
   <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
        }
        fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
   true period expectancies (those weighted with period prevalences are also\
    drawn in addition to the population based expectancies computed using\
    observed and cahotic prevalences: %s%d.png<br>\
   <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
    fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m0,cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
     int ng=0;
   /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   /*     printf("Problem with file %s",optionfilegnuplot); */
   /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   /*   } */
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
     m=pow(2,cptcoveff);
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
    /* 1eme*/
     for (cpt=1; cpt<= nlstate ; cpt ++) {
      for (k1=1; k1<= m ; k1 ++) {
        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
        fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
        fprintf(ficgp,"set xlabel \"Age\" \n\
   set ylabel \"Probability\" \n\
   set ter png small\n\
   set size 0.65,0.65\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else        fprintf(ficgp," \%%*lf (\%%*lf)");
        }
        fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        } 
        fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }  
        fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
      }
     }
     /*2 eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
       fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
       
       for (i=1; i<= nlstate+1 ; i ++) {
         k=2*i;
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         fprintf(ficgp,"\" t\"\" w l 0,");
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
         else fprintf(ficgp,"\" t\"\" w l 0,");
       }
     }
     
     /*3eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<= nlstate ; cpt ++) {
         /*       k=2+nlstate*(2*cpt-2); */
         k=2+(nlstate+1)*(cpt-1);
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
         fprintf(ficgp,"set ter png small\n\
   set size 0.65,0.65\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           
         */
         for (i=1; i< nlstate ; i ++) {
           fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1);
           /*      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
           
         } 
         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
       }
     }
     
     /* CV preval stable (period) */
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<=nlstate ; cpt ++) {
         k=3;
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   set ter png small\nset size 0.65,0.65\n\
   unset log y\n\
   plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
         
         for (i=1; i< nlstate ; i ++)
           fprintf(ficgp,"+$%d",k+i+1);
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
         
         l=3+(nlstate+ndeath)*cpt;
         fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
         for (i=1; i< nlstate ; i ++) {
           l=3+(nlstate+ndeath)*cpt;
           fprintf(ficgp,"+$%d",l+i+1);
         }
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
       } 
     }  
     
     /* proba elementaires */
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             jk++; 
             fprintf(ficgp,"\n");
           }
         }
       }
      }
   
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        for(jk=1; jk <=m; jk++) {
          fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
          if (ng==2)
            fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
          else
            fprintf(ficgp,"\nset title \"Probability\"\n");
          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
          for(k2=1; k2<=nlstate; k2++) {
            k3=i;
            for(k=1; k<=(nlstate+ndeath); k++) {
              if (k != k2){
                if(ng==2)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                else
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;
                for(j=3; j <=ncovmodel; j++) {
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                    fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                    ij++;
                  }
                  else
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
                fprintf(ficgp,")/(1");
                
                for(k1=1; k1 <=nlstate; k1++){   
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
                  for(j=3; j <=ncovmodel; j++){
                    if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                      fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                      ij++;
                    }
                    else
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                  }
                  fprintf(ficgp,")");
                }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
              }
            } /* end k */
          } /* end k2 */
        } /* end jk */
      } /* end ng */
      fflush(ficgp); 
   }  /* end gnuplot */
   
   
   /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
     int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
     double age;
   
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          we use a 5 terms etc. until the borders are no more concerned. 
       */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
           }
         }/* end age */
       }/* end mob */
     }else return -1;
     return 0;
   }/* End movingaverage */
   
   
   /************** Forecasting ******************/
   prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
     int *popage;
     double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   
   
   /**************** function prwizard **********************/
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     /* Wizard to print covariance matrix template */
   
     char ca[32], cb[32], cc[32];
     int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
   } /* end of prwizard */
   /******************* Gompertz Likelihood ******************************/
   double gompertz(double x[])
   { 
     double A,B,L=0.0,sump=0.,num=0.;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
   
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
                +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           L=L+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
    
     return -2*L*num/sump;
   }
   
   /******************* Printing html file ***********/
   void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,  double p[],double **matcov,double agemortsup){
     int i,k;
   
     fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
     fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
     for (i=1;i<=2;i++) 
       fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
     fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
     fprintf(fichtm,"</ul>");
   
   fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
   
    fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
   
    for (k=agegomp;k<(agemortsup-2);k++) 
      fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
   
    
     fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
     fprintf(ficgp,"set out \"graphmort.png\"\n "); 
     fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
     fprintf(ficgp, "set ter png small\n set log y\n"); 
     fprintf(ficgp, "set size 0.65,0.65\n");
     fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
   
   } 
   
   
   
   
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
     int linei, month, year,iout;
     int jj, ll, li, lj, lk, imk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int itimes;
     int NDIM=2;
     int vpopbased=0;
   
     char ca[32], cb[32], cc[32];
     char dummy[]="                         ";
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     struct stat info;
     double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE], pathimach[MAXLINE]; 
     char **bp, *tok, *val; /* pathtot */
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     int agemortsup;
     float  sumlpop=0.;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double *severity;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
     double **ximort;
     char *alph[]={"a","a","b","c","d","e"}, str[4];
     int *dcwave;
   
     char z[1]="c", occ;
   
     char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
     char  *strt, strtend[80];
     char *stratrunc;
     int lstra;
   
     long total_usecs;
    
   /*   setlocale (LC_ALL, ""); */
   /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   /*   textdomain (PACKAGE); */
   /*   setlocale (LC_CTYPE, ""); */
   /*   setlocale (LC_MESSAGES, ""); */
   
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     (void) gettimeofday(&start_time,&tzp);
     curr_time=start_time;
     tm = *localtime(&start_time.tv_sec);
     tmg = *gmtime(&start_time.tv_sec);
     strcpy(strstart,asctime(&tm));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tv_sec = tp.tv_sec +86400; */
   /*  tm = *localtime(&start_time.tv_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tv_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     nberr=0; /* Number of errors and warnings */
     nbwarn=0;
     getcwd(pathcd, size);
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       fgets(pathr,FILENAMELENGTH,stdin);
       i=strlen(pathr);
       if(pathr[i-1]=='\n')
         pathr[i-1]='\0';
      for (tok = pathr; tok != NULL; ){
         printf("Pathr |%s|\n",pathr);
         while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
         printf("val= |%s| pathr=%s\n",val,pathr);
         strcpy (pathtot, val);
         if(pathr[0] == '\0') break; /* Dirty */
       }
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     /* Split argv[0], imach program to get pathimach */
     printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
     split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
     printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
    /*   strcpy(pathimach,argv[0]); */
     /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path); /* Can be a relative path */
     if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
       printf("Current directory %s!\n",pathcd);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s\n%s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: \n");
     fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     printf("Local time (at start):%s",strstart);
     fprintf(ficlog,"Local time (at start): %s",strstart);
     fflush(ficlog);
   /*   (void) gettimeofday(&curr_time,&tzp); */
   /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile %s\n",optionfile);
       fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       fflush(ficlog);
       goto end;
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n); 
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
     if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
   
     ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
     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;
       }
   
       for (j=maxwav;j>=1;j--){
         cutv(stra, strb,line,' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
         /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
             fprintf(ficlog,"Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);
             goto end;
           }
         }
         s[j][i]=lval;
         
         strcpy(line,stra);
         cutv(stra, strb,line,' ');
         if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
         }
         else  if(iout=sscanf(strb,"%s.") != 0){
           month=99;
           year=9999;
         }else{
           printf("Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
           fprintf(ficlog,"Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);fflush(ficlog);
           goto end;
         }
         anint[j][i]= (double) year; 
         mint[j][i]= (double)month; 
         strcpy(line,stra);
       } /* ENd Waves */
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.",dummy) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
           fprintf(ficlog,"Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
           goto end;
       }
       andc[i]=(double) year; 
       moisdc[i]=(double) month; 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.") != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line,j);
         fprintf(ficlog,"Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line,j);fflush(ficlog);
           goto end;
       }
       annais[i]=(double)(year);
       moisnais[i]=(double)(month); 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       errno=0;
       dval=strtod(strb,&endptr); 
       if( strb[0]=='\0' || (*endptr != '\0')){
         printf("Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fprintf(ficlog,"Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fflush(ficlog);
         goto end;
       }
       weight[i]=dval; 
       strcpy(line,stra);
       
       for (j=ncovcol;j>=1;j--){
         cutv(stra, strb,line,' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);
             fprintf(ficlog,"Error reading data around '%d' at line number %ld for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);fflush(ficlog);
             goto end;
           }
         }
         if(lval <-1 || lval >1){
           printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);
           fprintf(ficlog,"Error reading data around '%d' at line number %ld for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
           goto end;
         }
         covar[j][i]=(double)(lval);
         strcpy(line,stra);
       }  
       lstra=strlen(stra);
        
       if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
         stratrunc = &(stra[lstra-9]);
         num[i]=atol(stratrunc);
       }
       else
         num[i]=atol(stra);
       /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
         printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
       
       i=i+1;
     } /* End loop reading  data */
     fclose(fic);
     /* printf("ii=%d", ij);
        scanf("%d",i);*/
     imx=i-1; /* Number of individuals */
   
     /* for (i=1; i<=imx; i++){
       if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
       if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
       if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
       }*/
      /*  for (i=1; i<=imx; i++){
        if (s[4][i]==9)  s[4][i]=-1; 
        printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
     
     /* for (i=1; i<=imx; i++) */
    
      /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
        else weight[i]=1;*/
   
     /* Calculation of the number of parameters from char model */
     Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. Stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
     Tprod=ivector(1,15); 
     Tvaraff=ivector(1,15); 
     Tvard=imatrix(1,15,1,2);
     Tage=ivector(1,15);      
      
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=1, k2=1;
       j=nbocc(model,'+'); /* j=Number of '+' */
       j1=nbocc(model,'*'); /* j1=Number of '*' */
       cptcovn=j+1; /* Number of covariates V1+V2+V3 =>2+1=3 */
       cptcovprod=j1; /*Number of products  V1*V2 =1 */
       
       strcpy(modelsav,model); 
       if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
         printf("Error. Non available option model=%s ",model);
         fprintf(ficlog,"Error. Non available option model=%s ",model);fflush(ficlog);
         goto end;
       }
       
       /* This loop fills the array Tvar from the string 'model'.*/
       /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
       for(i=(j+1); i>=1;i--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' 
                                        modelsav=V2+V3*age+V1+V4 strb=V3*age+V1+V4 
                                        stra=V2
                                       */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /* Model includes a product V1+V3*age+V2 strb=V3*age*/
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn: V3*age strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
           if (strcmp(strc,"age")==0) { /* Vn*age */
             cptcovprod--;
             cutv(strb,stre,strd,'V');
             Tvar[i]=atoi(stre);  /* V1+V3*age+V2 Tvar[2]=3 */
             cptcovage++; /* Sum the number of covariates including ages 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=1;/* debug */
       /*    likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone);*/ /* Prints the contributions to the likelihood */
       printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       globpr=1; /* to print the contributions */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       if(mle>=1){ /* Could be 1 or 2 */
         mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
       }
       
       /*--------- results files --------------*/
       fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
       
       
       fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(k=1; k <=(nlstate+ndeath); k++){
           if (k != i) {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%lf ",p[jk]);
               fprintf(ficlog,"%lf ",p[jk]);
               fprintf(ficres,"%lf ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       if(mle!=0){
         /* Computing hessian and covariance matrix */
         ftolhess=ftol; /* Usually correct */
         hesscov(matcov, p, npar, delti, ftolhess, func);
       }
       fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
       printf("# Scales (for hessian or gradient estimation)\n");
       fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if (j!=i) {
             fprintf(ficres,"%1d%1d",i,j);
             printf("%1d%1d",i,j);
             fprintf(ficlog,"%1d%1d",i,j);
             for(k=1; k<=ncovmodel;k++){
               printf(" %.5e",delti[jk]);
               fprintf(ficlog," %.5e",delti[jk]);
               fprintf(ficres," %.5e",delti[jk]);
               jk++;
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       
       fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       if(mle>=1)
         printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       /* # 121 Var(a12)\n\ */
       /* # 122 Cov(b12,a12) Var(b12)\n\ */
       /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
       /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
       /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
       /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
       /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
       /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
       
       
       /* Just to have a covariance matrix which will be more understandable
          even is we still don't want to manage dictionary of variables
       */
       for(itimes=1;itimes<=2;itimes++){
         jj=0;
         for(i=1; i <=nlstate; i++){
           for(j=1; j <=nlstate+ndeath; j++){
             if(j==i) continue;
             for(k=1; k<=ncovmodel;k++){
               jj++;
               ca[0]= k+'a'-1;ca[1]='\0';
               if(itimes==1){
                 if(mle>=1)
                   printf("#%1d%1d%d",i,j,k);
                 fprintf(ficlog,"#%1d%1d%d",i,j,k);
                 fprintf(ficres,"#%1d%1d%d",i,j,k);
               }else{
                 if(mle>=1)
                   printf("%1d%1d%d",i,j,k);
                 fprintf(ficlog,"%1d%1d%d",i,j,k);
                 fprintf(ficres,"%1d%1d%d",i,j,k);
               }
               ll=0;
               for(li=1;li <=nlstate; li++){
                 for(lj=1;lj <=nlstate+ndeath; lj++){
                   if(lj==li) continue;
                   for(lk=1;lk<=ncovmodel;lk++){
                     ll++;
                     if(ll<=jj){
                       cb[0]= lk +'a'-1;cb[1]='\0';
                       if(ll<jj){
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }else{
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }
                     }
                   } /* end lk */
                 } /* end lj */
               } /* end li */
               if(mle>=1)
                 printf("\n");
               fprintf(ficlog,"\n");
               fprintf(ficres,"\n");
               numlinepar++;
             } /* end k*/
           } /*end j */
         } /* end i */
       } /* end itimes */
       
       fflush(ficlog);
       fflush(ficres);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       estepm=0;
       fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
       if (estepm==0 || estepm < stepm) estepm=stepm;
       if (fage <= 2) {
         bage = ageminpar;
         fage = agemaxpar;
       }
       
       fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
       fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
       fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       
       dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
       dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
       
       fscanf(ficpar,"pop_based=%d\n",&popbased);
       fprintf(ficparo,"pop_based=%d\n",popbased);   
       fprintf(ficres,"pop_based=%d\n",popbased);   
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
       fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       /* day and month of proj2 are not used but only year anproj2.*/
       
       
       
       /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
       /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                    model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                    jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
         
      /*------------ free_vector  -------------*/
      /*  chdir(path); */
    
       free_ivector(wav,1,imx);
       free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
       free_lvector(num,1,n);
       free_vector(agedc,1,n);
       /*free_matrix(covar,0,NCOVMAX,1,n);*/
       /*free_matrix(covar,1,NCOVMAX,1,n);*/
       fclose(ficparo);
       fclose(ficres);
   
   
       /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
     
       strcpy(filerespl,"pl");
       strcat(filerespl,fileres);
       if((ficrespl=fopen(filerespl,"w"))==NULL) {
         printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
         fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
       }
       printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
       fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
       pstamp(ficrespl);
       fprintf(ficrespl,"# Period (stable) prevalence \n");
       fprintf(ficrespl,"#Age ");
       for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
       fprintf(ficrespl,"\n");
     
       prlim=matrix(1,nlstate,1,nlstate);
   
       agebase=ageminpar;
       agelim=agemaxpar;
       ftolpl=1.e-10;
       i1=cptcoveff;
       if (cptcovn < 1){i1=1;}
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           /* to clean */
           printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,codtab[cptcod][cptcov],nbcode);
           fprintf(ficrespl,"\n#******");
           printf("\n#******");
           fprintf(ficlog,"\n#******");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficrespl,"******\n");
           printf("******\n");
           fprintf(ficlog,"******\n");
           
           for (age=agebase; age<=agelim; age++){
             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
             fprintf(ficrespl,"%.0f ",age );
             for(j=1;j<=cptcoveff;j++)
               fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             for(i=1; i<=nlstate;i++)
               fprintf(ficrespl," %.5f", prlim[i][i]);
             fprintf(ficrespl,"\n");
           }
         }
       }
       fclose(ficrespl);
   
       /*------------- h Pij x at various ages ------------*/
     
       strcpy(filerespij,"pij");  strcat(filerespij,fileres);
       if((ficrespij=fopen(filerespij,"w"))==NULL) {
         printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
         fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
       }
       printf("Computing pij: result on file '%s' \n", filerespij);
       fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
       stepsize=(int) (stepm+YEARM-1)/YEARM;
       /*if (stepm<=24) stepsize=2;*/
   
       agelim=AGESUP;
       hstepm=stepsize*YEARM; /* Every year of age */
       hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
       /* hstepm=1;   aff par mois*/
       pstamp(ficrespij);
       fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           fprintf(ficrespij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrespij,"******\n");
           
           for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
             nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   
             /*      nhstepm=nhstepm*YEARM; aff par mois*/
   
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %1d-%1d",i,j);
             fprintf(ficrespij,"\n");
             for (h=0; h<=nhstepm; h++){
               fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
               for(i=1; i<=nlstate;i++)
                 for(j=1; j<=nlstate+ndeath;j++)
                   fprintf(ficrespij," %.5f", p3mat[i][j][h]);
               fprintf(ficrespij,"\n");
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             fprintf(ficrespij,"\n");
           }
         }
       }
   
       varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
   
       fclose(ficrespij);
   
       probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for(i=1;i<=AGESUP;i++)
         for(j=1;j<=NCOVMAX;j++)
           for(k=1;k<=NCOVMAX;k++)
             probs[i][j][k]=0.;
   
       /*---------- Forecasting ------------------*/
       /*if((stepm == 1) && (strcmp(model,".")==0)){*/
       if(prevfcast==1){
         /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
         /*      }  */
         /*      else{ */
         /*        erreur=108; */
         /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*      } */
       }
     
   
       /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
   
       prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
       /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
           ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
       */
   
       if (mobilav!=0) {
         mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
           fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
           printf(" Error in movingaverage mobilav=%d\n",mobilav);
         }
       }
   
   
       /*---------- Health expectancies, no variances ------------*/
   
       strcpy(filerese,"e");
       strcat(filerese,fileres);
       if((ficreseij=fopen(filerese,"w"))==NULL) {
         printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
         fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       }
       printf("Computing Health Expectancies: result on file '%s' \n", filerese);
       fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1; 
           fprintf(ficreseij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficreseij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);  
         
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         }
       }
       fclose(ficreseij);
   
   
       /*---------- Health expectancies and variances ------------*/
   
   
       strcpy(filerest,"t");
       strcat(filerest,fileres);
       if((ficrest=fopen(filerest,"w"))==NULL) {
         printf("Problem with total LE resultfile: %s\n", filerest);goto end;
         fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
       }
       printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
       fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
   
   
       strcpy(fileresstde,"stde");
       strcat(fileresstde,fileres);
       if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
         printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
         fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
       }
       printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
       fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
   
       strcpy(filerescve,"cve");
       strcat(filerescve,fileres);
       if((ficrescveij=fopen(filerescve,"w"))==NULL) {
         printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
         fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
       }
       printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
       fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
   
       strcpy(fileresv,"v");
       strcat(fileresv,fileres);
       if((ficresvij=fopen(fileresv,"w"))==NULL) {
         printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
         fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
       }
       printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
       fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1; 
           fprintf(ficrest,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrest,"******\n");
   
           fprintf(ficresstdeij,"\n#****** ");
           fprintf(ficrescveij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficresstdeij,"******\n");
           fprintf(ficrescveij,"******\n");
   
           fprintf(ficresvij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);  
    
           vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           pstamp(ficrest);
           for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
             oldm=oldms;savm=savms;
             varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart);   fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");
             if(vpopbased==1)
               fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
             else
               fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
             fprintf(ficrest,"# Age e.. (std) ");
             for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
             fprintf(ficrest,"\n");
   
             epj=vector(1,nlstate+1);
             for(age=bage; age <=fage ;age++){
               prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
               if (vpopbased==1) {
                 if(mobilav ==0){
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=probs[(int)age][i][k];
                 }else{ /* mobilav */ 
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=mobaverage[(int)age][i][k];
                 }
               }
           
               fprintf(ficrest," %4.0f",age);
               for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
                 for(i=1, epj[j]=0.;i <=nlstate;i++) {
                   epj[j] += prlim[i][i]*eij[i][j][(int)age];
                   /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
                 }
                 epj[nlstate+1] +=epj[j];
               }
   
               for(i=1, vepp=0.;i <=nlstate;i++)
                 for(j=1;j <=nlstate;j++)
                   vepp += vareij[i][j][(int)age];
               fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
               for(j=1;j <=nlstate;j++){
                 fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
               }
               fprintf(ficrest,"\n");
             }
           }
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_vector(epj,1,nlstate+1);
         }
       }
       free_vector(weight,1,n);
       free_imatrix(Tvard,1,15,1,2);
       free_imatrix(s,1,maxwav+1,1,n);
       free_matrix(anint,1,maxwav,1,n); 
       free_matrix(mint,1,maxwav,1,n);
       free_ivector(cod,1,n);
       free_ivector(tab,1,NCOVMAX);
       fclose(ficresstdeij);
       fclose(ficrescveij);
       fclose(ficresvij);
       fclose(ficrest);
       fclose(ficpar);
     
       /*------- Variance of period (stable) prevalence------*/   
   
       strcpy(fileresvpl,"vpl");
       strcat(fileresvpl,fileres);
       if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
         printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
         exit(0);
       }
       printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           fprintf(ficresvpl,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvpl,"******\n");
         
           varpl=matrix(1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
           free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
         }
       }
   
       fclose(ficresvpl);
   
       /*---------- End : free ----------------*/
       if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     }  /* mle==-3 arrives here for freeing */
    endfree:
     free_matrix(prlim,1,nlstate,1,nlstate);
       free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(covar,0,NCOVMAX,1,n);
       free_matrix(matcov,1,npar,1,npar);
       /*free_vector(delti,1,npar);*/
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       free_matrix(agev,1,maxwav,1,imx);
       free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   
       free_ivector(ncodemax,1,8);
       free_ivector(Tvar,1,15);
       free_ivector(Tprod,1,15);
       free_ivector(Tvaraff,1,15);
       free_ivector(Tage,1,15);
   
       free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
       free_imatrix(codtab,1,100,1,10);
     fflush(fichtm);
     fflush(ficgp);
     
   
     if((nberr >0) || (nbwarn>0)){
       printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
       fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
     }else{
       printf("End of Imach\n");
       fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     (void) gettimeofday(&end_time,&tzp);
     tm = *localtime(&end_time.tv_sec);
     tmg = *gmtime(&end_time.tv_sec);
     strcpy(strtend,asctime(&tm));
     printf("Local time at start %s\nLocal time at end   %s",strstart, strtend); 
     fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
     printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
   
     printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
     fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
     fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
     /*  printf("Total time was %d uSec.\n", total_usecs);*/
   /*   if(fileappend(fichtm,optionfilehtm)){ */
     fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtm);
     fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtmcov);
     fclose(ficgp);
     fclose(ficlog);
     /*------ End -----------*/
   
   
      printf("Before Current directory %s!\n",pathcd);
      if(chdir(pathcd) != 0)
       printf("Can't move to directory %s!\n",path);
     if(getcwd(pathcd,MAXLINE) > 0)
       printf("Current directory %s!\n",pathcd);
     /*strcat(plotcmd,CHARSEPARATOR);*/
     sprintf(plotcmd,"gnuplot");
   #ifndef UNIX
     sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
   #endif
     if(!stat(plotcmd,&info)){
       printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
       if(!stat(getenv("GNUPLOTBIN"),&info)){
         printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #ifdef UNIX
       strcpy(plotcmd,GNUPLOTPROGRAM);
       if(!stat(plotcmd,&info)){
         printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #endif
     }else
       strcpy(pplotcmd,plotcmd);
     
     sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
     printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
   
     if((outcmd=system(plotcmd)) != 0){
       printf("\n Problem with gnuplot\n");
     }
     printf(" Wait...");
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again and q for exiting: ");
       scanf("%s",z);
   /*     if (z[0] == 'c') system("./imach"); */
       if (z[0] == 'e') {
         printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
         system(optionfilehtm);
       }
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     end:
     while (z[0] != 'q') {
       printf("\nType  q for exiting: ");
       scanf("%s",z);
     }
   }
   
   
   
Removed from v.1.15  
changed lines
  Added in v.1.131

FreeBSD-CVSweb <freebsd-cvsweb@FreeBSD.org>