Diff for /imach/src/imach.c between versions 1.42 and 1.133

version 1.42, 2002/05/21 18:44:41 version 1.133, 2009/07/06 10:21:25
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.133  2009/07/06 10:21:25  brouard
      just nforces
   This program computes Healthy Life Expectancies from  
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    Revision 1.132  2009/07/06 08:22:05  brouard
   first survey ("cross") where individuals from different ages are    Many tings
   interviewed on their health status or degree of disability (in the  
   case of a health survey which is our main interest) -2- at least a    Revision 1.131  2009/06/20 16:22:47  brouard
   second wave of interviews ("longitudinal") which measure each change    Some dimensions resccaled
   (if any) in individual health status.  Health expectancies are  
   computed from the time spent in each health state according to a    Revision 1.130  2009/05/26 06:44:34  brouard
   model. More health states you consider, more time is necessary to reach the    (Module): Max Covariate is now set to 20 instead of 8. A
   Maximum Likelihood of the parameters involved in the model.  The    lot of cleaning with variables initialized to 0. Trying to make
   simplest model is the multinomial logistic model where pij is the    V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
   probability to be observed in state j at the second wave  
   conditional to be observed in state i at the first wave. Therefore    Revision 1.129  2007/08/31 13:49:27  lievre
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
   'age' is age and 'sex' is a covariate. If you want to have a more  
   complex model than "constant and age", you should modify the program    Revision 1.128  2006/06/30 13:02:05  brouard
   where the markup *Covariates have to be included here again* invites    (Module): Clarifications on computing e.j
   you to do it.  More covariates you add, slower the  
   convergence.    Revision 1.127  2006/04/28 18:11:50  brouard
     (Module): Yes the sum of survivors was wrong since
   The advantage of this computer programme, compared to a simple    imach-114 because nhstepm was no more computed in the age
   multinomial logistic model, is clear when the delay between waves is not    loop. Now we define nhstepma in the age loop.
   identical for each individual. Also, if a individual missed an    (Module): In order to speed up (in case of numerous covariates) we
   intermediate interview, the information is lost, but taken into    compute health expectancies (without variances) in a first step
   account using an interpolation or extrapolation.      and then all the health expectancies with variances or standard
     deviation (needs data from the Hessian matrices) which slows the
   hPijx is the probability to be observed in state i at age x+h    computation.
   conditional to the observed state i at age x. The delay 'h' can be    In the future we should be able to stop the program is only health
   split into an exact number (nh*stepm) of unobserved intermediate    expectancies and graph are needed without standard deviations.
   states. This elementary transition (by month or quarter trimester,  
   semester or year) is model as a multinomial logistic.  The hPx    Revision 1.126  2006/04/28 17:23:28  brouard
   matrix is simply the matrix product of nh*stepm elementary matrices    (Module): Yes the sum of survivors was wrong since
   and the contribution of each individual to the likelihood is simply    imach-114 because nhstepm was no more computed in the age
   hPijx.    loop. Now we define nhstepma in the age loop.
     Version 0.98h
   Also this programme outputs the covariance matrix of the parameters but also  
   of the life expectancies. It also computes the prevalence limits.    Revision 1.125  2006/04/04 15:20:31  lievre
      Errors in calculation of health expectancies. Age was not initialized.
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    Forecasting file added.
            Institut national d'études démographiques, Paris.  
   This software have been partly granted by Euro-REVES, a concerted action    Revision 1.124  2006/03/22 17:13:53  lievre
   from the European Union.    Parameters are printed with %lf instead of %f (more numbers after the comma).
   It is copyrighted identically to a GNU software product, ie programme and    The log-likelihood is printed in the log file
   software can be distributed freely for non commercial use. Latest version  
   can be accessed at http://euroreves.ined.fr/imach .    Revision 1.123  2006/03/20 10:52:43  brouard
   **********************************************************************/    * imach.c (Module): <title> changed, corresponds to .htm file
      name. <head> headers where missing.
 #include <math.h>  
 #include <stdio.h>    * imach.c (Module): Weights can have a decimal point as for
 #include <stdlib.h>    English (a comma might work with a correct LC_NUMERIC environment,
 #include <unistd.h>    otherwise the weight is truncated).
     Modification of warning when the covariates values are not 0 or
 #define MAXLINE 256    1.
 #define GNUPLOTPROGRAM "gnuplot"    Version 0.98g
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/  
 #define FILENAMELENGTH 80    Revision 1.122  2006/03/20 09:45:41  brouard
 /*#define DEBUG*/    (Module): Weights can have a decimal point as for
 #define windows    English (a comma might work with a correct LC_NUMERIC environment,
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    otherwise the weight is truncated).
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    Modification of warning when the covariates values are not 0 or
     1.
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    Version 0.98g
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */  
     Revision 1.121  2006/03/16 17:45:01  lievre
 #define NINTERVMAX 8    * imach.c (Module): Comments concerning covariates added
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */  
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    * imach.c (Module): refinements in the computation of lli if
 #define NCOVMAX 8 /* Maximum number of covariates */    status=-2 in order to have more reliable computation if stepm is
 #define MAXN 20000    not 1 month. Version 0.98f
 #define YEARM 12. /* Number of months per year */  
 #define AGESUP 130    Revision 1.120  2006/03/16 15:10:38  lievre
 #define AGEBASE 40    (Module): refinements in the computation of lli if
     status=-2 in order to have more reliable computation if stepm is
     not 1 month. Version 0.98f
 int erreur; /* Error number */  
 int nvar;    Revision 1.119  2006/03/15 17:42:26  brouard
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    (Module): Bug if status = -2, the loglikelihood was
 int npar=NPARMAX;    computed as likelihood omitting the logarithm. Version O.98e
 int nlstate=2; /* Number of live states */  
 int ndeath=1; /* Number of dead states */    Revision 1.118  2006/03/14 18:20:07  brouard
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    (Module): varevsij Comments added explaining the second
 int popbased=0;    table of variances if popbased=1 .
     (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 int *wav; /* Number of waves for this individuual 0 is possible */    (Module): Function pstamp added
 int maxwav; /* Maxim number of waves */    (Module): Version 0.98d
 int jmin, jmax; /* min, max spacing between 2 waves */  
 int mle, weightopt;    Revision 1.117  2006/03/14 17:16:22  brouard
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    (Module): varevsij Comments added explaining the second
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    table of variances if popbased=1 .
 double jmean; /* Mean space between 2 waves */    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 double **oldm, **newm, **savm; /* Working pointers to matrices */    (Module): Function pstamp added
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    (Module): Version 0.98d
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;  
 FILE *ficgp,*ficresprob,*ficpop;    Revision 1.116  2006/03/06 10:29:27  brouard
 FILE *ficreseij;    (Module): Variance-covariance wrong links and
   char filerese[FILENAMELENGTH];    varian-covariance of ej. is needed (Saito).
  FILE  *ficresvij;  
   char fileresv[FILENAMELENGTH];    Revision 1.115  2006/02/27 12:17:45  brouard
  FILE  *ficresvpl;    (Module): One freematrix added in mlikeli! 0.98c
   char fileresvpl[FILENAMELENGTH];  
     Revision 1.114  2006/02/26 12:57:58  brouard
 #define NR_END 1    (Module): Some improvements in processing parameter
 #define FREE_ARG char*    filename with strsep.
 #define FTOL 1.0e-10  
     Revision 1.113  2006/02/24 14:20:24  brouard
 #define NRANSI    (Module): Memory leaks checks with valgrind and:
 #define ITMAX 200    datafile was not closed, some imatrix were not freed and on matrix
     allocation too.
 #define TOL 2.0e-4  
     Revision 1.112  2006/01/30 09:55:26  brouard
 #define CGOLD 0.3819660    (Module): Back to gnuplot.exe instead of wgnuplot.exe
 #define ZEPS 1.0e-10  
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    Revision 1.111  2006/01/25 20:38:18  brouard
     (Module): Lots of cleaning and bugs added (Gompertz)
 #define GOLD 1.618034    (Module): Comments can be added in data file. Missing date values
 #define GLIMIT 100.0    can be a simple dot '.'.
 #define TINY 1.0e-20  
     Revision 1.110  2006/01/25 00:51:50  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))  
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    Revision 1.109  2006/01/24 19:37:15  brouard
      (Module): Comments (lines starting with a #) are allowed in data.
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  
 #define rint(a) floor(a+0.5)    Revision 1.108  2006/01/19 18:05:42  lievre
     Gnuplot problem appeared...
 static double sqrarg;    To be fixed
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    Revision 1.107  2006/01/19 16:20:37  brouard
     Test existence of gnuplot in imach path
 int imx;  
 int stepm;    Revision 1.106  2006/01/19 13:24:36  brouard
 /* Stepm, step in month: minimum step interpolation*/    Some cleaning and links added in html output
   
 int estepm;    Revision 1.105  2006/01/05 20:23:19  lievre
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/    *** empty log message ***
   
 int m,nb;    Revision 1.104  2005/09/30 16:11:43  lievre
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    (Module): sump fixed, loop imx fixed, and simplifications.
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    (Module): If the status is missing at the last wave but we know
 double **pmmij, ***probs, ***mobaverage;    that the person is alive, then we can code his/her status as -2
 double dateintmean=0;    (instead of missing=-1 in earlier versions) and his/her
     contributions to the likelihood is 1 - Prob of dying from last
 double *weight;    health status (= 1-p13= p11+p12 in the easiest case of somebody in
 int **s; /* Status */    the healthy state at last known wave). Version is 0.98
 double *agedc, **covar, idx;  
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    Revision 1.103  2005/09/30 15:54:49  lievre
     (Module): sump fixed, loop imx fixed, and simplifications.
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  
 double ftolhess; /* Tolerance for computing hessian */    Revision 1.102  2004/09/15 17:31:30  brouard
     Add the possibility to read data file including tab characters.
 /**************** split *************************/  
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    Revision 1.101  2004/09/15 10:38:38  brouard
 {    Fix on curr_time
    char *s;                             /* pointer */  
    int  l1, l2;                         /* length counters */    Revision 1.100  2004/07/12 18:29:06  brouard
     Add version for Mac OS X. Just define UNIX in Makefile
    l1 = strlen( path );                 /* length of path */  
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    Revision 1.99  2004/06/05 08:57:40  brouard
 #ifdef windows    *** empty log message ***
    s = strrchr( path, '\\' );           /* find last / */  
 #else    Revision 1.98  2004/05/16 15:05:56  brouard
    s = strrchr( path, '/' );            /* find last / */    New version 0.97 . First attempt to estimate force of mortality
 #endif    directly from the data i.e. without the need of knowing the health
    if ( s == NULL ) {                   /* no directory, so use current */    state at each age, but using a Gompertz model: log u =a + b*age .
 #if     defined(__bsd__)                /* get current working directory */    This is the basic analysis of mortality and should be done before any
       extern char       *getwd( );    other analysis, in order to test if the mortality estimated from the
     cross-longitudinal survey is different from the mortality estimated
       if ( getwd( dirc ) == NULL ) {    from other sources like vital statistic data.
 #else  
       extern char       *getcwd( );    The same imach parameter file can be used but the option for mle should be -3.
   
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    Agnès, who wrote this part of the code, tried to keep most of the
 #endif    former routines in order to include the new code within the former code.
          return( GLOCK_ERROR_GETCWD );  
       }    The output is very simple: only an estimate of the intercept and of
       strcpy( name, path );             /* we've got it */    the slope with 95% confident intervals.
    } else {                             /* strip direcotry from path */  
       s++;                              /* after this, the filename */    Current limitations:
       l2 = strlen( s );                 /* length of filename */    A) Even if you enter covariates, i.e. with the
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
       strcpy( name, s );                /* save file name */    B) There is no computation of Life Expectancy nor Life Table.
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  
       dirc[l1-l2] = 0;                  /* add zero */    Revision 1.97  2004/02/20 13:25:42  lievre
    }    Version 0.96d. Population forecasting command line is (temporarily)
    l1 = strlen( dirc );                 /* length of directory */    suppressed.
 #ifdef windows  
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    Revision 1.96  2003/07/15 15:38:55  brouard
 #else    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }    rewritten within the same printf. Workaround: many printfs.
 #endif  
    s = strrchr( name, '.' );            /* find last / */    Revision 1.95  2003/07/08 07:54:34  brouard
    s++;    * imach.c (Repository):
    strcpy(ext,s);                       /* save extension */    (Repository): Using imachwizard code to output a more meaningful covariance
    l1= strlen( name);    matrix (cov(a12,c31) instead of numbers.
    l2= strlen( s)+1;  
    strncpy( finame, name, l1-l2);    Revision 1.94  2003/06/27 13:00:02  brouard
    finame[l1-l2]= 0;    Just cleaning
    return( 0 );                         /* we're done */  
 }    Revision 1.93  2003/06/25 16:33:55  brouard
     (Module): On windows (cygwin) function asctime_r doesn't
     exist so I changed back to asctime which exists.
 /******************************************/    (Module): Version 0.96b
   
 void replace(char *s, char*t)    Revision 1.92  2003/06/25 16:30:45  brouard
 {    (Module): On windows (cygwin) function asctime_r doesn't
   int i;    exist so I changed back to asctime which exists.
   int lg=20;  
   i=0;    Revision 1.91  2003/06/25 15:30:29  brouard
   lg=strlen(t);    * imach.c (Repository): Duplicated warning errors corrected.
   for(i=0; i<= lg; i++) {    (Repository): Elapsed time after each iteration is now output. It
     (s[i] = t[i]);    helps to forecast when convergence will be reached. Elapsed time
     if (t[i]== '\\') s[i]='/';    is stamped in powell.  We created a new html file for the graphs
   }    concerning matrix of covariance. It has extension -cov.htm.
 }  
     Revision 1.90  2003/06/24 12:34:15  brouard
 int nbocc(char *s, char occ)    (Module): Some bugs corrected for windows. Also, when
 {    mle=-1 a template is output in file "or"mypar.txt with the design
   int i,j=0;    of the covariance matrix to be input.
   int lg=20;  
   i=0;    Revision 1.89  2003/06/24 12:30:52  brouard
   lg=strlen(s);    (Module): Some bugs corrected for windows. Also, when
   for(i=0; i<= lg; i++) {    mle=-1 a template is output in file "or"mypar.txt with the design
   if  (s[i] == occ ) j++;    of the covariance matrix to be input.
   }  
   return j;    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.
   
 void cutv(char *u,char *v, char*t, char occ)    Revision 1.87  2003/06/18 12:26:01  brouard
 {    Version 0.96
   int i,lg,j,p=0;  
   i=0;    Revision 1.86  2003/06/17 20:04:08  brouard
   for(j=0; j<=strlen(t)-1; j++) {    (Module): Change position of html and gnuplot routines and added
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    routine fileappend.
   }  
     Revision 1.85  2003/06/17 13:12:43  brouard
   lg=strlen(t);    * imach.c (Repository): Check when date of death was earlier that
   for(j=0; j<p; j++) {    current date of interview. It may happen when the death was just
     (u[j] = t[j]);    prior to the death. In this case, dh was negative and likelihood
   }    was wrong (infinity). We still send an "Error" but patch by
      u[p]='\0';    assuming that the date of death was just one stepm after the
     interview.
    for(j=0; j<= lg; j++) {    (Repository): Because some people have very long ID (first column)
     if (j>=(p+1))(v[j-p-1] = t[j]);    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)
     (Repository): No more line truncation errors.
 /********************** nrerror ********************/  
     Revision 1.84  2003/06/13 21:44:43  brouard
 void nrerror(char error_text[])    * imach.c (Repository): Replace "freqsummary" at a correct
 {    place. It differs from routine "prevalence" which may be called
   fprintf(stderr,"ERREUR ...\n");    many times. Probs is memory consuming and must be used with
   fprintf(stderr,"%s\n",error_text);    parcimony.
   exit(1);    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
 }  
 /*********************** vector *******************/    Revision 1.83  2003/06/10 13:39:11  lievre
 double *vector(int nl, int nh)    *** empty log message ***
 {  
   double *v;    Revision 1.82  2003/06/05 15:57:20  brouard
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    Add log in  imach.c and  fullversion number is now printed.
   if (!v) nrerror("allocation failure in vector");  
   return v-nl+NR_END;  */
 }  /*
      Interpolated Markov Chain
 /************************ free vector ******************/  
 void free_vector(double*v, int nl, int nh)    Short summary of the programme:
 {    
   free((FREE_ARG)(v+nl-NR_END));    This program computes Healthy Life Expectancies from
 }    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
     first survey ("cross") where individuals from different ages are
 /************************ivector *******************************/    interviewed on their health status or degree of disability (in the
 int *ivector(long nl,long nh)    case of a health survey which is our main interest) -2- at least a
 {    second wave of interviews ("longitudinal") which measure each change
   int *v;    (if any) in individual health status.  Health expectancies are
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    computed from the time spent in each health state according to a
   if (!v) nrerror("allocation failure in ivector");    model. More health states you consider, more time is necessary to reach the
   return v-nl+NR_END;    Maximum Likelihood of the parameters involved in the model.  The
 }    simplest model is the multinomial logistic model where pij is the
     probability to be observed in state j at the second wave
 /******************free ivector **************************/    conditional to be observed in state i at the first wave. Therefore
 void free_ivector(int *v, long nl, long nh)    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
 {    'age' is age and 'sex' is a covariate. If you want to have a more
   free((FREE_ARG)(v+nl-NR_END));    complex model than "constant and age", you should modify the program
 }    where the markup *Covariates have to be included here again* invites
     you to do it.  More covariates you add, slower the
 /******************* imatrix *******************************/    convergence.
 int **imatrix(long nrl, long nrh, long ncl, long nch)  
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    The advantage of this computer programme, compared to a simple
 {    multinomial logistic model, is clear when the delay between waves is not
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    identical for each individual. Also, if a individual missed an
   int **m;    intermediate interview, the information is lost, but taken into
      account using an interpolation or extrapolation.  
   /* allocate pointers to rows */  
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    hPijx is the probability to be observed in state i at age x+h
   if (!m) nrerror("allocation failure 1 in matrix()");    conditional to the observed state i at age x. The delay 'h' can be
   m += NR_END;    split into an exact number (nh*stepm) of unobserved intermediate
   m -= nrl;    states. This elementary transition (by month, quarter,
      semester or year) is modelled as a multinomial logistic.  The hPx
      matrix is simply the matrix product of nh*stepm elementary matrices
   /* allocate rows and set pointers to them */    and the contribution of each individual to the likelihood is simply
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    hPijx.
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;    Also this programme outputs the covariance matrix of the parameters but also
   m[nrl] -= ncl;    of the life expectancies. It also computes the period (stable) prevalence. 
      
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
               Institut national d'études démographiques, Paris.
   /* return pointer to array of pointers to rows */    This software have been partly granted by Euro-REVES, a concerted action
   return m;    from the European Union.
 }    It is copyrighted identically to a GNU software product, ie programme and
     software can be distributed freely for non commercial use. Latest version
 /****************** free_imatrix *************************/    can be accessed at http://euroreves.ined.fr/imach .
 void free_imatrix(m,nrl,nrh,ncl,nch)  
       int **m;    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
       long nch,ncl,nrh,nrl;    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
      /* free an int matrix allocated by imatrix() */    
 {    **********************************************************************/
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  /*
   free((FREE_ARG) (m+nrl-NR_END));    main
 }    read parameterfile
     read datafile
 /******************* matrix *******************************/    concatwav
 double **matrix(long nrl, long nrh, long ncl, long nch)    freqsummary
 {    if (mle >= 1)
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;      mlikeli
   double **m;    print results files
     if mle==1 
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));       computes hessian
   if (!m) nrerror("allocation failure 1 in matrix()");    read end of parameter file: agemin, agemax, bage, fage, estepm
   m += NR_END;        begin-prev-date,...
   m -= nrl;    open gnuplot file
     open html file
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    period (stable) prevalence
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");     for age prevalim()
   m[nrl] += NR_END;    h Pij x
   m[nrl] -= ncl;    variance of p varprob
     forecasting if prevfcast==1 prevforecast call prevalence()
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    health expectancies
   return m;    Variance-covariance of DFLE
 }    prevalence()
      movingaverage()
 /*************************free matrix ************************/    varevsij() 
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    if popbased==1 varevsij(,popbased)
 {    total life expectancies
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    Variance of period (stable) prevalence
   free((FREE_ARG)(m+nrl-NR_END));   end
 }  */
   
 /******************* ma3x *******************************/  
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  
 {   
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  #include <math.h>
   double ***m;  #include <stdio.h>
   #include <stdlib.h>
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  #include <string.h>
   if (!m) nrerror("allocation failure 1 in matrix()");  #include <unistd.h>
   m += NR_END;  
   m -= nrl;  #include <limits.h>
   #include <sys/types.h>
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  #include <sys/stat.h>
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  #include <errno.h>
   m[nrl] += NR_END;  extern int errno;
   m[nrl] -= ncl;  
   /* #include <sys/time.h> */
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  #include <time.h>
   #include "timeval.h"
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  /* #include <libintl.h> */
   m[nrl][ncl] += NR_END;  /* #define _(String) gettext (String) */
   m[nrl][ncl] -= nll;  
   for (j=ncl+1; j<=nch; j++)  #define MAXLINE 256
     m[nrl][j]=m[nrl][j-1]+nlay;  
    #define GNUPLOTPROGRAM "gnuplot"
   for (i=nrl+1; i<=nrh; i++) {  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  #define FILENAMELENGTH 132
     for (j=ncl+1; j<=nch; j++)  
       m[i][j]=m[i][j-1]+nlay;  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
   }  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   return m;  
 }  #define MAXPARM 128 /* Maximum number of parameters for the optimization */
   #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
 /*************************free ma3x ************************/  
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  #define NINTERVMAX 8
 {  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  #define NCOVMAX 20 /* Maximum number of covariates */
   free((FREE_ARG)(m+nrl-NR_END));  #define MAXN 20000
 }  #define YEARM 12. /* Number of months per year */
   #define AGESUP 130
 /***************** f1dim *************************/  #define AGEBASE 40
 extern int ncom;  #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
 extern double *pcom,*xicom;  #ifdef UNIX
 extern double (*nrfunc)(double []);  #define DIRSEPARATOR '/'
    #define CHARSEPARATOR "/"
 double f1dim(double x)  #define ODIRSEPARATOR '\\'
 {  #else
   int j;  #define DIRSEPARATOR '\\'
   double f;  #define CHARSEPARATOR "\\"
   double *xt;  #define ODIRSEPARATOR '/'
    #endif
   xt=vector(1,ncom);  
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  /* $Id$ */
   f=(*nrfunc)(xt);  /* $State$ */
   free_vector(xt,1,ncom);  
   return f;  char version[]="Imach version 0.98k, June 2009, INED-EUROREVES-Institut de longevite ";
 }  char fullversion[]="$Revision$ $Date$"; 
   char strstart[80];
 /*****************brent *************************/  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
 {  int nvar=0, nforce=0; /* Number of variables, number of forces */
   int iter;  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov=0; /* Number of covariates, of covariates with '*age' */
   double a,b,d,etemp;  int npar=NPARMAX;
   double fu,fv,fw,fx;  int nlstate=2; /* Number of live states */
   double ftemp;  int ndeath=1; /* Number of dead states */
   double p,q,r,tol1,tol2,u,v,w,x,xm;  int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   double e=0.0;  int popbased=0;
    
   a=(ax < cx ? ax : cx);  int *wav; /* Number of waves for this individuual 0 is possible */
   b=(ax > cx ? ax : cx);  int maxwav=0; /* Maxim number of waves */
   x=w=v=bx;  int jmin=0, jmax=0; /* min, max spacing between 2 waves */
   fw=fv=fx=(*f)(x);  int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
   for (iter=1;iter<=ITMAX;iter++) {  int gipmx=0, gsw=0; /* Global variables on the number of contributions 
     xm=0.5*(a+b);                     to the likelihood and the sum of weights (done by funcone)*/
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  int mle=1, weightopt=0;
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
     printf(".");fflush(stdout);  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
 #ifdef DEBUG  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
     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);             * wave mi and wave mi+1 is not an exact multiple of stepm. */
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  double jmean=1; /* Mean space between 2 waves */
 #endif  double **oldm, **newm, **savm; /* Working pointers to matrices */
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
       *xmin=x;  FILE *fic,*ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
       return fx;  FILE *ficlog, *ficrespow;
     }  int globpr=0; /* Global variable for printing or not */
     ftemp=fu;  double fretone; /* Only one call to likelihood */
     if (fabs(e) > tol1) {  long ipmx=0; /* Number of contributions */
       r=(x-w)*(fx-fv);  double sw; /* Sum of weights */
       q=(x-v)*(fx-fw);  char filerespow[FILENAMELENGTH];
       p=(x-v)*q-(x-w)*r;  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
       q=2.0*(q-r);  FILE *ficresilk;
       if (q > 0.0) p = -p;  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
       q=fabs(q);  FILE *ficresprobmorprev;
       etemp=e;  FILE *fichtm, *fichtmcov; /* Html File */
       e=d;  FILE *ficreseij;
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  char filerese[FILENAMELENGTH];
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  FILE *ficresstdeij;
       else {  char fileresstde[FILENAMELENGTH];
         d=p/q;  FILE *ficrescveij;
         u=x+d;  char filerescve[FILENAMELENGTH];
         if (u-a < tol2 || b-u < tol2)  FILE  *ficresvij;
           d=SIGN(tol1,xm-x);  char fileresv[FILENAMELENGTH];
       }  FILE  *ficresvpl;
     } else {  char fileresvpl[FILENAMELENGTH];
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  char title[MAXLINE];
     }  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
     fu=(*f)(u);  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
     if (fu <= fx) {  char command[FILENAMELENGTH];
       if (u >= x) a=x; else b=x;  int  outcmd=0;
       SHFT(v,w,x,u)  
         SHFT(fv,fw,fx,fu)  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
         } else {  
           if (u < x) a=u; else b=u;  char filelog[FILENAMELENGTH]; /* Log file */
           if (fu <= fw || w == x) {  char filerest[FILENAMELENGTH];
             v=w;  char fileregp[FILENAMELENGTH];
             w=u;  char popfile[FILENAMELENGTH];
             fv=fw;  
             fw=fu;  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
           } else if (fu <= fv || v == x || v == w) {  
             v=u;  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
             fv=fu;  struct timezone tzp;
           }  extern int gettimeofday();
         }  struct tm tmg, tm, tmf, *gmtime(), *localtime();
   }  long time_value;
   nrerror("Too many iterations in brent");  extern long time();
   *xmin=x;  char strcurr[80], strfor[80];
   return fx;  
 }  char *endptr;
   long lval;
 /****************** mnbrak ***********************/  double dval;
   
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  #define NR_END 1
             double (*func)(double))  #define FREE_ARG char*
 {  #define FTOL 1.0e-10
   double ulim,u,r,q, dum;  
   double fu;  #define NRANSI 
    #define ITMAX 200 
   *fa=(*func)(*ax);  
   *fb=(*func)(*bx);  #define TOL 2.0e-4 
   if (*fb > *fa) {  
     SHFT(dum,*ax,*bx,dum)  #define CGOLD 0.3819660 
       SHFT(dum,*fb,*fa,dum)  #define ZEPS 1.0e-10 
       }  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
   *cx=(*bx)+GOLD*(*bx-*ax);  
   *fc=(*func)(*cx);  #define GOLD 1.618034 
   while (*fb > *fc) {  #define GLIMIT 100.0 
     r=(*bx-*ax)*(*fb-*fc);  #define TINY 1.0e-20 
     q=(*bx-*cx)*(*fb-*fa);  
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  static double maxarg1,maxarg2;
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
     ulim=(*bx)+GLIMIT*(*cx-*bx);  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
     if ((*bx-u)*(u-*cx) > 0.0) {    
       fu=(*func)(u);  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
     } else if ((*cx-u)*(u-ulim) > 0.0) {  #define rint(a) floor(a+0.5)
       fu=(*func)(u);  
       if (fu < *fc) {  static double sqrarg;
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
           SHFT(*fb,*fc,fu,(*func)(u))  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
           }  int agegomp= AGEGOMP;
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  
       u=ulim;  int imx; 
       fu=(*func)(u);  int stepm=1;
     } else {  /* Stepm, step in month: minimum step interpolation*/
       u=(*cx)+GOLD*(*cx-*bx);  
       fu=(*func)(u);  int estepm;
     }  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
     SHFT(*ax,*bx,*cx,u)  
       SHFT(*fa,*fb,*fc,fu)  int m,nb;
       }  long *num;
 }  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
   double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
 /*************** linmin ************************/  double **pmmij, ***probs;
   double *ageexmed,*agecens;
 int ncom;  double dateintmean=0;
 double *pcom,*xicom;  
 double (*nrfunc)(double []);  double *weight;
    int **s; /* Status */
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  double *agedc, **covar, idx;
 {  int **nbcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
   double brent(double ax, double bx, double cx,  double *lsurv, *lpop, *tpop;
                double (*f)(double), double tol, double *xmin);  
   double f1dim(double x);  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  double ftolhess; /* Tolerance for computing hessian */
               double *fc, double (*func)(double));  
   int j;  /**************** split *************************/
   double xx,xmin,bx,ax;  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   double fx,fb,fa;  {
      /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
   ncom=n;       the name of the file (name), its extension only (ext) and its first part of the name (finame)
   pcom=vector(1,n);    */ 
   xicom=vector(1,n);    char  *ss;                            /* pointer */
   nrfunc=func;    int   l1, l2;                         /* length counters */
   for (j=1;j<=n;j++) {  
     pcom[j]=p[j];    l1 = strlen(path );                   /* length of path */
     xicom[j]=xi[j];    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   }    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
   ax=0.0;    if ( ss == NULL ) {                   /* no directory, so determine current directory */
   xx=1.0;      strcpy( name, path );               /* we got the fullname name because no directory */
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
 #ifdef DEBUG      /* get current working directory */
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);      /*    extern  char* getcwd ( char *buf , int len);*/
 #endif      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
   for (j=1;j<=n;j++) {        return( GLOCK_ERROR_GETCWD );
     xi[j] *= xmin;      }
     p[j] += xi[j];      /* got dirc from getcwd*/
   }      printf(" DIRC = %s \n",dirc);
   free_vector(xicom,1,n);    } else {                              /* strip direcotry from path */
   free_vector(pcom,1,n);      ss++;                               /* after this, the filename */
 }      l2 = strlen( ss );                  /* length of filename */
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
 /*************** powell ************************/      strcpy( name, ss );         /* save file name */
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,      strncpy( dirc, path, l1 - l2 );     /* now the directory */
             double (*func)(double []))      dirc[l1-l2] = 0;                    /* add zero */
 {      printf(" DIRC2 = %s \n",dirc);
   void linmin(double p[], double xi[], int n, double *fret,    }
               double (*func)(double []));    /* We add a separator at the end of dirc if not exists */
   int i,ibig,j;    l1 = strlen( dirc );                  /* length of directory */
   double del,t,*pt,*ptt,*xit;    if( dirc[l1-1] != DIRSEPARATOR ){
   double fp,fptt;      dirc[l1] =  DIRSEPARATOR;
   double *xits;      dirc[l1+1] = 0; 
   pt=vector(1,n);      printf(" DIRC3 = %s \n",dirc);
   ptt=vector(1,n);    }
   xit=vector(1,n);    ss = strrchr( name, '.' );            /* find last / */
   xits=vector(1,n);    if (ss >0){
   *fret=(*func)(p);      ss++;
   for (j=1;j<=n;j++) pt[j]=p[j];      strcpy(ext,ss);                     /* save extension */
   for (*iter=1;;++(*iter)) {      l1= strlen( name);
     fp=(*fret);      l2= strlen(ss)+1;
     ibig=0;      strncpy( finame, name, l1-l2);
     del=0.0;      finame[l1-l2]= 0;
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);    }
     for (i=1;i<=n;i++)  
       printf(" %d %.12f",i, p[i]);    return( 0 );                          /* we're done */
     printf("\n");  }
     for (i=1;i<=n;i++) {  
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  
       fptt=(*fret);  /******************************************/
 #ifdef DEBUG  
       printf("fret=%lf \n",*fret);  void replace_back_to_slash(char *s, char*t)
 #endif  {
       printf("%d",i);fflush(stdout);    int i;
       linmin(p,xit,n,fret,func);    int lg=0;
       if (fabs(fptt-(*fret)) > del) {    i=0;
         del=fabs(fptt-(*fret));    lg=strlen(t);
         ibig=i;    for(i=0; i<= lg; i++) {
       }      (s[i] = t[i]);
 #ifdef DEBUG      if (t[i]== '\\') s[i]='/';
       printf("%d %.12e",i,(*fret));    }
       for (j=1;j<=n;j++) {  }
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  
         printf(" x(%d)=%.12e",j,xit[j]);  char *trimbb(char *out, char *in)
       }  { /* Trim multiple blanks in line */
       for(j=1;j<=n;j++)    char *s;
         printf(" p=%.12e",p[j]);    s=out;
       printf("\n");    while (*in != '\0'){
 #endif      while( *in == ' ' && *(in+1) == ' ' && *(in+1) != '\0'){
     }        in++;
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {      }
 #ifdef DEBUG      *out++ = *in++;
       int k[2],l;    }
       k[0]=1;    *out='\0';
       k[1]=-1;    return s;
       printf("Max: %.12e",(*func)(p));  }
       for (j=1;j<=n;j++)  
         printf(" %.12e",p[j]);  int nbocc(char *s, char occ)
       printf("\n");  {
       for(l=0;l<=1;l++) {    int i,j=0;
         for (j=1;j<=n;j++) {    int lg=20;
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];    i=0;
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);    lg=strlen(s);
         }    for(i=0; i<= lg; i++) {
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    if  (s[i] == occ ) j++;
       }    }
 #endif    return j;
   }
   
       free_vector(xit,1,n);  void cutv(char *u,char *v, char*t, char occ)
       free_vector(xits,1,n);  {
       free_vector(ptt,1,n);    /* cuts string t into u and v where u ends before first occurence of char 'occ' 
       free_vector(pt,1,n);       and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
       return;       gives u="abcedf" and v="ghi2j" */
     }    int i,lg,j,p=0;
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    i=0;
     for (j=1;j<=n;j++) {    for(j=0; j<=strlen(t)-1; j++) {
       ptt[j]=2.0*p[j]-pt[j];      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
       xit[j]=p[j]-pt[j];    }
       pt[j]=p[j];  
     }    lg=strlen(t);
     fptt=(*func)(ptt);    for(j=0; j<p; j++) {
     if (fptt < fp) {      (u[j] = t[j]);
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);    }
       if (t < 0.0) {       u[p]='\0';
         linmin(p,xit,n,fret,func);  
         for (j=1;j<=n;j++) {     for(j=0; j<= lg; j++) {
           xi[j][ibig]=xi[j][n];      if (j>=(p+1))(v[j-p-1] = t[j]);
           xi[j][n]=xit[j];    }
         }  }
 #ifdef DEBUG  
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  /********************** nrerror ********************/
         for(j=1;j<=n;j++)  
           printf(" %.12e",xit[j]);  void nrerror(char error_text[])
         printf("\n");  {
 #endif    fprintf(stderr,"ERREUR ...\n");
       }    fprintf(stderr,"%s\n",error_text);
     }    exit(EXIT_FAILURE);
   }  }
 }  /*********************** vector *******************/
   double *vector(int nl, int nh)
 /**** Prevalence limit ****************/  {
     double *v;
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
 {    if (!v) nrerror("allocation failure in vector");
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit    return v-nl+NR_END;
      matrix by transitions matrix until convergence is reached */  }
   
   int i, ii,j,k;  /************************ free vector ******************/
   double min, max, maxmin, maxmax,sumnew=0.;  void free_vector(double*v, int nl, int nh)
   double **matprod2();  {
   double **out, cov[NCOVMAX], **pmij();    free((FREE_ARG)(v+nl-NR_END));
   double **newm;  }
   double agefin, delaymax=50 ; /* Max number of years to converge */  
   /************************ivector *******************************/
   for (ii=1;ii<=nlstate+ndeath;ii++)  int *ivector(long nl,long nh)
     for (j=1;j<=nlstate+ndeath;j++){  {
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);    int *v;
     }    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
     if (!v) nrerror("allocation failure in ivector");
    cov[1]=1.;    return 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){  /******************free ivector **************************/
     newm=savm;  void free_ivector(int *v, long nl, long nh)
     /* Covariates have to be included here again */  {
      cov[2]=agefin;    free((FREE_ARG)(v+nl-NR_END));
    }
       for (k=1; k<=cptcovn;k++) {  
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  /************************lvector *******************************/
         /*      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]]);*/  long *lvector(long nl,long nh)
       }  {
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    long *v;
       for (k=1; k<=cptcovprod;k++)    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    if (!v) nrerror("allocation failure in ivector");
     return 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]);*/  
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/  /******************free lvector **************************/
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  void free_lvector(long *v, long nl, long nh)
   {
     savm=oldm;    free((FREE_ARG)(v+nl-NR_END));
     oldm=newm;  }
     maxmax=0.;  
     for(j=1;j<=nlstate;j++){  /******************* imatrix *******************************/
       min=1.;  int **imatrix(long nrl, long nrh, long ncl, long nch) 
       max=0.;       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
       for(i=1; i<=nlstate; i++) {  { 
         sumnew=0;    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];    int **m; 
         prlim[i][j]= newm[i][j]/(1-sumnew);    
         max=FMAX(max,prlim[i][j]);    /* allocate pointers to rows */ 
         min=FMIN(min,prlim[i][j]);    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
       }    if (!m) nrerror("allocation failure 1 in matrix()"); 
       maxmin=max-min;    m += NR_END; 
       maxmax=FMAX(maxmax,maxmin);    m -= nrl; 
     }    
     if(maxmax < ftolpl){    
       return prlim;    /* allocate rows and set pointers to them */ 
     }    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
   }    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
 }    m[nrl] += NR_END; 
     m[nrl] -= ncl; 
 /*************** transition probabilities ***************/    
     for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )    
 {    /* return pointer to array of pointers to rows */ 
   double s1, s2;    return m; 
   /*double t34;*/  } 
   int i,j,j1, nc, ii, jj;  
   /****************** free_imatrix *************************/
     for(i=1; i<= nlstate; i++){  void free_imatrix(m,nrl,nrh,ncl,nch)
     for(j=1; j<i;j++){        int **m;
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){        long nch,ncl,nrh,nrl; 
         /*s2 += param[i][j][nc]*cov[nc];*/       /* free an int matrix allocated by imatrix() */ 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  { 
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
       }    free((FREE_ARG) (m+nrl-NR_END)); 
       ps[i][j]=s2;  } 
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/  
     }  /******************* matrix *******************************/
     for(j=i+1; j<=nlstate+ndeath;j++){  double **matrix(long nrl, long nrh, long ncl, long nch)
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  {
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/    double **m;
       }  
       ps[i][j]=s2;    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     }    if (!m) nrerror("allocation failure 1 in matrix()");
   }    m += NR_END;
     /*ps[3][2]=1;*/    m -= nrl;
   
   for(i=1; i<= nlstate; i++){    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
      s1=0;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     for(j=1; j<i; j++)    m[nrl] += NR_END;
       s1+=exp(ps[i][j]);    m[nrl] -= ncl;
     for(j=i+1; j<=nlstate+ndeath; j++)  
       s1+=exp(ps[i][j]);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     ps[i][i]=1./(s1+1.);    return m;
     for(j=1; j<i; j++)    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
       ps[i][j]= exp(ps[i][j])*ps[i][i];     */
     for(j=i+1; j<=nlstate+ndeath; j++)  }
       ps[i][j]= exp(ps[i][j])*ps[i][i];  
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */  /*************************free matrix ************************/
   } /* end i */  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   {
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     for(jj=1; jj<= nlstate+ndeath; jj++){    free((FREE_ARG)(m+nrl-NR_END));
       ps[ii][jj]=0;  }
       ps[ii][ii]=1;  
     }  /******************* ma3x *******************************/
   }  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
   {
     long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){    double ***m;
     for(jj=1; jj<= nlstate+ndeath; jj++){  
      printf("%lf ",ps[ii][jj]);    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
    }    if (!m) nrerror("allocation failure 1 in matrix()");
     printf("\n ");    m += NR_END;
     }    m -= nrl;
     printf("\n ");printf("%lf ",cov[2]);*/  
 /*    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   for(i=1; i<= npar; i++) printf("%f ",x[i]);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   goto end;*/    m[nrl] += NR_END;
     return ps;    m[nrl] -= ncl;
 }  
     for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
 /**************** Product of 2 matrices ******************/  
     m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
 {    m[nrl][ncl] += NR_END;
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times    m[nrl][ncl] -= nll;
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */    for (j=ncl+1; j<=nch; j++) 
   /* in, b, out are matrice of pointers which should have been initialized      m[nrl][j]=m[nrl][j-1]+nlay;
      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++) {
   long i, j, k;      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
   for(i=nrl; i<= nrh; i++)      for (j=ncl+1; j<=nch; j++) 
     for(k=ncolol; k<=ncoloh; k++)        m[i][j]=m[i][j-1]+nlay;
       for(j=ncl,out[i][k]=0.; j<=nch; j++)    }
         out[i][k] +=in[i][j]*b[j][k];    return m; 
     /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
   return out;             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
 }    */
   }
   
 /************* Higher Matrix Product ***************/  /*************************free ma3x ************************/
   void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )  {
 {    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month    free((FREE_ARG)(m[nrl]+ncl-NR_END));
      duration (i.e. until    free((FREE_ARG)(m+nrl-NR_END));
      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).  /*************** function subdirf ***********/
      Model is determined by parameters x and covariates have to be  char *subdirf(char fileres[])
      included manually here.  {
     /* Caution optionfilefiname is hidden */
      */    strcpy(tmpout,optionfilefiname);
     strcat(tmpout,"/"); /* Add to the right */
   int i, j, d, h, k;    strcat(tmpout,fileres);
   double **out, cov[NCOVMAX];    return tmpout;
   double **newm;  }
   
   /* Hstepm could be zero and should return the unit matrix */  /*************** function subdirf2 ***********/
   for (i=1;i<=nlstate+ndeath;i++)  char *subdirf2(char fileres[], char *preop)
     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);    /* Caution optionfilefiname is hidden */
     }    strcpy(tmpout,optionfilefiname);
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    strcat(tmpout,"/");
   for(h=1; h <=nhstepm; h++){    strcat(tmpout,preop);
     for(d=1; d <=hstepm; d++){    strcat(tmpout,fileres);
       newm=savm;    return tmpout;
       /* Covariates have to be included here again */  }
       cov[1]=1.;  
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;  /*************** function subdirf3 ***********/
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  char *subdirf3(char fileres[], char *preop, char *preop2)
       for (k=1; k<=cptcovage;k++)  {
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    
       for (k=1; k<=cptcovprod;k++)    /* Caution optionfilefiname is hidden */
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    strcpy(tmpout,optionfilefiname);
     strcat(tmpout,"/");
     strcat(tmpout,preop);
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/    strcat(tmpout,preop2);
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/    strcat(tmpout,fileres);
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,    return tmpout;
                    pmij(pmmij,cov,ncovmodel,x,nlstate));  }
       savm=oldm;  
       oldm=newm;  /***************** f1dim *************************/
     }  extern int ncom; 
     for(i=1; i<=nlstate+ndeath; i++)  extern double *pcom,*xicom;
       for(j=1;j<=nlstate+ndeath;j++) {  extern double (*nrfunc)(double []); 
         po[i][j][h]=newm[i][j];   
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);  double f1dim(double x) 
          */  { 
       }    int j; 
   } /* end h */    double f;
   return po;    double *xt; 
 }   
     xt=vector(1,ncom); 
     for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
 /*************** log-likelihood *************/    f=(*nrfunc)(xt); 
 double func( double *x)    free_vector(xt,1,ncom); 
 {    return f; 
   int i, ii, j, k, mi, d, kk;  } 
   double l, ll[NLSTATEMAX], cov[NCOVMAX];  
   double **out;  /*****************brent *************************/
   double sw; /* Sum of weights */  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
   double lli; /* Individual log likelihood */  { 
   long ipmx;    int iter; 
   /*extern weight */    double a,b,d,etemp;
   /* We are differentiating ll according to initial status */    double fu,fv,fw,fx;
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    double ftemp;
   /*for(i=1;i<imx;i++)    double p,q,r,tol1,tol2,u,v,w,x,xm; 
     printf(" %d\n",s[4][i]);    double e=0.0; 
   */   
   cov[1]=1.;    a=(ax < cx ? ax : cx); 
     b=(ax > cx ? ax : cx); 
   for(k=1; k<=nlstate; k++) ll[k]=0.;    x=w=v=bx; 
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){    fw=fv=fx=(*f)(x); 
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];    for (iter=1;iter<=ITMAX;iter++) { 
     for(mi=1; mi<= wav[i]-1; mi++){      xm=0.5*(a+b); 
       for (ii=1;ii<=nlstate+ndeath;ii++)      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
       for(d=0; d<dh[mi][i]; d++){      printf(".");fflush(stdout);
         newm=savm;      fprintf(ficlog,".");fflush(ficlog);
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;  #ifdef DEBUG
         for (kk=1; kk<=cptcovage;kk++) {      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);
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
         }      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
          #endif
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));        *xmin=x; 
         savm=oldm;        return fx; 
         oldm=newm;      } 
              ftemp=fu;
              if (fabs(e) > tol1) { 
       } /* end mult */        r=(x-w)*(fx-fv); 
              q=(x-v)*(fx-fw); 
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);        p=(x-v)*q-(x-w)*r; 
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/        q=2.0*(q-r); 
       ipmx +=1;        if (q > 0.0) p = -p; 
       sw += weight[i];        q=fabs(q); 
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;        etemp=e; 
     } /* end of wave */        e=d; 
   } /* end of individual */        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)); 
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];        else { 
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */          d=p/q; 
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */          u=x+d; 
   return -l;          if (u-a < tol2 || b-u < tol2) 
 }            d=SIGN(tol1,xm-x); 
         } 
       } else { 
 /*********** Maximum Likelihood Estimation ***************/        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 []))      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
 {      fu=(*f)(u); 
   int i,j, iter;      if (fu <= fx) { 
   double **xi,*delti;        if (u >= x) a=x; else b=x; 
   double fret;        SHFT(v,w,x,u) 
   xi=matrix(1,npar,1,npar);          SHFT(fv,fw,fx,fu) 
   for (i=1;i<=npar;i++)          } else { 
     for (j=1;j<=npar;j++)            if (u < x) a=u; else b=u; 
       xi[i][j]=(i==j ? 1.0 : 0.0);            if (fu <= fw || w == x) { 
   printf("Powell\n");              v=w; 
   powell(p,xi,npar,ftol,&iter,&fret,func);              w=u; 
               fv=fw; 
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));              fw=fu; 
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));            } else if (fu <= fv || v == x || v == w) { 
               v=u; 
 }              fv=fu; 
             } 
 /**** Computes Hessian and covariance matrix ***/          } 
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))    } 
 {    nrerror("Too many iterations in brent"); 
   double  **a,**y,*x,pd;    *xmin=x; 
   double **hess;    return fx; 
   int i, j,jk;  } 
   int *indx;  
   /****************** mnbrak ***********************/
   double hessii(double p[], double delta, int theta, double delti[]);  
   double hessij(double p[], double delti[], int i, int j);  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
   void lubksb(double **a, int npar, int *indx, double b[]) ;              double (*func)(double)) 
   void ludcmp(double **a, int npar, int *indx, double *d) ;  { 
     double ulim,u,r,q, dum;
   hess=matrix(1,npar,1,npar);    double fu; 
    
   printf("\nCalculation of the hessian matrix. Wait...\n");    *fa=(*func)(*ax); 
   for (i=1;i<=npar;i++){    *fb=(*func)(*bx); 
     printf("%d",i);fflush(stdout);    if (*fb > *fa) { 
     hess[i][i]=hessii(p,ftolhess,i,delti);      SHFT(dum,*ax,*bx,dum) 
     /*printf(" %f ",p[i]);*/        SHFT(dum,*fb,*fa,dum) 
     /*printf(" %lf ",hess[i][i]);*/        } 
   }    *cx=(*bx)+GOLD*(*bx-*ax); 
      *fc=(*func)(*cx); 
   for (i=1;i<=npar;i++) {    while (*fb > *fc) { 
     for (j=1;j<=npar;j++)  {      r=(*bx-*ax)*(*fb-*fc); 
       if (j>i) {      q=(*bx-*cx)*(*fb-*fa); 
         printf(".%d%d",i,j);fflush(stdout);      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
         hess[i][j]=hessij(p,delti,i,j);        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
         hess[j][i]=hess[i][j];          ulim=(*bx)+GLIMIT*(*cx-*bx); 
         /*printf(" %lf ",hess[i][j]);*/      if ((*bx-u)*(u-*cx) > 0.0) { 
       }        fu=(*func)(u); 
     }      } else if ((*cx-u)*(u-ulim) > 0.0) { 
   }        fu=(*func)(u); 
   printf("\n");        if (fu < *fc) { 
           SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");            SHFT(*fb,*fc,fu,(*func)(u)) 
              } 
   a=matrix(1,npar,1,npar);      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
   y=matrix(1,npar,1,npar);        u=ulim; 
   x=vector(1,npar);        fu=(*func)(u); 
   indx=ivector(1,npar);      } else { 
   for (i=1;i<=npar;i++)        u=(*cx)+GOLD*(*cx-*bx); 
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];        fu=(*func)(u); 
   ludcmp(a,npar,indx,&pd);      } 
       SHFT(*ax,*bx,*cx,u) 
   for (j=1;j<=npar;j++) {        SHFT(*fa,*fb,*fc,fu) 
     for (i=1;i<=npar;i++) x[i]=0;        } 
     x[j]=1;  } 
     lubksb(a,npar,indx,x);  
     for (i=1;i<=npar;i++){  /*************** linmin ************************/
       matcov[i][j]=x[i];  
     }  int ncom; 
   }  double *pcom,*xicom;
   double (*nrfunc)(double []); 
   printf("\n#Hessian matrix#\n");   
   for (i=1;i<=npar;i++) {  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
     for (j=1;j<=npar;j++) {  { 
       printf("%.3e ",hess[i][j]);    double brent(double ax, double bx, double cx, 
     }                 double (*f)(double), double tol, double *xmin); 
     printf("\n");    double f1dim(double x); 
   }    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
                 double *fc, double (*func)(double)); 
   /* Recompute Inverse */    int j; 
   for (i=1;i<=npar;i++)    double xx,xmin,bx,ax; 
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];    double fx,fb,fa;
   ludcmp(a,npar,indx,&pd);   
     ncom=n; 
   /*  printf("\n#Hessian matrix recomputed#\n");    pcom=vector(1,n); 
     xicom=vector(1,n); 
   for (j=1;j<=npar;j++) {    nrfunc=func; 
     for (i=1;i<=npar;i++) x[i]=0;    for (j=1;j<=n;j++) { 
     x[j]=1;      pcom[j]=p[j]; 
     lubksb(a,npar,indx,x);      xicom[j]=xi[j]; 
     for (i=1;i<=npar;i++){    } 
       y[i][j]=x[i];    ax=0.0; 
       printf("%.3e ",y[i][j]);    xx=1.0; 
     }    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
     printf("\n");    *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);
   free_matrix(a,1,npar,1,npar);  #endif
   free_matrix(y,1,npar,1,npar);    for (j=1;j<=n;j++) { 
   free_vector(x,1,npar);      xi[j] *= xmin; 
   free_ivector(indx,1,npar);      p[j] += xi[j]; 
   free_matrix(hess,1,npar,1,npar);    } 
     free_vector(xicom,1,n); 
     free_vector(pcom,1,n); 
 }  } 
   
 /*************** hessian matrix ****************/  char *asc_diff_time(long time_sec, char ascdiff[])
 double hessii( double x[], double delta, int theta, double delti[])  {
 {    long sec_left, days, hours, minutes;
   int i;    days = (time_sec) / (60*60*24);
   int l=1, lmax=20;    sec_left = (time_sec) % (60*60*24);
   double k1,k2;    hours = (sec_left) / (60*60) ;
   double p2[NPARMAX+1];    sec_left = (sec_left) %(60*60);
   double res;    minutes = (sec_left) /60;
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;    sec_left = (sec_left) % (60);
   double fx;    sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
   int k=0,kmax=10;    return ascdiff;
   double l1;  }
   
   fx=func(x);  /*************** powell ************************/
   for (i=1;i<=npar;i++) p2[i]=x[i];  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
   for(l=0 ; l <=lmax; l++){              double (*func)(double [])) 
     l1=pow(10,l);  { 
     delts=delt;    void linmin(double p[], double xi[], int n, double *fret, 
     for(k=1 ; k <kmax; k=k+1){                double (*func)(double [])); 
       delt = delta*(l1*k);    int i,ibig,j; 
       p2[theta]=x[theta] +delt;    double del,t,*pt,*ptt,*xit;
       k1=func(p2)-fx;    double fp,fptt;
       p2[theta]=x[theta]-delt;    double *xits;
       k2=func(p2)-fx;    int niterf, itmp;
       /*res= (k1-2.0*fx+k2)/delt/delt; */  
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */    pt=vector(1,n); 
          ptt=vector(1,n); 
 #ifdef DEBUG    xit=vector(1,n); 
       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);    xits=vector(1,n); 
 #endif    *fret=(*func)(p); 
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */    for (j=1;j<=n;j++) pt[j]=p[j]; 
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){    for (*iter=1;;++(*iter)) { 
         k=kmax;      fp=(*fret); 
       }      ibig=0; 
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */      del=0.0; 
         k=kmax; l=lmax*10.;      last_time=curr_time;
       }      (void) gettimeofday(&curr_time,&tzp);
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){      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);
         delts=delt;      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec); fflush(ficlog);
       }  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
     }     for (i=1;i<=n;i++) {
   }        printf(" %d %.12f",i, p[i]);
   delti[theta]=delts;        fprintf(ficlog," %d %.12lf",i, p[i]);
   return res;        fprintf(ficrespow," %.12lf", p[i]);
        }
 }      printf("\n");
       fprintf(ficlog,"\n");
 double hessij( double x[], double delti[], int thetai,int thetaj)      fprintf(ficrespow,"\n");fflush(ficrespow);
 {      if(*iter <=3){
   int i;        tm = *localtime(&curr_time.tv_sec);
   int l=1, l1, lmax=20;        strcpy(strcurr,asctime(&tm));
   double k1,k2,k3,k4,res,fx;  /*       asctime_r(&tm,strcurr); */
   double p2[NPARMAX+1];        forecast_time=curr_time; 
   int k;        itmp = strlen(strcurr);
         if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
   fx=func(x);          strcurr[itmp-1]='\0';
   for (k=1; k<=2; k++) {        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
     for (i=1;i<=npar;i++) p2[i]=x[i];        fprintf(ficlog,"\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;        for(niterf=10;niterf<=30;niterf+=10){
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
     k1=func(p2)-fx;          tmf = *localtime(&forecast_time.tv_sec);
    /*      asctime_r(&tmf,strfor); */
     p2[thetai]=x[thetai]+delti[thetai]/k;          strcpy(strfor,asctime(&tmf));
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          itmp = strlen(strfor);
     k2=func(p2)-fx;          if(strfor[itmp-1]=='\n')
            strfor[itmp-1]='\0';
     p2[thetai]=x[thetai]-delti[thetai]/k;          printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;          fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
     k3=func(p2)-fx;        }
        }
     p2[thetai]=x[thetai]-delti[thetai]/k;      for (i=1;i<=n;i++) { 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
     k4=func(p2)-fx;        fptt=(*fret); 
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */  #ifdef DEBUG
 #ifdef DEBUG        printf("fret=%lf \n",*fret);
     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,"fret=%lf \n",*fret);
 #endif  #endif
   }        printf("%d",i);fflush(stdout);
   return res;        fprintf(ficlog,"%d",i);fflush(ficlog);
 }        linmin(p,xit,n,fret,func); 
         if (fabs(fptt-(*fret)) > del) { 
 /************** Inverse of matrix **************/          del=fabs(fptt-(*fret)); 
 void ludcmp(double **a, int n, int *indx, double *d)          ibig=i; 
 {        } 
   int i,imax,j,k;  #ifdef DEBUG
   double big,dum,sum,temp;        printf("%d %.12e",i,(*fret));
   double *vv;        fprintf(ficlog,"%d %.12e",i,(*fret));
          for (j=1;j<=n;j++) {
   vv=vector(1,n);          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
   *d=1.0;          printf(" x(%d)=%.12e",j,xit[j]);
   for (i=1;i<=n;i++) {          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
     big=0.0;        }
     for (j=1;j<=n;j++)        for(j=1;j<=n;j++) {
       if ((temp=fabs(a[i][j])) > big) big=temp;          printf(" p=%.12e",p[j]);
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");          fprintf(ficlog," p=%.12e",p[j]);
     vv[i]=1.0/big;        }
   }        printf("\n");
   for (j=1;j<=n;j++) {        fprintf(ficlog,"\n");
     for (i=1;i<j;i++) {  #endif
       sum=a[i][j];      } 
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
       a[i][j]=sum;  #ifdef DEBUG
     }        int k[2],l;
     big=0.0;        k[0]=1;
     for (i=j;i<=n;i++) {        k[1]=-1;
       sum=a[i][j];        printf("Max: %.12e",(*func)(p));
       for (k=1;k<j;k++)        fprintf(ficlog,"Max: %.12e",(*func)(p));
         sum -= a[i][k]*a[k][j];        for (j=1;j<=n;j++) {
       a[i][j]=sum;          printf(" %.12e",p[j]);
       if ( (dum=vv[i]*fabs(sum)) >= big) {          fprintf(ficlog," %.12e",p[j]);
         big=dum;        }
         imax=i;        printf("\n");
       }        fprintf(ficlog,"\n");
     }        for(l=0;l<=1;l++) {
     if (j != imax) {          for (j=1;j<=n;j++) {
       for (k=1;k<=n;k++) {            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
         dum=a[imax][k];            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
         a[imax][k]=a[j][k];            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
         a[j][k]=dum;          }
       }          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
       *d = -(*d);          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
       vv[imax]=vv[j];        }
     }  #endif
     indx[j]=imax;  
     if (a[j][j] == 0.0) a[j][j]=TINY;  
     if (j != n) {        free_vector(xit,1,n); 
       dum=1.0/(a[j][j]);        free_vector(xits,1,n); 
       for (i=j+1;i<=n;i++) a[i][j] *= dum;        free_vector(ptt,1,n); 
     }        free_vector(pt,1,n); 
   }        return; 
   free_vector(vv,1,n);  /* Doesn't work */      } 
 ;      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
 }      for (j=1;j<=n;j++) { 
         ptt[j]=2.0*p[j]-pt[j]; 
 void lubksb(double **a, int n, int *indx, double b[])        xit[j]=p[j]-pt[j]; 
 {        pt[j]=p[j]; 
   int i,ii=0,ip,j;      } 
   double sum;      fptt=(*func)(ptt); 
        if (fptt < fp) { 
   for (i=1;i<=n;i++) {        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
     ip=indx[i];        if (t < 0.0) { 
     sum=b[ip];          linmin(p,xit,n,fret,func); 
     b[ip]=b[i];          for (j=1;j<=n;j++) { 
     if (ii)            xi[j][ibig]=xi[j][n]; 
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];            xi[j][n]=xit[j]; 
     else if (sum) ii=i;          }
     b[i]=sum;  #ifdef DEBUG
   }          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   for (i=n;i>=1;i--) {          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
     sum=b[i];          for(j=1;j<=n;j++){
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];            printf(" %.12e",xit[j]);
     b[i]=sum/a[i][i];            fprintf(ficlog," %.12e",xit[j]);
   }          }
 }          printf("\n");
           fprintf(ficlog,"\n");
 /************ Frequencies ********************/  #endif
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)        }
 {  /* Some frequencies */      } 
      } 
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;  } 
   double ***freq; /* Frequencies */  
   double *pp;  /**** Prevalence limit (stable or period prevalence)  ****************/
   double pos, k2, dateintsum=0,k2cpt=0;  
   FILE *ficresp;  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
   char fileresp[FILENAMELENGTH];  {
      /* Computes the prevalence limit in each live state at age x by left multiplying the unit
   pp=vector(1,nlstate);       matrix by transitions matrix until convergence is reached */
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);  
   strcpy(fileresp,"p");    int i, ii,j,k;
   strcat(fileresp,fileres);    double min, max, maxmin, maxmax,sumnew=0.;
   if((ficresp=fopen(fileresp,"w"))==NULL) {    double **matprod2();
     printf("Problem with prevalence resultfile: %s\n", fileresp);    double **out, cov[NCOVMAX+1], **pmij();
     exit(0);    double **newm;
   }    double agefin, delaymax=50 ; /* Max number of years to converge */
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);  
   j1=0;    for (ii=1;ii<=nlstate+ndeath;ii++)
        for (j=1;j<=nlstate+ndeath;j++){
   j=cptcoveff;        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   if (cptcovn<1) {j=1;ncodemax[1]=1;}      }
    
   for(k1=1; k1<=j;k1++){     cov[1]=1.;
     for(i1=1; i1<=ncodemax[k1];i1++){   
       j1++;   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
         scanf("%d", i);*/      newm=savm;
       for (i=-1; i<=nlstate+ndeath; i++)        /* Covariates have to be included here again */
         for (jk=-1; jk<=nlstate+ndeath; jk++)         cov[2]=agefin;
           for(m=agemin; m <= agemax+3; m++)    
             freq[i][jk][m]=0;        for (k=1; k<=cptcovn;k++) {
                cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
       dateintsum=0;          /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
       k2cpt=0;        }
       for (i=1; i<=imx; i++) {        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
         bool=1;        for (k=1; k<=cptcovprod;k++)
         if  (cptcovn>0) {          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
           for (z1=1; z1<=cptcoveff; z1++)  
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
               bool=0;        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
         }        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
         if (bool==1) {      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
           for(m=firstpass; m<=lastpass; m++){  
             k2=anint[m][i]+(mint[m][i]/12.);      savm=oldm;
             if ((k2>=dateprev1) && (k2<=dateprev2)) {      oldm=newm;
               if(agev[m][i]==0) agev[m][i]=agemax+1;      maxmax=0.;
               if(agev[m][i]==1) agev[m][i]=agemax+2;      for(j=1;j<=nlstate;j++){
               if (m<lastpass) {        min=1.;
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];        max=0.;
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];        for(i=1; i<=nlstate; i++) {
               }          sumnew=0;
                        for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {          prlim[i][j]= newm[i][j]/(1-sumnew);
                 dateintsum=dateintsum+k2;          max=FMAX(max,prlim[i][j]);
                 k2cpt++;          min=FMIN(min,prlim[i][j]);
               }        }
             }        maxmin=max-min;
           }        maxmax=FMAX(maxmax,maxmin);
         }      }
       }      if(maxmax < ftolpl){
                return prlim;
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);      }
     }
       if  (cptcovn>0) {  }
         fprintf(ficresp, "\n#********** Variable ");  
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  /*************** transition probabilities ***************/ 
         fprintf(ficresp, "**********\n#");  
       }  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
       for(i=1; i<=nlstate;i++)  {
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);    double s1, s2;
       fprintf(ficresp, "\n");    /*double t34;*/
          int i,j,j1, nc, ii, jj;
       for(i=(int)agemin; i <= (int)agemax+3; i++){  
         if(i==(int)agemax+3)      for(i=1; i<= nlstate; i++){
           printf("Total");        for(j=1; j<i;j++){
         else          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
           printf("Age %d", i);            /*s2 += param[i][j][nc]*cov[nc];*/
         for(jk=1; jk <=nlstate ; jk++){            s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)  /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
             pp[jk] += freq[jk][m][i];          }
         }          ps[i][j]=s2;
         for(jk=1; jk <=nlstate ; jk++){  /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
           for(m=-1, pos=0; m <=0 ; m++)        }
             pos += freq[jk][m][i];        for(j=i+1; j<=nlstate+ndeath;j++){
           if(pp[jk]>=1.e-10)          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);            s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
           else  /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);          }
         }          ps[i][j]=s2;
         }
         for(jk=1; jk <=nlstate ; jk++){      }
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)      /*ps[3][2]=1;*/
             pp[jk] += freq[jk][m][i];      
         }      for(i=1; i<= nlstate; i++){
         s1=0;
         for(jk=1,pos=0; jk <=nlstate ; jk++)        for(j=1; j<i; j++){
           pos += pp[jk];          s1+=exp(ps[i][j]);
         for(jk=1; jk <=nlstate ; jk++){          /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
           if(pos>=1.e-5)        }
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);        for(j=i+1; j<=nlstate+ndeath; j++){
           else          s1+=exp(ps[i][j]);
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);          /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
           if( i <= (int) agemax){        }
             if(pos>=1.e-5){        ps[i][i]=1./(s1+1.);
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);        for(j=1; j<i; j++)
               probs[i][jk][j1]= pp[jk]/pos;          ps[i][j]= exp(ps[i][j])*ps[i][i];
               /*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++)
             }          ps[i][j]= exp(ps[i][j])*ps[i][i];
             else        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);      } /* end i */
           }      
         }      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
                for(jj=1; jj<= nlstate+ndeath; jj++){
         for(jk=-1; jk <=nlstate+ndeath; jk++)          ps[ii][jj]=0;
           for(m=-1; m <=nlstate+ndeath; m++)          ps[ii][ii]=1;
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);        }
         if(i <= (int) agemax)      }
           fprintf(ficresp,"\n");      
         printf("\n");  
       }  /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
     }  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
   }  /*         printf("ddd %lf ",ps[ii][jj]); */
   dateintmean=dateintsum/k2cpt;  /*       } */
    /*       printf("\n "); */
   fclose(ficresp);  /*        } */
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);  /*        printf("\n ");printf("%lf ",cov[2]); */
   free_vector(pp,1,nlstate);         /*
          for(i=1; i<= npar; i++) printf("%f ",x[i]);
   /* End of Freq */        goto end;*/
 }      return ps;
   }
 /************ Prevalence ********************/  
 void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)  /**************** Product of 2 matrices ******************/
 {  /* Some frequencies */  
    double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;  {
   double ***freq; /* Frequencies */    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
   double *pp;       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
   double pos, k2;    /* in, b, out are matrice of pointers which should have been initialized 
        before: only the contents of out is modified. The function returns
   pp=vector(1,nlstate);       a pointer to pointers identical to out */
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    long i, j, k;
      for(i=nrl; i<= nrh; i++)
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);      for(k=ncolol; k<=ncoloh; k++)
   j1=0;        for(j=ncl,out[i][k]=0.; j<=nch; j++)
            out[i][k] +=in[i][j]*b[j][k];
   j=cptcoveff;  
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    return out;
    }
   for(k1=1; k1<=j;k1++){  
     for(i1=1; i1<=ncodemax[k1];i1++){  
       j1++;  /************* Higher Matrix Product ***************/
        
       for (i=-1; i<=nlstate+ndeath; i++)    double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
         for (jk=-1; jk<=nlstate+ndeath; jk++)    {
           for(m=agemin; m <= agemax+3; m++)    /* Computes the transition matrix starting at age 'age' over 
             freq[i][jk][m]=0;       'nhstepm*hstepm*stepm' months (i.e. until
             age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
       for (i=1; i<=imx; i++) {       nhstepm*hstepm matrices. 
         bool=1;       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
         if  (cptcovn>0) {       (typically every 2 years instead of every month which is too big 
           for (z1=1; z1<=cptcoveff; z1++)       for the memory).
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])       Model is determined by parameters x and covariates have to be 
               bool=0;       included manually here. 
         }  
         if (bool==1) {       */
           for(m=firstpass; m<=lastpass; m++){  
             k2=anint[m][i]+(mint[m][i]/12.);    int i, j, d, h, k;
             if ((k2>=dateprev1) && (k2<=dateprev2)) {    double **out, cov[NCOVMAX+1];
               if(agev[m][i]==0) agev[m][i]=agemax+1;    double **newm;
               if(agev[m][i]==1) agev[m][i]=agemax+2;  
               if (m<lastpass) {    /* Hstepm could be zero and should return the unit matrix */
                 if (calagedate>0)    for (i=1;i<=nlstate+ndeath;i++)
                   freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];      for (j=1;j<=nlstate+ndeath;j++){
                 else        oldm[i][j]=(i==j ? 1.0 : 0.0);
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];        po[i][j][0]=(i==j ? 1.0 : 0.0);
                 freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];      }
               }    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
             }    for(h=1; h <=nhstepm; h++){
           }      for(d=1; d <=hstepm; d++){
         }        newm=savm;
       }        /* Covariates have to be included here again */
       for(i=(int)agemin; i <= (int)agemax+3; i++){        cov[1]=1.;
         for(jk=1; jk <=nlstate ; jk++){        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        for (k=1; k<=cptcovn;k++) 
             pp[jk] += freq[jk][m][i];          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
         }        for (k=1; k<=cptcovage;k++)
         for(jk=1; jk <=nlstate ; jk++){          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
           for(m=-1, pos=0; m <=0 ; m++)        for (k=1; k<=cptcovprod;k++)
             pos += freq[jk][m][i];          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
         }  
          
         for(jk=1; jk <=nlstate ; jk++){        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
             pp[jk] += freq[jk][m][i];        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
         }                     pmij(pmmij,cov,ncovmodel,x,nlstate));
                savm=oldm;
         for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];        oldm=newm;
              }
         for(jk=1; jk <=nlstate ; jk++){          for(i=1; i<=nlstate+ndeath; i++)
           if( i <= (int) agemax){        for(j=1;j<=nlstate+ndeath;j++) {
             if(pos>=1.e-5){          po[i][j][h]=newm[i][j];
               probs[i][jk][j1]= pp[jk]/pos;          /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
             }        }
           }      /*printf("h=%d ",h);*/
         }    } /* end h */
          /*     printf("\n H=%d \n",h); */
       }    return po;
     }  }
   }  
   
    /*************** log-likelihood *************/
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);  double func( double *x)
   free_vector(pp,1,nlstate);  {
      int i, ii, j, k, mi, d, kk;
 }  /* End of Freq */    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
     double **out;
 /************* Waves Concatenation ***************/    double sw; /* Sum of weights */
     double lli; /* Individual log likelihood */
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)    int s1, s2;
 {    double bbh, survp;
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.    long ipmx;
      Death is a valid wave (if date is known).    /*extern weight */
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i    /* We are differentiating ll according to initial status */
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
      and mw[mi+1][i]. dh depends on stepm.    /*for(i=1;i<imx;i++) 
      */      printf(" %d\n",s[4][i]);
     */
   int i, mi, m;    cov[1]=1.;
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;  
      double sum=0., jmean=0.;*/    for(k=1; k<=nlstate; k++) ll[k]=0.;
   
   int j, k=0,jk, ju, jl;    if(mle==1){
   double sum=0.;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   jmin=1e+5;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   jmax=-1;        for(mi=1; mi<= wav[i]-1; mi++){
   jmean=0.;          for (ii=1;ii<=nlstate+ndeath;ii++)
   for(i=1; i<=imx; i++){            for (j=1;j<=nlstate+ndeath;j++){
     mi=0;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     m=firstpass;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     while(s[m][i] <= nlstate){            }
       if(s[m][i]>=1)          for(d=0; d<dh[mi][i]; d++){
         mw[++mi][i]=m;            newm=savm;
       if(m >=lastpass)            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         break;            for (kk=1; kk<=cptcovage;kk++) {
       else              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         m++;            }
     }/* end while */            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     if (s[m][i] > nlstate){                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       mi++;     /* Death is another wave */            savm=oldm;
       /* if(mi==0)  never been interviewed correctly before death */            oldm=newm;
          /* Only death is a correct wave */          } /* end mult */
       mw[mi][i]=m;        
     }          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
           /* But now since version 0.9 we anticipate for bias at large stepm.
     wav[i]=mi;           * If stepm is larger than one month (smallest stepm) and if the exact delay 
     if(mi==0)           * (in months) between two waves is not a multiple of stepm, we rounded to 
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);           * the nearest (and in case of equal distance, to the lowest) interval but now
   }           * we keep into memory the bias bh[mi][i] and also the previous matrix product
            * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
   for(i=1; i<=imx; i++){           * probability in order to take into account the bias as a fraction of the way
     for(mi=1; mi<wav[i];mi++){           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
       if (stepm <=0)           * -stepm/2 to stepm/2 .
         dh[mi][i]=1;           * For stepm=1 the results are the same as for previous versions of Imach.
       else{           * For stepm > 1 the results are less biased than in previous versions. 
         if (s[mw[mi+1][i]][i] > nlstate) {           */
           if (agedc[i] < 2*AGESUP) {          s1=s[mw[mi][i]][i];
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);          s2=s[mw[mi+1][i]][i];
           if(j==0) j=1;  /* Survives at least one month after exam */          bbh=(double)bh[mi][i]/(double)stepm; 
           k=k+1;          /* bias bh is positive if real duration
           if (j >= jmax) jmax=j;           * is higher than the multiple of stepm and negative otherwise.
           if (j <= jmin) jmin=j;           */
           sum=sum+j;          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
           /*if (j<0) printf("j=%d num=%d \n",j,i); */          if( s2 > nlstate){ 
           }            /* i.e. if s2 is a death state and if the date of death is known 
         }               then the contribution to the likelihood is the probability to 
         else{               die between last step unit time and current  step unit time, 
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));               which is also equal to probability to die before dh 
           k=k+1;               minus probability to die before dh-stepm . 
           if (j >= jmax) jmax=j;               In version up to 0.92 likelihood was computed
           else if (j <= jmin)jmin=j;          as if date of death was unknown. Death was treated as any other
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */          health state: the date of the interview describes the actual state
           sum=sum+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
         jk= j/stepm;          (healthy, disable or death) and IMaCh was corrected; but when we
         jl= j -jk*stepm;          introduced the exact date of death then we should have modified
         ju= j -(jk+1)*stepm;          the contribution of an exact death to the likelihood. This new
         if(jl <= -ju)          contribution is smaller and very dependent of the step unit
           dh[mi][i]=jk;          stepm. It is no more the probability to die between last interview
         else          and month of death but the probability to survive from last
           dh[mi][i]=jk+1;          interview up to one month before death multiplied by the
         if(dh[mi][i]==0)          probability to die within a month. Thanks to Chris
           dh[mi][i]=1; /* At least one step */          Jackson for correcting this bug.  Former versions increased
       }          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.
   jmean=sum/k;            */
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);            lli=log(out[s1][s2] - savm[s1][s2]);
  }  
 /*********** Tricode ****************************/  
 void tricode(int *Tvar, int **nbcode, int imx)          } else if  (s2==-2) {
 {            for (j=1,survp=0. ; j<=nlstate; j++) 
   int Ndum[20],ij=1, k, j, i;              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   int cptcode=0;            /*survp += out[s1][j]; */
   cptcoveff=0;            lli= log(survp);
            }
   for (k=0; k<19; k++) Ndum[k]=0;          
   for (k=1; k<=7; k++) ncodemax[k]=0;          else if  (s2==-4) { 
             for (j=3,survp=0. ; j<=nlstate; j++)  
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
     for (i=1; i<=imx; i++) {            lli= log(survp); 
       ij=(int)(covar[Tvar[j]][i]);          } 
       Ndum[ij]++;  
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/          else if  (s2==-5) { 
       if (ij > cptcode) cptcode=ij;            for (j=1,survp=0. ; j<=2; j++)  
     }              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
             lli= log(survp); 
     for (i=0; i<=cptcode; i++) {          } 
       if(Ndum[i]!=0) ncodemax[j]++;          
     }          else{
     ij=1;            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
             /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
           } 
     for (i=1; i<=ncodemax[j]; i++) {          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
       for (k=0; k<=19; k++) {          /*if(lli ==000.0)*/
         if (Ndum[k] != 0) {          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
           nbcode[Tvar[j]][ij]=k;          ipmx +=1;
                    sw += weight[i];
           ij++;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         }        } /* end of wave */
         if (ij > ncodemax[j]) break;      } /* end of individual */
       }      }  else if(mle==2){
     }      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 (k=0; k<19; k++) Ndum[k]=0;          for (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
  for (i=1; i<=ncovmodel-2; i++) {              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       ij=Tvar[i];              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       Ndum[ij]++;            }
     }          for(d=0; d<=dh[mi][i]; d++){
             newm=savm;
  ij=1;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
  for (i=1; i<=10; i++) {            for (kk=1; kk<=cptcovage;kk++) {
    if((Ndum[i]!=0) && (i<=ncovcol)){              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
      Tvaraff[ij]=i;            }
      ij++;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
    }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
  }            savm=oldm;
              oldm=newm;
     cptcoveff=ij-1;          } /* end mult */
 }        
           s1=s[mw[mi][i]][i];
 /*********** Health Expectancies ****************/          s2=s[mw[mi+1][i]][i];
           bbh=(double)bh[mi][i]/(double)stepm; 
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
           ipmx +=1;
 {          sw += weight[i];
   /* Health expectancies */          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;        } /* end of wave */
   double age, agelim, hf;      } /* end of individual */
   double ***p3mat,***varhe;    }  else if(mle==3){  /* exponential inter-extrapolation */
   double **dnewm,**doldm;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   double *xp;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   double **gp, **gm;        for(mi=1; mi<= wav[i]-1; mi++){
   double ***gradg, ***trgradg;          for (ii=1;ii<=nlstate+ndeath;ii++)
   int theta;            for (j=1;j<=nlstate+ndeath;j++){
               oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   xp=vector(1,npar);            }
   dnewm=matrix(1,nlstate*2,1,npar);          for(d=0; d<dh[mi][i]; d++){
   doldm=matrix(1,nlstate*2,1,nlstate*2);            newm=savm;
              cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   fprintf(ficreseij,"# Health expectancies\n");            for (kk=1; kk<=cptcovage;kk++) {
   fprintf(ficreseij,"# Age");              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   for(i=1; i<=nlstate;i++)            }
     for(j=1; j<=nlstate;j++)            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       fprintf(ficreseij," %1d-%1d (SE)",i,j);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   fprintf(ficreseij,"\n");            savm=oldm;
             oldm=newm;
   if(estepm < stepm){          } /* end mult */
     printf ("Problem %d lower than %d\n",estepm, stepm);        
   }          s1=s[mw[mi][i]][i];
   else  hstepm=estepm;            s2=s[mw[mi+1][i]][i];
   /* We compute the life expectancy from trapezoids spaced every estepm months          bbh=(double)bh[mi][i]/(double)stepm; 
    * This is mainly to measure the difference between two models: for example          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 */
    * if stepm=24 months pijx are given only every 2 years and by summing them          ipmx +=1;
    * we are calculating an estimate of the Life Expectancy assuming a linear          sw += weight[i];
    * progression inbetween and thus overestimating or underestimating according          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
    * to the curvature of the survival function. If, for the same date, we        } /* end of wave */
    * estimate the model with stepm=1 month, we can keep estepm to 24 months      } /* end of individual */
    * to compare the new estimate of Life expectancy with the same linear    }else if (mle==4){  /* ml=4 no inter-extrapolation */
    * hypothesis. A more precise result, taking into account a more precise      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
    * curvature will be obtained if estepm is as small as stepm. */        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for(mi=1; mi<= wav[i]-1; mi++){
   /* For example we decided to compute the life expectancy with the smallest unit */          for (ii=1;ii<=nlstate+ndeath;ii++)
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.            for (j=1;j<=nlstate+ndeath;j++){
      nhstepm is the number of hstepm from age to agelim              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
      nstepm is the number of stepm from age to agelin.              savm[ii][j]=(ii==j ? 1.0 : 0.0);
      Look at hpijx to understand the reason of that which relies in memory size            }
      and note for a fixed period like estepm months */          for(d=0; d<dh[mi][i]; d++){
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the            newm=savm;
      survival function given by stepm (the optimization length). Unfortunately it            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
      means that if the survival funtion is printed only each two years of age and if            for (kk=1; kk<=cptcovage;kk++) {
      you sum them up and add 1 year (area under the trapezoids) you won't get the same              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
      results. So we changed our mind and took the option of the best precision.            }
   */          
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   agelim=AGESUP;            savm=oldm;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */            oldm=newm;
     /* nhstepm age range expressed in number of stepm */          } /* end mult */
     nstepm=(int) rint((agelim-age)*YEARM/stepm);        
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */          s1=s[mw[mi][i]][i];
     /* if (stepm >= YEARM) hstepm=1;*/          s2=s[mw[mi+1][i]][i];
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */          if( s2 > nlstate){ 
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            lli=log(out[s1][s2] - savm[s1][s2]);
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);          }else{
     gp=matrix(0,nhstepm,1,nlstate*2);            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
     gm=matrix(0,nhstepm,1,nlstate*2);          }
           ipmx +=1;
     /* Computed by stepm unit matrices, product of hstepm matrices, stored          sw += weight[i];
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);    /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
          } /* end of wave */
       } /* end of individual */
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     /* Computing Variances of health expectancies */        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for(mi=1; mi<= wav[i]-1; mi++){
      for(theta=1; theta <=npar; theta++){          for (ii=1;ii<=nlstate+ndeath;ii++)
       for(i=1; i<=npar; i++){            for (j=1;j<=nlstate+ndeath;j++){
         xp[i] = x[i] + (i==theta ?delti[theta]:0);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);              }
            for(d=0; d<dh[mi][i]; d++){
       cptj=0;            newm=savm;
       for(j=1; j<= nlstate; j++){            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         for(i=1; i<=nlstate; i++){            for (kk=1; kk<=cptcovage;kk++) {
           cptj=cptj+1;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){            }
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;          
           }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       }            savm=oldm;
                  oldm=newm;
                } /* end mult */
       for(i=1; i<=npar; i++)        
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          s1=s[mw[mi][i]][i];
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            s2=s[mw[mi+1][i]][i];
                lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
       cptj=0;          ipmx +=1;
       for(j=1; j<= nlstate; j++){          sw += weight[i];
         for(i=1;i<=nlstate;i++){          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           cptj=cptj+1;          /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){        } /* end of wave */
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;      } /* end of individual */
           }    } /* End of if */
         }    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
       }    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
          l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
        return -l;
   }
       for(j=1; j<= nlstate*2; j++)  
         for(h=0; h<=nhstepm-1; h++){  /*************** log-likelihood *************/
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];  double funcone( double *x)
         }  {
     /* Same as likeli but slower because of a lot of printf and if */
      }    int i, ii, j, k, mi, d, kk;
        double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
 /* End theta */    double **out;
     double lli; /* Individual log likelihood */
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);    double llt;
     int s1, s2;
      for(h=0; h<=nhstepm-1; h++)    double bbh, survp;
       for(j=1; j<=nlstate*2;j++)    /*extern weight */
         for(theta=1; theta <=npar; theta++)    /* We are differentiating ll according to initial status */
         trgradg[h][j][theta]=gradg[h][theta][j];    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     /*for(i=1;i<imx;i++) 
       printf(" %d\n",s[4][i]);
      for(i=1;i<=nlstate*2;i++)    */
       for(j=1;j<=nlstate*2;j++)    cov[1]=1.;
         varhe[i][j][(int)age] =0.;  
     for(k=1; k<=nlstate; k++) ll[k]=0.;
      printf("%d||",(int)age);fflush(stdout);  
     for(h=0;h<=nhstepm-1;h++){    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       for(k=0;k<=nhstepm-1;k++){      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);      for(mi=1; mi<= wav[i]-1; mi++){
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);        for (ii=1;ii<=nlstate+ndeath;ii++)
         for(i=1;i<=nlstate*2;i++)          for (j=1;j<=nlstate+ndeath;j++){
           for(j=1;j<=nlstate*2;j++)            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;            savm[ii][j]=(ii==j ? 1.0 : 0.0);
       }          }
     }        for(d=0; d<dh[mi][i]; d++){
           newm=savm;
                cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     /* Computing expectancies */          for (kk=1; kk<=cptcovage;kk++) {
     for(i=1; i<=nlstate;i++)            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       for(j=1; j<=nlstate;j++)          }
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
                    savm=oldm;
 /* 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]);*/          oldm=newm;
         } /* end mult */
         }        
         s1=s[mw[mi][i]][i];
     fprintf(ficreseij,"%3.0f",age );        s2=s[mw[mi+1][i]][i];
     cptj=0;        bbh=(double)bh[mi][i]/(double)stepm; 
     for(i=1; i<=nlstate;i++)        /* bias is positive if real duration
       for(j=1; j<=nlstate;j++){         * is higher than the multiple of stepm and negative otherwise.
         cptj++;         */
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );        if( s2 > nlstate && (mle <5) ){  /* Jackson */
       }          lli=log(out[s1][s2] - savm[s1][s2]);
     fprintf(ficreseij,"\n");        } else if  (s2==-2) {
              for (j=1,survp=0. ; j<=nlstate; j++) 
     free_matrix(gm,0,nhstepm,1,nlstate*2);            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
     free_matrix(gp,0,nhstepm,1,nlstate*2);          lli= log(survp);
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);        }else if (mle==1){
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        } else if(mle==2){
   }          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 */
   free_vector(xp,1,npar);        } else if(mle==3){  /* exponential inter-extrapolation */
   free_matrix(dnewm,1,nlstate*2,1,npar);          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 */
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);        } else if (mle==4){  /* mle=4 no inter-extrapolation */
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);          lli=log(out[s1][s2]); /* Original formula */
 }        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
           lli=log(out[s1][s2]); /* Original formula */
 /************ Variance ******************/        } /* End of if */
 void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm)        ipmx +=1;
 {        sw += weight[i];
   /* Variance of health expectancies */        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/        /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
   double **newm;        if(globpr){
   double **dnewm,**doldm;          fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
   int i, j, nhstepm, hstepm, h, nstepm ;   %11.6f %11.6f %11.6f ", \
   int k, cptcode;                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
   double *xp;                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
   double **gp, **gm;          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
   double ***gradg, ***trgradg;            llt +=ll[k]*gipmx/gsw;
   double ***p3mat;            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
   double age,agelim, hf;          }
   int theta;          fprintf(ficresilk," %10.6f\n", -llt);
         }
    fprintf(ficresvij,"# Covariances of life expectancies\n");      } /* end of wave */
   fprintf(ficresvij,"# Age");    } /* end of individual */
   for(i=1; i<=nlstate;i++)    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     for(j=1; j<=nlstate;j++)    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
   fprintf(ficresvij,"\n");    if(globpr==0){ /* First time we count the contributions and weights */
       gipmx=ipmx;
   xp=vector(1,npar);      gsw=sw;
   dnewm=matrix(1,nlstate,1,npar);    }
   doldm=matrix(1,nlstate,1,nlstate);    return -l;
    }
   if(estepm < stepm){  
     printf ("Problem %d lower than %d\n",estepm, stepm);  
   }  /*************** function likelione ***********/
   else  hstepm=estepm;    void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
   /* 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.    /* This routine should help understanding what is done with 
      nhstepm is the number of hstepm from age to agelim       the selection of individuals/waves and
      nstepm is the number of stepm from age to agelin.       to check the exact contribution to the likelihood.
      Look at hpijx to understand the reason of that which relies in memory size       Plotting could be done.
      and note for a fixed period like k years */     */
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the    int k;
      survival function given by stepm (the optimization length). Unfortunately it  
      means that if the survival funtion is printed only each two years of age and if    if(*globpri !=0){ /* Just counts and sums, no printings */
      you sum them up and add 1 year (area under the trapezoids) you won't get the same      strcpy(fileresilk,"ilk"); 
      results. So we changed our mind and took the option of the best precision.      strcat(fileresilk,fileres);
   */      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */        printf("Problem with resultfile: %s\n", fileresilk);
   agelim = AGESUP;        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      }
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      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");
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);      for(k=1; k<=nlstate; k++) 
     gp=matrix(0,nhstepm,1,nlstate);        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
     gm=matrix(0,nhstepm,1,nlstate);      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
     }
     for(theta=1; theta <=npar; theta++){  
       for(i=1; i<=npar; i++){ /* Computes gradient */    *fretone=(*funcone)(p);
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    if(*globpri !=0){
       }      fclose(ficresilk);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      fflush(fichtm); 
     } 
       if (popbased==1) {    return;
         for(i=1; i<=nlstate;i++)  }
           prlim[i][i]=probs[(int)age][i][ij];  
       }  
    /*********** Maximum Likelihood Estimation ***************/
       for(j=1; j<= nlstate; j++){  
         for(h=0; h<=nhstepm; h++){  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)  {
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];    int i,j, iter;
         }    double **xi;
       }    double fret;
        double fretone; /* Only one call to likelihood */
       for(i=1; i<=npar; i++) /* Computes gradient */    /*  char filerespow[FILENAMELENGTH];*/
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    xi=matrix(1,npar,1,npar);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      for (i=1;i<=npar;i++)
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      for (j=1;j<=npar;j++)
          xi[i][j]=(i==j ? 1.0 : 0.0);
       if (popbased==1) {    printf("Powell\n");  fprintf(ficlog,"Powell\n");
         for(i=1; i<=nlstate;i++)    strcpy(filerespow,"pow"); 
           prlim[i][i]=probs[(int)age][i][ij];    strcat(filerespow,fileres);
       }    if((ficrespow=fopen(filerespow,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", filerespow);
       for(j=1; j<= nlstate; j++){      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
         for(h=0; h<=nhstepm; h++){    }
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)    fprintf(ficrespow,"# Powell\n# iter -2*LL");
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];    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");
       for(j=1; j<= nlstate; j++)  
         for(h=0; h<=nhstepm; h++){    powell(p,xi,npar,ftol,&iter,&fret,func);
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];  
         }    free_matrix(xi,1,npar,1,npar);
     } /* End theta */    fclose(ficrespow);
     printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     for(h=0; h<=nhstepm; h++)  
       for(j=1; j<=nlstate;j++)  }
         for(theta=1; theta <=npar; theta++)  
           trgradg[h][j][theta]=gradg[h][theta][j];  /**** Computes Hessian and covariance matrix ***/
   void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */  {
     for(i=1;i<=nlstate;i++)    double  **a,**y,*x,pd;
       for(j=1;j<=nlstate;j++)    double **hess;
         vareij[i][j][(int)age] =0.;    int i, j,jk;
     int *indx;
     for(h=0;h<=nhstepm;h++){  
       for(k=0;k<=nhstepm;k++){    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);    void lubksb(double **a, int npar, int *indx, double b[]) ;
         for(i=1;i<=nlstate;i++)    void ludcmp(double **a, int npar, int *indx, double *d) ;
           for(j=1;j<=nlstate;j++)    double gompertz(double p[]);
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;    hess=matrix(1,npar,1,npar);
       }  
     }    printf("\nCalculation of the hessian matrix. Wait...\n");
     fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
     fprintf(ficresvij,"%.0f ",age );    for (i=1;i<=npar;i++){
     for(i=1; i<=nlstate;i++)      printf("%d",i);fflush(stdout);
       for(j=1; j<=nlstate;j++){      fprintf(ficlog,"%d",i);fflush(ficlog);
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);     
       }       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
     fprintf(ficresvij,"\n");      
     free_matrix(gp,0,nhstepm,1,nlstate);      /*  printf(" %f ",p[i]);
     free_matrix(gm,0,nhstepm,1,nlstate);          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
     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);    for (i=1;i<=npar;i++) {
   } /* End age */      for (j=1;j<=npar;j++)  {
          if (j>i) { 
   free_vector(xp,1,npar);          printf(".%d%d",i,j);fflush(stdout);
   free_matrix(doldm,1,nlstate,1,npar);          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
   free_matrix(dnewm,1,nlstate,1,nlstate);          hess[i][j]=hessij(p,delti,i,j,func,npar);
           
 }          hess[j][i]=hess[i][j];    
           /*printf(" %lf ",hess[i][j]);*/
 /************ 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)      }
 {    }
   /* Variance of prevalence limit */    printf("\n");
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    fprintf(ficlog,"\n");
   double **newm;  
   double **dnewm,**doldm;    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
   int i, j, nhstepm, hstepm;    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
   int k, cptcode;    
   double *xp;    a=matrix(1,npar,1,npar);
   double *gp, *gm;    y=matrix(1,npar,1,npar);
   double **gradg, **trgradg;    x=vector(1,npar);
   double age,agelim;    indx=ivector(1,npar);
   int theta;    for (i=1;i<=npar;i++)
          for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");    ludcmp(a,npar,indx,&pd);
   fprintf(ficresvpl,"# Age");  
   for(i=1; i<=nlstate;i++)    for (j=1;j<=npar;j++) {
       fprintf(ficresvpl," %1d-%1d",i,i);      for (i=1;i<=npar;i++) x[i]=0;
   fprintf(ficresvpl,"\n");      x[j]=1;
       lubksb(a,npar,indx,x);
   xp=vector(1,npar);      for (i=1;i<=npar;i++){ 
   dnewm=matrix(1,nlstate,1,npar);        matcov[i][j]=x[i];
   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 */    printf("\n#Hessian matrix#\n");
   agelim = AGESUP;    fprintf(ficlog,"\n#Hessian matrix#\n");
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    for (i=1;i<=npar;i++) { 
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      for (j=1;j<=npar;j++) { 
     if (stepm >= YEARM) hstepm=1;        printf("%.3e ",hess[i][j]);
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */        fprintf(ficlog,"%.3e ",hess[i][j]);
     gradg=matrix(1,npar,1,nlstate);      }
     gp=vector(1,nlstate);      printf("\n");
     gm=vector(1,nlstate);      fprintf(ficlog,"\n");
     }
     for(theta=1; theta <=npar; theta++){  
       for(i=1; i<=npar; i++){ /* Computes gradient */    /* Recompute Inverse */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    for (i=1;i<=npar;i++)
       }      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    ludcmp(a,npar,indx,&pd);
       for(i=1;i<=nlstate;i++)  
         gp[i] = prlim[i][i];    /*  printf("\n#Hessian matrix recomputed#\n");
      
       for(i=1; i<=npar; i++) /* Computes gradient */    for (j=1;j<=npar;j++) {
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      for (i=1;i<=npar;i++) x[i]=0;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      x[j]=1;
       for(i=1;i<=nlstate;i++)      lubksb(a,npar,indx,x);
         gm[i] = prlim[i][i];      for (i=1;i<=npar;i++){ 
         y[i][j]=x[i];
       for(i=1;i<=nlstate;i++)        printf("%.3e ",y[i][j]);
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];        fprintf(ficlog,"%.3e ",y[i][j]);
     } /* End theta */      }
       printf("\n");
     trgradg =matrix(1,nlstate,1,npar);      fprintf(ficlog,"\n");
     }
     for(j=1; j<=nlstate;j++)    */
       for(theta=1; theta <=npar; theta++)  
         trgradg[j][theta]=gradg[theta][j];    free_matrix(a,1,npar,1,npar);
     free_matrix(y,1,npar,1,npar);
     for(i=1;i<=nlstate;i++)    free_vector(x,1,npar);
       varpl[i][(int)age] =0.;    free_ivector(indx,1,npar);
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);    free_matrix(hess,1,npar,1,npar);
     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 );  /*************** hessian matrix ****************/
     for(i=1; i<=nlstate;i++)  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));  {
     fprintf(ficresvpl,"\n");    int i;
     free_vector(gp,1,nlstate);    int l=1, lmax=20;
     free_vector(gm,1,nlstate);    double k1,k2;
     free_matrix(gradg,1,npar,1,nlstate);    double p2[MAXPARM+1]; /* identical to x */
     free_matrix(trgradg,1,nlstate,1,npar);    double res;
   } /* End age */    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
     double fx;
   free_vector(xp,1,npar);    int k=0,kmax=10;
   free_matrix(doldm,1,nlstate,1,npar);    double l1;
   free_matrix(dnewm,1,nlstate,1,nlstate);  
     fx=func(x);
 }    for (i=1;i<=npar;i++) p2[i]=x[i];
     for(l=0 ; l <=lmax; l++){
 /************ Variance of one-step probabilities  ******************/      l1=pow(10,l);
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)      delts=delt;
 {      for(k=1 ; k <kmax; k=k+1){
   int i, j, i1, k1, j1, z1;        delt = delta*(l1*k);
   int k=0, cptcode;        p2[theta]=x[theta] +delt;
   double **dnewm,**doldm;        k1=func(p2)-fx;
   double *xp;        p2[theta]=x[theta]-delt;
   double *gp, *gm;        k2=func(p2)-fx;
   double **gradg, **trgradg;        /*res= (k1-2.0*fx+k2)/delt/delt; */
   double age,agelim, cov[NCOVMAX];        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
   int theta;        
   char fileresprob[FILENAMELENGTH];  #ifdef DEBUGHESS
         printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
   strcpy(fileresprob,"prob");        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);
   strcat(fileresprob,fileres);  #endif
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
     printf("Problem with resultfile: %s\n", fileresprob);        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
   }          k=kmax;
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);        }
          else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
 fprintf(ficresprob,"#One-step probabilities and standard deviation in parentheses\n");          k=kmax; l=lmax*10.;
   fprintf(ficresprob,"# Age");        }
   for(i=1; i<=nlstate;i++)        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
     for(j=1; j<=(nlstate+ndeath);j++)          delts=delt;
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);        }
       }
     }
   fprintf(ficresprob,"\n");    delti[theta]=delts;
     return res; 
     
   xp=vector(1,npar);  }
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);  
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
    {
   cov[1]=1;    int i;
   j=cptcoveff;    int l=1, l1, lmax=20;
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    double k1,k2,k3,k4,res,fx;
   j1=0;    double p2[MAXPARM+1];
   for(k1=1; k1<=1;k1++){    int k;
     for(i1=1; i1<=ncodemax[k1];i1++){  
     j1++;    fx=func(x);
     for (k=1; k<=2; k++) {
     if  (cptcovn>0) {      for (i=1;i<=npar;i++) p2[i]=x[i];
       fprintf(ficresprob, "\n#********** Variable ");      p2[thetai]=x[thetai]+delti[thetai]/k;
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       fprintf(ficresprob, "**********\n#");      k1=func(p2)-fx;
     }    
          p2[thetai]=x[thetai]+delti[thetai]/k;
       for (age=bage; age<=fage; age ++){      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
         cov[2]=age;      k2=func(p2)-fx;
         for (k=1; k<=cptcovn;k++) {    
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];      p2[thetai]=x[thetai]-delti[thetai]/k;
                p2[thetaj]=x[thetaj]+delti[thetaj]/k;
         }      k3=func(p2)-fx;
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    
         for (k=1; k<=cptcovprod;k++)      p2[thetai]=x[thetai]-delti[thetai]/k;
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
              k4=func(p2)-fx;
         gradg=matrix(1,npar,1,9);      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
         trgradg=matrix(1,9,1,npar);  #ifdef DEBUG
         gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));      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);
         gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));      fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
      #endif
         for(theta=1; theta <=npar; theta++){    }
           for(i=1; i<=npar; i++)    return res;
             xp[i] = x[i] + (i==theta ?delti[theta]:0);  }
            
           pmij(pmmij,cov,ncovmodel,xp,nlstate);  /************** Inverse of matrix **************/
            void ludcmp(double **a, int n, int *indx, double *d) 
           k=0;  { 
           for(i=1; i<= (nlstate+ndeath); i++){    int i,imax,j,k; 
             for(j=1; j<=(nlstate+ndeath);j++){    double big,dum,sum,temp; 
               k=k+1;    double *vv; 
               gp[k]=pmmij[i][j];   
             }    vv=vector(1,n); 
           }    *d=1.0; 
              for (i=1;i<=n;i++) { 
           for(i=1; i<=npar; i++)      big=0.0; 
             xp[i] = x[i] - (i==theta ?delti[theta]:0);      for (j=1;j<=n;j++) 
            if ((temp=fabs(a[i][j])) > big) big=temp; 
           pmij(pmmij,cov,ncovmodel,xp,nlstate);      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
           k=0;      vv[i]=1.0/big; 
           for(i=1; i<=(nlstate+ndeath); i++){    } 
             for(j=1; j<=(nlstate+ndeath);j++){    for (j=1;j<=n;j++) { 
               k=k+1;      for (i=1;i<j;i++) { 
               gm[k]=pmmij[i][j];        sum=a[i][j]; 
             }        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
           }        a[i][j]=sum; 
            } 
           for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)      big=0.0; 
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];        for (i=j;i<=n;i++) { 
         }        sum=a[i][j]; 
         for (k=1;k<j;k++) 
         for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)          sum -= a[i][k]*a[k][j]; 
           for(theta=1; theta <=npar; theta++)        a[i][j]=sum; 
             trgradg[j][theta]=gradg[theta][j];        if ( (dum=vv[i]*fabs(sum)) >= big) { 
                  big=dum; 
         matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);          imax=i; 
         matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);        } 
              } 
         pmij(pmmij,cov,ncovmodel,x,nlstate);      if (j != imax) { 
                for (k=1;k<=n;k++) { 
         k=0;          dum=a[imax][k]; 
         for(i=1; i<=(nlstate+ndeath); i++){          a[imax][k]=a[j][k]; 
           for(j=1; j<=(nlstate+ndeath);j++){          a[j][k]=dum; 
             k=k+1;        } 
             gm[k]=pmmij[i][j];        *d = -(*d); 
           }        vv[imax]=vv[j]; 
         }      } 
            indx[j]=imax; 
      /*printf("\n%d ",(int)age);      if (a[j][j] == 0.0) a[j][j]=TINY; 
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){      if (j != n) { 
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));        dum=1.0/(a[j][j]); 
      }*/        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
       } 
         fprintf(ficresprob,"\n%d ",(int)age);    } 
     free_vector(vv,1,n);  /* Doesn't work */
         for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++)  ;
           fprintf(ficresprob,"%.3e (%.3e) ",gm[i],sqrt(doldm[i][i]));  } 
    
       }  void lubksb(double **a, int n, int *indx, double b[]) 
     }  { 
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));    int i,ii=0,ip,j; 
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));    double sum; 
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);   
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    for (i=1;i<=n;i++) { 
   }      ip=indx[i]; 
   free_vector(xp,1,npar);      sum=b[ip]; 
   fclose(ficresprob);      b[ip]=b[i]; 
        if (ii) 
 }        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
       else if (sum) ii=i; 
 /******************* Printing html file ***********/      b[i]=sum; 
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \    } 
  int lastpass, int stepm, int weightopt, char model[],\    for (i=n;i>=1;i--) { 
  int imx,int jmin, int jmax, double jmeanint,char optionfile[], \      sum=b[i]; 
  char optionfilehtm[],char rfileres[], char optionfilegnuplot[],\      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
  char version[], int popforecast, int estepm ){      b[i]=sum/a[i][i]; 
   int jj1, k1, i1, cpt;    } 
   FILE *fichtm;  } 
   /*char optionfilehtm[FILENAMELENGTH];*/  
   void pstamp(FILE *fichier)
   strcpy(optionfilehtm,optionfile);  {
   strcat(optionfilehtm,".htm");    fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {  }
     printf("Problem with %s \n",optionfilehtm), exit(0);  
   }  /************ Frequencies ********************/
   void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])
  fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n  {  /* Some frequencies */
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n    
 \n    int i, m, jk, k1,i1, j1, bool, z1,j;
 Total number of observations=%d <br>\n    int first;
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n    double ***freq; /* Frequencies */
 <hr  size=\"2\" color=\"#EC5E5E\">    double *pp, **prop;
  <ul><li>Outputs files<br>\n    double pos,posprop, k2, dateintsum=0,k2cpt=0;
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n    char fileresp[FILENAMELENGTH];
  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n    
  - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n    pp=vector(1,nlstate);
  - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>\n    prop=matrix(1,nlstate,iagemin,iagemax+3);
  - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>\n    strcpy(fileresp,"p");
  - Life expectancies by age and initial health status (estepm=%2d months): <a href=\"e%s\">e%s</a> <br>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot,fileres,fileres,fileres,fileres,fileres,fileres,estepm,fileres,fileres);    strcat(fileresp,fileres);
     if((ficresp=fopen(fileresp,"w"))==NULL) {
  fprintf(fichtm,"\n      printf("Problem with prevalence resultfile: %s\n", fileresp);
  - Parameter file with estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>\n      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
   - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n      exit(0);
  - Variances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n    }
  - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>\n    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
  - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);    j1=0;
     
  if(popforecast==1) fprintf(fichtm,"\n    j=cptcoveff;
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n    if (cptcovn<1) {j=1;ncodemax[1]=1;}
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n  
         <br>",fileres,fileres,fileres,fileres);    first=1;
  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);    for(k1=1; k1<=j;k1++){
 fprintf(fichtm," <li>Graphs</li><p>");      for(i1=1; i1<=ncodemax[k1];i1++){
         j1++;
  m=cptcoveff;        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}          scanf("%d", i);*/
         for (i=-5; i<=nlstate+ndeath; i++)  
  jj1=0;          for (jk=-5; jk<=nlstate+ndeath; jk++)  
  for(k1=1; k1<=m;k1++){            for(m=iagemin; m <= iagemax+3; m++)
    for(i1=1; i1<=ncodemax[k1];i1++){              freq[i][jk][m]=0;
        jj1++;  
        if (cptcovn > 0) {      for (i=1; i<=nlstate; i++)  
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");        for(m=iagemin; m <= iagemax+3; m++)
          for (cpt=1; cpt<=cptcoveff;cpt++)          prop[i][m]=0;
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);        
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");        dateintsum=0;
        }        k2cpt=0;
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.png<br>        for (i=1; i<=imx; i++) {
 <img src=\"pe%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);              bool=1;
        for(cpt=1; cpt<nlstate;cpt++){          if  (cptcovn>0) {
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.png<br>            for (z1=1; z1<=cptcoveff; z1++) 
 <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
        }                bool=0;
     for(cpt=1; cpt<=nlstate;cpt++) {          }
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident          if (bool==1){
 interval) in state (%d): v%s%d%d.png <br>            for(m=firstpass; m<=lastpass; m++){
 <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);                k2=anint[m][i]+(mint[m][i]/12.);
      }              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
      for(cpt=1; cpt<=nlstate;cpt++) {                if(agev[m][i]==0) agev[m][i]=iagemax+1;
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>                if(agev[m][i]==1) agev[m][i]=iagemax+2;
 <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
      }                if (m<lastpass) {
      fprintf(fichtm,"\n<br>- Total life expectancy by age and                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
 health expectancies in states (1) and (2): e%s%d.png<br>                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
 <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);                }
 fprintf(fichtm,"\n</body>");                
    }                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
    }                  dateintsum=dateintsum+k2;
 fclose(fichtm);                  k2cpt++;
 }                }
                 /*}*/
 /******************* Gnuplot file **************/            }
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){          }
         }
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;         
         /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
   strcpy(optionfilegnuplot,optionfilefiname);        pstamp(ficresp);
   strcat(optionfilegnuplot,".gp.txt");        if  (cptcovn>0) {
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {          fprintf(ficresp, "\n#********** Variable "); 
     printf("Problem with file %s",optionfilegnuplot);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   }          fprintf(ficresp, "**********\n#");
         }
 #ifdef windows        for(i=1; i<=nlstate;i++) 
     fprintf(ficgp,"cd \"%s\" \n",pathc);          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
 #endif        fprintf(ficresp, "\n");
 m=pow(2,cptcoveff);        
          for(i=iagemin; i <= iagemax+3; i++){
  /* 1eme*/          if(i==iagemax+3){
   for (cpt=1; cpt<= nlstate ; cpt ++) {            fprintf(ficlog,"Total");
    for (k1=1; k1<= m ; k1 ++) {          }else{
             if(first==1){
 #ifdef windows              first=0;
      fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n\n",strtok(optionfile, "."),cpt,k1);              printf("See log file for details...\n");
      fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);            }
 #endif            fprintf(ficlog,"Age %d", i);
 #ifdef unix          }
 fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n\n",strtok(optionfile, "."),cpt,k1);          for(jk=1; jk <=nlstate ; jk++){
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
 #endif              pp[jk] += freq[jk][m][i]; 
           }
 for (i=1; i<= nlstate ; i ++) {          for(jk=1; jk <=nlstate ; jk++){
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");            for(m=-1, pos=0; m <=0 ; m++)
   else fprintf(ficgp," \%%*lf (\%%*lf)");              pos += freq[jk][m][i];
 }            if(pp[jk]>=1.e-10){
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);              if(first==1){
     for (i=1; i<= nlstate ; i ++) {                printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");              }
   else fprintf(ficgp," \%%*lf (\%%*lf)");              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
 }            }else{
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);              if(first==1)
      for (i=1; i<= nlstate ; i ++) {                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   else fprintf(ficgp," \%%*lf (\%%*lf)");            }
 }            }
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));  
 #ifdef unix          for(jk=1; jk <=nlstate ; jk++){
 fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
 #endif              pp[jk] += freq[jk][m][i];
    }          }       
   }          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
   /*2 eme*/            pos += pp[jk];
             posprop += prop[jk][i];
   for (k1=1; k1<= m ; k1 ++) {          }
     fprintf(ficgp,"\nset out \"e%s%d.png\" \n\n",strtok(optionfile, "."),k1);          for(jk=1; jk <=nlstate ; jk++){
     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);            if(pos>=1.e-5){
                  if(first==1)
     for (i=1; i<= nlstate+1 ; i ++) {                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
       k=2*i;              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);            }else{
       for (j=1; j<= nlstate+1 ; j ++) {              if(first==1)
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   else fprintf(ficgp," \%%*lf (\%%*lf)");              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
 }              }
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");            if( i <= iagemax){
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);              if(pos>=1.e-5){
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
       for (j=1; j<= nlstate+1 ; j ++) {                /*probs[i][jk][j1]= pp[jk]/pos;*/
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
         else fprintf(ficgp," \%%*lf (\%%*lf)");              }
 }                else
       fprintf(ficgp,"\" t\"\" w l 0,");                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);            }
       for (j=1; j<= nlstate+1 ; j ++) {          }
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          
   else fprintf(ficgp," \%%*lf (\%%*lf)");          for(jk=-1; jk <=nlstate+ndeath; jk++)
 }              for(m=-1; m <=nlstate+ndeath; m++)
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");              if(freq[jk][m][i] !=0 ) {
       else fprintf(ficgp,"\" t\"\" w l 0,");              if(first==1)
     }                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
   }                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
                }
   /*3eme*/          if(i <= iagemax)
             fprintf(ficresp,"\n");
   for (k1=1; k1<= m ; k1 ++) {          if(first==1)
     for (cpt=1; cpt<= nlstate ; cpt ++) {            printf("Others in log...\n");
       k=2+nlstate*(2*cpt-2);          fprintf(ficlog,"\n");
       fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n\n",strtok(optionfile, "."),cpt,k1);        }
       fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);      }
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);    }
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");    dateintmean=dateintsum/k2cpt; 
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);   
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);    fclose(ficresp);
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);    free_vector(pp,1,nlstate);
     free_matrix(prop,1,nlstate,iagemin, iagemax+3);
 */    /* End of Freq */
       for (i=1; i< nlstate ; i ++) {  }
         fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);  
   /************ Prevalence ********************/
       }  void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
     }  {  
   }    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
         in each health status at the date of interview (if between dateprev1 and dateprev2).
   /* CV preval stat */       We still use firstpass and lastpass as another selection.
     for (k1=1; k1<= m ; k1 ++) {    */
     for (cpt=1; cpt<nlstate ; cpt ++) {   
       k=3;    int i, m, jk, k1, i1, j1, bool, z1,j;
       fprintf(ficgp,"set out \"p%s%d%d.png\" \n\n",strtok(optionfile, "."),cpt,k1);    double ***freq; /* Frequencies */
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);    double *pp, **prop;
     double pos,posprop; 
       for (i=1; i< nlstate ; i ++)    double  y2; /* in fractional years */
         fprintf(ficgp,"+$%d",k+i+1);    int iagemin, iagemax;
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);  
          iagemin= (int) agemin;
       l=3+(nlstate+ndeath)*cpt;    iagemax= (int) agemax;
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);    /*pp=vector(1,nlstate);*/
       for (i=1; i< nlstate ; i ++) {    prop=matrix(1,nlstate,iagemin,iagemax+3); 
         l=3+(nlstate+ndeath)*cpt;    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
         fprintf(ficgp,"+$%d",l+i+1);    j1=0;
       }    
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);      j=cptcoveff;
     }    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   }      
      for(k1=1; k1<=j;k1++){
   /* proba elementaires */      for(i1=1; i1<=ncodemax[k1];i1++){
    for(i=1,jk=1; i <=nlstate; i++){        j1++;
     for(k=1; k <=(nlstate+ndeath); k++){        
       if (k != i) {        for (i=1; i<=nlstate; i++)  
         for(j=1; j <=ncovmodel; j++){          for(m=iagemin; m <= iagemax+3; m++)
                    prop[i][m]=0.0;
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);       
           jk++;        for (i=1; i<=imx; i++) { /* Each individual */
           fprintf(ficgp,"\n");          bool=1;
         }          if  (cptcovn>0) {
       }            for (z1=1; z1<=cptcoveff; z1++) 
     }              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
    }                bool=0;
           } 
    for(jk=1; jk <=m; jk++) {          if (bool==1) { 
      fprintf(ficgp,"\nset out \"pe%s%d.png\" \n\n",strtok(optionfile, "."),jk);            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
      i=1;              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
      for(k2=1; k2<=nlstate; k2++) {                if(agev[m][i]==0) agev[m][i]=iagemax+1;
        k3=i;                if(agev[m][i]==1) agev[m][i]=iagemax+2;
        for(k=1; k<=(nlstate+ndeath); k++) {                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 (k != k2){                if (s[m][i]>0 && s[m][i]<=nlstate) { 
            fprintf(ficgp," exp(p%d+p%d*x",i,i+1);                  /*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]]);*/
            ij=1;                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
            for(j=3; j <=ncovmodel; j++) {                  prop[s[m][i]][iagemax+3] += weight[i]; 
              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++;            } /* end selection of waves */
              }          }
              else        }
                fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);        for(i=iagemin; i <= iagemax+3; i++){  
            }          
            fprintf(ficgp,")/(1");          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
                        posprop += prop[jk][i]; 
            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(jk=1; jk <=nlstate ; jk++){     
              for(j=3; j <=ncovmodel; j++){            if( i <=  iagemax){ 
                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {              if(posprop>=1.e-5){ 
                  fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);                probs[i][jk][j1]= prop[jk][i]/posprop;
                  ij++;              } else
                }                printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\n",jk,i,j1,probs[i][jk][j1]);
                else            } 
                  fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);          }/* end jk */ 
              }        }/* end i */ 
              fprintf(ficgp,")");      } /* end i1 */
            }    } /* end k1 */
            fprintf(ficgp,") t \"p%d%d\" ", k2,k);    
            if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
            i=i+ncovmodel;    /*free_vector(pp,1,nlstate);*/
          }    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
        }  }  /* End of prevalence */
      }  
    }  /************* Waves Concatenation ***************/
      
    fclose(ficgp);  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)
 }  /* end gnuplot */  {
     /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
        Death is a valid wave (if date is known).
 /*************** Moving average **************/       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){       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.
   int i, cpt, cptcod;       */
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)  
       for (i=1; i<=nlstate;i++)    int i, mi, m;
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
           mobaverage[(int)agedeb][i][cptcod]=0.;       double sum=0., jmean=0.;*/
        int first;
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){    int j, k=0,jk, ju, jl;
       for (i=1; i<=nlstate;i++){    double sum=0.;
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    first=0;
           for (cpt=0;cpt<=4;cpt++){    jmin=1e+5;
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];    jmax=-1;
           }    jmean=0.;
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;    for(i=1; i<=imx; i++){
         }      mi=0;
       }      m=firstpass;
     }      while(s[m][i] <= nlstate){
            if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
 }          mw[++mi][i]=m;
         if(m >=lastpass)
           break;
 /************** Forecasting ******************/        else
 prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){          m++;
        }/* end while */
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;      if (s[m][i] > nlstate){
   int *popage;        mi++;     /* Death is another wave */
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;        /* if(mi==0)  never been interviewed correctly before death */
   double *popeffectif,*popcount;           /* Only death is a correct wave */
   double ***p3mat;        mw[mi][i]=m;
   char fileresf[FILENAMELENGTH];      }
   
  agelim=AGESUP;      wav[i]=mi;
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;      if(mi==0){
         nbwarn++;
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);        if(first==0){
            printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
            first=1;
   strcpy(fileresf,"f");        }
   strcat(fileresf,fileres);        if(first==1){
   if((ficresf=fopen(fileresf,"w"))==NULL) {          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
     printf("Problem with forecast resultfile: %s\n", fileresf);        }
   }      } /* end mi==0 */
   printf("Computing forecasting: result on file '%s' \n", fileresf);    } /* End individuals */
   
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    for(i=1; i<=imx; i++){
       for(mi=1; mi<wav[i];mi++){
   if (mobilav==1) {        if (stepm <=0)
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          dh[mi][i]=1;
     movingaverage(agedeb, fage, ageminpar, mobaverage);        else{
   }          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
             if (agedc[i] < 2*AGESUP) {
   stepsize=(int) (stepm+YEARM-1)/YEARM;              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
   if (stepm<=12) stepsize=1;              if(j==0) j=1;  /* Survives at least one month after exam */
                else if(j<0){
   agelim=AGESUP;                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]);
   hstepm=1;                j=1; /* Temporary Dangerous patch */
   hstepm=hstepm/stepm;                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);
   yp1=modf(dateintmean,&yp);                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]);
   anprojmean=yp;                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);
   yp2=modf((yp1*12),&yp);              }
   mprojmean=yp;              k=k+1;
   yp1=modf((yp2*30.5),&yp);              if (j >= jmax){
   jprojmean=yp;                jmax=j;
   if(jprojmean==0) jprojmean=1;                ijmax=i;
   if(mprojmean==0) jprojmean=1;              }
                if (j <= jmin){
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);                jmin=j;
                  ijmin=i;
   for(cptcov=1;cptcov<=i2;cptcov++){              }
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){              sum=sum+j;
       k=k+1;              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
       fprintf(ficresf,"\n#******");              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
       for(j=1;j<=cptcoveff;j++) {            }
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          }
       }          else{
       fprintf(ficresf,"******\n");            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
       fprintf(ficresf,"# StartingAge FinalAge");  /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);  
                  k=k+1;
                  if (j >= jmax) {
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {              jmax=j;
         fprintf(ficresf,"\n");              ijmax=i;
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);              }
             else if (j <= jmin){
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){              jmin=j;
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);              ijmin=i;
           nhstepm = nhstepm/hstepm;            }
                      /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            /*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]);*/
           oldm=oldms;savm=savms;            if(j<0){
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);                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]);
           for (h=0; h<=nhstepm; h++){              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]);
             if (h==(int) (calagedate+YEARM*cpt)) {            }
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);            sum=sum+j;
             }          }
             for(j=1; j<=nlstate+ndeath;j++) {          jk= j/stepm;
               kk1=0.;kk2=0;          jl= j -jk*stepm;
               for(i=1; i<=nlstate;i++) {                        ju= j -(jk+1)*stepm;
                 if (mobilav==1)          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];            if(jl==0){
                 else {              dh[mi][i]=jk;
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];              bh[mi][i]=0;
                 }            }else{ /* We want a negative bias in order to only have interpolation ie
                                    * at the price of an extra matrix product in likelihood */
               }              dh[mi][i]=jk+1;
               if (h==(int)(calagedate+12*cpt)){              bh[mi][i]=ju;
                 fprintf(ficresf," %.3f", kk1);            }
                                  }else{
               }            if(jl <= -ju){
             }              dh[mi][i]=jk;
           }              bh[mi][i]=jl;       /* bias is positive if real duration
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                                   * is higher than the multiple of stepm and negative otherwise.
         }                                   */
       }            }
     }            else{
   }              dh[mi][i]=jk+1;
                      bh[mi][i]=ju;
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            }
             if(dh[mi][i]==0){
   fclose(ficresf);              dh[mi][i]=1; /* At least one step */
 }              bh[mi][i]=ju; /* At least one step */
 /************** Forecasting ******************/              /*  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);*/
 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){            }
            } /* end if mle */
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;        }
   int *popage;      } /* end wave */
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;    }
   double *popeffectif,*popcount;    jmean=sum/k;
   double ***p3mat,***tabpop,***tabpopprev;    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);
   char filerespop[FILENAMELENGTH];    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);
    }
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  /*********** Tricode ****************************/
   agelim=AGESUP;  void tricode(int *Tvar, int **nbcode, int imx)
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;  {
      
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    /*      Tvar[i]=atoi(stre); /* find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 */
    
      int Ndum[20],ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
   strcpy(filerespop,"pop");    int cptcode=0;
   strcat(filerespop,fileres);    cptcoveff=0; 
   if((ficrespop=fopen(filerespop,"w"))==NULL) {   
     printf("Problem with forecast resultfile: %s\n", filerespop);    for (k=0; k<maxncov; k++) Ndum[k]=0;
   }    for (k=1; k<=7; k++) ncodemax[k]=0; /* Horrible constant again */
   printf("Computing forecasting: result on file '%s' \n", filerespop);  
     for (j=1; j<=(cptcovn+2*cptcovprod); j++) { /* For each covariate */
   if (cptcoveff==0) ncodemax[cptcoveff]=1;      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
                                  modality*/ 
   if (mobilav==1) {        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual, might be -1*/
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        Ndum[ij]++; /*counts the occurence of this modality */
     movingaverage(agedeb, fage, ageminpar, mobaverage);        /*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) 
                                          Tvar[j]. If V=sex and male is 0 and 
   stepsize=(int) (stepm+YEARM-1)/YEARM;                                         female is 1, then  cptcode=1.*/
   if (stepm<=12) stepsize=1;      }
    
   agelim=AGESUP;      for (i=0; i<=cptcode; i++) { /* i=-1 ?*/
          if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j
   hstepm=1;                                         th covariate. In fact
   hstepm=hstepm/stepm;                                         ncodemax[j]=2
                                           (dichotom. variables only) but
   if (popforecast==1) {                                         it can be more */
     if((ficpop=fopen(popfile,"r"))==NULL) {      } /* Ndum[-1] number of undefined modalities */
       printf("Problem with population file : %s\n",popfile);exit(0);  
     }      ij=1; 
     popage=ivector(0,AGESUP);      for (i=1; i<=ncodemax[j]; i++) { /* i= 1 to 2 */
     popeffectif=vector(0,AGESUP);        for (k=0; k<= maxncov; k++) { /* k=-1 ?*/
     popcount=vector(0,AGESUP);          if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
                nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode. 
     i=1;                                         k is a modality. If we have model=V1+V1*sex 
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;                                       then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
                ij++;
     imx=i;          }
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];          if (ij > ncodemax[j]) break; 
   }        }  
       } 
   for(cptcov=1;cptcov<=i2;cptcov++){    }  
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){  
       k=k+1;   for (k=0; k< maxncov; k++) Ndum[k]=0;
       fprintf(ficrespop,"\n#******");  
       for(j=1;j<=cptcoveff;j++) {   for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
       }     ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
       fprintf(ficrespop,"******\n");     Ndum[ij]++;
       fprintf(ficrespop,"# Age");   }
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);  
       if (popforecast==1)  fprintf(ficrespop," [Population]");   ij=1;
         for (i=1; i<= maxncov; i++) {
       for (cpt=0; cpt<=0;cpt++) {     if((Ndum[i]!=0) && (i<=ncovcol)){
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);         Tvaraff[ij]=i; /*For printing */
               ij++;
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){     }
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);   }
           nhstepm = nhstepm/hstepm;   ij--;
             cptcoveff=ij; /*Number of simple covariates*/
           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);    /*********** Health Expectancies ****************/
          
           for (h=0; h<=nhstepm; h++){  void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
             if (h==(int) (calagedate+YEARM*cpt)) {  
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);  {
             }    /* Health expectancies, no variances */
             for(j=1; j<=nlstate+ndeath;j++) {    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
               kk1=0.;kk2=0;    int nhstepma, nstepma; /* Decreasing with age */
               for(i=1; i<=nlstate;i++) {                  double age, agelim, hf;
                 if (mobilav==1)    double ***p3mat;
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];    double eip;
                 else {  
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];    pstamp(ficreseij);
                 }    fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
               }    fprintf(ficreseij,"# Age");
               if (h==(int)(calagedate+12*cpt)){    for(i=1; i<=nlstate;i++){
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;      for(j=1; j<=nlstate;j++){
                   /*fprintf(ficrespop," %.3f", kk1);        fprintf(ficreseij," e%1d%1d ",i,j);
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/      }
               }      fprintf(ficreseij," e%1d. ",i);
             }    }
             for(i=1; i<=nlstate;i++){    fprintf(ficreseij,"\n");
               kk1=0.;  
                 for(j=1; j<=nlstate;j++){    
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];    if(estepm < stepm){
                 }      printf ("Problem %d lower than %d\n",estepm, stepm);
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];    }
             }    else  hstepm=estepm;   
     /* We compute the life expectancy from trapezoids spaced every estepm months
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)     * This is mainly to measure the difference between two models: for example
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);     * if stepm=24 months pijx are given only every 2 years and by summing them
           }     * we are calculating an estimate of the Life Expectancy assuming a linear 
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);     * 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 (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {  
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);      /* For example we decided to compute the life expectancy with the smallest unit */
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);       nhstepm is the number of hstepm from age to agelim 
           nhstepm = nhstepm/hstepm;       nstepm is the number of stepm from age to agelin. 
                 Look at hpijx to understand the reason of that which relies in memory size
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);       and note for a fixed period like estepm months */
           oldm=oldms;savm=savms;    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);         survival function given by stepm (the optimization length). Unfortunately it
           for (h=0; h<=nhstepm; h++){       means that if the survival funtion is printed only each two years of age and if
             if (h==(int) (calagedate+YEARM*cpt)) {       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);       results. So we changed our mind and took the option of the best precision.
             }    */
             for(j=1; j<=nlstate+ndeath;j++) {    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
               kk1=0.;kk2=0;  
               for(i=1; i<=nlstate;i++) {                  agelim=AGESUP;
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];        /* If stepm=6 months */
               }      /* Computed by stepm unit matrices, product of hstepm matrices, stored
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
             }      
           }  /* nhstepm age range expressed in number of stepm */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
         }    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       }    /* if (stepm >= YEARM) hstepm=1;*/
    }    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   }    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
    
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    for (age=bage; age<=fage; age ++){ 
       nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
   if (popforecast==1) {      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     free_ivector(popage,0,AGESUP);      /* if (stepm >= YEARM) hstepm=1;*/
     free_vector(popeffectif,0,AGESUP);      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
     free_vector(popcount,0,AGESUP);  
   }      /* If stepm=6 months */
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      /* Computed by stepm unit matrices, product of hstepma matrices, stored
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
   fclose(ficrespop);      
 }      hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
       
 /***********************************************/      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
 /**************** Main Program *****************/      
 /***********************************************/      printf("%d|",(int)age);fflush(stdout);
       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
 int main(int argc, char *argv[])      
 {      /* Computing expectancies */
       for(i=1; i<=nlstate;i++)
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;        for(j=1; j<=nlstate;j++)
   double agedeb, agefin,hf;          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
             
   double fret;            /* 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]);*/
   double **xi,tmp,delta;  
           }
   double dum; /* Dummy variable */  
   double ***p3mat;      fprintf(ficreseij,"%3.0f",age );
   int *indx;      for(i=1; i<=nlstate;i++){
   char line[MAXLINE], linepar[MAXLINE];        eip=0;
   char title[MAXLINE];        for(j=1; j<=nlstate;j++){
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];          eip +=eij[i][j][(int)age];
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];          fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
          }
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];        fprintf(ficreseij,"%9.4f", eip );
       }
   char filerest[FILENAMELENGTH];      fprintf(ficreseij,"\n");
   char fileregp[FILENAMELENGTH];      
   char popfile[FILENAMELENGTH];    }
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];    free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   int firstobs=1, lastobs=10;    printf("\n");
   int sdeb, sfin; /* Status at beginning and end */    fprintf(ficlog,"\n");
   int c,  h , cpt,l;    
   int ju,jl, mi;  }
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;  
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;  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[] )
   int mobilav=0,popforecast=0;  
   int hstepm, nhstepm;  {
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;    /* Covariances of health expectancies eij and of total life expectancies according
      to initial status i, ei. .
   double bage, fage, age, agelim, agebase;    */
   double ftolpl=FTOL;    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
   double **prlim;    int nhstepma, nstepma; /* Decreasing with age */
   double *severity;    double age, agelim, hf;
   double ***param; /* Matrix of parameters */    double ***p3matp, ***p3matm, ***varhe;
   double  *p;    double **dnewm,**doldm;
   double **matcov; /* Matrix of covariance */    double *xp, *xm;
   double ***delti3; /* Scale */    double **gp, **gm;
   double *delti; /* Scale */    double ***gradg, ***trgradg;
   double ***eij, ***vareij;    int theta;
   double **varpl; /* Variances of prevalence limits by age */  
   double *epj, vepp;    double eip, vip;
   double kk1, kk2;  
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
      xp=vector(1,npar);
     xm=vector(1,npar);
   char version[80]="Imach version 0.8d, May 2002, INED-EUROREVES ";    dnewm=matrix(1,nlstate*nlstate,1,npar);
   char *alph[]={"a","a","b","c","d","e"}, str[4];    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
     
     pstamp(ficresstdeij);
   char z[1]="c", occ;    fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
 #include <sys/time.h>    fprintf(ficresstdeij,"# Age");
 #include <time.h>    for(i=1; i<=nlstate;i++){
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];      for(j=1; j<=nlstate;j++)
          fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
   /* long total_usecs;      fprintf(ficresstdeij," e%1d. ",i);
   struct timeval start_time, end_time;    }
      fprintf(ficresstdeij,"\n");
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */  
   getcwd(pathcd, size);    pstamp(ficrescveij);
     fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
   printf("\n%s",version);    fprintf(ficrescveij,"# Age");
   if(argc <=1){    for(i=1; i<=nlstate;i++)
     printf("\nEnter the parameter file name: ");      for(j=1; j<=nlstate;j++){
     scanf("%s",pathtot);        cptj= (j-1)*nlstate+i;
   }        for(i2=1; i2<=nlstate;i2++)
   else{          for(j2=1; j2<=nlstate;j2++){
     strcpy(pathtot,argv[1]);            cptj2= (j2-1)*nlstate+i2;
   }            if(cptj2 <= cptj)
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/              fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
   /*cygwin_split_path(pathtot,path,optionfile);          }
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/      }
   /* cutv(path,optionfile,pathtot,'\\');*/    fprintf(ficrescveij,"\n");
     
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);    if(estepm < stepm){
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);      printf ("Problem %d lower than %d\n",estepm, stepm);
   chdir(path);    }
   replace(pathc,path);    else  hstepm=estepm;   
     /* We compute the life expectancy from trapezoids spaced every estepm months
 /*-------- arguments in the command line --------*/     * 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
   strcpy(fileres,"r");     * we are calculating an estimate of the Life Expectancy assuming a linear 
   strcat(fileres, optionfilefiname);     * progression in between and thus overestimating or underestimating according
   strcat(fileres,".txt");    /* Other files have txt extension */     * to the curvature of the survival function. If, for the same date, we 
      * estimate the model with stepm=1 month, we can keep estepm to 24 months
   /*---------arguments file --------*/     * to compare the new estimate of Life expectancy with the same linear 
      * hypothesis. A more precise result, taking into account a more precise
   if((ficpar=fopen(optionfile,"r"))==NULL)    {     * curvature will be obtained if estepm is as small as stepm. */
     printf("Problem with optionfile %s\n",optionfile);  
     goto end;    /* 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. 
        nhstepm is the number of hstepm from age to agelim 
   strcpy(filereso,"o");       nstepm is the number of stepm from age to agelin. 
   strcat(filereso,fileres);       Look at hpijx to understand the reason of that which relies in memory size
   if((ficparo=fopen(filereso,"w"))==NULL) {       and note for a fixed period like estepm months */
     printf("Problem with Output resultfile: %s\n", filereso);goto end;    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   }       survival function given by stepm (the optimization length). Unfortunately it
        means that if the survival funtion is printed only each two years of age and if
   /* Reads comments: lines beginning with '#' */       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   while((c=getc(ficpar))=='#' && c!= EOF){       results. So we changed our mind and took the option of the best precision.
     ungetc(c,ficpar);    */
     fgets(line, MAXLINE, ficpar);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     puts(line);  
     fputs(line,ficparo);    /* If stepm=6 months */
   }    /* nhstepm age range expressed in number of stepm */
   ungetc(c,ficpar);    agelim=AGESUP;
     nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   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);    /* if (stepm >= YEARM) hstepm=1;*/
   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);    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
 while((c=getc(ficpar))=='#' && c!= EOF){    
     ungetc(c,ficpar);    p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     fgets(line, MAXLINE, ficpar);    p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     puts(line);    gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
     fputs(line,ficparo);    trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
   }    gp=matrix(0,nhstepm,1,nlstate*nlstate);
   ungetc(c,ficpar);    gm=matrix(0,nhstepm,1,nlstate*nlstate);
    
        for (age=bage; age<=fage; age ++){ 
   covar=matrix(0,NCOVMAX,1,n);      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
   cptcovn=0;      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;      /* if (stepm >= YEARM) hstepm=1;*/
       nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
   ncovmodel=2+cptcovn;  
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */      /* If stepm=6 months */
        /* Computed by stepm unit matrices, product of hstepma matrices, stored
   /* Read guess parameters */         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
   /* Reads comments: lines beginning with '#' */      
   while((c=getc(ficpar))=='#' && c!= EOF){      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);      /* Computing  Variances of health expectancies */
     puts(line);      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
     fputs(line,ficparo);         decrease memory allocation */
   }      for(theta=1; theta <=npar; theta++){
   ungetc(c,ficpar);        for(i=1; i<=npar; i++){ 
            xp[i] = x[i] + (i==theta ?delti[theta]:0);
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);          xm[i] = x[i] - (i==theta ?delti[theta]:0);
     for(i=1; i <=nlstate; i++)        }
     for(j=1; j <=nlstate+ndeath-1; j++){        hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
       fscanf(ficpar,"%1d%1d",&i1,&j1);        hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
       fprintf(ficparo,"%1d%1d",i1,j1);    
       printf("%1d%1d",i,j);        for(j=1; j<= nlstate; j++){
       for(k=1; k<=ncovmodel;k++){          for(i=1; i<=nlstate; i++){
         fscanf(ficpar," %lf",&param[i][j][k]);            for(h=0; h<=nhstepm-1; h++){
         printf(" %lf",param[i][j][k]);              gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
         fprintf(ficparo," %lf",param[i][j][k]);              gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
       }            }
       fscanf(ficpar,"\n");          }
       printf("\n");        }
       fprintf(ficparo,"\n");       
     }        for(ij=1; ij<= nlstate*nlstate; ij++)
            for(h=0; h<=nhstepm-1; h++){
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;            gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
           }
   p=param[1][1];      }/* End theta */
        
   /* Reads comments: lines beginning with '#' */      
   while((c=getc(ficpar))=='#' && c!= EOF){      for(h=0; h<=nhstepm-1; h++)
     ungetc(c,ficpar);        for(j=1; j<=nlstate*nlstate;j++)
     fgets(line, MAXLINE, ficpar);          for(theta=1; theta <=npar; theta++)
     puts(line);            trgradg[h][j][theta]=gradg[h][theta][j];
     fputs(line,ficparo);      
   }  
   ungetc(c,ficpar);       for(ij=1;ij<=nlstate*nlstate;ij++)
         for(ji=1;ji<=nlstate*nlstate;ji++)
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);          varhe[ij][ji][(int)age] =0.;
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */  
   for(i=1; i <=nlstate; i++){       printf("%d|",(int)age);fflush(stdout);
     for(j=1; j <=nlstate+ndeath-1; j++){       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
       fscanf(ficpar,"%1d%1d",&i1,&j1);       for(h=0;h<=nhstepm-1;h++){
       printf("%1d%1d",i,j);        for(k=0;k<=nhstepm-1;k++){
       fprintf(ficparo,"%1d%1d",i1,j1);          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
       for(k=1; k<=ncovmodel;k++){          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
         fscanf(ficpar,"%le",&delti3[i][j][k]);          for(ij=1;ij<=nlstate*nlstate;ij++)
         printf(" %le",delti3[i][j][k]);            for(ji=1;ji<=nlstate*nlstate;ji++)
         fprintf(ficparo," %le",delti3[i][j][k]);              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
       }        }
       fscanf(ficpar,"\n");      }
       printf("\n");  
       fprintf(ficparo,"\n");      /* Computing expectancies */
     }      hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
   }      for(i=1; i<=nlstate;i++)
   delti=delti3[1][1];        for(j=1; j<=nlstate;j++)
            for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
   /* Reads comments: lines beginning with '#' */            eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
   while((c=getc(ficpar))=='#' && c!= EOF){            
     ungetc(c,ficpar);            /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
     fgets(line, MAXLINE, ficpar);  
     puts(line);          }
     fputs(line,ficparo);  
   }      fprintf(ficresstdeij,"%3.0f",age );
   ungetc(c,ficpar);      for(i=1; i<=nlstate;i++){
          eip=0.;
   matcov=matrix(1,npar,1,npar);        vip=0.;
   for(i=1; i <=npar; i++){        for(j=1; j<=nlstate;j++){
     fscanf(ficpar,"%s",&str);          eip += eij[i][j][(int)age];
     printf("%s",str);          for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
     fprintf(ficparo,"%s",str);            vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
     for(j=1; j <=i; j++){          fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
       fscanf(ficpar," %le",&matcov[i][j]);        }
       printf(" %.5le",matcov[i][j]);        fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
       fprintf(ficparo," %.5le",matcov[i][j]);      }
     }      fprintf(ficresstdeij,"\n");
     fscanf(ficpar,"\n");  
     printf("\n");      fprintf(ficrescveij,"%3.0f",age );
     fprintf(ficparo,"\n");      for(i=1; i<=nlstate;i++)
   }        for(j=1; j<=nlstate;j++){
   for(i=1; i <=npar; i++)          cptj= (j-1)*nlstate+i;
     for(j=i+1;j<=npar;j++)          for(i2=1; i2<=nlstate;i2++)
       matcov[i][j]=matcov[j][i];            for(j2=1; j2<=nlstate;j2++){
                  cptj2= (j2-1)*nlstate+i2;
   printf("\n");              if(cptj2 <= cptj)
                 fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
             }
     /*-------- Rewriting paramater file ----------*/        }
      strcpy(rfileres,"r");    /* "Rparameterfile */      fprintf(ficrescveij,"\n");
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/     
      strcat(rfileres,".");    /* */    }
      strcat(rfileres,optionfilext);    /* Other files have txt extension */    free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
     if((ficres =fopen(rfileres,"w"))==NULL) {    free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
       printf("Problem writing new parameter file: %s\n", fileres);goto end;    free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
     }    free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
     fprintf(ficres,"#%s\n",version);    free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
        free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     /*-------- data file ----------*/    printf("\n");
     if((fic=fopen(datafile,"r"))==NULL)    {    fprintf(ficlog,"\n");
       printf("Problem with datafile: %s\n", datafile);goto end;  
     }    free_vector(xm,1,npar);
     free_vector(xp,1,npar);
     n= lastobs;    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
     severity = vector(1,maxwav);    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
     outcome=imatrix(1,maxwav+1,1,n);    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
     num=ivector(1,n);  }
     moisnais=vector(1,n);  
     annais=vector(1,n);  /************ Variance ******************/
     moisdc=vector(1,n);  void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
     andc=vector(1,n);  {
     agedc=vector(1,n);    /* Variance of health expectancies */
     cod=ivector(1,n);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
     weight=vector(1,n);    /* double **newm;*/
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */    double **dnewm,**doldm;
     mint=matrix(1,maxwav,1,n);    double **dnewmp,**doldmp;
     anint=matrix(1,maxwav,1,n);    int i, j, nhstepm, hstepm, h, nstepm ;
     s=imatrix(1,maxwav+1,1,n);    int k, cptcode;
     adl=imatrix(1,maxwav+1,1,n);        double *xp;
     tab=ivector(1,NCOVMAX);    double **gp, **gm;  /* for var eij */
     ncodemax=ivector(1,8);    double ***gradg, ***trgradg; /*for var eij */
     double **gradgp, **trgradgp; /* for var p point j */
     i=1;    double *gpp, *gmp; /* for var p point j */
     while (fgets(line, MAXLINE, fic) != NULL)    {    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
       if ((i >= firstobs) && (i <=lastobs)) {    double ***p3mat;
            double age,agelim, hf;
         for (j=maxwav;j>=1;j--){    double ***mobaverage;
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);    int theta;
           strcpy(line,stra);    char digit[4];
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    char digitp[25];
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);  
         }    char fileresprobmorprev[FILENAMELENGTH];
          
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);    if(popbased==1){
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);      if(mobilav!=0)
         strcpy(digitp,"-populbased-mobilav-");
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);      else strcpy(digitp,"-populbased-nomobil-");
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);    }
     else 
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);      strcpy(digitp,"-stablbased-");
         for (j=ncovcol;j>=1;j--){  
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);    if (mobilav!=0) {
         }      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         num[i]=atol(stra);      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
                fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){        printf(" Error in movingaverage mobilav=%d\n",mobilav);
           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;}*/      }
     }
         i=i+1;  
       }    strcpy(fileresprobmorprev,"prmorprev"); 
     }    sprintf(digit,"%-d",ij);
     /* printf("ii=%d", ij);    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
        scanf("%d",i);*/    strcat(fileresprobmorprev,digit); /* Tvar to be done */
   imx=i-1; /* Number of individuals */    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
     strcat(fileresprobmorprev,fileres);
   /* for (i=1; i<=imx; i++){    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;      printf("Problem with resultfile: %s\n", fileresprobmorprev);
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;    }
     }*/    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
    /*  for (i=1; i<=imx; i++){   
      if (s[4][i]==9)  s[4][i]=-1;    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
      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]));}*/    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);
      fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
   /* Calculation of the number of parameter from char model*/    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
   Tvar=ivector(1,15);      fprintf(ficresprobmorprev," p.%-d SE",j);
   Tprod=ivector(1,15);      for(i=1; i<=nlstate;i++)
   Tvaraff=ivector(1,15);        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
   Tvard=imatrix(1,15,1,2);    }  
   Tage=ivector(1,15);          fprintf(ficresprobmorprev,"\n");
        fprintf(ficgp,"\n# Routine varevsij");
   if (strlen(model) >1){    /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
     j=0, j1=0, k1=1, k2=1;    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");
     j=nbocc(model,'+');    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
     j1=nbocc(model,'*');  /*   } */
     cptcovn=j+1;    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     cptcovprod=j1;    pstamp(ficresvij);
        fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
     strcpy(modelsav,model);    if(popbased==1)
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){      fprintf(ficresvij,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d\n",mobilav);
       printf("Error. Non available option model=%s ",model);    else
       goto end;      fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
     }    fprintf(ficresvij,"# Age");
        for(i=1; i<=nlstate;i++)
     for(i=(j+1); i>=1;i--){      for(j=1; j<=nlstate;j++)
       cutv(stra,strb,modelsav,'+');        fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);    fprintf(ficresvij,"\n");
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/  
       /*scanf("%d",i);*/    xp=vector(1,npar);
       if (strchr(strb,'*')) {    dnewm=matrix(1,nlstate,1,npar);
         cutv(strd,strc,strb,'*');    doldm=matrix(1,nlstate,1,nlstate);
         if (strcmp(strc,"age")==0) {    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
           cptcovprod--;    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
           cutv(strb,stre,strd,'V');  
           Tvar[i]=atoi(stre);    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
           cptcovage++;    gpp=vector(nlstate+1,nlstate+ndeath);
             Tage[cptcovage]=i;    gmp=vector(nlstate+1,nlstate+ndeath);
             /*printf("stre=%s ", stre);*/    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
         }    
         else if (strcmp(strd,"age")==0) {    if(estepm < stepm){
           cptcovprod--;      printf ("Problem %d lower than %d\n",estepm, stepm);
           cutv(strb,stre,strc,'V');    }
           Tvar[i]=atoi(stre);    else  hstepm=estepm;   
           cptcovage++;    /* For example we decided to compute the life expectancy with the smallest unit */
           Tage[cptcovage]=i;    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
         }       nhstepm is the number of hstepm from age to agelim 
         else {       nstepm is the number of stepm from age to agelin. 
           cutv(strb,stre,strc,'V');       Look at function hpijx to understand why (it is linked to memory size questions) */
           Tvar[i]=ncovcol+k1;    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
           cutv(strb,strc,strd,'V');       survival function given by stepm (the optimization length). Unfortunately it
           Tprod[k1]=i;       means that if the survival funtion is printed every two years of age and if
           Tvard[k1][1]=atoi(strc);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
           Tvard[k1][2]=atoi(stre);       results. So we changed our mind and took the option of the best precision.
           Tvar[cptcovn+k2]=Tvard[k1][1];    */
           Tvar[cptcovn+k2+1]=Tvard[k1][2];    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
           for (k=1; k<=lastobs;k++)    agelim = AGESUP;
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
           k1++;      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
           k2=k2+2;      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
         }      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       }      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
       else {      gp=matrix(0,nhstepm,1,nlstate);
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/      gm=matrix(0,nhstepm,1,nlstate);
        /*  scanf("%d",i);*/  
       cutv(strd,strc,strb,'V');  
       Tvar[i]=atoi(strc);      for(theta=1; theta <=npar; theta++){
       }        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
       strcpy(modelsav,stra);            xp[i] = x[i] + (i==theta ?delti[theta]:0);
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);        }
         scanf("%d",i);*/        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     }        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
 }  
          if (popbased==1) {
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);          if(mobilav ==0){
   printf("cptcovprod=%d ", cptcovprod);            for(i=1; i<=nlstate;i++)
   scanf("%d ",i);*/              prlim[i][i]=probs[(int)age][i][ij];
     fclose(fic);          }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)
     /*  if(mle==1){*/              prlim[i][i]=mobaverage[(int)age][i][ij];
     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 -*/        for(j=1; j<= nlstate; j++){
     agev=matrix(1,maxwav,1,imx);          for(h=0; h<=nhstepm; h++){
             for(i=1, gp[h][j]=0.;i<=nlstate;i++)
     for (i=1; i<=imx; i++) {              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
       for(m=2; (m<= maxwav); m++) {          }
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){        }
          anint[m][i]=9999;        /* This for computing probability of death (h=1 means
          s[m][i]=-1;           computed over hstepm matrices product = hstepm*stepm months) 
        }           as a weighted average of prlim.
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;        */
       }        for(j=nlstate+1;j<=nlstate+ndeath;j++){
     }          for(i=1,gpp[j]=0.; i<= nlstate; i++)
             gpp[j] += prlim[i][i]*p3mat[i][j][1];
     for (i=1; i<=imx; i++)  {        }    
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);        /* end probability of death */
       for(m=1; (m<= maxwav); m++){  
         if(s[m][i] >0){        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
           if (s[m][i] >= nlstate+1) {          xp[i] = x[i] - (i==theta ?delti[theta]:0);
             if(agedc[i]>0)        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
               if(moisdc[i]!=99 && andc[i]!=9999)        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
                 agev[m][i]=agedc[i];   
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/        if (popbased==1) {
            else {          if(mobilav ==0){
               if (andc[i]!=9999){            for(i=1; i<=nlstate;i++)
               printf("Warning negative age at death: %d line:%d\n",num[i],i);              prlim[i][i]=probs[(int)age][i][ij];
               agev[m][i]=-1;          }else{ /* mobilav */ 
               }            for(i=1; i<=nlstate;i++)
             }              prlim[i][i]=mobaverage[(int)age][i][ij];
           }          }
           else if(s[m][i] !=9){ /* Should no more exist */        }
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);  
             if(mint[m][i]==99 || anint[m][i]==9999)        for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
               agev[m][i]=1;          for(h=0; h<=nhstepm; h++){
             else if(agev[m][i] <agemin){            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
               agemin=agev[m][i];              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
               /*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){        /* This for computing probability of death (h=1 means
               agemax=agev[m][i];           computed over hstepm matrices product = hstepm*stepm months) 
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/           as a weighted average of prlim.
             }        */
             /*agev[m][i]=anint[m][i]-annais[i];*/        for(j=nlstate+1;j<=nlstate+ndeath;j++){
             /*   agev[m][i] = age[i]+2*m;*/          for(i=1,gmp[j]=0.; i<= nlstate; i++)
           }           gmp[j] += prlim[i][i]*p3mat[i][j][1];
           else { /* =9 */        }    
             agev[m][i]=1;        /* end probability of death */
             s[m][i]=-1;  
           }        for(j=1; j<= nlstate; j++) /* vareij */
         }          for(h=0; h<=nhstepm; h++){
         else /*= 0 Unknown */            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
           agev[m][i]=1;          }
       }  
            for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
     }          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
     for (i=1; i<=imx; i++)  {        }
       for(m=1; (m<= maxwav); m++){  
         if (s[m][i] > (nlstate+ndeath)) {      } /* End theta */
           printf("Error: Wrong value in nlstate or ndeath\n");    
           goto end;      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
         }  
       }      for(h=0; h<=nhstepm; h++) /* veij */
     }        for(j=1; j<=nlstate;j++)
           for(theta=1; theta <=npar; theta++)
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);            trgradg[h][j][theta]=gradg[h][theta][j];
   
     free_vector(severity,1,maxwav);      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
     free_imatrix(outcome,1,maxwav+1,1,n);        for(theta=1; theta <=npar; theta++)
     free_vector(moisnais,1,n);          trgradgp[j][theta]=gradgp[theta][j];
     free_vector(annais,1,n);    
     /* free_matrix(mint,1,maxwav,1,n);  
        free_matrix(anint,1,maxwav,1,n);*/      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     free_vector(moisdc,1,n);      for(i=1;i<=nlstate;i++)
     free_vector(andc,1,n);        for(j=1;j<=nlstate;j++)
           vareij[i][j][(int)age] =0.;
      
     wav=ivector(1,imx);      for(h=0;h<=nhstepm;h++){
     dh=imatrix(1,lastpass-firstpass+1,1,imx);        for(k=0;k<=nhstepm;k++){
     mw=imatrix(1,lastpass-firstpass+1,1,imx);          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
              matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
     /* Concatenates waves */          for(i=1;i<=nlstate;i++)
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);            for(j=1;j<=nlstate;j++)
               vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
         }
       Tcode=ivector(1,100);      }
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);    
       ncodemax[1]=1;      /* pptj */
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);      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);
    codtab=imatrix(1,100,1,10);      for(j=nlstate+1;j<=nlstate+ndeath;j++)
    h=0;        for(i=nlstate+1;i<=nlstate+ndeath;i++)
    m=pow(2,cptcoveff);          varppt[j][i]=doldmp[j][i];
        /* end ppptj */
    for(k=1;k<=cptcoveff; k++){      /*  x centered again */
      for(i=1; i <=(m/pow(2,k));i++){      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
        for(j=1; j <= ncodemax[k]; j++){      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){   
            h++;      if (popbased==1) {
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;        if(mobilav ==0){
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/          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];
    /* 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++){      /* This for computing probability of death (h=1 means
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
       }         as a weighted average of prlim.
       printf("\n");      */
       }      for(j=nlstate+1;j<=nlstate+ndeath;j++){
       scanf("%d",i);*/        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
              gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
    /* Calculates basic frequencies. Computes observed prevalence at single age      }    
        and prints on file fileres'p'. */      /* end probability of death */
   
          fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
          for(j=nlstate+1; j<=(nlstate+ndeath);j++){
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        for(i=1; i<=nlstate;i++){
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        }
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */      } 
            fprintf(ficresprobmorprev,"\n");
     /* 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] */      fprintf(ficresvij,"%.0f ",age );
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */      for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
     if(mle==1){          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);        }
     }      fprintf(ficresvij,"\n");
          free_matrix(gp,0,nhstepm,1,nlstate);
     /*--------- results files --------------*/      free_matrix(gm,0,nhstepm,1,nlstate);
     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);      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);
    jk=1;    } /* End age */
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    free_vector(gpp,nlstate+1,nlstate+ndeath);
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    free_vector(gmp,nlstate+1,nlstate+ndeath);
    for(i=1,jk=1; i <=nlstate; i++){    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
      for(k=1; k <=(nlstate+ndeath); k++){    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
        if (k != i)    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 */
            printf("%d%d ",i,k);    fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
            fprintf(ficres,"%1d%1d ",i,k);  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
            for(j=1; j <=ncovmodel; j++){  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
              printf("%f ",p[jk]);  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
              fprintf(ficres,"%f ",p[jk]);    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
              jk++;    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));
            printf("\n");    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
            fprintf(ficres,"\n");    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
          }    /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
      }  */
    }  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
  if(mle==1){    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
     /* Computing hessian and covariance matrix */  
     ftolhess=ftol; /* Usually correct */    free_vector(xp,1,npar);
     hesscov(matcov, p, npar, delti, ftolhess, func);    free_matrix(doldm,1,nlstate,1,nlstate);
  }    free_matrix(dnewm,1,nlstate,1,npar);
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     printf("# Scales (for hessian or gradient estimation)\n");    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
      for(i=1,jk=1; i <=nlstate; i++){    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
       for(j=1; j <=nlstate+ndeath; j++){    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         if (j!=i) {    fclose(ficresprobmorprev);
           fprintf(ficres,"%1d%1d",i,j);    fflush(ficgp);
           printf("%1d%1d",i,j);    fflush(fichtm); 
           for(k=1; k<=ncovmodel;k++){  }  /* end varevsij */
             printf(" %.5e",delti[jk]);  
             fprintf(ficres," %.5e",delti[jk]);  /************ Variance of prevlim ******************/
             jk++;  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[])
           }  {
           printf("\n");    /* Variance of prevalence limit */
           fprintf(ficres,"\n");    /*  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;
     k=1;    double *xp;
     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");    double *gp, *gm;
     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");    double **gradg, **trgradg;
     for(i=1;i<=npar;i++){    double age,agelim;
       /*  if (k>nlstate) k=1;    int theta;
       i1=(i-1)/(ncovmodel*nlstate)+1;    
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);    pstamp(ficresvpl);
       printf("%s%d%d",alph[k],i1,tab[i]);*/    fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
       fprintf(ficres,"%3d",i);    fprintf(ficresvpl,"# Age");
       printf("%3d",i);    for(i=1; i<=nlstate;i++)
       for(j=1; j<=i;j++){        fprintf(ficresvpl," %1d-%1d",i,i);
         fprintf(ficres," %.5e",matcov[i][j]);    fprintf(ficresvpl,"\n");
         printf(" %.5e",matcov[i][j]);  
       }    xp=vector(1,npar);
       fprintf(ficres,"\n");    dnewm=matrix(1,nlstate,1,npar);
       printf("\n");    doldm=matrix(1,nlstate,1,nlstate);
       k++;    
     }    hstepm=1*YEARM; /* Every year of age */
        hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
     while((c=getc(ficpar))=='#' && c!= EOF){    agelim = AGESUP;
       ungetc(c,ficpar);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       fgets(line, MAXLINE, ficpar);      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       puts(line);      if (stepm >= YEARM) hstepm=1;
       fputs(line,ficparo);      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
     }      gradg=matrix(1,npar,1,nlstate);
     ungetc(c,ficpar);      gp=vector(1,nlstate);
     estepm=0;      gm=vector(1,nlstate);
     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;      for(theta=1; theta <=npar; theta++){
     if (fage <= 2) {        for(i=1; i<=npar; i++){ /* Computes gradient */
       bage = ageminpar;          xp[i] = x[i] + (i==theta ?delti[theta]:0);
       fage = agemaxpar;        }
     }        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
            for(i=1;i<=nlstate;i++)
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");          gp[i] = prlim[i][i];
     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);        for(i=1; i<=npar; i++) /* Computes gradient */
            xp[i] = x[i] - (i==theta ?delti[theta]:0);
     while((c=getc(ficpar))=='#' && c!= EOF){        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     ungetc(c,ficpar);        for(i=1;i<=nlstate;i++)
     fgets(line, MAXLINE, ficpar);          gm[i] = prlim[i][i];
     puts(line);  
     fputs(line,ficparo);        for(i=1;i<=nlstate;i++)
   }          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
   ungetc(c,ficpar);      } /* End theta */
    
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);      trgradg =matrix(1,nlstate,1,npar);
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);  
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);      for(j=1; j<=nlstate;j++)
              for(theta=1; theta <=npar; theta++)
   while((c=getc(ficpar))=='#' && c!= EOF){          trgradg[j][theta]=gradg[theta][j];
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);      for(i=1;i<=nlstate;i++)
     puts(line);        varpl[i][(int)age] =0.;
     fputs(line,ficparo);      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
   }      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
   ungetc(c,ficpar);      for(i=1;i<=nlstate;i++)
          varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   
    dateprev1=anprev1+mprev1/12.+jprev1/365.;      fprintf(ficresvpl,"%.0f ",age );
    dateprev2=anprev2+mprev2/12.+jprev2/365.;      for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
   fscanf(ficpar,"pop_based=%d\n",&popbased);      fprintf(ficresvpl,"\n");
   fprintf(ficparo,"pop_based=%d\n",popbased);        free_vector(gp,1,nlstate);
   fprintf(ficres,"pop_based=%d\n",popbased);        free_vector(gm,1,nlstate);
        free_matrix(gradg,1,npar,1,nlstate);
   while((c=getc(ficpar))=='#' && c!= EOF){      free_matrix(trgradg,1,nlstate,1,npar);
     ungetc(c,ficpar);    } /* End age */
     fgets(line, MAXLINE, ficpar);  
     puts(line);    free_vector(xp,1,npar);
     fputs(line,ficparo);    free_matrix(doldm,1,nlstate,1,npar);
   }    free_matrix(dnewm,1,nlstate,1,nlstate);
   ungetc(c,ficpar);  
   }
   fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mov_average=%d\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);  
 fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);  /************ Variance of one-step probabilities  ******************/
 fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);  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;
 while((c=getc(ficpar))=='#' && c!= EOF){    int k2, l2, j1,  z1;
     ungetc(c,ficpar);    int k=0,l, cptcode;
     fgets(line, MAXLINE, ficpar);    int first=1, first1;
     puts(line);    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
     fputs(line,ficparo);    double **dnewm,**doldm;
   }    double *xp;
   ungetc(c,ficpar);    double *gp, *gm;
     double **gradg, **trgradg;
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);    double **mu;
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);    double age,agelim, cov[NCOVMAX];
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
     int theta;
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    char fileresprob[FILENAMELENGTH];
     char fileresprobcov[FILENAMELENGTH];
 /*------------ gnuplot -------------*/    char fileresprobcor[FILENAMELENGTH];
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, ageminpar,agemaxpar,fage, pathc,p);  
      double ***varpij;
 /*------------ free_vector  -------------*/  
  chdir(path);    strcpy(fileresprob,"prob"); 
      strcat(fileresprob,fileres);
  free_ivector(wav,1,imx);    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);      printf("Problem with resultfile: %s\n", fileresprob);
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);        fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
  free_ivector(num,1,n);    }
  free_vector(agedc,1,n);    strcpy(fileresprobcov,"probcov"); 
  /*free_matrix(covar,1,NCOVMAX,1,n);*/    strcat(fileresprobcov,fileres);
  fclose(ficparo);    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
  fclose(ficres);      printf("Problem with resultfile: %s\n", fileresprobcov);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
 /*--------- index.htm --------*/    }
     strcpy(fileresprobcor,"probcor"); 
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres,optionfilegnuplot,version,popforecast,estepm);    strcat(fileresprobcor,fileres);
     if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
        printf("Problem with resultfile: %s\n", fileresprobcor);
   /*--------------- Prevalence limit --------------*/      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
      }
   strcpy(filerespl,"pl");    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
   strcat(filerespl,fileres);    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
   if((ficrespl=fopen(filerespl,"w"))==NULL) {    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;    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);
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   fprintf(ficrespl,"#Prevalence limit\n");    pstamp(ficresprob);
   fprintf(ficrespl,"#Age ");    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);    fprintf(ficresprob,"# Age");
   fprintf(ficrespl,"\n");    pstamp(ficresprobcov);
      fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
   prlim=matrix(1,nlstate,1,nlstate);    fprintf(ficresprobcov,"# Age");
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    pstamp(ficresprobcor);
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    fprintf(ficresprobcor,"# Age");
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */  
   k=0;    for(i=1; i<=nlstate;i++)
   agebase=ageminpar;      for(j=1; j<=(nlstate+ndeath);j++){
   agelim=agemaxpar;        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
   ftolpl=1.e-10;        fprintf(ficresprobcov," p%1d-%1d ",i,j);
   i1=cptcoveff;        fprintf(ficresprobcor," p%1d-%1d ",i,j);
   if (cptcovn < 1){i1=1;}      }  
    /* fprintf(ficresprob,"\n");
   for(cptcov=1;cptcov<=i1;cptcov++){    fprintf(ficresprobcov,"\n");
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    fprintf(ficresprobcor,"\n");
         k=k+1;   */
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/    xp=vector(1,npar);
         fprintf(ficrespl,"\n#******");    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
         for(j=1;j<=cptcoveff;j++)    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
         fprintf(ficrespl,"******\n");    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
            first=1;
         for (age=agebase; age<=agelim; age++){    fprintf(ficgp,"\n# Routine varprob");
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
           fprintf(ficrespl,"%.0f",age );    fprintf(fichtm,"\n");
           for(i=1; i<=nlstate;i++)  
           fprintf(ficrespl," %.5f", prlim[i][i]);    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
           fprintf(ficrespl,"\n");    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.\
   fclose(ficrespl);   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. \
   /*------------- h Pij x at various ages ------------*/  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 \
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);  standard deviations wide on each axis. <br>\
   if((ficrespij=fopen(filerespij,"w"))==NULL) {   Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;   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");
   printf("Computing pij: result on file '%s' \n", filerespij);  
      cov[1]=1;
   stepsize=(int) (stepm+YEARM-1)/YEARM;    tj=cptcoveff;
   /*if (stepm<=24) stepsize=2;*/    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
     j1=0;
   agelim=AGESUP;    for(t=1; t<=tj;t++){
   hstepm=stepsize*YEARM; /* Every year of age */      for(i1=1; i1<=ncodemax[t];i1++){ 
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */        j1++;
          if  (cptcovn>0) {
   k=0;          fprintf(ficresprob, "\n#********** Variable "); 
   for(cptcov=1;cptcov<=i1;cptcov++){          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          fprintf(ficresprob, "**********\n#\n");
       k=k+1;          fprintf(ficresprobcov, "\n#********** Variable "); 
         fprintf(ficrespij,"\n#****** ");          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         for(j=1;j<=cptcoveff;j++)          fprintf(ficresprobcov, "**********\n#\n");
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          
         fprintf(ficrespij,"******\n");          fprintf(ficgp, "\n#********** Variable "); 
                  for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */          fprintf(ficgp, "**********\n#\n");
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */          
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
           oldm=oldms;savm=savms;          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
           fprintf(ficrespij,"# Age");          
           for(i=1; i<=nlstate;i++)          fprintf(ficresprobcor, "\n#********** Variable ");    
             for(j=1; j<=nlstate+ndeath;j++)          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
               fprintf(ficrespij," %1d-%1d",i,j);          fprintf(ficresprobcor, "**********\n#");    
           fprintf(ficrespij,"\n");        }
            for (h=0; h<=nhstepm; h++){        
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );        for (age=bage; age<=fage; age ++){ 
             for(i=1; i<=nlstate;i++)          cov[2]=age;
               for(j=1; j<=nlstate+ndeath;j++)          for (k=1; k<=cptcovn;k++) {
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
             fprintf(ficrespij,"\n");          }
              }          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          for (k=1; k<=cptcovprod;k++)
           fprintf(ficrespij,"\n");            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));
   varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);          gm=vector(1,(nlstate)*(nlstate+ndeath));
       
   fclose(ficrespij);          for(theta=1; theta <=npar; theta++){
             for(i=1; i<=npar; i++)
               xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
   /*---------- Forecasting ------------------*/            
   if((stepm == 1) && (strcmp(model,".")==0)){            pmij(pmmij,cov,ncovmodel,xp,nlstate);
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);            
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);            k=0;
   }            for(i=1; i<= (nlstate); i++){
   else{              for(j=1; j<=(nlstate+ndeath);j++){
     erreur=108;                k=k+1;
     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);                gp[k]=pmmij[i][j];
   }              }
              }
             
   /*---------- Health expectancies and variances ------------*/            for(i=1; i<=npar; i++)
               xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
   strcpy(filerest,"t");      
   strcat(filerest,fileres);            pmij(pmmij,cov,ncovmodel,xp,nlstate);
   if((ficrest=fopen(filerest,"w"))==NULL) {            k=0;
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;            for(i=1; i<=(nlstate); i++){
   }              for(j=1; j<=(nlstate+ndeath);j++){
   printf("Computing Total LEs with variances: file '%s' \n", filerest);                k=k+1;
                 gm[k]=pmmij[i][j];
               }
   strcpy(filerese,"e");            }
   strcat(filerese,fileres);       
   if((ficreseij=fopen(filerese,"w"))==NULL) {            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
   }          }
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);  
           for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
  strcpy(fileresv,"v");            for(theta=1; theta <=npar; theta++)
   strcat(fileresv,fileres);              trgradg[j][theta]=gradg[theta][j];
   if((ficresvij=fopen(fileresv,"w"))==NULL) {          
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);          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);
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
   calagedate=-1;          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
 prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
           free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   k=0;  
   for(cptcov=1;cptcov<=i1;cptcov++){          pmij(pmmij,cov,ncovmodel,x,nlstate);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          
       k=k+1;          k=0;
       fprintf(ficrest,"\n#****** ");          for(i=1; i<=(nlstate); i++){
       for(j=1;j<=cptcoveff;j++)            for(j=1; j<=(nlstate+ndeath);j++){
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);              k=k+1;
       fprintf(ficrest,"******\n");              mu[k][(int) age]=pmmij[i][j];
             }
       fprintf(ficreseij,"\n#****** ");          }
       for(j=1;j<=cptcoveff;j++)          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
       fprintf(ficreseij,"******\n");              varpij[i][j][(int)age] = doldm[i][j];
   
       fprintf(ficresvij,"\n#****** ");          /*printf("\n%d ",(int)age);
       for(j=1;j<=cptcoveff;j++)            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
       fprintf(ficresvij,"******\n");            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             }*/
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);  
       oldm=oldms;savm=savms;          fprintf(ficresprob,"\n%d ",(int)age);
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);            fprintf(ficresprobcov,"\n%d ",(int)age);
            fprintf(ficresprobcor,"\n%d ",(int)age);
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);  
       oldm=oldms;savm=savms;          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);            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]);
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");          }
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);          i=0;
       fprintf(ficrest,"\n");          for (k=1; k<=(nlstate);k++){
             for (l=1; l<=(nlstate+ndeath);l++){ 
       epj=vector(1,nlstate+1);              i=i++;
       for(age=bage; age <=fage ;age++){              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
         if (popbased==1) {              for (j=1; j<=i;j++){
           for(i=1; i<=nlstate;i++)                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
             prlim[i][i]=probs[(int)age][i][k];                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
         }              }
                    }
         fprintf(ficrest," %4.0f",age);          }/* end of loop for state */
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){        } /* end of loop for age */
           for(i=1, epj[j]=0.;i <=nlstate;i++) {  
             epj[j] += prlim[i][i]*eij[i][j][(int)age];        /* Confidence intervalle of pij  */
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/        /*
           }          fprintf(ficgp,"\nunset parametric;unset label");
           epj[nlstate+1] +=epj[j];          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);
         for(i=1, vepp=0.;i <=nlstate;i++)          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
           for(j=1;j <=nlstate;j++)          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
             vepp += vareij[i][j][(int)age];          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
         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]));        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
         }        first1=1;
         fprintf(ficrest,"\n");        for (k2=1; k2<=(nlstate);k2++){
       }          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
     }            if(l2==k2) continue;
   }            j=(k2-1)*(nlstate+ndeath)+l2;
 free_matrix(mint,1,maxwav,1,n);            for (k1=1; k1<=(nlstate);k1++){
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
     free_vector(weight,1,n);                if(l1==k1) continue;
   fclose(ficreseij);                i=(k1-1)*(nlstate+ndeath)+l1;
   fclose(ficresvij);                if(i<=j) continue;
   fclose(ficrest);                for (age=bage; age<=fage; age ++){ 
   fclose(ficpar);                  if ((int)age %5==0){
   free_vector(epj,1,nlstate+1);                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                      v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
   /*------- Variance limit prevalence------*/                      cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     mu1=mu[i][(int) age]/stepm*YEARM ;
   strcpy(fileresvpl,"vpl");                    mu2=mu[j][(int) age]/stepm*YEARM;
   strcat(fileresvpl,fileres);                    c12=cv12/sqrt(v1*v2);
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {                    /* Computing eigen value of matrix of covariance */
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
     exit(0);                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
   }                    /* Eigen vectors */
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                     /*v21=sqrt(1.-v11*v11); *//* error */
   k=0;                    v21=(lc1-v1)/cv12*v11;
   for(cptcov=1;cptcov<=i1;cptcov++){                    v12=-v21;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){                    v22=v11;
       k=k+1;                    tnalp=v21/v11;
       fprintf(ficresvpl,"\n#****** ");                    if(first1==1){
       for(j=1;j<=cptcoveff;j++)                      first1=0;
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                      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(ficresvpl,"******\n");                    }
                          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);
       varpl=matrix(1,nlstate,(int) bage, (int) fage);                    /*printf(fignu*/
       oldm=oldms;savm=savms;                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
     }                    if(first==1){
  }                      first=0;
                       fprintf(ficgp,"\nset parametric;unset label");
   fclose(ficresvpl);                      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");
   /*---------- End : free ----------------*/                      fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);   :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
    %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);                              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);
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);                      fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);                      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),\
   free_matrix(matcov,1,npar,1,npar);                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
   free_vector(delti,1,npar);                    }else{
   free_matrix(agev,1,maxwav,1,imx);                      first=0;
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);                      fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
   if(erreur >0)                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
     printf("End of Imach with error or warning %d\n",erreur);                      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",\
   else   printf("End of Imach\n");                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                      }/* if first */
   /* 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);*/                  } /* age mod 5 */
   /*printf("Total time was %d uSec.\n", total_usecs);*/                } /* end loop age */
   /*------ End -----------*/                fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                 first=1;
               } /*l12 */
  end:            } /* k12 */
 #ifdef windows          } /*l1 */
   /* chdir(pathcd);*/        }/* k1 */
 #endif      } /* loop covariates */
  /*system("wgnuplot graph.plt");*/    }
  /*system("../gp37mgw/wgnuplot graph.plt");*/    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
  /*system("cd ../gp37mgw");*/    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/    free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
  strcpy(plotcmd,GNUPLOTPROGRAM);    free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
  strcat(plotcmd," ");    free_vector(xp,1,npar);
  strcat(plotcmd,optionfilegnuplot);    fclose(ficresprob);
  system(plotcmd);    fclose(ficresprobcov);
     fclose(ficresprobcor);
 #ifdef windows    fflush(ficgp);
   while (z[0] != 'q') {    fflush(fichtmcov);
     /* chdir(path); */  }
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");  
     scanf("%s",z);  
     if (z[0] == 'c') system("./imach");  /******************* Printing html file ***********/
     else if (z[0] == 'e') system(optionfilehtm);  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
     else if (z[0] == 'g') system(plotcmd);                    int lastpass, int stepm, int weightopt, char model[],\
     else if (z[0] == 'q') exit(0);                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
   }                    int popforecast, int estepm ,\
 #endif                    double jprev1, double mprev1,double anprev1, \
 }                    double jprev2, double mprev2,double anprev2){
     int jj1, k1, i1, cpt;
   
      fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
      <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
   </ul>");
      fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
    - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
              jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
      fprintf(fichtm,"\
    - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
              stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
      fprintf(fichtm,"\
    - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
              subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
      fprintf(fichtm,"\
    - (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n",
              estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
      fprintf(fichtm,"\
    - Population projections by age and states: \
      <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
   
   fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
    m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        /* Pij */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d1.png\">%s%d1.png</a><br> \
   <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
        /* Quasi-incidences */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
    before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d2.png\">%s%d2.png</a><br> \
   <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
          /* Period (stable) prevalence in each health state */
          for(cpt=1; cpt<nlstate;cpt++){
            fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
   <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
          }
        for(cpt=1; cpt<=nlstate;cpt++) {
           fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
   <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
        }
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
   
   
    fprintf(fichtm,"\
   \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
    - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
   
    fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
    fprintf(fichtm,"\
    - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
   
    fprintf(fichtm,"\
    - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
    fprintf(fichtm,"\
    - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
            estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
    fprintf(fichtm,"\
    - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",
            estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
    fprintf(fichtm,"\
    - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
            subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   
   /*  if(popforecast==1) fprintf(fichtm,"\n */
   /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
   /*      <br>",fileres,fileres,fileres,fileres); */
   /*  else  */
   /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
    fflush(fichtm);
    fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   
    m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        for(cpt=1; cpt<=nlstate;cpt++) {
          fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
   prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
   <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
        }
        fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
   true period expectancies (those weighted with period prevalences are also\
    drawn in addition to the population based expectancies computed using\
    observed and cahotic prevalences: %s%d.png<br>\
   <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
    fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m0,cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
     int ng=0;
   /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   /*     printf("Problem with file %s",optionfilegnuplot); */
   /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   /*   } */
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
     m=pow(2,cptcoveff);
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
    /* 1eme*/
     for (cpt=1; cpt<= nlstate ; cpt ++) {
      for (k1=1; k1<= m ; k1 ++) {
        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
        fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
        fprintf(ficgp,"set xlabel \"Age\" \n\
   set ylabel \"Probability\" \n\
   set ter png small\n\
   set size 0.65,0.65\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else        fprintf(ficgp," \%%*lf (\%%*lf)");
        }
        fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        } 
        fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }  
        fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
      }
     }
     /*2 eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
       fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
       
       for (i=1; i<= nlstate+1 ; i ++) {
         k=2*i;
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         fprintf(ficgp,"\" t\"\" w l 0,");
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
         else fprintf(ficgp,"\" t\"\" w l 0,");
       }
     }
     
     /*3eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<= nlstate ; cpt ++) {
         /*       k=2+nlstate*(2*cpt-2); */
         k=2+(nlstate+1)*(cpt-1);
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
         fprintf(ficgp,"set ter png small\n\
   set size 0.65,0.65\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           
         */
         for (i=1; i< nlstate ; i ++) {
           fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1);
           /*      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
           
         } 
         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
       }
     }
     
     /* CV preval stable (period) */
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<=nlstate ; cpt ++) {
         k=3;
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   set ter png small\nset size 0.65,0.65\n\
   unset log y\n\
   plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
         
         for (i=1; i< nlstate ; i ++)
           fprintf(ficgp,"+$%d",k+i+1);
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
         
         l=3+(nlstate+ndeath)*cpt;
         fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
         for (i=1; i< nlstate ; i ++) {
           l=3+(nlstate+ndeath)*cpt;
           fprintf(ficgp,"+$%d",l+i+1);
         }
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
       } 
     }  
     
     /* proba elementaires */
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             jk++; 
             fprintf(ficgp,"\n");
           }
         }
       }
      }
   
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        for(jk=1; jk <=m; jk++) {
          fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
          if (ng==2)
            fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
          else
            fprintf(ficgp,"\nset title \"Probability\"\n");
          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
          for(k2=1; k2<=nlstate; k2++) {
            k3=i;
            for(k=1; k<=(nlstate+ndeath); k++) {
              if (k != k2){
                if(ng==2)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                else
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;
                for(j=3; j <=ncovmodel; j++) {
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                    fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                    ij++;
                  }
                  else
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
                fprintf(ficgp,")/(1");
                
                for(k1=1; k1 <=nlstate; k1++){   
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
                  for(j=3; j <=ncovmodel; j++){
                    if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                      fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                      ij++;
                    }
                    else
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                  }
                  fprintf(ficgp,")");
                }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
              }
            } /* end k */
          } /* end k2 */
        } /* end jk */
      } /* end ng */
      fflush(ficgp); 
   }  /* end gnuplot */
   
   
   /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
     int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
     double age;
   
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          we use a 5 terms etc. until the borders are no more concerned. 
       */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
           }
         }/* end age */
       }/* end mob */
     }else return -1;
     return 0;
   }/* End movingaverage */
   
   
   /************** Forecasting ******************/
   prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
     int *popage;
     double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   
   
   /**************** function prwizard **********************/
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     /* Wizard to print covariance matrix template */
   
     char ca[32], cb[32], cc[32];
     int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
   } /* end of prwizard */
   /******************* Gompertz Likelihood ******************************/
   double gompertz(double x[])
   { 
     double A,B,L=0.0,sump=0.,num=0.;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
   
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
                +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           L=L+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
    
     return -2*L*num/sump;
   }
   
   /******************* Printing html file ***********/
   void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,  double p[],double **matcov,double agemortsup){
     int i,k;
   
     fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
     fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
     for (i=1;i<=2;i++) 
       fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
     fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
     fprintf(fichtm,"</ul>");
   
   fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
   
    fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
   
    for (k=agegomp;k<(agemortsup-2);k++) 
      fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
   
    
     fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
     fprintf(ficgp,"set out \"graphmort.png\"\n "); 
     fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
     fprintf(ficgp, "set ter png small\n set log y\n"); 
     fprintf(ficgp, "set size 0.65,0.65\n");
     fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
   
   } 
   
   
   
   
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
     int linei, month, year,iout;
     int jj, ll, li, lj, lk, imk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int itimes;
     int NDIM=2;
     int vpopbased=0;
   
     char ca[32], cb[32], cc[32];
     char dummy[]="                         ";
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     struct stat info;
     double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char linetmp[MAXLINE];
       char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE], pathimach[MAXLINE]; 
     char **bp, *tok, *val; /* pathtot */
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     int agemortsup;
     float  sumlpop=0.;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double *severity;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
     double **ximort;
     char *alph[]={"a","a","b","c","d","e"}, str[4];
     int *dcwave;
   
     char z[1]="c", occ;
   
     char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
     char  *strt, strtend[80];
     char *stratrunc;
     int lstra;
   
     long total_usecs;
    
   /*   setlocale (LC_ALL, ""); */
   /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   /*   textdomain (PACKAGE); */
   /*   setlocale (LC_CTYPE, ""); */
   /*   setlocale (LC_MESSAGES, ""); */
   
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     (void) gettimeofday(&start_time,&tzp);
     curr_time=start_time;
     tm = *localtime(&start_time.tv_sec);
     tmg = *gmtime(&start_time.tv_sec);
     strcpy(strstart,asctime(&tm));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tv_sec = tp.tv_sec +86400; */
   /*  tm = *localtime(&start_time.tv_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tv_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     nberr=0; /* Number of errors and warnings */
     nbwarn=0;
     getcwd(pathcd, size);
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       fgets(pathr,FILENAMELENGTH,stdin);
       i=strlen(pathr);
       if(pathr[i-1]=='\n')
         pathr[i-1]='\0';
      for (tok = pathr; tok != NULL; ){
         printf("Pathr |%s|\n",pathr);
         while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
         printf("val= |%s| pathr=%s\n",val,pathr);
         strcpy (pathtot, val);
         if(pathr[0] == '\0') break; /* Dirty */
       }
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     /* Split argv[0], imach program to get pathimach */
     printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
     split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
     printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
    /*   strcpy(pathimach,argv[0]); */
     /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path); /* Can be a relative path */
     if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
       printf("Current directory %s!\n",pathcd);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s\n%s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: \n");
     fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     printf("Local time (at start):%s",strstart);
     fprintf(ficlog,"Local time (at start): %s",strstart);
     fflush(ficlog);
   /*   (void) gettimeofday(&curr_time,&tzp); */
   /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile %s\n",optionfile);
       fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       fflush(ficlog);
       goto end;
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n); 
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
     if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
     /* where is ncovprod ?*/
     ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7*/
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
     npar= nforce*ncovmodel; /* Number of parameters like aij*/
     if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
       printf("Too complex model for current IMaCh: npar=(nlstate+ndeath-1)*nlstate*ncovmodel=%d >= %d(MAXPARM) or nlstate=%d >= %d(NLSTATEMAX) or ndeath=%d >= %d(NDEATHMAX) or ncovmodel=(k+age+#of+signs)=%d(NCOVMAX) >= %d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fprintf(ficlog,"Too complex model for current IMaCh: %d >=%d(MAXPARM) or %d >=%d(NLSTATEMAX) or %d >=%d(NDEATHMAX) or %d(NCOVMAX) >=%d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fflush(stdout);
       fclose (ficlog);
       goto end;
     }
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     delti=delti3[1][1];
     /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
     if(mle==-1){ /* Print a wizard for help writing covariance matrix */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       fclose (ficparo);
       fclose (ficlog);
       goto end;
       exit(0);
     }
     else if(mle==-3) {
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       matcov=matrix(1,npar,1,npar);
     }
     else{
       /* Read guess parameters */
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
       
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       for(i=1; i <=nlstate; i++){
         j=0;
         for(jj=1; jj <=nlstate+ndeath; jj++){
           if(jj==i) continue;
           j++;
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1 != i) && (j1 != j)){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
   It might be a problem of design; if ncovcol and the model are correct\n \
   run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           fprintf(ficparo,"%1d%1d",i1,j1);
           if(mle==1)
             printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar," %lf",&param[i][j][k]);
             if(mle==1){
               printf(" %lf",param[i][j][k]);
               fprintf(ficlog," %lf",param[i][j][k]);
             }
             else
               fprintf(ficlog," %lf",param[i][j][k]);
             fprintf(ficparo," %lf",param[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           if(mle==1)
             printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficparo,"\n");
         }
       }  
       fflush(ficlog);
   
       p=param[1][1];
       
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
   
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath-1; j++){
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1-i)*(j1-j)!=0){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           printf("%1d%1d",i,j);
           fprintf(ficparo,"%1d%1d",i1,j1);
           fprintf(ficlog,"%1d%1d",i1,j1);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar,"%le",&delti3[i][j][k]);
             printf(" %le",delti3[i][j][k]);
             fprintf(ficparo," %le",delti3[i][j][k]);
             fprintf(ficlog," %le",delti3[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           printf("\n");
           fprintf(ficparo,"\n");
           fprintf(ficlog,"\n");
         }
       }
       fflush(ficlog);
   
       delti=delti3[1][1];
   
   
       /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
     
       matcov=matrix(1,npar,1,npar);
       for(i=1; i <=npar; i++)
         for(j=1; j <=npar; j++) matcov[i][j]=0.;
         
       for(i=1; i <=npar; i++){
         fscanf(ficpar,"%s",&str);
         if(mle==1)
           printf("%s",str);
         fprintf(ficlog,"%s",str);
         fprintf(ficparo,"%s",str);
         for(j=1; j <=i; j++){
           fscanf(ficpar," %le",&matcov[i][j]);
           if(mle==1){
             printf(" %.5le",matcov[i][j]);
           }
           fprintf(ficlog," %.5le",matcov[i][j]);
           fprintf(ficparo," %.5le",matcov[i][j]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
       for(i=1; i <=npar; i++)
         for(j=i+1;j<=npar;j++)
           matcov[i][j]=matcov[j][i];
       
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       
       fflush(ficlog);
       
       /*-------- Rewriting parameter file ----------*/
       strcpy(rfileres,"r");    /* "Rparameterfile */
       strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
       strcat(rfileres,".");    /* */
       strcat(rfileres,optionfilext);    /* Other files have txt extension */
       if((ficres =fopen(rfileres,"w"))==NULL) {
         printf("Problem writing new parameter file: %s\n", fileres);goto end;
         fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
       }
       fprintf(ficres,"#%s\n",version);
     }    /* End of mle != -3 */
   
     /*-------- data file ----------*/
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem while opening datafile: %s\n", datafile);goto end;
       fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);goto end;
     }
   
     n= lastobs;
     severity = vector(1,maxwav);
     outcome=imatrix(1,maxwav+1,1,n);
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */ 
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,8);
   
     i=1;
     linei=0;
     while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
       linei=linei+1;
       for(j=strlen(line); j>=0;j--){  /* Untabifies line */
         if(line[j] == '\t')
           line[j] = ' ';
       }
       for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
         ;
       };
       line[j+1]=0;  /* Trims blanks at end of line */
       if(line[0]=='#'){
         fprintf(ficlog,"Comment line\n%s\n",line);
         printf("Comment line\n%s\n",line);
         continue;
       }
       trimbb(linetmp,line); /* Trims multiple blanks in line */
       for (j=0; line[j]!='\0';j++){
         line[j]=linetmp[j];
       }
     
   
       for (j=maxwav;j>=1;j--){
         cutv(stra, strb,line,' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
         /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
             fprintf(ficlog,"Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);
             goto end;
           }
         }
         s[j][i]=lval;
         
         strcpy(line,stra);
         cutv(stra, strb,line,' ');
         if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
         }
         else  if(iout=sscanf(strb,"%s.") != 0){
           month=99;
           year=9999;
         }else{
           printf("Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
           fprintf(ficlog,"Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);fflush(ficlog);
           goto end;
         }
         anint[j][i]= (double) year; 
         mint[j][i]= (double)month; 
         strcpy(line,stra);
       } /* ENd Waves */
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.",dummy) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
           fprintf(ficlog,"Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
           goto end;
       }
       andc[i]=(double) year; 
       moisdc[i]=(double) month; 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.") != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line,j);
         fprintf(ficlog,"Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line,j);fflush(ficlog);
           goto end;
       }
       annais[i]=(double)(year);
       moisnais[i]=(double)(month); 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       errno=0;
       dval=strtod(strb,&endptr); 
       if( strb[0]=='\0' || (*endptr != '\0')){
         printf("Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fprintf(ficlog,"Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fflush(ficlog);
         goto end;
       }
       weight[i]=dval; 
       strcpy(line,stra);
       
       for (j=ncovcol;j>=1;j--){
         cutv(stra, strb,line,' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);
             fprintf(ficlog,"Error reading data around '%d' at line number %ld for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);fflush(ficlog);
             goto end;
           }
         }
         if(lval <-1 || lval >1){
           printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);
           fprintf(ficlog,"Error reading data around '%d' at line number %ld for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
           goto end;
         }
         covar[j][i]=(double)(lval);
         strcpy(line,stra);
       }  
       lstra=strlen(stra);
        
       if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
         stratrunc = &(stra[lstra-9]);
         num[i]=atol(stratrunc);
       }
       else
         num[i]=atol(stra);
       /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
         printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
       
       i=i+1;
     } /* End loop reading  data */
     fclose(fic);
     /* printf("ii=%d", ij);
        scanf("%d",i);*/
     imx=i-1; /* Number of individuals */
   
     /* for (i=1; i<=imx; i++){
       if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
       if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
       if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
       }*/
      /*  for (i=1; i<=imx; i++){
        if (s[4][i]==9)  s[4][i]=-1; 
        printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
     
     /* for (i=1; i<=imx; i++) */
    
      /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
        else weight[i]=1;*/
   
     /* Calculation of the number of parameters from char model */
     Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. Stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
     Tprod=ivector(1,15); 
     Tvaraff=ivector(1,15); 
     Tvard=imatrix(1,15,1,2);
     Tage=ivector(1,15);      
      
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=1, k2=1;
       j=nbocc(model,'+'); /* j=Number of '+' */
       j1=nbocc(model,'*'); /* j1=Number of '*' */
       cptcovn=j+1; /* Number of covariates V1+V2+V3 =>2+1=3 */
       cptcovprod=j1; /*Number of products  V1*V2 =1 */
       
       strcpy(modelsav,model); 
       if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
         printf("Error. Non available option model=%s ",model);
         fprintf(ficlog,"Error. Non available option model=%s ",model);fflush(ficlog);
         goto end;
       }
       
       /* This loop fills the array Tvar from the string 'model'.*/
       /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
       for(i=(j+1); i>=1;i--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' 
                                        modelsav=V2+V3*age+V1+V4 strb=V3*age+V1+V4 
                                        stra=V2
                                       */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /* Model includes a product V1+V3*age+V2 strb=V3*age*/
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn: V3*age strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
           if (strcmp(strc,"age")==0) { /* Vn*age */
             cptcovprod--;
             cutv(strb,stre,strd,'V');
             Tvar[i]=atoi(stre);  /* V1+V3*age+V2 Tvar[2]=3 */
             cptcovage++; /* Sums the number of covariates including age as a product */
             Tage[cptcovage]=i;  /* Tage[1] =2 */
             /*printf("stre=%s ", stre);*/
           }
           else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutv(strb,stre,strc,'V');
             Tvar[i]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=i;
           }
           else {  /* Age is not in the model V1+V3*V2+V2  strb=V3*V2*/
             cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
             Tvar[i]=ncovcol+k1;  /* find 'n' in Vn and stores in Tvar. 
                                     If already ncovcol=2 and model=V2*V1 Tvar[1]=2+1 and Tvar[2]=2+2 etc */
             cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=i;  /* Tprod[1]  */
             Tvard[k1][1]=atoi(strc); /* m*/
             Tvard[k1][2]=atoi(stre); /* n */
             Tvar[cptcovn+k2]=Tvard[k1][1];
             Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
             for (k=1; k<=lastobs;k++) 
               covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
             k1++;
             k2=k2+2;
           }
         }
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
         cutv(strd,strc,strb,'V');
         Tvar[i]=atoi(strc);
         }
         strcpy(modelsav,stra);  /* modelsav=V2+V3*age+V1+V4 strb=V3*age+V1+V4 */ 
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);*/
   
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights*/
       for(i=1;i<=n;i++) weight[i]=1.0;
     }
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           nberr++;
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           nberr++;
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if ((int)andc[i]!=9999){
                   nbwarn++;
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] <agemin){ 
               agemin=agev[m][i];
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
             }
             else if(agev[m][i] >agemax){
               agemax=agev[m][i];
               /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           nberr++;
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           goto end;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
   
     agegomp=(int)agemin;
     free_vector(severity,1,maxwav);
     free_imatrix(outcome,1,maxwav+1,1,n);
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
   
      
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     if (cptcovn > 0) tricode(Tvar,nbcode,imx);
         
     codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
                                    the estimations*/
     h=0;
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
       for(i=1; i <=(m/pow(2,k));i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */ 
         for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate */
           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){  /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */ 
             h++;
             if (h>m) 
               h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
             printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]);
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
          printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
       
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     if(mle==-3)
       strcat(optionfilegnuplot,"-mort");
     strcat(optionfilegnuplot,".gp");
   
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       fprintf(ficgp,"set missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname); /* Main html file */
     if(mle==-3)
       strcat(optionfilehtm,"-mort");
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm);
       exit(0);
     }
   
     strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
     strcat(optionfilehtmcov,"-cov.htm");
     if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtmcov), exit(0);
     }
     else{
     fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
             optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
    - Log file of the run: <a href=\"%s\">%s</a><br>\n\
    - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
    - Date and time at start: %s</ul>\n",\
             optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
             optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
             fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
     chdir(optionfilefiname); /* Move to directory named optionfile */
     
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
   
     fprintf(fichtm,"\n");
     fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
             imx,agemin,agemax,jmin,jmax,jmean);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
   
     if (mle==-3){
       ximort=matrix(1,NDIM,1,NDIM);
       cens=ivector(1,n);
       ageexmed=vector(1,n);
       agecens=vector(1,n);
       dcwave=ivector(1,n);
    
       for (i=1; i<=imx; i++){
         dcwave[i]=-1;
         for (m=firstpass; m<=lastpass; m++)
           if (s[m][i]>nlstate) {
             dcwave[i]=m;
             /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
             break;
           }
       }
   
       for (i=1; i<=imx; i++) {
         if (wav[i]>0){
           ageexmed[i]=agev[mw[1][i]][i];
           j=wav[i];
           agecens[i]=1.; 
   
           if (ageexmed[i]> 1 && wav[i] > 0){
             agecens[i]=agev[mw[j][i]][i];
             cens[i]= 1;
           }else if (ageexmed[i]< 1) 
             cens[i]= -1;
           if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
             cens[i]=0 ;
         }
         else cens[i]=-1;
       }
       
       for (i=1;i<=NDIM;i++) {
         for (j=1;j<=NDIM;j++)
           ximort[i][j]=(i == j ? 1.0 : 0.0);
       }
       
       p[1]=0.0268; p[NDIM]=0.083;
       /*printf("%lf %lf", p[1], p[2]);*/
       
       
       printf("Powell\n");  fprintf(ficlog,"Powell\n");
       strcpy(filerespow,"pow-mort"); 
       strcat(filerespow,fileres);
       if((ficrespow=fopen(filerespow,"w"))==NULL) {
         printf("Problem with resultfile: %s\n", filerespow);
         fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
       }
       fprintf(ficrespow,"# Powell\n# iter -2*LL");
       /*  for (i=1;i<=nlstate;i++)
           for(j=1;j<=nlstate+ndeath;j++)
           if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       */
       fprintf(ficrespow,"\n");
       
       powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
       fclose(ficrespow);
       
       hesscov(matcov, p, NDIM, delti, 1e-4, gompertz); 
   
       for(i=1; i <=NDIM; i++)
         for(j=i+1;j<=NDIM;j++)
           matcov[i][j]=matcov[j][i];
       
       printf("\nCovariance matrix\n ");
       for(i=1; i <=NDIM; i++) {
         for(j=1;j<=NDIM;j++){ 
           printf("%f ",matcov[i][j]);
         }
         printf("\n ");
       }
       
       printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
       for (i=1;i<=NDIM;i++) 
         printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
   
       lsurv=vector(1,AGESUP);
       lpop=vector(1,AGESUP);
       tpop=vector(1,AGESUP);
       lsurv[agegomp]=100000;
       
       for (k=agegomp;k<=AGESUP;k++) {
         agemortsup=k;
         if (p[1]*exp(p[2]*(k-agegomp))>1) break;
       }
       
       for (k=agegomp;k<agemortsup;k++)
         lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
       
       for (k=agegomp;k<agemortsup;k++){
         lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
         sumlpop=sumlpop+lpop[k];
       }
       
       tpop[agegomp]=sumlpop;
       for (k=agegomp;k<(agemortsup-3);k++){
         /*  tpop[k+1]=2;*/
         tpop[k+1]=tpop[k]-lpop[k];
       }
       
       
       printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
       for (k=agegomp;k<(agemortsup-2);k++) 
         printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
       
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
                        stepm, weightopt,\
                        model,imx,p,matcov,agemortsup);
       
       free_vector(lsurv,1,AGESUP);
       free_vector(lpop,1,AGESUP);
       free_vector(tpop,1,AGESUP);
     } /* Endof if mle==-3 */
     
     else{ /* For mle >=1 */
       globpr=0;/* debug */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       globpr=1; /* to print the contributions */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       if(mle>=1){ /* Could be 1 or 2 */
         mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
       }
       
       /*--------- results files --------------*/
       fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
       
       
       fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(k=1; k <=(nlstate+ndeath); k++){
           if (k != i) {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%lf ",p[jk]);
               fprintf(ficlog,"%lf ",p[jk]);
               fprintf(ficres,"%lf ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       if(mle!=0){
         /* Computing hessian and covariance matrix */
         ftolhess=ftol; /* Usually correct */
         hesscov(matcov, p, npar, delti, ftolhess, func);
       }
       fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
       printf("# Scales (for hessian or gradient estimation)\n");
       fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if (j!=i) {
             fprintf(ficres,"%1d%1d",i,j);
             printf("%1d%1d",i,j);
             fprintf(ficlog,"%1d%1d",i,j);
             for(k=1; k<=ncovmodel;k++){
               printf(" %.5e",delti[jk]);
               fprintf(ficlog," %.5e",delti[jk]);
               fprintf(ficres," %.5e",delti[jk]);
               jk++;
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       
       fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       if(mle>=1)
         printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       /* # 121 Var(a12)\n\ */
       /* # 122 Cov(b12,a12) Var(b12)\n\ */
       /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
       /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
       /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
       /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
       /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
       /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
       
       
       /* Just to have a covariance matrix which will be more understandable
          even is we still don't want to manage dictionary of variables
       */
       for(itimes=1;itimes<=2;itimes++){
         jj=0;
         for(i=1; i <=nlstate; i++){
           for(j=1; j <=nlstate+ndeath; j++){
             if(j==i) continue;
             for(k=1; k<=ncovmodel;k++){
               jj++;
               ca[0]= k+'a'-1;ca[1]='\0';
               if(itimes==1){
                 if(mle>=1)
                   printf("#%1d%1d%d",i,j,k);
                 fprintf(ficlog,"#%1d%1d%d",i,j,k);
                 fprintf(ficres,"#%1d%1d%d",i,j,k);
               }else{
                 if(mle>=1)
                   printf("%1d%1d%d",i,j,k);
                 fprintf(ficlog,"%1d%1d%d",i,j,k);
                 fprintf(ficres,"%1d%1d%d",i,j,k);
               }
               ll=0;
               for(li=1;li <=nlstate; li++){
                 for(lj=1;lj <=nlstate+ndeath; lj++){
                   if(lj==li) continue;
                   for(lk=1;lk<=ncovmodel;lk++){
                     ll++;
                     if(ll<=jj){
                       cb[0]= lk +'a'-1;cb[1]='\0';
                       if(ll<jj){
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }else{
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }
                     }
                   } /* end lk */
                 } /* end lj */
               } /* end li */
               if(mle>=1)
                 printf("\n");
               fprintf(ficlog,"\n");
               fprintf(ficres,"\n");
               numlinepar++;
             } /* end k*/
           } /*end j */
         } /* end i */
       } /* end itimes */
       
       fflush(ficlog);
       fflush(ficres);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       estepm=0;
       fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
       if (estepm==0 || estepm < stepm) estepm=stepm;
       if (fage <= 2) {
         bage = ageminpar;
         fage = agemaxpar;
       }
       
       fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
       fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
       fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       
       dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
       dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
       
       fscanf(ficpar,"pop_based=%d\n",&popbased);
       fprintf(ficparo,"pop_based=%d\n",popbased);   
       fprintf(ficres,"pop_based=%d\n",popbased);   
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
       fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       /* day and month of proj2 are not used but only year anproj2.*/
       
       
       
       /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
       /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                    model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                    jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
         
      /*------------ free_vector  -------------*/
      /*  chdir(path); */
    
       free_ivector(wav,1,imx);
       free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
       free_lvector(num,1,n);
       free_vector(agedc,1,n);
       /*free_matrix(covar,0,NCOVMAX,1,n);*/
       /*free_matrix(covar,1,NCOVMAX,1,n);*/
       fclose(ficparo);
       fclose(ficres);
   
   
       /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
     
       strcpy(filerespl,"pl");
       strcat(filerespl,fileres);
       if((ficrespl=fopen(filerespl,"w"))==NULL) {
         printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
         fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
       }
       printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
       fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
       pstamp(ficrespl);
       fprintf(ficrespl,"# Period (stable) prevalence \n");
       fprintf(ficrespl,"#Age ");
       for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
       fprintf(ficrespl,"\n");
     
       prlim=matrix(1,nlstate,1,nlstate);
   
       agebase=ageminpar;
       agelim=agemaxpar;
       ftolpl=1.e-10;
       i1=cptcoveff;
       if (cptcovn < 1){i1=1;}
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           /* to clean */
           printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,codtab[cptcod][cptcov],nbcode);
           fprintf(ficrespl,"\n#******");
           printf("\n#******");
           fprintf(ficlog,"\n#******");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficrespl,"******\n");
           printf("******\n");
           fprintf(ficlog,"******\n");
           
           for (age=agebase; age<=agelim; age++){
             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
             fprintf(ficrespl,"%.0f ",age );
             for(j=1;j<=cptcoveff;j++)
               fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             for(i=1; i<=nlstate;i++)
               fprintf(ficrespl," %.5f", prlim[i][i]);
             fprintf(ficrespl,"\n");
           }
         }
       }
       fclose(ficrespl);
   
       /*------------- h Pij x at various ages ------------*/
     
       strcpy(filerespij,"pij");  strcat(filerespij,fileres);
       if((ficrespij=fopen(filerespij,"w"))==NULL) {
         printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
         fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
       }
       printf("Computing pij: result on file '%s' \n", filerespij);
       fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
       stepsize=(int) (stepm+YEARM-1)/YEARM;
       /*if (stepm<=24) stepsize=2;*/
   
       agelim=AGESUP;
       hstepm=stepsize*YEARM; /* Every year of age */
       hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
       /* hstepm=1;   aff par mois*/
       pstamp(ficrespij);
       fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           fprintf(ficrespij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrespij,"******\n");
           
           for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
             nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   
             /*      nhstepm=nhstepm*YEARM; aff par mois*/
   
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %1d-%1d",i,j);
             fprintf(ficrespij,"\n");
             for (h=0; h<=nhstepm; h++){
               fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
               for(i=1; i<=nlstate;i++)
                 for(j=1; j<=nlstate+ndeath;j++)
                   fprintf(ficrespij," %.5f", p3mat[i][j][h]);
               fprintf(ficrespij,"\n");
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             fprintf(ficrespij,"\n");
           }
         }
       }
   
       varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
   
       fclose(ficrespij);
   
       probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for(i=1;i<=AGESUP;i++)
         for(j=1;j<=NCOVMAX;j++)
           for(k=1;k<=NCOVMAX;k++)
             probs[i][j][k]=0.;
   
       /*---------- Forecasting ------------------*/
       /*if((stepm == 1) && (strcmp(model,".")==0)){*/
       if(prevfcast==1){
         /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
         /*      }  */
         /*      else{ */
         /*        erreur=108; */
         /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*      } */
       }
     
   
       /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
   
       prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
       /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
           ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
       */
   
       if (mobilav!=0) {
         mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
           fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
           printf(" Error in movingaverage mobilav=%d\n",mobilav);
         }
       }
   
   
       /*---------- Health expectancies, no variances ------------*/
   
       strcpy(filerese,"e");
       strcat(filerese,fileres);
       if((ficreseij=fopen(filerese,"w"))==NULL) {
         printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
         fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       }
       printf("Computing Health Expectancies: result on file '%s' \n", filerese);
       fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1; 
           fprintf(ficreseij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficreseij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);  
         
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         }
       }
       fclose(ficreseij);
   
   
       /*---------- Health expectancies and variances ------------*/
   
   
       strcpy(filerest,"t");
       strcat(filerest,fileres);
       if((ficrest=fopen(filerest,"w"))==NULL) {
         printf("Problem with total LE resultfile: %s\n", filerest);goto end;
         fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
       }
       printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
       fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
   
   
       strcpy(fileresstde,"stde");
       strcat(fileresstde,fileres);
       if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
         printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
         fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
       }
       printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
       fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
   
       strcpy(filerescve,"cve");
       strcat(filerescve,fileres);
       if((ficrescveij=fopen(filerescve,"w"))==NULL) {
         printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
         fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
       }
       printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
       fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
   
       strcpy(fileresv,"v");
       strcat(fileresv,fileres);
       if((ficresvij=fopen(fileresv,"w"))==NULL) {
         printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
         fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
       }
       printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
       fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1; 
           fprintf(ficrest,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrest,"******\n");
   
           fprintf(ficresstdeij,"\n#****** ");
           fprintf(ficrescveij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficresstdeij,"******\n");
           fprintf(ficrescveij,"******\n");
   
           fprintf(ficresvij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);  
    
           vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           pstamp(ficrest);
           for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
             oldm=oldms;savm=savms;
             varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart);   fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");
             if(vpopbased==1)
               fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
             else
               fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
             fprintf(ficrest,"# Age e.. (std) ");
             for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
             fprintf(ficrest,"\n");
   
             epj=vector(1,nlstate+1);
             for(age=bage; age <=fage ;age++){
               prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
               if (vpopbased==1) {
                 if(mobilav ==0){
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=probs[(int)age][i][k];
                 }else{ /* mobilav */ 
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=mobaverage[(int)age][i][k];
                 }
               }
           
               fprintf(ficrest," %4.0f",age);
               for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
                 for(i=1, epj[j]=0.;i <=nlstate;i++) {
                   epj[j] += prlim[i][i]*eij[i][j][(int)age];
                   /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
                 }
                 epj[nlstate+1] +=epj[j];
               }
   
               for(i=1, vepp=0.;i <=nlstate;i++)
                 for(j=1;j <=nlstate;j++)
                   vepp += vareij[i][j][(int)age];
               fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
               for(j=1;j <=nlstate;j++){
                 fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
               }
               fprintf(ficrest,"\n");
             }
           }
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_vector(epj,1,nlstate+1);
         }
       }
       free_vector(weight,1,n);
       free_imatrix(Tvard,1,15,1,2);
       free_imatrix(s,1,maxwav+1,1,n);
       free_matrix(anint,1,maxwav,1,n); 
       free_matrix(mint,1,maxwav,1,n);
       free_ivector(cod,1,n);
       free_ivector(tab,1,NCOVMAX);
       fclose(ficresstdeij);
       fclose(ficrescveij);
       fclose(ficresvij);
       fclose(ficrest);
       fclose(ficpar);
     
       /*------- Variance of period (stable) prevalence------*/   
   
       strcpy(fileresvpl,"vpl");
       strcat(fileresvpl,fileres);
       if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
         printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
         exit(0);
       }
       printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           fprintf(ficresvpl,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvpl,"******\n");
         
           varpl=matrix(1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
           free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
         }
       }
   
       fclose(ficresvpl);
   
       /*---------- End : free ----------------*/
       if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     }  /* mle==-3 arrives here for freeing */
    endfree:
     free_matrix(prlim,1,nlstate,1,nlstate);
       free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(covar,0,NCOVMAX,1,n);
       free_matrix(matcov,1,npar,1,npar);
       /*free_vector(delti,1,npar);*/
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       free_matrix(agev,1,maxwav,1,imx);
       free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   
       free_ivector(ncodemax,1,8);
       free_ivector(Tvar,1,15);
       free_ivector(Tprod,1,15);
       free_ivector(Tvaraff,1,15);
       free_ivector(Tage,1,15);
   
       free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
       free_imatrix(codtab,1,100,1,10);
     fflush(fichtm);
     fflush(ficgp);
     
   
     if((nberr >0) || (nbwarn>0)){
       printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
       fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
     }else{
       printf("End of Imach\n");
       fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     (void) gettimeofday(&end_time,&tzp);
     tm = *localtime(&end_time.tv_sec);
     tmg = *gmtime(&end_time.tv_sec);
     strcpy(strtend,asctime(&tm));
     printf("Local time at start %s\nLocal time at end   %s",strstart, strtend); 
     fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
     printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
   
     printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
     fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
     fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
     /*  printf("Total time was %d uSec.\n", total_usecs);*/
   /*   if(fileappend(fichtm,optionfilehtm)){ */
     fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtm);
     fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtmcov);
     fclose(ficgp);
     fclose(ficlog);
     /*------ End -----------*/
   
   
      printf("Before Current directory %s!\n",pathcd);
      if(chdir(pathcd) != 0)
       printf("Can't move to directory %s!\n",path);
     if(getcwd(pathcd,MAXLINE) > 0)
       printf("Current directory %s!\n",pathcd);
     /*strcat(plotcmd,CHARSEPARATOR);*/
     sprintf(plotcmd,"gnuplot");
   #ifndef UNIX
     sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
   #endif
     if(!stat(plotcmd,&info)){
       printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
       if(!stat(getenv("GNUPLOTBIN"),&info)){
         printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #ifdef UNIX
       strcpy(plotcmd,GNUPLOTPROGRAM);
       if(!stat(plotcmd,&info)){
         printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #endif
     }else
       strcpy(pplotcmd,plotcmd);
     
     sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
     printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
   
     if((outcmd=system(plotcmd)) != 0){
       printf("\n Problem with gnuplot\n");
     }
     printf(" Wait...");
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again and q for exiting: ");
       scanf("%s",z);
   /*     if (z[0] == 'c') system("./imach"); */
       if (z[0] == 'e') {
         printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
         system(optionfilehtm);
       }
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     end:
     while (z[0] != 'q') {
       printf("\nType  q for exiting: ");
       scanf("%s",z);
     }
   }
   
   
   

Removed from v.1.42  
changed lines
  Added in v.1.133


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