Diff for /imach/src/imach.c between versions 1.36 and 1.130

version 1.36, 2002/03/29 15:27:27 version 1.130, 2009/05/26 06:44:34
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.130  2009/05/26 06:44:34  brouard
      (Module): Max Covariate is now set to 20 instead of 8. A
   This program computes Healthy Life Expectancies from    lot of cleaning with variables initialized to 0. Trying to make
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
   first survey ("cross") where individuals from different ages are  
   interviewed on their health status or degree of disability (in the    Revision 1.129  2007/08/31 13:49:27  lievre
   case of a health survey which is our main interest) -2- at least a    Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
   second wave of interviews ("longitudinal") which measure each change  
   (if any) in individual health status.  Health expectancies are    Revision 1.128  2006/06/30 13:02:05  brouard
   computed from the time spent in each health state according to a    (Module): Clarifications on computing e.j
   model. More health states you consider, more time is necessary to reach the  
   Maximum Likelihood of the parameters involved in the model.  The    Revision 1.127  2006/04/28 18:11:50  brouard
   simplest model is the multinomial logistic model where pij is the    (Module): Yes the sum of survivors was wrong since
   probabibility to be observed in state j at the second wave    imach-114 because nhstepm was no more computed in the age
   conditional to be observed in state i at the first wave. Therefore    loop. Now we define nhstepma in the age loop.
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    (Module): In order to speed up (in case of numerous covariates) we
   'age' is age and 'sex' is a covariate. If you want to have a more    compute health expectancies (without variances) in a first step
   complex model than "constant and age", you should modify the program    and then all the health expectancies with variances or standard
   where the markup *Covariates have to be included here again* invites    deviation (needs data from the Hessian matrices) which slows the
   you to do it.  More covariates you add, slower the    computation.
   convergence.    In the future we should be able to stop the program is only health
     expectancies and graph are needed without standard deviations.
   The advantage of this computer programme, compared to a simple  
   multinomial logistic model, is clear when the delay between waves is not    Revision 1.126  2006/04/28 17:23:28  brouard
   identical for each individual. Also, if a individual missed an    (Module): Yes the sum of survivors was wrong since
   intermediate interview, the information is lost, but taken into    imach-114 because nhstepm was no more computed in the age
   account using an interpolation or extrapolation.      loop. Now we define nhstepma in the age loop.
     Version 0.98h
   hPijx is the probability to be observed in state i at age x+h  
   conditional to the observed state i at age x. The delay 'h' can be    Revision 1.125  2006/04/04 15:20:31  lievre
   split into an exact number (nh*stepm) of unobserved intermediate    Errors in calculation of health expectancies. Age was not initialized.
   states. This elementary transition (by month or quarter trimester,    Forecasting file added.
   semester or year) is model as a multinomial logistic.  The hPx  
   matrix is simply the matrix product of nh*stepm elementary matrices    Revision 1.124  2006/03/22 17:13:53  lievre
   and the contribution of each individual to the likelihood is simply    Parameters are printed with %lf instead of %f (more numbers after the comma).
   hPijx.    The log-likelihood is printed in the log file
   
   Also this programme outputs the covariance matrix of the parameters but also    Revision 1.123  2006/03/20 10:52:43  brouard
   of the life expectancies. It also computes the prevalence limits.    * imach.c (Module): <title> changed, corresponds to .htm file
      name. <head> headers where missing.
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).  
            Institut national d'études démographiques, Paris.    * imach.c (Module): Weights can have a decimal point as for
   This software have been partly granted by Euro-REVES, a concerted action    English (a comma might work with a correct LC_NUMERIC environment,
   from the European Union.    otherwise the weight is truncated).
   It is copyrighted identically to a GNU software product, ie programme and    Modification of warning when the covariates values are not 0 or
   software can be distributed freely for non commercial use. Latest version    1.
   can be accessed at http://euroreves.ined.fr/imach .    Version 0.98g
   **********************************************************************/  
      Revision 1.122  2006/03/20 09:45:41  brouard
 #include <math.h>    (Module): Weights can have a decimal point as for
 #include <stdio.h>    English (a comma might work with a correct LC_NUMERIC environment,
 #include <stdlib.h>    otherwise the weight is truncated).
 #include <unistd.h>    Modification of warning when the covariates values are not 0 or
     1.
 #define MAXLINE 256    Version 0.98g
 #define GNUPLOTPROGRAM "wgnuplot"  
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/    Revision 1.121  2006/03/16 17:45:01  lievre
 #define FILENAMELENGTH 80    * imach.c (Module): Comments concerning covariates added
 /*#define DEBUG*/  
 #define windows    * imach.c (Module): refinements in the computation of lli if
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    status=-2 in order to have more reliable computation if stepm is
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    not 1 month. Version 0.98f
   
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    Revision 1.120  2006/03/16 15:10:38  lievre
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    (Module): refinements in the computation of lli if
     status=-2 in order to have more reliable computation if stepm is
 #define NINTERVMAX 8    not 1 month. Version 0.98f
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */  
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    Revision 1.119  2006/03/15 17:42:26  brouard
 #define NCOVMAX 8 /* Maximum number of covariates */    (Module): Bug if status = -2, the loglikelihood was
 #define MAXN 20000    computed as likelihood omitting the logarithm. Version O.98e
 #define YEARM 12. /* Number of months per year */  
 #define AGESUP 130    Revision 1.118  2006/03/14 18:20:07  brouard
 #define AGEBASE 40    (Module): varevsij Comments added explaining the second
     table of variances if popbased=1 .
     (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 int erreur; /* Error number */    (Module): Function pstamp added
 int nvar;    (Module): Version 0.98d
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;  
 int npar=NPARMAX;    Revision 1.117  2006/03/14 17:16:22  brouard
 int nlstate=2; /* Number of live states */    (Module): varevsij Comments added explaining the second
 int ndeath=1; /* Number of dead states */    table of variances if popbased=1 .
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 int popbased=0;    (Module): Function pstamp added
     (Module): Version 0.98d
 int *wav; /* Number of waves for this individuual 0 is possible */  
 int maxwav; /* Maxim number of waves */    Revision 1.116  2006/03/06 10:29:27  brouard
 int jmin, jmax; /* min, max spacing between 2 waves */    (Module): Variance-covariance wrong links and
 int mle, weightopt;    varian-covariance of ej. is needed (Saito).
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */  
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    Revision 1.115  2006/02/27 12:17:45  brouard
 double jmean; /* Mean space between 2 waves */    (Module): One freematrix added in mlikeli! 0.98c
 double **oldm, **newm, **savm; /* Working pointers to matrices */  
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    Revision 1.114  2006/02/26 12:57:58  brouard
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    (Module): Some improvements in processing parameter
 FILE *ficgp,*ficresprob,*ficpop;    filename with strsep.
 FILE *ficreseij;  
   char filerese[FILENAMELENGTH];    Revision 1.113  2006/02/24 14:20:24  brouard
  FILE  *ficresvij;    (Module): Memory leaks checks with valgrind and:
   char fileresv[FILENAMELENGTH];    datafile was not closed, some imatrix were not freed and on matrix
  FILE  *ficresvpl;    allocation too.
   char fileresvpl[FILENAMELENGTH];  
     Revision 1.112  2006/01/30 09:55:26  brouard
 #define NR_END 1    (Module): Back to gnuplot.exe instead of wgnuplot.exe
 #define FREE_ARG char*  
 #define FTOL 1.0e-10    Revision 1.111  2006/01/25 20:38:18  brouard
     (Module): Lots of cleaning and bugs added (Gompertz)
 #define NRANSI    (Module): Comments can be added in data file. Missing date values
 #define ITMAX 200    can be a simple dot '.'.
   
 #define TOL 2.0e-4    Revision 1.110  2006/01/25 00:51:50  brouard
     (Module): Lots of cleaning and bugs added (Gompertz)
 #define CGOLD 0.3819660  
 #define ZEPS 1.0e-10    Revision 1.109  2006/01/24 19:37:15  brouard
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    (Module): Comments (lines starting with a #) are allowed in data.
   
 #define GOLD 1.618034    Revision 1.108  2006/01/19 18:05:42  lievre
 #define GLIMIT 100.0    Gnuplot problem appeared...
 #define TINY 1.0e-20    To be fixed
   
 static double maxarg1,maxarg2;    Revision 1.107  2006/01/19 16:20:37  brouard
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    Test existence of gnuplot in imach path
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  
      Revision 1.106  2006/01/19 13:24:36  brouard
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    Some cleaning and links added in html output
 #define rint(a) floor(a+0.5)  
     Revision 1.105  2006/01/05 20:23:19  lievre
 static double sqrarg;    *** empty log message ***
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    Revision 1.104  2005/09/30 16:11:43  lievre
     (Module): sump fixed, loop imx fixed, and simplifications.
 int imx;    (Module): If the status is missing at the last wave but we know
 int stepm;    that the person is alive, then we can code his/her status as -2
 /* Stepm, step in month: minimum step interpolation*/    (instead of missing=-1 in earlier versions) and his/her
     contributions to the likelihood is 1 - Prob of dying from last
 int estepm;    health status (= 1-p13= p11+p12 in the easiest case of somebody in
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/    the healthy state at last known wave). Version is 0.98
   
 int m,nb;    Revision 1.103  2005/09/30 15:54:49  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;  
 double **pmmij, ***probs, ***mobaverage;    Revision 1.102  2004/09/15 17:31:30  brouard
 double dateintmean=0;    Add the possibility to read data file including tab characters.
   
 double *weight;    Revision 1.101  2004/09/15 10:38:38  brouard
 int **s; /* Status */    Fix on curr_time
 double *agedc, **covar, idx;  
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    Revision 1.100  2004/07/12 18:29:06  brouard
     Add version for Mac OS X. Just define UNIX in Makefile
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  
 double ftolhess; /* Tolerance for computing hessian */    Revision 1.99  2004/06/05 08:57:40  brouard
     *** empty log message ***
 /**************** split *************************/  
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    Revision 1.98  2004/05/16 15:05:56  brouard
 {    New version 0.97 . First attempt to estimate force of mortality
    char *s;                             /* pointer */    directly from the data i.e. without the need of knowing the health
    int  l1, l2;                         /* length counters */    state at each age, but using a Gompertz model: log u =a + b*age .
     This is the basic analysis of mortality and should be done before any
    l1 = strlen( path );                 /* length of path */    other analysis, in order to test if the mortality estimated from the
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    cross-longitudinal survey is different from the mortality estimated
 #ifdef windows    from other sources like vital statistic data.
    s = strrchr( path, '\\' );           /* find last / */  
 #else    The same imach parameter file can be used but the option for mle should be -3.
    s = strrchr( path, '/' );            /* find last / */  
 #endif    Agnès, who wrote this part of the code, tried to keep most of the
    if ( s == NULL ) {                   /* no directory, so use current */    former routines in order to include the new code within the former code.
 #if     defined(__bsd__)                /* get current working directory */  
       extern char       *getwd( );    The output is very simple: only an estimate of the intercept and of
     the slope with 95% confident intervals.
       if ( getwd( dirc ) == NULL ) {  
 #else    Current limitations:
       extern char       *getcwd( );    A) Even if you enter covariates, i.e. with the
     model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    B) There is no computation of Life Expectancy nor Life Table.
 #endif  
          return( GLOCK_ERROR_GETCWD );    Revision 1.97  2004/02/20 13:25:42  lievre
       }    Version 0.96d. Population forecasting command line is (temporarily)
       strcpy( name, path );             /* we've got it */    suppressed.
    } else {                             /* strip direcotry from path */  
       s++;                              /* after this, the filename */    Revision 1.96  2003/07/15 15:38:55  brouard
       l2 = strlen( s );                 /* length of filename */    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    rewritten within the same printf. Workaround: many printfs.
       strcpy( name, s );                /* save file name */  
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    Revision 1.95  2003/07/08 07:54:34  brouard
       dirc[l1-l2] = 0;                  /* add zero */    * imach.c (Repository):
    }    (Repository): Using imachwizard code to output a more meaningful covariance
    l1 = strlen( dirc );                 /* length of directory */    matrix (cov(a12,c31) instead of numbers.
 #ifdef windows  
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    Revision 1.94  2003/06/27 13:00:02  brouard
 #else    Just cleaning
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }  
 #endif    Revision 1.93  2003/06/25 16:33:55  brouard
    s = strrchr( name, '.' );            /* find last / */    (Module): On windows (cygwin) function asctime_r doesn't
    s++;    exist so I changed back to asctime which exists.
    strcpy(ext,s);                       /* save extension */    (Module): Version 0.96b
    l1= strlen( name);  
    l2= strlen( s)+1;    Revision 1.92  2003/06/25 16:30:45  brouard
    strncpy( finame, name, l1-l2);    (Module): On windows (cygwin) function asctime_r doesn't
    finame[l1-l2]= 0;    exist so I changed back to asctime which exists.
    return( 0 );                         /* we're done */  
 }    Revision 1.91  2003/06/25 15:30:29  brouard
     * imach.c (Repository): Duplicated warning errors corrected.
     (Repository): Elapsed time after each iteration is now output. It
 /******************************************/    helps to forecast when convergence will be reached. Elapsed time
     is stamped in powell.  We created a new html file for the graphs
 void replace(char *s, char*t)    concerning matrix of covariance. It has extension -cov.htm.
 {  
   int i;    Revision 1.90  2003/06/24 12:34:15  brouard
   int lg=20;    (Module): Some bugs corrected for windows. Also, when
   i=0;    mle=-1 a template is output in file "or"mypar.txt with the design
   lg=strlen(t);    of the covariance matrix to be input.
   for(i=0; i<= lg; i++) {  
     (s[i] = t[i]);    Revision 1.89  2003/06/24 12:30:52  brouard
     if (t[i]== '\\') s[i]='/';    (Module): Some bugs corrected for windows. Also, when
   }    mle=-1 a template is output in file "or"mypar.txt with the design
 }    of the covariance matrix to be input.
   
 int nbocc(char *s, char occ)    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.
   int i,j=0;  
   int lg=20;    Revision 1.87  2003/06/18 12:26:01  brouard
   i=0;    Version 0.96
   lg=strlen(s);  
   for(i=0; i<= lg; i++) {    Revision 1.86  2003/06/17 20:04:08  brouard
   if  (s[i] == occ ) j++;    (Module): Change position of html and gnuplot routines and added
   }    routine fileappend.
   return j;  
 }    Revision 1.85  2003/06/17 13:12:43  brouard
     * imach.c (Repository): Check when date of death was earlier that
 void cutv(char *u,char *v, char*t, char occ)    current date of interview. It may happen when the death was just
 {    prior to the death. In this case, dh was negative and likelihood
   int i,lg,j,p=0;    was wrong (infinity). We still send an "Error" but patch by
   i=0;    assuming that the date of death was just one stepm after the
   for(j=0; j<=strlen(t)-1; j++) {    interview.
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    (Repository): Because some people have very long ID (first column)
   }    we changed int to long in num[] and we added a new lvector for
     memory allocation. But we also truncated to 8 characters (left
   lg=strlen(t);    truncation)
   for(j=0; j<p; j++) {    (Repository): No more line truncation errors.
     (u[j] = t[j]);  
   }    Revision 1.84  2003/06/13 21:44:43  brouard
      u[p]='\0';    * imach.c (Repository): Replace "freqsummary" at a correct
     place. It differs from routine "prevalence" which may be called
    for(j=0; j<= lg; j++) {    many times. Probs is memory consuming and must be used with
     if (j>=(p+1))(v[j-p-1] = t[j]);    parcimony.
   }    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
 }  
     Revision 1.83  2003/06/10 13:39:11  lievre
 /********************** nrerror ********************/    *** empty log message ***
   
 void nrerror(char error_text[])    Revision 1.82  2003/06/05 15:57:20  brouard
 {    Add log in  imach.c and  fullversion number is now printed.
   fprintf(stderr,"ERREUR ...\n");  
   fprintf(stderr,"%s\n",error_text);  */
   exit(1);  /*
 }     Interpolated Markov Chain
 /*********************** vector *******************/  
 double *vector(int nl, int nh)    Short summary of the programme:
 {    
   double *v;    This program computes Healthy Life Expectancies from
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
   if (!v) nrerror("allocation failure in vector");    first survey ("cross") where individuals from different ages are
   return v-nl+NR_END;    interviewed on their health status or degree of disability (in the
 }    case of a health survey which is our main interest) -2- at least a
     second wave of interviews ("longitudinal") which measure each change
 /************************ free vector ******************/    (if any) in individual health status.  Health expectancies are
 void free_vector(double*v, int nl, int nh)    computed from the time spent in each health state according to a
 {    model. More health states you consider, more time is necessary to reach the
   free((FREE_ARG)(v+nl-NR_END));    Maximum Likelihood of the parameters involved in the model.  The
 }    simplest model is the multinomial logistic model where pij is the
     probability to be observed in state j at the second wave
 /************************ivector *******************************/    conditional to be observed in state i at the first wave. Therefore
 int *ivector(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
   int *v;    complex model than "constant and age", you should modify the program
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    where the markup *Covariates have to be included here again* invites
   if (!v) nrerror("allocation failure in ivector");    you to do it.  More covariates you add, slower the
   return v-nl+NR_END;    convergence.
 }  
     The advantage of this computer programme, compared to a simple
 /******************free ivector **************************/    multinomial logistic model, is clear when the delay between waves is not
 void free_ivector(int *v, long nl, long nh)    identical for each individual. Also, if a individual missed an
 {    intermediate interview, the information is lost, but taken into
   free((FREE_ARG)(v+nl-NR_END));    account using an interpolation or extrapolation.  
 }  
     hPijx is the probability to be observed in state i at age x+h
 /******************* imatrix *******************************/    conditional to the observed state i at age x. The delay 'h' can be
 int **imatrix(long nrl, long nrh, long ncl, long nch)    split into an exact number (nh*stepm) of unobserved intermediate
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    states. This elementary transition (by month, quarter,
 {    semester or year) is modelled as a multinomial logistic.  The hPx
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    matrix is simply the matrix product of nh*stepm elementary matrices
   int **m;    and the contribution of each individual to the likelihood is simply
      hPijx.
   /* allocate pointers to rows */  
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    Also this programme outputs the covariance matrix of the parameters but also
   if (!m) nrerror("allocation failure 1 in matrix()");    of the life expectancies. It also computes the period (stable) prevalence. 
   m += NR_END;    
   m -= nrl;    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
               Institut national d'études démographiques, Paris.
      This software have been partly granted by Euro-REVES, a concerted action
   /* allocate rows and set pointers to them */    from the European Union.
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    It is copyrighted identically to a GNU software product, ie programme and
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    software can be distributed freely for non commercial use. Latest version
   m[nrl] += NR_END;    can be accessed at http://euroreves.ined.fr/imach .
   m[nrl] -= ncl;  
      Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
      
   /* return pointer to array of pointers to rows */    **********************************************************************/
   return m;  /*
 }    main
     read parameterfile
 /****************** free_imatrix *************************/    read datafile
 void free_imatrix(m,nrl,nrh,ncl,nch)    concatwav
       int **m;    freqsummary
       long nch,ncl,nrh,nrl;    if (mle >= 1)
      /* free an int matrix allocated by imatrix() */      mlikeli
 {    print results files
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    if mle==1 
   free((FREE_ARG) (m+nrl-NR_END));       computes hessian
 }    read end of parameter file: agemin, agemax, bage, fage, estepm
         begin-prev-date,...
 /******************* matrix *******************************/    open gnuplot file
 double **matrix(long nrl, long nrh, long ncl, long nch)    open html file
 {    period (stable) prevalence
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;     for age prevalim()
   double **m;    h Pij x
     variance of p varprob
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    forecasting if prevfcast==1 prevforecast call prevalence()
   if (!m) nrerror("allocation failure 1 in matrix()");    health expectancies
   m += NR_END;    Variance-covariance of DFLE
   m -= nrl;    prevalence()
      movingaverage()
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    varevsij() 
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    if popbased==1 varevsij(,popbased)
   m[nrl] += NR_END;    total life expectancies
   m[nrl] -= ncl;    Variance of period (stable) prevalence
    end
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  */
   return m;  
 }  
   
 /*************************free matrix ************************/   
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  #include <math.h>
 {  #include <stdio.h>
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  #include <stdlib.h>
   free((FREE_ARG)(m+nrl-NR_END));  #include <string.h>
 }  #include <unistd.h>
   
 /******************* ma3x *******************************/  #include <limits.h>
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  #include <sys/types.h>
 {  #include <sys/stat.h>
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  #include <errno.h>
   double ***m;  extern int errno;
   
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  /* #include <sys/time.h> */
   if (!m) nrerror("allocation failure 1 in matrix()");  #include <time.h>
   m += NR_END;  #include "timeval.h"
   m -= nrl;  
   /* #include <libintl.h> */
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  /* #define _(String) gettext (String) */
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;  #define MAXLINE 256
   m[nrl] -= ncl;  
   #define GNUPLOTPROGRAM "gnuplot"
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
   #define FILENAMELENGTH 132
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
   m[nrl][ncl] += NR_END;  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   m[nrl][ncl] -= nll;  
   for (j=ncl+1; j<=nch; j++)  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
     m[nrl][j]=m[nrl][j-1]+nlay;  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
    
   for (i=nrl+1; i<=nrh; i++) {  #define NINTERVMAX 8
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
     for (j=ncl+1; j<=nch; j++)  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
       m[i][j]=m[i][j-1]+nlay;  #define NCOVMAX 20 /* Maximum number of covariates */
   }  #define MAXN 20000
   return m;  #define YEARM 12. /* Number of months per year */
 }  #define AGESUP 130
   #define AGEBASE 40
 /*************************free ma3x ************************/  #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  #ifdef UNIX
 {  #define DIRSEPARATOR '/'
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  #define CHARSEPARATOR "/"
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  #define ODIRSEPARATOR '\\'
   free((FREE_ARG)(m+nrl-NR_END));  #else
 }  #define DIRSEPARATOR '\\'
   #define CHARSEPARATOR "\\"
 /***************** f1dim *************************/  #define ODIRSEPARATOR '/'
 extern int ncom;  #endif
 extern double *pcom,*xicom;  
 extern double (*nrfunc)(double []);  /* $Id$ */
    /* $State$ */
 double f1dim(double x)  
 {  char version[]="Imach version 0.98i, June 2006, INED-EUROREVES-Institut de longevite ";
   int j;  char fullversion[]="$Revision$ $Date$"; 
   double f;  char strstart[80];
   double *xt;  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
    int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
   xt=vector(1,ncom);  int nvar=0;
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov=0; /* Number of covariates, of covariates with '*age' */
   f=(*nrfunc)(xt);  int npar=NPARMAX;
   free_vector(xt,1,ncom);  int nlstate=2; /* Number of live states */
   return f;  int ndeath=1; /* Number of dead states */
 }  int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   int popbased=0;
 /*****************brent *************************/  
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  int *wav; /* Number of waves for this individuual 0 is possible */
 {  int maxwav=0; /* Maxim number of waves */
   int iter;  int jmin=0, jmax=0; /* min, max spacing between 2 waves */
   double a,b,d,etemp;  int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
   double fu,fv,fw,fx;  int gipmx=0, gsw=0; /* Global variables on the number of contributions 
   double ftemp;                     to the likelihood and the sum of weights (done by funcone)*/
   double p,q,r,tol1,tol2,u,v,w,x,xm;  int mle=1, weightopt=0;
   double e=0.0;  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
    int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
   a=(ax < cx ? ax : cx);  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
   b=(ax > cx ? ax : cx);             * wave mi and wave mi+1 is not an exact multiple of stepm. */
   x=w=v=bx;  double jmean=1; /* Mean space between 2 waves */
   fw=fv=fx=(*f)(x);  double **oldm, **newm, **savm; /* Working pointers to matrices */
   for (iter=1;iter<=ITMAX;iter++) {  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
     xm=0.5*(a+b);  FILE *fic,*ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  FILE *ficlog, *ficrespow;
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  int globpr=0; /* Global variable for printing or not */
     printf(".");fflush(stdout);  double fretone; /* Only one call to likelihood */
 #ifdef DEBUG  long ipmx=0; /* Number of contributions */
     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);  double sw; /* Sum of weights */
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  char filerespow[FILENAMELENGTH];
 #endif  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  FILE *ficresilk;
       *xmin=x;  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
       return fx;  FILE *ficresprobmorprev;
     }  FILE *fichtm, *fichtmcov; /* Html File */
     ftemp=fu;  FILE *ficreseij;
     if (fabs(e) > tol1) {  char filerese[FILENAMELENGTH];
       r=(x-w)*(fx-fv);  FILE *ficresstdeij;
       q=(x-v)*(fx-fw);  char fileresstde[FILENAMELENGTH];
       p=(x-v)*q-(x-w)*r;  FILE *ficrescveij;
       q=2.0*(q-r);  char filerescve[FILENAMELENGTH];
       if (q > 0.0) p = -p;  FILE  *ficresvij;
       q=fabs(q);  char fileresv[FILENAMELENGTH];
       etemp=e;  FILE  *ficresvpl;
       e=d;  char fileresvpl[FILENAMELENGTH];
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  char title[MAXLINE];
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
       else {  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
         d=p/q;  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
         u=x+d;  char command[FILENAMELENGTH];
         if (u-a < tol2 || b-u < tol2)  int  outcmd=0;
           d=SIGN(tol1,xm-x);  
       }  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
     } else {  
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  char filelog[FILENAMELENGTH]; /* Log file */
     }  char filerest[FILENAMELENGTH];
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  char fileregp[FILENAMELENGTH];
     fu=(*f)(u);  char popfile[FILENAMELENGTH];
     if (fu <= fx) {  
       if (u >= x) a=x; else b=x;  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
       SHFT(v,w,x,u)  
         SHFT(fv,fw,fx,fu)  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
         } else {  struct timezone tzp;
           if (u < x) a=u; else b=u;  extern int gettimeofday();
           if (fu <= fw || w == x) {  struct tm tmg, tm, tmf, *gmtime(), *localtime();
             v=w;  long time_value;
             w=u;  extern long time();
             fv=fw;  char strcurr[80], strfor[80];
             fw=fu;  
           } else if (fu <= fv || v == x || v == w) {  char *endptr;
             v=u;  long lval;
             fv=fu;  double dval;
           }  
         }  #define NR_END 1
   }  #define FREE_ARG char*
   nrerror("Too many iterations in brent");  #define FTOL 1.0e-10
   *xmin=x;  
   return fx;  #define NRANSI 
 }  #define ITMAX 200 
   
 /****************** mnbrak ***********************/  #define TOL 2.0e-4 
   
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  #define CGOLD 0.3819660 
             double (*func)(double))  #define ZEPS 1.0e-10 
 {  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
   double ulim,u,r,q, dum;  
   double fu;  #define GOLD 1.618034 
    #define GLIMIT 100.0 
   *fa=(*func)(*ax);  #define TINY 1.0e-20 
   *fb=(*func)(*bx);  
   if (*fb > *fa) {  static double maxarg1,maxarg2;
     SHFT(dum,*ax,*bx,dum)  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
       SHFT(dum,*fb,*fa,dum)  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
       }    
   *cx=(*bx)+GOLD*(*bx-*ax);  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   *fc=(*func)(*cx);  #define rint(a) floor(a+0.5)
   while (*fb > *fc) {  
     r=(*bx-*ax)*(*fb-*fc);  static double sqrarg;
     q=(*bx-*cx)*(*fb-*fa);  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  int agegomp= AGEGOMP;
     ulim=(*bx)+GLIMIT*(*cx-*bx);  
     if ((*bx-u)*(u-*cx) > 0.0) {  int imx; 
       fu=(*func)(u);  int stepm=1;
     } else if ((*cx-u)*(u-ulim) > 0.0) {  /* Stepm, step in month: minimum step interpolation*/
       fu=(*func)(u);  
       if (fu < *fc) {  int estepm;
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
           SHFT(*fb,*fc,fu,(*func)(u))  
           }  int m,nb;
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  long *num;
       u=ulim;  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
       fu=(*func)(u);  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
     } else {  double **pmmij, ***probs;
       u=(*cx)+GOLD*(*cx-*bx);  double *ageexmed,*agecens;
       fu=(*func)(u);  double dateintmean=0;
     }  
     SHFT(*ax,*bx,*cx,u)  double *weight;
       SHFT(*fa,*fb,*fc,fu)  int **s; /* Status */
       }  double *agedc, **covar, idx;
 }  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
   double *lsurv, *lpop, *tpop;
 /*************** linmin ************************/  
   double ftol=FTOL; /* Tolerance for computing Max Likelihood */
 int ncom;  double ftolhess; /* Tolerance for computing hessian */
 double *pcom,*xicom;  
 double (*nrfunc)(double []);  /**************** split *************************/
    static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  {
 {    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
   double brent(double ax, double bx, double cx,       the name of the file (name), its extension only (ext) and its first part of the name (finame)
                double (*f)(double), double tol, double *xmin);    */ 
   double f1dim(double x);    char  *ss;                            /* pointer */
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,    int   l1, l2;                         /* length counters */
               double *fc, double (*func)(double));  
   int j;    l1 = strlen(path );                   /* length of path */
   double xx,xmin,bx,ax;    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   double fx,fb,fa;    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
      if ( ss == NULL ) {                   /* no directory, so determine current directory */
   ncom=n;      strcpy( name, path );               /* we got the fullname name because no directory */
   pcom=vector(1,n);      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
   xicom=vector(1,n);        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
   nrfunc=func;      /* get current working directory */
   for (j=1;j<=n;j++) {      /*    extern  char* getcwd ( char *buf , int len);*/
     pcom[j]=p[j];      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
     xicom[j]=xi[j];        return( GLOCK_ERROR_GETCWD );
   }      }
   ax=0.0;      /* got dirc from getcwd*/
   xx=1.0;      printf(" DIRC = %s \n",dirc);
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);    } else {                              /* strip direcotry from path */
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);      ss++;                               /* after this, the filename */
 #ifdef DEBUG      l2 = strlen( ss );                  /* length of filename */
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
 #endif      strcpy( name, ss );         /* save file name */
   for (j=1;j<=n;j++) {      strncpy( dirc, path, l1 - l2 );     /* now the directory */
     xi[j] *= xmin;      dirc[l1-l2] = 0;                    /* add zero */
     p[j] += xi[j];      printf(" DIRC2 = %s \n",dirc);
   }    }
   free_vector(xicom,1,n);    /* We add a separator at the end of dirc if not exists */
   free_vector(pcom,1,n);    l1 = strlen( dirc );                  /* length of directory */
 }    if( dirc[l1-1] != DIRSEPARATOR ){
       dirc[l1] =  DIRSEPARATOR;
 /*************** powell ************************/      dirc[l1+1] = 0; 
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,      printf(" DIRC3 = %s \n",dirc);
             double (*func)(double []))    }
 {    ss = strrchr( name, '.' );            /* find last / */
   void linmin(double p[], double xi[], int n, double *fret,    if (ss >0){
               double (*func)(double []));      ss++;
   int i,ibig,j;      strcpy(ext,ss);                     /* save extension */
   double del,t,*pt,*ptt,*xit;      l1= strlen( name);
   double fp,fptt;      l2= strlen(ss)+1;
   double *xits;      strncpy( finame, name, l1-l2);
   pt=vector(1,n);      finame[l1-l2]= 0;
   ptt=vector(1,n);    }
   xit=vector(1,n);  
   xits=vector(1,n);    return( 0 );                          /* we're done */
   *fret=(*func)(p);  }
   for (j=1;j<=n;j++) pt[j]=p[j];  
   for (*iter=1;;++(*iter)) {  
     fp=(*fret);  /******************************************/
     ibig=0;  
     del=0.0;  void replace_back_to_slash(char *s, char*t)
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  {
     for (i=1;i<=n;i++)    int i;
       printf(" %d %.12f",i, p[i]);    int lg=0;
     printf("\n");    i=0;
     for (i=1;i<=n;i++) {    lg=strlen(t);
       for (j=1;j<=n;j++) xit[j]=xi[j][i];    for(i=0; i<= lg; i++) {
       fptt=(*fret);      (s[i] = t[i]);
 #ifdef DEBUG      if (t[i]== '\\') s[i]='/';
       printf("fret=%lf \n",*fret);    }
 #endif  }
       printf("%d",i);fflush(stdout);  
       linmin(p,xit,n,fret,func);  int nbocc(char *s, char occ)
       if (fabs(fptt-(*fret)) > del) {  {
         del=fabs(fptt-(*fret));    int i,j=0;
         ibig=i;    int lg=20;
       }    i=0;
 #ifdef DEBUG    lg=strlen(s);
       printf("%d %.12e",i,(*fret));    for(i=0; i<= lg; i++) {
       for (j=1;j<=n;j++) {    if  (s[i] == occ ) j++;
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);    }
         printf(" x(%d)=%.12e",j,xit[j]);    return j;
       }  }
       for(j=1;j<=n;j++)  
         printf(" p=%.12e",p[j]);  void cutv(char *u,char *v, char*t, char occ)
       printf("\n");  {
 #endif    /* cuts string t into u and v where u ends before first occurence of char 'occ' 
     }       and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {       gives u="abcedf" and v="ghi2j" */
 #ifdef DEBUG    int i,lg,j,p=0;
       int k[2],l;    i=0;
       k[0]=1;    for(j=0; j<=strlen(t)-1; j++) {
       k[1]=-1;      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
       printf("Max: %.12e",(*func)(p));    }
       for (j=1;j<=n;j++)  
         printf(" %.12e",p[j]);    lg=strlen(t);
       printf("\n");    for(j=0; j<p; j++) {
       for(l=0;l<=1;l++) {      (u[j] = t[j]);
         for (j=1;j<=n;j++) {    }
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];       u[p]='\0';
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  
         }     for(j=0; j<= lg; j++) {
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));      if (j>=(p+1))(v[j-p-1] = t[j]);
       }    }
 #endif  }
   
   /********************** nrerror ********************/
       free_vector(xit,1,n);  
       free_vector(xits,1,n);  void nrerror(char error_text[])
       free_vector(ptt,1,n);  {
       free_vector(pt,1,n);    fprintf(stderr,"ERREUR ...\n");
       return;    fprintf(stderr,"%s\n",error_text);
     }    exit(EXIT_FAILURE);
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  }
     for (j=1;j<=n;j++) {  /*********************** vector *******************/
       ptt[j]=2.0*p[j]-pt[j];  double *vector(int nl, int nh)
       xit[j]=p[j]-pt[j];  {
       pt[j]=p[j];    double *v;
     }    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
     fptt=(*func)(ptt);    if (!v) nrerror("allocation failure in vector");
     if (fptt < fp) {    return v-nl+NR_END;
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  }
       if (t < 0.0) {  
         linmin(p,xit,n,fret,func);  /************************ free vector ******************/
         for (j=1;j<=n;j++) {  void free_vector(double*v, int nl, int nh)
           xi[j][ibig]=xi[j][n];  {
           xi[j][n]=xit[j];    free((FREE_ARG)(v+nl-NR_END));
         }  }
 #ifdef DEBUG  
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  /************************ivector *******************************/
         for(j=1;j<=n;j++)  int *ivector(long nl,long nh)
           printf(" %.12e",xit[j]);  {
         printf("\n");    int *v;
 #endif    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
       }    if (!v) nrerror("allocation failure in ivector");
     }    return v-nl+NR_END;
   }  }
 }  
   /******************free ivector **************************/
 /**** Prevalence limit ****************/  void free_ivector(int *v, long nl, long nh)
   {
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)    free((FREE_ARG)(v+nl-NR_END));
 {  }
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit  
      matrix by transitions matrix until convergence is reached */  /************************lvector *******************************/
   long *lvector(long nl,long nh)
   int i, ii,j,k;  {
   double min, max, maxmin, maxmax,sumnew=0.;    long *v;
   double **matprod2();    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
   double **out, cov[NCOVMAX], **pmij();    if (!v) nrerror("allocation failure in ivector");
   double **newm;    return v-nl+NR_END;
   double agefin, delaymax=50 ; /* Max number of years to converge */  }
   
   for (ii=1;ii<=nlstate+ndeath;ii++)  /******************free lvector **************************/
     for (j=1;j<=nlstate+ndeath;j++){  void free_lvector(long *v, long nl, long nh)
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);  {
     }    free((FREE_ARG)(v+nl-NR_END));
   }
    cov[1]=1.;  
    /******************* imatrix *******************************/
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */  int **imatrix(long nrl, long nrh, long ncl, long nch) 
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
     newm=savm;  { 
     /* Covariates have to be included here again */    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
      cov[2]=agefin;    int **m; 
      
       for (k=1; k<=cptcovn;k++) {    /* allocate pointers to rows */ 
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
         /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/    if (!m) nrerror("allocation failure 1 in matrix()"); 
       }    m += NR_END; 
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    m -= nrl; 
       for (k=1; k<=cptcovprod;k++)    
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    
     /* allocate rows and set pointers to them */ 
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/    m[nrl] += NR_END; 
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);    m[nrl] -= ncl; 
     
     savm=oldm;    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
     oldm=newm;    
     maxmax=0.;    /* return pointer to array of pointers to rows */ 
     for(j=1;j<=nlstate;j++){    return m; 
       min=1.;  } 
       max=0.;  
       for(i=1; i<=nlstate; i++) {  /****************** free_imatrix *************************/
         sumnew=0;  void free_imatrix(m,nrl,nrh,ncl,nch)
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];        int **m;
         prlim[i][j]= newm[i][j]/(1-sumnew);        long nch,ncl,nrh,nrl; 
         max=FMAX(max,prlim[i][j]);       /* free an int matrix allocated by imatrix() */ 
         min=FMIN(min,prlim[i][j]);  { 
       }    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
       maxmin=max-min;    free((FREE_ARG) (m+nrl-NR_END)); 
       maxmax=FMAX(maxmax,maxmin);  } 
     }  
     if(maxmax < ftolpl){  /******************* matrix *******************************/
       return prlim;  double **matrix(long nrl, long nrh, long ncl, long nch)
     }  {
   }    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
 }    double **m;
   
 /*************** transition probabilities ***************/    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     if (!m) nrerror("allocation failure 1 in matrix()");
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )    m += NR_END;
 {    m -= nrl;
   double s1, s2;  
   /*double t34;*/    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   int i,j,j1, nc, ii, jj;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     m[nrl] += NR_END;
     for(i=1; i<= nlstate; i++){    m[nrl] -= ncl;
     for(j=1; j<i;j++){  
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
         /*s2 += param[i][j][nc]*cov[nc];*/    return m;
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/     */
       }  }
       ps[i][j]=s2;  
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/  /*************************free matrix ************************/
     }  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
     for(j=i+1; j<=nlstate+ndeath;j++){  {
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    free((FREE_ARG)(m[nrl]+ncl-NR_END));
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    free((FREE_ARG)(m+nrl-NR_END));
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/  }
       }  
       ps[i][j]=s2;  /******************* ma3x *******************************/
     }  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
   }  {
     /*ps[3][2]=1;*/    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
     double ***m;
   for(i=1; i<= nlstate; i++){  
      s1=0;    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     for(j=1; j<i; j++)    if (!m) nrerror("allocation failure 1 in matrix()");
       s1+=exp(ps[i][j]);    m += NR_END;
     for(j=i+1; j<=nlstate+ndeath; j++)    m -= nrl;
       s1+=exp(ps[i][j]);  
     ps[i][i]=1./(s1+1.);    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     for(j=1; j<i; j++)    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
       ps[i][j]= exp(ps[i][j])*ps[i][i];    m[nrl] += NR_END;
     for(j=i+1; j<=nlstate+ndeath; j++)    m[nrl] -= ncl;
       ps[i][j]= exp(ps[i][j])*ps[i][i];  
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   } /* end i */  
     m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
     for(jj=1; jj<= nlstate+ndeath; jj++){    m[nrl][ncl] += NR_END;
       ps[ii][jj]=0;    m[nrl][ncl] -= nll;
       ps[ii][ii]=1;    for (j=ncl+1; j<=nch; j++) 
     }      m[nrl][j]=m[nrl][j-1]+nlay;
   }    
     for (i=nrl+1; i<=nrh; i++) {
       m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){      for (j=ncl+1; j<=nch; j++) 
     for(jj=1; jj<= nlstate+ndeath; jj++){        m[i][j]=m[i][j-1]+nlay;
      printf("%lf ",ps[ii][jj]);    }
    }    return m; 
     printf("\n ");    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
     }             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
     printf("\n ");printf("%lf ",cov[2]);*/    */
 /*  }
   for(i=1; i<= npar; i++) printf("%f ",x[i]);  
   goto end;*/  /*************************free ma3x ************************/
     return ps;  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
 }  {
     free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
 /**************** Product of 2 matrices ******************/    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     free((FREE_ARG)(m+nrl-NR_END));
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)  }
 {  
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times  /*************** function subdirf ***********/
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */  char *subdirf(char fileres[])
   /* in, b, out are matrice of pointers which should have been initialized  {
      before: only the contents of out is modified. The function returns    /* Caution optionfilefiname is hidden */
      a pointer to pointers identical to out */    strcpy(tmpout,optionfilefiname);
   long i, j, k;    strcat(tmpout,"/"); /* Add to the right */
   for(i=nrl; i<= nrh; i++)    strcat(tmpout,fileres);
     for(k=ncolol; k<=ncoloh; k++)    return tmpout;
       for(j=ncl,out[i][k]=0.; j<=nch; j++)  }
         out[i][k] +=in[i][j]*b[j][k];  
   /*************** function subdirf2 ***********/
   return out;  char *subdirf2(char fileres[], char *preop)
 }  {
     
     /* Caution optionfilefiname is hidden */
 /************* Higher Matrix Product ***************/    strcpy(tmpout,optionfilefiname);
     strcat(tmpout,"/");
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )    strcat(tmpout,preop);
 {    strcat(tmpout,fileres);
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month    return tmpout;
      duration (i.e. until  }
      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  /*************** function subdirf3 ***********/
      (typically every 2 years instead of every month which is too big).  char *subdirf3(char fileres[], char *preop, char *preop2)
      Model is determined by parameters x and covariates have to be  {
      included manually here.    
     /* Caution optionfilefiname is hidden */
      */    strcpy(tmpout,optionfilefiname);
     strcat(tmpout,"/");
   int i, j, d, h, k;    strcat(tmpout,preop);
   double **out, cov[NCOVMAX];    strcat(tmpout,preop2);
   double **newm;    strcat(tmpout,fileres);
     return tmpout;
   /* Hstepm could be zero and should return the unit matrix */  }
   for (i=1;i<=nlstate+ndeath;i++)  
     for (j=1;j<=nlstate+ndeath;j++){  /***************** f1dim *************************/
       oldm[i][j]=(i==j ? 1.0 : 0.0);  extern int ncom; 
       po[i][j][0]=(i==j ? 1.0 : 0.0);  extern double *pcom,*xicom;
     }  extern double (*nrfunc)(double []); 
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */   
   for(h=1; h <=nhstepm; h++){  double f1dim(double x) 
     for(d=1; d <=hstepm; d++){  { 
       newm=savm;    int j; 
       /* Covariates have to be included here again */    double f;
       cov[1]=1.;    double *xt; 
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;   
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    xt=vector(1,ncom); 
       for (k=1; k<=cptcovage;k++)    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    f=(*nrfunc)(xt); 
       for (k=1; k<=cptcovprod;k++)    free_vector(xt,1,ncom); 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    return f; 
   } 
   
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/  /*****************brent *************************/
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,  { 
                    pmij(pmmij,cov,ncovmodel,x,nlstate));    int iter; 
       savm=oldm;    double a,b,d,etemp;
       oldm=newm;    double fu,fv,fw,fx;
     }    double ftemp;
     for(i=1; i<=nlstate+ndeath; i++)    double p,q,r,tol1,tol2,u,v,w,x,xm; 
       for(j=1;j<=nlstate+ndeath;j++) {    double e=0.0; 
         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]);    a=(ax < cx ? ax : cx); 
          */    b=(ax > cx ? ax : cx); 
       }    x=w=v=bx; 
   } /* end h */    fw=fv=fx=(*f)(x); 
   return po;    for (iter=1;iter<=ITMAX;iter++) { 
 }      xm=0.5*(a+b); 
       tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
       /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
 /*************** log-likelihood *************/      printf(".");fflush(stdout);
 double func( double *x)      fprintf(ficlog,".");fflush(ficlog);
 {  #ifdef DEBUG
   int i, ii, j, k, mi, d, 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);
   double l, ll[NLSTATEMAX], cov[NCOVMAX];      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);
   double **out;      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
   double sw; /* Sum of weights */  #endif
   double lli; /* Individual log likelihood */      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
   long ipmx;        *xmin=x; 
   /*extern weight */        return fx; 
   /* We are differentiating ll according to initial status */      } 
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/      ftemp=fu;
   /*for(i=1;i<imx;i++)      if (fabs(e) > tol1) { 
     printf(" %d\n",s[4][i]);        r=(x-w)*(fx-fv); 
   */        q=(x-v)*(fx-fw); 
   cov[1]=1.;        p=(x-v)*q-(x-w)*r; 
         q=2.0*(q-r); 
   for(k=1; k<=nlstate; k++) ll[k]=0.;        if (q > 0.0) p = -p; 
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){        q=fabs(q); 
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];        etemp=e; 
     for(mi=1; mi<= wav[i]-1; mi++){        e=d; 
       for (ii=1;ii<=nlstate+ndeath;ii++)        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       for(d=0; d<dh[mi][i]; d++){        else { 
         newm=savm;          d=p/q; 
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;          u=x+d; 
         for (kk=1; kk<=cptcovage;kk++) {          if (u-a < tol2 || b-u < tol2) 
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];            d=SIGN(tol1,xm-x); 
         }        } 
              } else { 
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));      } 
         savm=oldm;      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
         oldm=newm;      fu=(*f)(u); 
              if (fu <= fx) { 
                if (u >= x) a=x; else b=x; 
       } /* end mult */        SHFT(v,w,x,u) 
                SHFT(fv,fw,fx,fu) 
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);          } else { 
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/            if (u < x) a=u; else b=u; 
       ipmx +=1;            if (fu <= fw || w == x) { 
       sw += weight[i];              v=w; 
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;              w=u; 
     } /* end of wave */              fv=fw; 
   } /* end of individual */              fw=fu; 
             } else if (fu <= fv || v == x || v == w) { 
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];              v=u; 
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */              fv=fu; 
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */            } 
   return -l;          } 
 }    } 
     nrerror("Too many iterations in brent"); 
     *xmin=x; 
 /*********** Maximum Likelihood Estimation ***************/    return fx; 
   } 
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))  
 {  /****************** mnbrak ***********************/
   int i,j, iter;  
   double **xi,*delti;  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
   double fret;              double (*func)(double)) 
   xi=matrix(1,npar,1,npar);  { 
   for (i=1;i<=npar;i++)    double ulim,u,r,q, dum;
     for (j=1;j<=npar;j++)    double fu; 
       xi[i][j]=(i==j ? 1.0 : 0.0);   
   printf("Powell\n");    *fa=(*func)(*ax); 
   powell(p,xi,npar,ftol,&iter,&fret,func);    *fb=(*func)(*bx); 
     if (*fb > *fa) { 
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));      SHFT(dum,*ax,*bx,dum) 
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));        SHFT(dum,*fb,*fa,dum) 
         } 
 }    *cx=(*bx)+GOLD*(*bx-*ax); 
     *fc=(*func)(*cx); 
 /**** Computes Hessian and covariance matrix ***/    while (*fb > *fc) { 
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))      r=(*bx-*ax)*(*fb-*fc); 
 {      q=(*bx-*cx)*(*fb-*fa); 
   double  **a,**y,*x,pd;      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
   double **hess;        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
   int i, j,jk;      ulim=(*bx)+GLIMIT*(*cx-*bx); 
   int *indx;      if ((*bx-u)*(u-*cx) > 0.0) { 
         fu=(*func)(u); 
   double hessii(double p[], double delta, int theta, double delti[]);      } else if ((*cx-u)*(u-ulim) > 0.0) { 
   double hessij(double p[], double delti[], int i, int j);        fu=(*func)(u); 
   void lubksb(double **a, int npar, int *indx, double b[]) ;        if (fu < *fc) { 
   void ludcmp(double **a, int npar, int *indx, double *d) ;          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
             SHFT(*fb,*fc,fu,(*func)(u)) 
   hess=matrix(1,npar,1,npar);            } 
       } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
   printf("\nCalculation of the hessian matrix. Wait...\n");        u=ulim; 
   for (i=1;i<=npar;i++){        fu=(*func)(u); 
     printf("%d",i);fflush(stdout);      } else { 
     hess[i][i]=hessii(p,ftolhess,i,delti);        u=(*cx)+GOLD*(*cx-*bx); 
     /*printf(" %f ",p[i]);*/        fu=(*func)(u); 
     /*printf(" %lf ",hess[i][i]);*/      } 
   }      SHFT(*ax,*bx,*cx,u) 
          SHFT(*fa,*fb,*fc,fu) 
   for (i=1;i<=npar;i++) {        } 
     for (j=1;j<=npar;j++)  {  } 
       if (j>i) {  
         printf(".%d%d",i,j);fflush(stdout);  /*************** linmin ************************/
         hess[i][j]=hessij(p,delti,i,j);  
         hess[j][i]=hess[i][j];      int ncom; 
         /*printf(" %lf ",hess[i][j]);*/  double *pcom,*xicom;
       }  double (*nrfunc)(double []); 
     }   
   }  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
   printf("\n");  { 
     double brent(double ax, double bx, double cx, 
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");                 double (*f)(double), double tol, double *xmin); 
      double f1dim(double x); 
   a=matrix(1,npar,1,npar);    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
   y=matrix(1,npar,1,npar);                double *fc, double (*func)(double)); 
   x=vector(1,npar);    int j; 
   indx=ivector(1,npar);    double xx,xmin,bx,ax; 
   for (i=1;i<=npar;i++)    double fx,fb,fa;
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];   
   ludcmp(a,npar,indx,&pd);    ncom=n; 
     pcom=vector(1,n); 
   for (j=1;j<=npar;j++) {    xicom=vector(1,n); 
     for (i=1;i<=npar;i++) x[i]=0;    nrfunc=func; 
     x[j]=1;    for (j=1;j<=n;j++) { 
     lubksb(a,npar,indx,x);      pcom[j]=p[j]; 
     for (i=1;i<=npar;i++){      xicom[j]=xi[j]; 
       matcov[i][j]=x[i];    } 
     }    ax=0.0; 
   }    xx=1.0; 
     mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
   printf("\n#Hessian matrix#\n");    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
   for (i=1;i<=npar;i++) {  #ifdef DEBUG
     for (j=1;j<=npar;j++) {    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
       printf("%.3e ",hess[i][j]);    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     }  #endif
     printf("\n");    for (j=1;j<=n;j++) { 
   }      xi[j] *= xmin; 
       p[j] += xi[j]; 
   /* Recompute Inverse */    } 
   for (i=1;i<=npar;i++)    free_vector(xicom,1,n); 
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];    free_vector(pcom,1,n); 
   ludcmp(a,npar,indx,&pd);  } 
   
   /*  printf("\n#Hessian matrix recomputed#\n");  char *asc_diff_time(long time_sec, char ascdiff[])
   {
   for (j=1;j<=npar;j++) {    long sec_left, days, hours, minutes;
     for (i=1;i<=npar;i++) x[i]=0;    days = (time_sec) / (60*60*24);
     x[j]=1;    sec_left = (time_sec) % (60*60*24);
     lubksb(a,npar,indx,x);    hours = (sec_left) / (60*60) ;
     for (i=1;i<=npar;i++){    sec_left = (sec_left) %(60*60);
       y[i][j]=x[i];    minutes = (sec_left) /60;
       printf("%.3e ",y[i][j]);    sec_left = (sec_left) % (60);
     }    sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
     printf("\n");    return ascdiff;
   }  }
   */  
   /*************** powell ************************/
   free_matrix(a,1,npar,1,npar);  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
   free_matrix(y,1,npar,1,npar);              double (*func)(double [])) 
   free_vector(x,1,npar);  { 
   free_ivector(indx,1,npar);    void linmin(double p[], double xi[], int n, double *fret, 
   free_matrix(hess,1,npar,1,npar);                double (*func)(double [])); 
     int i,ibig,j; 
     double del,t,*pt,*ptt,*xit;
 }    double fp,fptt;
     double *xits;
 /*************** hessian matrix ****************/    int niterf, itmp;
 double hessii( double x[], double delta, int theta, double delti[])  
 {    pt=vector(1,n); 
   int i;    ptt=vector(1,n); 
   int l=1, lmax=20;    xit=vector(1,n); 
   double k1,k2;    xits=vector(1,n); 
   double p2[NPARMAX+1];    *fret=(*func)(p); 
   double res;    for (j=1;j<=n;j++) pt[j]=p[j]; 
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;    for (*iter=1;;++(*iter)) { 
   double fx;      fp=(*fret); 
   int k=0,kmax=10;      ibig=0; 
   double l1;      del=0.0; 
       last_time=curr_time;
   fx=func(x);      (void) gettimeofday(&curr_time,&tzp);
   for (i=1;i<=npar;i++) p2[i]=x[i];      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);
   for(l=0 ; l <=lmax; l++){      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);
     l1=pow(10,l);  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
     delts=delt;     for (i=1;i<=n;i++) {
     for(k=1 ; k <kmax; k=k+1){        printf(" %d %.12f",i, p[i]);
       delt = delta*(l1*k);        fprintf(ficlog," %d %.12lf",i, p[i]);
       p2[theta]=x[theta] +delt;        fprintf(ficrespow," %.12lf", p[i]);
       k1=func(p2)-fx;      }
       p2[theta]=x[theta]-delt;      printf("\n");
       k2=func(p2)-fx;      fprintf(ficlog,"\n");
       /*res= (k1-2.0*fx+k2)/delt/delt; */      fprintf(ficrespow,"\n");fflush(ficrespow);
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */      if(*iter <=3){
              tm = *localtime(&curr_time.tv_sec);
 #ifdef DEBUG        strcpy(strcurr,asctime(&tm));
       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);  /*       asctime_r(&tm,strcurr); */
 #endif        forecast_time=curr_time; 
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */        itmp = strlen(strcurr);
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
         k=kmax;          strcurr[itmp-1]='\0';
       }        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
         k=kmax; l=lmax*10.;        for(niterf=10;niterf<=30;niterf+=10){
       }          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){          tmf = *localtime(&forecast_time.tv_sec);
         delts=delt;  /*      asctime_r(&tmf,strfor); */
       }          strcpy(strfor,asctime(&tmf));
     }          itmp = strlen(strfor);
   }          if(strfor[itmp-1]=='\n')
   delti[theta]=delts;          strfor[itmp-1]='\0';
   return res;          printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
            fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
 }        }
       }
 double hessij( double x[], double delti[], int thetai,int thetaj)      for (i=1;i<=n;i++) { 
 {        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
   int i;        fptt=(*fret); 
   int l=1, l1, lmax=20;  #ifdef DEBUG
   double k1,k2,k3,k4,res,fx;        printf("fret=%lf \n",*fret);
   double p2[NPARMAX+1];        fprintf(ficlog,"fret=%lf \n",*fret);
   int k;  #endif
         printf("%d",i);fflush(stdout);
   fx=func(x);        fprintf(ficlog,"%d",i);fflush(ficlog);
   for (k=1; k<=2; k++) {        linmin(p,xit,n,fret,func); 
     for (i=1;i<=npar;i++) p2[i]=x[i];        if (fabs(fptt-(*fret)) > del) { 
     p2[thetai]=x[thetai]+delti[thetai]/k;          del=fabs(fptt-(*fret)); 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;          ibig=i; 
     k1=func(p2)-fx;        } 
    #ifdef DEBUG
     p2[thetai]=x[thetai]+delti[thetai]/k;        printf("%d %.12e",i,(*fret));
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;        fprintf(ficlog,"%d %.12e",i,(*fret));
     k2=func(p2)-fx;        for (j=1;j<=n;j++) {
            xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
     p2[thetai]=x[thetai]-delti[thetai]/k;          printf(" x(%d)=%.12e",j,xit[j]);
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
     k3=func(p2)-fx;        }
          for(j=1;j<=n;j++) {
     p2[thetai]=x[thetai]-delti[thetai]/k;          printf(" p=%.12e",p[j]);
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          fprintf(ficlog," p=%.12e",p[j]);
     k4=func(p2)-fx;        }
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */        printf("\n");
 #ifdef DEBUG        fprintf(ficlog,"\n");
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);  #endif
 #endif      } 
   }      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
   return res;  #ifdef DEBUG
 }        int k[2],l;
         k[0]=1;
 /************** Inverse of matrix **************/        k[1]=-1;
 void ludcmp(double **a, int n, int *indx, double *d)        printf("Max: %.12e",(*func)(p));
 {        fprintf(ficlog,"Max: %.12e",(*func)(p));
   int i,imax,j,k;        for (j=1;j<=n;j++) {
   double big,dum,sum,temp;          printf(" %.12e",p[j]);
   double *vv;          fprintf(ficlog," %.12e",p[j]);
          }
   vv=vector(1,n);        printf("\n");
   *d=1.0;        fprintf(ficlog,"\n");
   for (i=1;i<=n;i++) {        for(l=0;l<=1;l++) {
     big=0.0;          for (j=1;j<=n;j++) {
     for (j=1;j<=n;j++)            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
       if ((temp=fabs(a[i][j])) > big) big=temp;            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
     vv[i]=1.0/big;          }
   }          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   for (j=1;j<=n;j++) {          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     for (i=1;i<j;i++) {        }
       sum=a[i][j];  #endif
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];  
       a[i][j]=sum;  
     }        free_vector(xit,1,n); 
     big=0.0;        free_vector(xits,1,n); 
     for (i=j;i<=n;i++) {        free_vector(ptt,1,n); 
       sum=a[i][j];        free_vector(pt,1,n); 
       for (k=1;k<j;k++)        return; 
         sum -= a[i][k]*a[k][j];      } 
       a[i][j]=sum;      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
       if ( (dum=vv[i]*fabs(sum)) >= big) {      for (j=1;j<=n;j++) { 
         big=dum;        ptt[j]=2.0*p[j]-pt[j]; 
         imax=i;        xit[j]=p[j]-pt[j]; 
       }        pt[j]=p[j]; 
     }      } 
     if (j != imax) {      fptt=(*func)(ptt); 
       for (k=1;k<=n;k++) {      if (fptt < fp) { 
         dum=a[imax][k];        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
         a[imax][k]=a[j][k];        if (t < 0.0) { 
         a[j][k]=dum;          linmin(p,xit,n,fret,func); 
       }          for (j=1;j<=n;j++) { 
       *d = -(*d);            xi[j][ibig]=xi[j][n]; 
       vv[imax]=vv[j];            xi[j][n]=xit[j]; 
     }          }
     indx[j]=imax;  #ifdef DEBUG
     if (a[j][j] == 0.0) a[j][j]=TINY;          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
     if (j != n) {          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
       dum=1.0/(a[j][j]);          for(j=1;j<=n;j++){
       for (i=j+1;i<=n;i++) a[i][j] *= dum;            printf(" %.12e",xit[j]);
     }            fprintf(ficlog," %.12e",xit[j]);
   }          }
   free_vector(vv,1,n);  /* Doesn't work */          printf("\n");
 ;          fprintf(ficlog,"\n");
 }  #endif
         }
 void lubksb(double **a, int n, int *indx, double b[])      } 
 {    } 
   int i,ii=0,ip,j;  } 
   double sum;  
    /**** Prevalence limit (stable or period prevalence)  ****************/
   for (i=1;i<=n;i++) {  
     ip=indx[i];  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
     sum=b[ip];  {
     b[ip]=b[i];    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
     if (ii)       matrix by transitions matrix until convergence is reached */
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];  
     else if (sum) ii=i;    int i, ii,j,k;
     b[i]=sum;    double min, max, maxmin, maxmax,sumnew=0.;
   }    double **matprod2();
   for (i=n;i>=1;i--) {    double **out, cov[NCOVMAX], **pmij();
     sum=b[i];    double **newm;
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];    double agefin, delaymax=50 ; /* Max number of years to converge */
     b[i]=sum/a[i][i];  
   }    for (ii=1;ii<=nlstate+ndeath;ii++)
 }      for (j=1;j<=nlstate+ndeath;j++){
         oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 /************ Frequencies ********************/      }
 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 */     cov[1]=1.;
     
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   double ***freq; /* Frequencies */    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
   double *pp;      newm=savm;
   double pos, k2, dateintsum=0,k2cpt=0;      /* Covariates have to be included here again */
   FILE *ficresp;       cov[2]=agefin;
   char fileresp[FILENAMELENGTH];    
          for (k=1; k<=cptcovn;k++) {
   pp=vector(1,nlstate);          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);          /*      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]]);*/
   strcpy(fileresp,"p");        }
   strcat(fileresp,fileres);        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   if((ficresp=fopen(fileresp,"w"))==NULL) {        for (k=1; k<=cptcovprod;k++)
     printf("Problem with prevalence resultfile: %s\n", fileresp);          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
     exit(0);  
   }        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
   j1=0;        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
        out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
   j=cptcoveff;  
   if (cptcovn<1) {j=1;ncodemax[1]=1;}      savm=oldm;
        oldm=newm;
   for(k1=1; k1<=j;k1++){      maxmax=0.;
     for(i1=1; i1<=ncodemax[k1];i1++){      for(j=1;j<=nlstate;j++){
       j1++;        min=1.;
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);        max=0.;
         scanf("%d", i);*/        for(i=1; i<=nlstate; i++) {
       for (i=-1; i<=nlstate+ndeath; i++)            sumnew=0;
         for (jk=-1; jk<=nlstate+ndeath; jk++)            for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
           for(m=agemin; m <= agemax+3; m++)          prlim[i][j]= newm[i][j]/(1-sumnew);
             freq[i][jk][m]=0;          max=FMAX(max,prlim[i][j]);
                min=FMIN(min,prlim[i][j]);
       dateintsum=0;        }
       k2cpt=0;        maxmin=max-min;
       for (i=1; i<=imx; i++) {        maxmax=FMAX(maxmax,maxmin);
         bool=1;      }
         if  (cptcovn>0) {      if(maxmax < ftolpl){
           for (z1=1; z1<=cptcoveff; z1++)        return prlim;
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])      }
               bool=0;    }
         }  }
         if (bool==1) {  
           for(m=firstpass; m<=lastpass; m++){  /*************** transition probabilities ***************/ 
             k2=anint[m][i]+(mint[m][i]/12.);  
             if ((k2>=dateprev1) && (k2<=dateprev2)) {  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
               if(agev[m][i]==0) agev[m][i]=agemax+1;  {
               if(agev[m][i]==1) agev[m][i]=agemax+2;    double s1, s2;
               if (m<lastpass) {    /*double t34;*/
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    int i,j,j1, nc, ii, jj;
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];  
               }      for(i=1; i<= nlstate; i++){
                      for(j=1; j<i;j++){
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
                 dateintsum=dateintsum+k2;            /*s2 += param[i][j][nc]*cov[nc];*/
                 k2cpt++;            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); */
             }          }
           }          ps[i][j]=s2;
         }  /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
       }        }
                for(j=i+1; j<=nlstate+ndeath;j++){
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
             s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
       if  (cptcovn>0) {  /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
         fprintf(ficresp, "\n#********** Variable ");          }
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          ps[i][j]=s2;
         fprintf(ficresp, "**********\n#");        }
       }      }
       for(i=1; i<=nlstate;i++)      /*ps[3][2]=1;*/
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);      
       fprintf(ficresp, "\n");      for(i=1; i<= nlstate; i++){
              s1=0;
       for(i=(int)agemin; i <= (int)agemax+3; i++){        for(j=1; j<i; j++)
         if(i==(int)agemax+3)          s1+=exp(ps[i][j]);
           printf("Total");        for(j=i+1; j<=nlstate+ndeath; j++)
         else          s1+=exp(ps[i][j]);
           printf("Age %d", i);        ps[i][i]=1./(s1+1.);
         for(jk=1; jk <=nlstate ; jk++){        for(j=1; j<i; j++)
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)          ps[i][j]= exp(ps[i][j])*ps[i][i];
             pp[jk] += freq[jk][m][i];        for(j=i+1; j<=nlstate+ndeath; j++)
         }          ps[i][j]= exp(ps[i][j])*ps[i][i];
         for(jk=1; jk <=nlstate ; jk++){        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
           for(m=-1, pos=0; m <=0 ; m++)      } /* end i */
             pos += freq[jk][m][i];      
           if(pp[jk]>=1.e-10)      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);        for(jj=1; jj<= nlstate+ndeath; jj++){
           else          ps[ii][jj]=0;
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);          ps[ii][ii]=1;
         }        }
       }
         for(jk=1; jk <=nlstate ; jk++){      
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)  
             pp[jk] += freq[jk][m][i];  /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
         }  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
   /*         printf("ddd %lf ",ps[ii][jj]); */
         for(jk=1,pos=0; jk <=nlstate ; jk++)  /*       } */
           pos += pp[jk];  /*       printf("\n "); */
         for(jk=1; jk <=nlstate ; jk++){  /*        } */
           if(pos>=1.e-5)  /*        printf("\n ");printf("%lf ",cov[2]); */
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);         /*
           else        for(i=1; i<= npar; i++) printf("%f ",x[i]);
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);        goto end;*/
           if( i <= (int) agemax){      return ps;
             if(pos>=1.e-5){  }
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);  
               probs[i][jk][j1]= pp[jk]/pos;  /**************** Product of 2 matrices ******************/
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/  
             }  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
             else  {
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
           }       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
         }    /* in, b, out are matrice of pointers which should have been initialized 
               before: only the contents of out is modified. The function returns
         for(jk=-1; jk <=nlstate+ndeath; jk++)       a pointer to pointers identical to out */
           for(m=-1; m <=nlstate+ndeath; m++)    long i, j, k;
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);    for(i=nrl; i<= nrh; i++)
         if(i <= (int) agemax)      for(k=ncolol; k<=ncoloh; k++)
           fprintf(ficresp,"\n");        for(j=ncl,out[i][k]=0.; j<=nch; j++)
         printf("\n");          out[i][k] +=in[i][j]*b[j][k];
       }  
     }    return out;
   }  }
   dateintmean=dateintsum/k2cpt;  
    
   fclose(ficresp);  /************* Higher Matrix Product ***************/
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);  
   free_vector(pp,1,nlstate);  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
    {
   /* End of Freq */    /* Computes the transition matrix starting at age 'age' over 
 }       'nhstepm*hstepm*stepm' months (i.e. until
        age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
 /************ Prevalence ********************/       nhstepm*hstepm matrices. 
 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)       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
 {  /* Some frequencies */       (typically every 2 years instead of every month which is too big 
         for the memory).
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;       Model is determined by parameters x and covariates have to be 
   double ***freq; /* Frequencies */       included manually here. 
   double *pp;  
   double pos, k2;       */
   
   pp=vector(1,nlstate);    int i, j, d, h, k;
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    double **out, cov[NCOVMAX];
      double **newm;
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);  
   j1=0;    /* Hstepm could be zero and should return the unit matrix */
      for (i=1;i<=nlstate+ndeath;i++)
   j=cptcoveff;      for (j=1;j<=nlstate+ndeath;j++){
   if (cptcovn<1) {j=1;ncodemax[1]=1;}        oldm[i][j]=(i==j ? 1.0 : 0.0);
          po[i][j][0]=(i==j ? 1.0 : 0.0);
  for(k1=1; k1<=j;k1++){      }
     for(i1=1; i1<=ncodemax[k1];i1++){    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
       j1++;    for(h=1; h <=nhstepm; h++){
        for(d=1; d <=hstepm; d++){
       for (i=-1; i<=nlstate+ndeath; i++)          newm=savm;
         for (jk=-1; jk<=nlstate+ndeath; jk++)          /* Covariates have to be included here again */
           for(m=agemin; m <= agemax+3; m++)        cov[1]=1.;
             freq[i][jk][m]=0;        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
              for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
       for (i=1; i<=imx; i++) {        for (k=1; k<=cptcovage;k++)
         bool=1;          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
         if  (cptcovn>0) {        for (k=1; k<=cptcovprod;k++)
           for (z1=1; z1<=cptcoveff; z1++)          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])  
               bool=0;  
         }        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
         if (bool==1) {        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
           for(m=firstpass; m<=lastpass; m++){        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
             k2=anint[m][i]+(mint[m][i]/12.);                     pmij(pmmij,cov,ncovmodel,x,nlstate));
             if ((k2>=dateprev1) && (k2<=dateprev2)) {        savm=oldm;
               if(agev[m][i]==0) agev[m][i]=agemax+1;        oldm=newm;
               if(agev[m][i]==1) agev[m][i]=agemax+2;      }
               if (m<lastpass) freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];      for(i=1; i<=nlstate+ndeath; i++)
               /* freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];  */        for(j=1;j<=nlstate+ndeath;j++) {
             }          po[i][j][h]=newm[i][j];
           }          /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
         }        }
       }      /*printf("h=%d ",h);*/
         for(i=(int)agemin; i <= (int)agemax+3; i++){    } /* end h */
           for(jk=1; jk <=nlstate ; jk++){  /*     printf("\n H=%d \n",h); */
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    return po;
               pp[jk] += freq[jk][m][i];  }
           }  
           for(jk=1; jk <=nlstate ; jk++){  
             for(m=-1, pos=0; m <=0 ; m++)  /*************** log-likelihood *************/
             pos += freq[jk][m][i];  double func( double *x)
         }  {
            int i, ii, j, k, mi, d, kk;
          for(jk=1; jk <=nlstate ; jk++){    double l, ll[NLSTATEMAX], cov[NCOVMAX];
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)    double **out;
              pp[jk] += freq[jk][m][i];    double sw; /* Sum of weights */
          }    double lli; /* Individual log likelihood */
              int s1, s2;
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];    double bbh, survp;
     long ipmx;
          for(jk=1; jk <=nlstate ; jk++){              /*extern weight */
            if( i <= (int) agemax){    /* We are differentiating ll according to initial status */
              if(pos>=1.e-5){    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
                probs[i][jk][j1]= pp[jk]/pos;    /*for(i=1;i<imx;i++) 
              }      printf(" %d\n",s[4][i]);
            }    */
          }    cov[1]=1.;
            
         }    for(k=1; k<=nlstate; k++) ll[k]=0.;
     }  
   }    if(mle==1){
        for (i=1,ipmx=0, sw=0.; i<=imx; i++){
          for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);        for(mi=1; mi<= wav[i]-1; mi++){
   free_vector(pp,1,nlstate);          for (ii=1;ii<=nlstate+ndeath;ii++)
              for (j=1;j<=nlstate+ndeath;j++){
 }  /* End of Freq */              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               savm[ii][j]=(ii==j ? 1.0 : 0.0);
 /************* Waves Concatenation ***************/            }
           for(d=0; d<dh[mi][i]; d++){
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)            newm=savm;
 {            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.            for (kk=1; kk<=cptcovage;kk++) {
      Death is a valid wave (if date is known).              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i            }
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
      and mw[mi+1][i]. dh depends on stepm.                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
      */            savm=oldm;
             oldm=newm;
   int i, mi, m;          } /* end mult */
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;        
      double sum=0., jmean=0.;*/          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
           /* But now since version 0.9 we anticipate for bias at large stepm.
   int j, k=0,jk, ju, jl;           * If stepm is larger than one month (smallest stepm) and if the exact delay 
   double sum=0.;           * (in months) between two waves is not a multiple of stepm, we rounded to 
   jmin=1e+5;           * the nearest (and in case of equal distance, to the lowest) interval but now
   jmax=-1;           * we keep into memory the bias bh[mi][i] and also the previous matrix product
   jmean=0.;           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
   for(i=1; i<=imx; i++){           * probability in order to take into account the bias as a fraction of the way
     mi=0;           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
     m=firstpass;           * -stepm/2 to stepm/2 .
     while(s[m][i] <= nlstate){           * For stepm=1 the results are the same as for previous versions of Imach.
       if(s[m][i]>=1)           * For stepm > 1 the results are less biased than in previous versions. 
         mw[++mi][i]=m;           */
       if(m >=lastpass)          s1=s[mw[mi][i]][i];
         break;          s2=s[mw[mi+1][i]][i];
       else          bbh=(double)bh[mi][i]/(double)stepm; 
         m++;          /* bias bh is positive if real duration
     }/* end while */           * is higher than the multiple of stepm and negative otherwise.
     if (s[m][i] > nlstate){           */
       mi++;     /* Death is another wave */          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
       /* if(mi==0)  never been interviewed correctly before death */          if( s2 > nlstate){ 
          /* Only death is a correct wave */            /* i.e. if s2 is a death state and if the date of death is known 
       mw[mi][i]=m;               then the contribution to the likelihood is the probability to 
     }               die between last step unit time and current  step unit time, 
                which is also equal to probability to die before dh 
     wav[i]=mi;               minus probability to die before dh-stepm . 
     if(mi==0)               In version up to 0.92 likelihood was computed
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);          as if date of death was unknown. Death was treated as any other
   }          health state: the date of the interview describes the actual state
           and not the date of a change in health state. The former idea was
   for(i=1; i<=imx; i++){          to consider that at each interview the state was recorded
     for(mi=1; mi<wav[i];mi++){          (healthy, disable or death) and IMaCh was corrected; but when we
       if (stepm <=0)          introduced the exact date of death then we should have modified
         dh[mi][i]=1;          the contribution of an exact death to the likelihood. This new
       else{          contribution is smaller and very dependent of the step unit
         if (s[mw[mi+1][i]][i] > nlstate) {          stepm. It is no more the probability to die between last interview
           if (agedc[i] < 2*AGESUP) {          and month of death but the probability to survive from last
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);          interview up to one month before death multiplied by the
           if(j==0) j=1;  /* Survives at least one month after exam */          probability to die within a month. Thanks to Chris
           k=k+1;          Jackson for correcting this bug.  Former versions increased
           if (j >= jmax) jmax=j;          mortality artificially. The bad side is that we add another loop
           if (j <= jmin) jmin=j;          which slows down the processing. The difference can be up to 10%
           sum=sum+j;          lower mortality.
           /*if (j<0) printf("j=%d num=%d \n",j,i); */            */
           }            lli=log(out[s1][s2] - savm[s1][s2]);
         }  
         else{  
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));          } else if  (s2==-2) {
           k=k+1;            for (j=1,survp=0. ; j<=nlstate; j++) 
           if (j >= jmax) jmax=j;              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
           else if (j <= jmin)jmin=j;            /*survp += out[s1][j]; */
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */            lli= log(survp);
           sum=sum+j;          }
         }          
         jk= j/stepm;          else if  (s2==-4) { 
         jl= j -jk*stepm;            for (j=3,survp=0. ; j<=nlstate; j++)  
         ju= j -(jk+1)*stepm;              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
         if(jl <= -ju)            lli= log(survp); 
           dh[mi][i]=jk;          } 
         else  
           dh[mi][i]=jk+1;          else if  (s2==-5) { 
         if(dh[mi][i]==0)            for (j=1,survp=0. ; j<=2; j++)  
           dh[mi][i]=1; /* At least one step */              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
       }            lli= log(survp); 
     }          } 
   }          
   jmean=sum/k;          else{
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
  }            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
 /*********** Tricode ****************************/          } 
 void tricode(int *Tvar, int **nbcode, int imx)          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
 {          /*if(lli ==000.0)*/
   int Ndum[20],ij=1, k, j, i;          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
   int cptcode=0;          ipmx +=1;
   cptcoveff=0;          sw += weight[i];
            ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   for (k=0; k<19; k++) Ndum[k]=0;        } /* end of wave */
   for (k=1; k<=7; k++) ncodemax[k]=0;      } /* end of individual */
     }  else if(mle==2){
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     for (i=1; i<=imx; i++) {        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       ij=(int)(covar[Tvar[j]][i]);        for(mi=1; mi<= wav[i]-1; mi++){
       Ndum[ij]++;          for (ii=1;ii<=nlstate+ndeath;ii++)
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/            for (j=1;j<=nlstate+ndeath;j++){
       if (ij > cptcode) cptcode=ij;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             }
     for (i=0; i<=cptcode; i++) {          for(d=0; d<=dh[mi][i]; d++){
       if(Ndum[i]!=0) ncodemax[j]++;            newm=savm;
     }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     ij=1;            for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             }
     for (i=1; i<=ncodemax[j]; i++) {            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       for (k=0; k<=19; k++) {                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         if (Ndum[k] != 0) {            savm=oldm;
           nbcode[Tvar[j]][ij]=k;            oldm=newm;
           /*     printf("nbcodeaaaaaaaaaaa=%d Tvar[j]=%d ij=%d j=%d",nbcode[Tvar[j]][ij],Tvar[j],ij,j);*/          } /* end mult */
           ij++;        
         }          s1=s[mw[mi][i]][i];
         if (ij > ncodemax[j]) break;          s2=s[mw[mi+1][i]][i];
       }            bbh=(double)bh[mi][i]/(double)stepm; 
     }          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
   }            ipmx +=1;
           sw += weight[i];
  for (k=0; k<19; k++) Ndum[k]=0;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         } /* end of wave */
  for (i=1; i<=ncovmodel-2; i++) {      } /* end of individual */
       ij=Tvar[i];    }  else if(mle==3){  /* exponential inter-extrapolation */
       Ndum[ij]++;      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++){
  ij=1;          for (ii=1;ii<=nlstate+ndeath;ii++)
  for (i=1; i<=10; i++) {            for (j=1;j<=nlstate+ndeath;j++){
    if((Ndum[i]!=0) && (i<=ncovcol)){              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
      Tvaraff[ij]=i;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
      ij++;            }
    }          for(d=0; d<dh[mi][i]; d++){
  }            newm=savm;
              cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     cptcoveff=ij-1;            for (kk=1; kk<=cptcovage;kk++) {
 }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             }
 /*********** Health Expectancies ****************/            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm)            savm=oldm;
 {            oldm=newm;
   /* Health expectancies */          } /* end mult */
   int i, j, nhstepm, hstepm, h, nstepm;        
   double age, agelim, hf;          s1=s[mw[mi][i]][i];
   double ***p3mat;          s2=s[mw[mi+1][i]][i];
            bbh=(double)bh[mi][i]/(double)stepm; 
   fprintf(ficreseij,"# Health expectancies\n");          lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
   fprintf(ficreseij,"# Age");          ipmx +=1;
   for(i=1; i<=nlstate;i++)          sw += weight[i];
     for(j=1; j<=nlstate;j++)          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       fprintf(ficreseij," %1d-%1d",i,j);        } /* end of wave */
   fprintf(ficreseij,"\n");      } /* end of individual */
     }else if (mle==4){  /* ml=4 no inter-extrapolation */
   if(estepm < stepm){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     printf ("Problem %d lower than %d\n",estepm, stepm);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   }        for(mi=1; mi<= wav[i]-1; mi++){
   else  hstepm=estepm;            for (ii=1;ii<=nlstate+ndeath;ii++)
   /* We compute the life expectancy from trapezoids spaced every estepm months            for (j=1;j<=nlstate+ndeath;j++){
    * This is mainly to measure the difference between two models: for example              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
    * if stepm=24 months pijx are given only every 2 years and by summing them              savm[ii][j]=(ii==j ? 1.0 : 0.0);
    * we are calculating an estimate of the Life Expectancy assuming a linear            }
    * progression inbetween and thus overestimating or underestimating according          for(d=0; d<dh[mi][i]; d++){
    * to the curvature of the survival function. If, for the same date, we            newm=savm;
    * estimate the model with stepm=1 month, we can keep estepm to 24 months            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
    * to compare the new estimate of Life expectancy with the same linear            for (kk=1; kk<=cptcovage;kk++) {
    * hypothesis. A more precise result, taking into account a more precise              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
    * curvature will be obtained if estepm is as small as stepm. */            }
           
   /* For example we decided to compute the life expectancy with the smallest unit */            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
      nhstepm is the number of hstepm from age to agelim            savm=oldm;
      nstepm is the number of stepm from age to agelin.            oldm=newm;
      Look at hpijx to understand the reason of that which relies in memory size          } /* end mult */
      and note for a fixed period like estepm months */        
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the          s1=s[mw[mi][i]][i];
      survival function given by stepm (the optimization length). Unfortunately it          s2=s[mw[mi+1][i]][i];
      means that if the survival funtion is printed only each two years of age and if          if( s2 > nlstate){ 
      you sum them up and add 1 year (area under the trapezoids) you won't get the same            lli=log(out[s1][s2] - savm[s1][s2]);
      results. So we changed our mind and took the option of the best precision.          }else{
   */            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */          }
           ipmx +=1;
   agelim=AGESUP;          sw += weight[i];
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     /* nhstepm age range expressed in number of stepm */  /*      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]); */
     nstepm=(int) rint((agelim-age)*YEARM/stepm);        } /* end of wave */
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */      } /* end of individual */
     /* if (stepm >= YEARM) hstepm=1;*/    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     /* Computed by stepm unit matrices, product of hstepm matrices, stored        for(mi=1; mi<= wav[i]-1; mi++){
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */          for (ii=1;ii<=nlstate+ndeath;ii++)
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);              for (j=1;j<=nlstate+ndeath;j++){
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     for(i=1; i<=nlstate;i++)              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       for(j=1; j<=nlstate;j++)            }
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){          for(d=0; d<dh[mi][i]; d++){
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;            newm=savm;
           /* 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]);*/            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         }            for (kk=1; kk<=cptcovage;kk++) {
     fprintf(ficreseij,"%3.0f",age );              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     for(i=1; i<=nlstate;i++)            }
       for(j=1; j<=nlstate;j++){          
         fprintf(ficreseij," %9.4f", eij[i][j][(int)age]);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     fprintf(ficreseij,"\n");            savm=oldm;
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            oldm=newm;
   }          } /* end mult */
 }        
           s1=s[mw[mi][i]][i];
 /************ Variance ******************/          s2=s[mw[mi+1][i]][i];
 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)          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
 {          ipmx +=1;
   /* Variance of health expectancies */          sw += weight[i];
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   double **newm;          /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
   double **dnewm,**doldm;        } /* end of wave */
   int i, j, nhstepm, hstepm, h, nstepm ;      } /* end of individual */
   int k, cptcode;    } /* End of if */
   double *xp;    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   double **gp, **gm;    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   double ***gradg, ***trgradg;    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
   double ***p3mat;    return -l;
   double age,agelim, hf;  }
   int theta;  
   /*************** log-likelihood *************/
    fprintf(ficresvij,"# Covariances of life expectancies\n");  double funcone( double *x)
   fprintf(ficresvij,"# Age");  {
   for(i=1; i<=nlstate;i++)    /* Same as likeli but slower because of a lot of printf and if */
     for(j=1; j<=nlstate;j++)    int i, ii, j, k, mi, d, kk;
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);    double l, ll[NLSTATEMAX], cov[NCOVMAX];
   fprintf(ficresvij,"\n");    double **out;
     double lli; /* Individual log likelihood */
   xp=vector(1,npar);    double llt;
   dnewm=matrix(1,nlstate,1,npar);    int s1, s2;
   doldm=matrix(1,nlstate,1,nlstate);    double bbh, survp;
      /*extern weight */
   if(estepm < stepm){    /* We are differentiating ll according to initial status */
     printf ("Problem %d lower than %d\n",estepm, stepm);    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   }    /*for(i=1;i<imx;i++) 
   else  hstepm=estepm;        printf(" %d\n",s[4][i]);
   /* 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.    cov[1]=1.;
      nhstepm is the number of hstepm from age to agelim  
      nstepm is the number of stepm from age to agelin.    for(k=1; k<=nlstate; k++) ll[k]=0.;
      Look at hpijx to understand the reason of that which relies in memory size  
      and note for a fixed period like k years */    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
      survival function given by stepm (the optimization length). Unfortunately it      for(mi=1; mi<= wav[i]-1; mi++){
      means that if the survival funtion is printed only each two years of age and if        for (ii=1;ii<=nlstate+ndeath;ii++)
      you sum them up and add 1 year (area under the trapezoids) you won't get the same          for (j=1;j<=nlstate+ndeath;j++){
      results. So we changed our mind and took the option of the best precision.            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   */            savm[ii][j]=(ii==j ? 1.0 : 0.0);
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */          }
   agelim = AGESUP;        for(d=0; d<dh[mi][i]; d++){
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          newm=savm;
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */          for (kk=1; kk<=cptcovage;kk++) {
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);          }
     gp=matrix(0,nhstepm,1,nlstate);          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     gm=matrix(0,nhstepm,1,nlstate);                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           savm=oldm;
     for(theta=1; theta <=npar; theta++){          oldm=newm;
       for(i=1; i<=npar; i++){ /* Computes gradient */        } /* end mult */
         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];
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        bbh=(double)bh[mi][i]/(double)stepm; 
         /* bias is positive if real duration
       if (popbased==1) {         * is higher than the multiple of stepm and negative otherwise.
         for(i=1; i<=nlstate;i++)         */
           prlim[i][i]=probs[(int)age][i][ij];        if( s2 > nlstate && (mle <5) ){  /* Jackson */
       }          lli=log(out[s1][s2] - savm[s1][s2]);
          } else if  (s2==-2) {
       for(j=1; j<= nlstate; j++){          for (j=1,survp=0. ; j<=nlstate; j++) 
         for(h=0; h<=nhstepm; h++){            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)          lli= log(survp);
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];        }else if (mle==1){
         }          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
       }        } 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 */
       for(i=1; i<=npar; i++) /* Computes gradient */        } else if(mle==3){  /* exponential inter-extrapolation */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          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 */
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          } else if (mle==4){  /* mle=4 no inter-extrapolation */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          lli=log(out[s1][s2]); /* Original formula */
          } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
       if (popbased==1) {          lli=log(out[s1][s2]); /* Original formula */
         for(i=1; i<=nlstate;i++)        } /* End of if */
           prlim[i][i]=probs[(int)age][i][ij];        ipmx +=1;
       }        sw += weight[i];
         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       for(j=1; j<= nlstate; j++){  /*       printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
         for(h=0; h<=nhstepm; h++){        if(globpr){
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)          fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];   %11.6f %11.6f %11.6f ", \
         }                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
       }                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
           for(k=1,llt=0.,l=0.; k<=nlstate; k++){
       for(j=1; j<= nlstate; j++)            llt +=ll[k]*gipmx/gsw;
         for(h=0; h<=nhstepm; h++){            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];          }
         }          fprintf(ficresilk," %10.6f\n", -llt);
     } /* End theta */        }
       } /* end of wave */
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);    } /* end of individual */
     for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     for(h=0; h<=nhstepm; h++)    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
       for(j=1; j<=nlstate;j++)    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
         for(theta=1; theta <=npar; theta++)    if(globpr==0){ /* First time we count the contributions and weights */
           trgradg[h][j][theta]=gradg[h][theta][j];      gipmx=ipmx;
       gsw=sw;
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */    }
     for(i=1;i<=nlstate;i++)    return -l;
       for(j=1;j<=nlstate;j++)  }
         vareij[i][j][(int)age] =0.;  
   
     for(h=0;h<=nhstepm;h++){  /*************** function likelione ***********/
       for(k=0;k<=nhstepm;k++){  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);  {
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);    /* This routine should help understanding what is done with 
         for(i=1;i<=nlstate;i++)       the selection of individuals/waves and
           for(j=1;j<=nlstate;j++)       to check the exact contribution to the likelihood.
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;       Plotting could be done.
       }     */
     }    int k;
   
     fprintf(ficresvij,"%.0f ",age );    if(*globpri !=0){ /* Just counts and sums, no printings */
     for(i=1; i<=nlstate;i++)      strcpy(fileresilk,"ilk"); 
       for(j=1; j<=nlstate;j++){      strcat(fileresilk,fileres);
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
       }        printf("Problem with resultfile: %s\n", fileresilk);
     fprintf(ficresvij,"\n");        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
     free_matrix(gp,0,nhstepm,1,nlstate);      }
     free_matrix(gm,0,nhstepm,1,nlstate);      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");
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      for(k=1; k<=nlstate; k++) 
   } /* End age */        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
        fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
   free_vector(xp,1,npar);    }
   free_matrix(doldm,1,nlstate,1,npar);  
   free_matrix(dnewm,1,nlstate,1,nlstate);    *fretone=(*funcone)(p);
     if(*globpri !=0){
 }      fclose(ficresilk);
       fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
 /************ Variance of prevlim ******************/      fflush(fichtm); 
 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)    } 
 {    return;
   /* Variance of prevalence limit */  }
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/  
   double **newm;  
   double **dnewm,**doldm;  /*********** Maximum Likelihood Estimation ***************/
   int i, j, nhstepm, hstepm;  
   int k, cptcode;  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   double *xp;  {
   double *gp, *gm;    int i,j, iter;
   double **gradg, **trgradg;    double **xi;
   double age,agelim;    double fret;
   int theta;    double fretone; /* Only one call to likelihood */
        /*  char filerespow[FILENAMELENGTH];*/
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");    xi=matrix(1,npar,1,npar);
   fprintf(ficresvpl,"# Age");    for (i=1;i<=npar;i++)
   for(i=1; i<=nlstate;i++)      for (j=1;j<=npar;j++)
       fprintf(ficresvpl," %1d-%1d",i,i);        xi[i][j]=(i==j ? 1.0 : 0.0);
   fprintf(ficresvpl,"\n");    printf("Powell\n");  fprintf(ficlog,"Powell\n");
     strcpy(filerespow,"pow"); 
   xp=vector(1,npar);    strcat(filerespow,fileres);
   dnewm=matrix(1,nlstate,1,npar);    if((ficrespow=fopen(filerespow,"w"))==NULL) {
   doldm=matrix(1,nlstate,1,nlstate);      printf("Problem with resultfile: %s\n", filerespow);
        fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
   hstepm=1*YEARM; /* Every year of age */    }
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    fprintf(ficrespow,"# Powell\n# iter -2*LL");
   agelim = AGESUP;    for (i=1;i<=nlstate;i++)
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      for(j=1;j<=nlstate+ndeath;j++)
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
     if (stepm >= YEARM) hstepm=1;    fprintf(ficrespow,"\n");
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */  
     gradg=matrix(1,npar,1,nlstate);    powell(p,xi,npar,ftol,&iter,&fret,func);
     gp=vector(1,nlstate);  
     gm=vector(1,nlstate);    free_matrix(xi,1,npar,1,npar);
     fclose(ficrespow);
     for(theta=1; theta <=npar; theta++){    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
       for(i=1; i<=npar; i++){ /* Computes gradient */    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
       }  
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  }
       for(i=1;i<=nlstate;i++)  
         gp[i] = prlim[i][i];  /**** Computes Hessian and covariance matrix ***/
      void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
       for(i=1; i<=npar; i++) /* Computes gradient */  {
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    double  **a,**y,*x,pd;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    double **hess;
       for(i=1;i<=nlstate;i++)    int i, j,jk;
         gm[i] = prlim[i][i];    int *indx;
   
       for(i=1;i<=nlstate;i++)    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
     } /* End theta */    void lubksb(double **a, int npar, int *indx, double b[]) ;
     void ludcmp(double **a, int npar, int *indx, double *d) ;
     trgradg =matrix(1,nlstate,1,npar);    double gompertz(double p[]);
     hess=matrix(1,npar,1,npar);
     for(j=1; j<=nlstate;j++)  
       for(theta=1; theta <=npar; theta++)    printf("\nCalculation of the hessian matrix. Wait...\n");
         trgradg[j][theta]=gradg[theta][j];    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
     for (i=1;i<=npar;i++){
     for(i=1;i<=nlstate;i++)      printf("%d",i);fflush(stdout);
       varpl[i][(int)age] =0.;      fprintf(ficlog,"%d",i);fflush(ficlog);
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);     
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
     for(i=1;i<=nlstate;i++)      
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */      /*  printf(" %f ",p[i]);
           printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
     fprintf(ficresvpl,"%.0f ",age );    }
     for(i=1; i<=nlstate;i++)    
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));    for (i=1;i<=npar;i++) {
     fprintf(ficresvpl,"\n");      for (j=1;j<=npar;j++)  {
     free_vector(gp,1,nlstate);        if (j>i) { 
     free_vector(gm,1,nlstate);          printf(".%d%d",i,j);fflush(stdout);
     free_matrix(gradg,1,npar,1,nlstate);          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
     free_matrix(trgradg,1,nlstate,1,npar);          hess[i][j]=hessij(p,delti,i,j,func,npar);
   } /* End age */          
           hess[j][i]=hess[i][j];    
   free_vector(xp,1,npar);          /*printf(" %lf ",hess[i][j]);*/
   free_matrix(doldm,1,nlstate,1,npar);        }
   free_matrix(dnewm,1,nlstate,1,nlstate);      }
     }
 }    printf("\n");
     fprintf(ficlog,"\n");
 /************ Variance of one-step probabilities  ******************/  
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
 {    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
   int i, j;    
   int k=0, cptcode;    a=matrix(1,npar,1,npar);
   double **dnewm,**doldm;    y=matrix(1,npar,1,npar);
   double *xp;    x=vector(1,npar);
   double *gp, *gm;    indx=ivector(1,npar);
   double **gradg, **trgradg;    for (i=1;i<=npar;i++)
   double age,agelim, cov[NCOVMAX];      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
   int theta;    ludcmp(a,npar,indx,&pd);
   char fileresprob[FILENAMELENGTH];  
     for (j=1;j<=npar;j++) {
   strcpy(fileresprob,"prob");      for (i=1;i<=npar;i++) x[i]=0;
   strcat(fileresprob,fileres);      x[j]=1;
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {      lubksb(a,npar,indx,x);
     printf("Problem with resultfile: %s\n", fileresprob);      for (i=1;i<=npar;i++){ 
   }        matcov[i][j]=x[i];
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);      }
      }
   
   xp=vector(1,npar);    printf("\n#Hessian matrix#\n");
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    fprintf(ficlog,"\n#Hessian matrix#\n");
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));    for (i=1;i<=npar;i++) { 
        for (j=1;j<=npar;j++) { 
   cov[1]=1;        printf("%.3e ",hess[i][j]);
   for (age=bage; age<=fage; age ++){        fprintf(ficlog,"%.3e ",hess[i][j]);
     cov[2]=age;      }
     gradg=matrix(1,npar,1,9);      printf("\n");
     trgradg=matrix(1,9,1,npar);      fprintf(ficlog,"\n");
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));    }
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));  
        /* Recompute Inverse */
     for(theta=1; theta <=npar; theta++){    for (i=1;i<=npar;i++)
       for(i=1; i<=npar; i++)      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    ludcmp(a,npar,indx,&pd);
        
       pmij(pmmij,cov,ncovmodel,xp,nlstate);    /*  printf("\n#Hessian matrix recomputed#\n");
      
       k=0;    for (j=1;j<=npar;j++) {
       for(i=1; i<= (nlstate+ndeath); i++){      for (i=1;i<=npar;i++) x[i]=0;
         for(j=1; j<=(nlstate+ndeath);j++){      x[j]=1;
            k=k+1;      lubksb(a,npar,indx,x);
           gp[k]=pmmij[i][j];      for (i=1;i<=npar;i++){ 
         }        y[i][j]=x[i];
       }        printf("%.3e ",y[i][j]);
         fprintf(ficlog,"%.3e ",y[i][j]);
       for(i=1; i<=npar; i++)      }
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      printf("\n");
          fprintf(ficlog,"\n");
     }
       pmij(pmmij,cov,ncovmodel,xp,nlstate);    */
       k=0;  
       for(i=1; i<=(nlstate+ndeath); i++){    free_matrix(a,1,npar,1,npar);
         for(j=1; j<=(nlstate+ndeath);j++){    free_matrix(y,1,npar,1,npar);
           k=k+1;    free_vector(x,1,npar);
           gm[k]=pmmij[i][j];    free_ivector(indx,1,npar);
         }    free_matrix(hess,1,npar,1,npar);
       }  
        
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)  }
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];    
     }  /*************** hessian matrix ****************/
   double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)  {
       for(theta=1; theta <=npar; theta++)    int i;
       trgradg[j][theta]=gradg[theta][j];    int l=1, lmax=20;
      double k1,k2;
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);    double p2[NPARMAX+1];
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);    double res;
     double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
      pmij(pmmij,cov,ncovmodel,x,nlstate);    double fx;
     int k=0,kmax=10;
      k=0;    double l1;
      for(i=1; i<=(nlstate+ndeath); i++){  
        for(j=1; j<=(nlstate+ndeath);j++){    fx=func(x);
          k=k+1;    for (i=1;i<=npar;i++) p2[i]=x[i];
          gm[k]=pmmij[i][j];    for(l=0 ; l <=lmax; l++){
         }      l1=pow(10,l);
      }      delts=delt;
            for(k=1 ; k <kmax; k=k+1){
      /*printf("\n%d ",(int)age);        delt = delta*(l1*k);
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){        p2[theta]=x[theta] +delt;
                k1=func(p2)-fx;
         p2[theta]=x[theta]-delt;
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));        k2=func(p2)-fx;
      }*/        /*res= (k1-2.0*fx+k2)/delt/delt; */
         res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
   fprintf(ficresprob,"\n%d ",(int)age);        
   #ifdef DEBUG
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){        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);
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);        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);
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);  #endif
   }        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
         if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));          k=kmax;
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));        }
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);          k=kmax; l=lmax*10.;
 }        }
  free_vector(xp,1,npar);        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
 fclose(ficresprob);          delts=delt;
         }
 }      }
     }
 /******************* Printing html file ***********/    delti[theta]=delts;
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \    return res; 
  int lastpass, int stepm, int weightopt, char model[],\    
  int imx,int jmin, int jmax, double jmeanint,char optionfile[], \  }
  char optionfilehtm[],char rfileres[], char optionfilegnuplot[],\  
  char version[], int popforecast, int estepm ){  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
   int jj1, k1, i1, cpt;  {
   FILE *fichtm;    int i;
   /*char optionfilehtm[FILENAMELENGTH];*/    int l=1, l1, lmax=20;
     double k1,k2,k3,k4,res,fx;
   strcpy(optionfilehtm,optionfile);    double p2[NPARMAX+1];
   strcat(optionfilehtm,".htm");    int k;
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {  
     printf("Problem with %s \n",optionfilehtm), exit(0);    fx=func(x);
   }    for (k=1; k<=2; k++) {
       for (i=1;i<=npar;i++) p2[i]=x[i];
  fprintf(fichtm,"<body> <font size=\"2\">Imach, Version %s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n      p2[thetai]=x[thetai]+delti[thetai]/k;
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
 \n      k1=func(p2)-fx;
 Total number of observations=%d <br>\n    
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n      p2[thetai]=x[thetai]+delti[thetai]/k;
 <hr  size=\"2\" color=\"#EC5E5E\">      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
  <ul><li>Outputs files<br>\n      k2=func(p2)-fx;
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n    
  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n      p2[thetai]=x[thetai]-delti[thetai]/k;
  - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
  - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>\n      k3=func(p2)-fx;
  - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>\n    
  - 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,fileres,fileres,estepm);      p2[thetai]=x[thetai]-delti[thetai]/k;
       p2[thetaj]=x[thetaj]-delti[thetaj]/k;
  fprintf(fichtm,"\n      k4=func(p2)-fx;
  - Parameter file with estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>\n      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
  - Variances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n  #ifdef DEBUG
  - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>\n      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);
  - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);      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
  if(popforecast==1) fprintf(fichtm,"\n    }
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n    return res;
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n  }
         <br>",fileres,fileres,fileres,fileres);  
  else  /************** Inverse of matrix **************/
    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);  void ludcmp(double **a, int n, int *indx, double *d) 
 fprintf(fichtm," <li>Graphs</li><p>");  { 
     int i,imax,j,k; 
  m=cptcoveff;    double big,dum,sum,temp; 
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}    double *vv; 
    
  jj1=0;    vv=vector(1,n); 
  for(k1=1; k1<=m;k1++){    *d=1.0; 
    for(i1=1; i1<=ncodemax[k1];i1++){    for (i=1;i<=n;i++) { 
        jj1++;      big=0.0; 
        if (cptcovn > 0) {      for (j=1;j<=n;j++) 
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");        if ((temp=fabs(a[i][j])) > big) big=temp; 
          for (cpt=1; cpt<=cptcoveff;cpt++)      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);      vv[i]=1.0/big; 
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");    } 
        }    for (j=1;j<=n;j++) { 
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>      for (i=1;i<j;i++) { 
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);            sum=a[i][j]; 
        for(cpt=1; cpt<nlstate;cpt++){        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>        a[i][j]=sum; 
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);      } 
        }      big=0.0; 
     for(cpt=1; cpt<=nlstate;cpt++) {      for (i=j;i<=n;i++) { 
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident        sum=a[i][j]; 
 interval) in state (%d): v%s%d%d.gif <br>        for (k=1;k<j;k++) 
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);            sum -= a[i][k]*a[k][j]; 
      }        a[i][j]=sum; 
      for(cpt=1; cpt<=nlstate;cpt++) {        if ( (dum=vv[i]*fabs(sum)) >= big) { 
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>          big=dum; 
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);          imax=i; 
      }        } 
      fprintf(fichtm,"\n<br>- Total life expectancy by age and      } 
 health expectancies in states (1) and (2): e%s%d.gif<br>      if (j != imax) { 
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);        for (k=1;k<=n;k++) { 
 fprintf(fichtm,"\n</body>");          dum=a[imax][k]; 
    }          a[imax][k]=a[j][k]; 
    }          a[j][k]=dum; 
 fclose(fichtm);        } 
 }        *d = -(*d); 
         vv[imax]=vv[j]; 
 /******************* Gnuplot file **************/      } 
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){      indx[j]=imax; 
       if (a[j][j] == 0.0) a[j][j]=TINY; 
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;      if (j != n) { 
         dum=1.0/(a[j][j]); 
   strcpy(optionfilegnuplot,optionfilefiname);        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
   strcat(optionfilegnuplot,".gp.txt");      } 
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {    } 
     printf("Problem with file %s",optionfilegnuplot);    free_vector(vv,1,n);  /* Doesn't work */
   }  ;
   } 
 #ifdef windows  
     fprintf(ficgp,"cd \"%s\" \n",pathc);  void lubksb(double **a, int n, int *indx, double b[]) 
 #endif  { 
 m=pow(2,cptcoveff);    int i,ii=0,ip,j; 
      double sum; 
  /* 1eme*/   
   for (cpt=1; cpt<= nlstate ; cpt ++) {    for (i=1;i<=n;i++) { 
    for (k1=1; k1<= m ; k1 ++) {      ip=indx[i]; 
       sum=b[ip]; 
 #ifdef windows      b[ip]=b[i]; 
     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);      if (ii) 
 #endif        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
 #ifdef unix      else if (sum) ii=i; 
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);      b[i]=sum; 
 #endif    } 
     for (i=n;i>=1;i--) { 
 for (i=1; i<= nlstate ; i ++) {      sum=b[i]; 
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
   else fprintf(ficgp," \%%*lf (\%%*lf)");      b[i]=sum/a[i][i]; 
 }    } 
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);  } 
     for (i=1; i<= nlstate ; i ++) {  
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");  void pstamp(FILE *fichier)
   else fprintf(ficgp," \%%*lf (\%%*lf)");  {
 }    fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);  }
      for (i=1; i<= nlstate ; i ++) {  
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");  /************ Frequencies ********************/
   else fprintf(ficgp," \%%*lf (\%%*lf)");  void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])
 }    {  /* Some frequencies */
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));    
 #ifdef unix    int i, m, jk, k1,i1, j1, bool, z1,j;
 fprintf(ficgp,"\nset ter gif small size 400,300");    int first;
 #endif    double ***freq; /* Frequencies */
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    double *pp, **prop;
    }    double pos,posprop, k2, dateintsum=0,k2cpt=0;
   }    char fileresp[FILENAMELENGTH];
   /*2 eme*/    
     pp=vector(1,nlstate);
   for (k1=1; k1<= m ; k1 ++) {    prop=matrix(1,nlstate,iagemin,iagemax+3);
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",ageminpar,fage);    strcpy(fileresp,"p");
        strcat(fileresp,fileres);
     for (i=1; i<= nlstate+1 ; i ++) {    if((ficresp=fopen(fileresp,"w"))==NULL) {
       k=2*i;      printf("Problem with prevalence resultfile: %s\n", fileresp);
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
       for (j=1; j<= nlstate+1 ; j ++) {      exit(0);
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    }
   else fprintf(ficgp," \%%*lf (\%%*lf)");    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
 }      j1=0;
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");    
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);    j=cptcoveff;
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
       for (j=1; j<= nlstate+1 ; j ++) {  
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    first=1;
         else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }      for(k1=1; k1<=j;k1++){
       fprintf(ficgp,"\" t\"\" w l 0,");      for(i1=1; i1<=ncodemax[k1];i1++){
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);        j1++;
       for (j=1; j<= nlstate+1 ; j ++) {        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          scanf("%d", i);*/
   else fprintf(ficgp," \%%*lf (\%%*lf)");        for (i=-5; i<=nlstate+ndeath; i++)  
 }            for (jk=-5; jk<=nlstate+ndeath; jk++)  
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");            for(m=iagemin; m <= iagemax+3; m++)
       else fprintf(ficgp,"\" t\"\" w l 0,");              freq[i][jk][m]=0;
     }  
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);      for (i=1; i<=nlstate; i++)  
   }        for(m=iagemin; m <= iagemax+3; m++)
            prop[i][m]=0;
   /*3eme*/        
         dateintsum=0;
   for (k1=1; k1<= m ; k1 ++) {        k2cpt=0;
     for (cpt=1; cpt<= nlstate ; cpt ++) {        for (i=1; i<=imx; i++) {
       k=2+nlstate*(cpt-1);          bool=1;
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);          if  (cptcovn>0) {
       for (i=1; i< nlstate ; i ++) {            for (z1=1; z1<=cptcoveff; z1++) 
         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
       }                bool=0;
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);          }
     }          if (bool==1){
     }            for(m=firstpass; m<=lastpass; m++){
                k2=anint[m][i]+(mint[m][i]/12.);
   /* CV preval stat */              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
     for (k1=1; k1<= m ; k1 ++) {                if(agev[m][i]==0) agev[m][i]=iagemax+1;
     for (cpt=1; cpt<nlstate ; cpt ++) {                if(agev[m][i]==1) agev[m][i]=iagemax+2;
       k=3;                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);                if (m<lastpass) {
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
       for (i=1; i< nlstate ; i ++)                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
         fprintf(ficgp,"+$%d",k+i+1);                }
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);                
                      if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
       l=3+(nlstate+ndeath)*cpt;                  dateintsum=dateintsum+k2;
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);                  k2cpt++;
       for (i=1; i< nlstate ; i ++) {                }
         l=3+(nlstate+ndeath)*cpt;                /*}*/
         fprintf(ficgp,"+$%d",l+i+1);            }
       }          }
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);          }
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);         
     }        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
   }          pstamp(ficresp);
          if  (cptcovn>0) {
   /* proba elementaires */          fprintf(ficresp, "\n#********** Variable "); 
    for(i=1,jk=1; i <=nlstate; i++){          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     for(k=1; k <=(nlstate+ndeath); k++){          fprintf(ficresp, "**********\n#");
       if (k != i) {        }
         for(j=1; j <=ncovmodel; j++){        for(i=1; i<=nlstate;i++) 
                  fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);        fprintf(ficresp, "\n");
           jk++;        
           fprintf(ficgp,"\n");        for(i=iagemin; i <= iagemax+3; i++){
         }          if(i==iagemax+3){
       }            fprintf(ficlog,"Total");
     }          }else{
     }            if(first==1){
               first=0;
     for(jk=1; jk <=m; jk++) {              printf("See log file for details...\n");
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);            }
    i=1;            fprintf(ficlog,"Age %d", i);
    for(k2=1; k2<=nlstate; k2++) {          }
      k3=i;          for(jk=1; jk <=nlstate ; jk++){
      for(k=1; k<=(nlstate+ndeath); k++) {            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
        if (k != k2){              pp[jk] += freq[jk][m][i]; 
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);          }
 ij=1;          for(jk=1; jk <=nlstate ; jk++){
         for(j=3; j <=ncovmodel; j++) {            for(m=-1, pos=0; m <=0 ; m++)
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {              pos += freq[jk][m][i];
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);            if(pp[jk]>=1.e-10){
             ij++;              if(first==1){
           }              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
           else              }
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
         }            }else{
           fprintf(ficgp,")/(1");              if(first==1)
                        printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
         for(k1=1; k1 <=nlstate; k1++){                fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
           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)) {          for(jk=1; jk <=nlstate ; jk++){
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
             ij++;              pp[jk] += freq[jk][m][i];
           }          }       
           else          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);            pos += pp[jk];
           }            posprop += prop[jk][i];
           fprintf(ficgp,")");          }
         }          for(jk=1; jk <=nlstate ; jk++){
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);            if(pos>=1.e-5){
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");              if(first==1)
         i=i+ncovmodel;                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
        }              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
      }            }else{
    }              if(first==1)
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
    }              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
                }
   fclose(ficgp);            if( i <= iagemax){
 }  /* end gnuplot */              if(pos>=1.e-5){
                 fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
                 /*probs[i][jk][j1]= pp[jk]/pos;*/
 /*************** Moving average **************/                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){              }
               else
   int i, cpt, cptcod;                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)            }
       for (i=1; i<=nlstate;i++)          }
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)          
           mobaverage[(int)agedeb][i][cptcod]=0.;          for(jk=-1; jk <=nlstate+ndeath; jk++)
                for(m=-1; m <=nlstate+ndeath; m++)
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){              if(freq[jk][m][i] !=0 ) {
       for (i=1; i<=nlstate;i++){              if(first==1)
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
           for (cpt=0;cpt<=4;cpt++){                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];              }
           }          if(i <= iagemax)
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;            fprintf(ficresp,"\n");
         }          if(first==1)
       }            printf("Others in log...\n");
     }          fprintf(ficlog,"\n");
            }
 }      }
     }
     dateintmean=dateintsum/k2cpt; 
 /************** Forecasting ******************/   
 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){    fclose(ficresp);
      free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;    free_vector(pp,1,nlstate);
   int *popage;    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;    /* End of Freq */
   double *popeffectif,*popcount;  }
   double ***p3mat;  
   char fileresf[FILENAMELENGTH];  /************ 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)
  agelim=AGESUP;  {  
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;    /* 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).
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);       We still use firstpass and lastpass as another selection.
      */
     
   strcpy(fileresf,"f");    int i, m, jk, k1, i1, j1, bool, z1,j;
   strcat(fileresf,fileres);    double ***freq; /* Frequencies */
   if((ficresf=fopen(fileresf,"w"))==NULL) {    double *pp, **prop;
     printf("Problem with forecast resultfile: %s\n", fileresf);    double pos,posprop; 
   }    double  y2; /* in fractional years */
   printf("Computing forecasting: result on file '%s' \n", fileresf);    int iagemin, iagemax;
   
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    iagemin= (int) agemin;
     iagemax= (int) agemax;
   if (mobilav==1) {    /*pp=vector(1,nlstate);*/
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    prop=matrix(1,nlstate,iagemin,iagemax+3); 
     movingaverage(agedeb, fage, ageminpar, mobaverage);    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
   }    j1=0;
     
   stepsize=(int) (stepm+YEARM-1)/YEARM;    j=cptcoveff;
   if (stepm<=12) stepsize=1;    if (cptcovn<1) {j=1;ncodemax[1]=1;}
      
   agelim=AGESUP;    for(k1=1; k1<=j;k1++){
        for(i1=1; i1<=ncodemax[k1];i1++){
   hstepm=1;        j1++;
   hstepm=hstepm/stepm;        
   yp1=modf(dateintmean,&yp);        for (i=1; i<=nlstate; i++)  
   anprojmean=yp;          for(m=iagemin; m <= iagemax+3; m++)
   yp2=modf((yp1*12),&yp);            prop[i][m]=0.0;
   mprojmean=yp;       
   yp1=modf((yp2*30.5),&yp);        for (i=1; i<=imx; i++) { /* Each individual */
   jprojmean=yp;          bool=1;
   if(jprojmean==0) jprojmean=1;          if  (cptcovn>0) {
   if(mprojmean==0) jprojmean=1;            for (z1=1; z1<=cptcoveff; z1++) 
                if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);                bool=0;
            } 
   for(cptcov=1;cptcov<=i2;cptcov++){          if (bool==1) { 
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
       k=k+1;              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
       fprintf(ficresf,"\n#******");              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
       for(j=1;j<=cptcoveff;j++) {                if(agev[m][i]==0) agev[m][i]=iagemax+1;
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
       }                if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
       fprintf(ficresf,"******\n");                if (s[m][i]>0 && s[m][i]<=nlstate) { 
       fprintf(ficresf,"# StartingAge FinalAge");                  /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
                        prop[s[m][i]][iagemax+3] += weight[i]; 
                      } 
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {              }
         fprintf(ficresf,"\n");            } /* end selection of waves */
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);            }
         }
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){        for(i=iagemin; i <= iagemax+3; i++){  
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);          
           nhstepm = nhstepm/hstepm;          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
                      posprop += prop[jk][i]; 
           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(jk=1; jk <=nlstate ; jk++){     
                    if( i <=  iagemax){ 
           for (h=0; h<=nhstepm; h++){              if(posprop>=1.e-5){ 
             if (h==(int) (calagedate+YEARM*cpt)) {                probs[i][jk][j1]= prop[jk][i]/posprop;
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);              } else
             }                printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\n",jk,i,j1,probs[i][jk][j1]);
             for(j=1; j<=nlstate+ndeath;j++) {            } 
               kk1=0.;kk2=0;          }/* end jk */ 
               for(i=1; i<=nlstate;i++) {                      }/* end i */ 
                 if (mobilav==1)      } /* end i1 */
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];    } /* end k1 */
                 else {    
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
                 }    /*free_vector(pp,1,nlstate);*/
                    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
               }  }  /* End of prevalence */
               if (h==(int)(calagedate+12*cpt)){  
                 fprintf(ficresf," %.3f", kk1);  /************* Waves Concatenation ***************/
                          
               }  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)
             }  {
           }    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);       Death is a valid wave (if date is known).
         }       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
       }       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
     }       and mw[mi+1][i]. dh depends on stepm.
   }       */
          
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    int i, mi, m;
     /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
   fclose(ficresf);       double sum=0., jmean=0.;*/
 }    int first;
 /************** Forecasting ******************/    int j, k=0,jk, ju, jl;
 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){    double sum=0.;
      first=0;
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;    jmin=1e+5;
   int *popage;    jmax=-1;
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;    jmean=0.;
   double *popeffectif,*popcount;    for(i=1; i<=imx; i++){
   double ***p3mat,***tabpop,***tabpopprev;      mi=0;
   char filerespop[FILENAMELENGTH];      m=firstpass;
       while(s[m][i] <= nlstate){
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          mw[++mi][i]=m;
   agelim=AGESUP;        if(m >=lastpass)
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;          break;
          else
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);          m++;
        }/* end while */
        if (s[m][i] > nlstate){
   strcpy(filerespop,"pop");        mi++;     /* Death is another wave */
   strcat(filerespop,fileres);        /* if(mi==0)  never been interviewed correctly before death */
   if((ficrespop=fopen(filerespop,"w"))==NULL) {           /* Only death is a correct wave */
     printf("Problem with forecast resultfile: %s\n", filerespop);        mw[mi][i]=m;
   }      }
   printf("Computing forecasting: result on file '%s' \n", filerespop);  
       wav[i]=mi;
   if (cptcoveff==0) ncodemax[cptcoveff]=1;      if(mi==0){
         nbwarn++;
   if (mobilav==1) {        if(first==0){
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
     movingaverage(agedeb, fage, ageminpar, mobaverage);          first=1;
   }        }
         if(first==1){
   stepsize=(int) (stepm+YEARM-1)/YEARM;          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
   if (stepm<=12) stepsize=1;        }
        } /* end mi==0 */
   agelim=AGESUP;    } /* End individuals */
    
   hstepm=1;    for(i=1; i<=imx; i++){
   hstepm=hstepm/stepm;      for(mi=1; mi<wav[i];mi++){
          if (stepm <=0)
   if (popforecast==1) {          dh[mi][i]=1;
     if((ficpop=fopen(popfile,"r"))==NULL) {        else{
       printf("Problem with population file : %s\n",popfile);exit(0);          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
     }            if (agedc[i] < 2*AGESUP) {
     popage=ivector(0,AGESUP);              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
     popeffectif=vector(0,AGESUP);              if(j==0) j=1;  /* Survives at least one month after exam */
     popcount=vector(0,AGESUP);              else if(j<0){
                    nberr++;
     i=1;                  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]);
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;                j=1; /* Temporary Dangerous patch */
                    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);
     imx=i;                fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];                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);
   }              }
               k=k+1;
   for(cptcov=1;cptcov<=i2;cptcov++){              if (j >= jmax){
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){                jmax=j;
       k=k+1;                ijmax=i;
       fprintf(ficrespop,"\n#******");              }
       for(j=1;j<=cptcoveff;j++) {              if (j <= jmin){
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                jmin=j;
       }                ijmin=i;
       fprintf(ficrespop,"******\n");              }
       fprintf(ficrespop,"# Age");              sum=sum+j;
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
       if (popforecast==1)  fprintf(ficrespop," [Population]");              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
                  }
       for (cpt=0; cpt<=0;cpt++) {          }
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);            else{
                    j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){  /*        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]); */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);  
           nhstepm = nhstepm/hstepm;            k=k+1;
                      if (j >= jmax) {
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              jmax=j;
           oldm=oldms;savm=savms;              ijmax=i;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);              }
                    else if (j <= jmin){
           for (h=0; h<=nhstepm; h++){              jmin=j;
             if (h==(int) (calagedate+YEARM*cpt)) {              ijmin=i;
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);            }
             }            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
             for(j=1; j<=nlstate+ndeath;j++) {            /*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]);*/
               kk1=0.;kk2=0;            if(j<0){
               for(i=1; i<=nlstate;i++) {                            nberr++;
                 if (mobilav==1)              printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];              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]);
                 else {            }
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];            sum=sum+j;
                 }          }
               }          jk= j/stepm;
               if (h==(int)(calagedate+12*cpt)){          jl= j -jk*stepm;
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;          ju= j -(jk+1)*stepm;
                   /*fprintf(ficrespop," %.3f", kk1);          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/            if(jl==0){
               }              dh[mi][i]=jk;
             }              bh[mi][i]=0;
             for(i=1; i<=nlstate;i++){            }else{ /* We want a negative bias in order to only have interpolation ie
               kk1=0.;                    * at the price of an extra matrix product in likelihood */
                 for(j=1; j<=nlstate;j++){              dh[mi][i]=jk+1;
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];              bh[mi][i]=ju;
                 }            }
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];          }else{
             }            if(jl <= -ju){
               dh[mi][i]=jk;
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)              bh[mi][i]=jl;       /* bias is positive if real duration
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);                                   * is higher than the multiple of stepm and negative otherwise.
           }                                   */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            }
         }            else{
       }              dh[mi][i]=jk+1;
                bh[mi][i]=ju;
   /******/            }
             if(dh[mi][i]==0){
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {              dh[mi][i]=1; /* At least one step */
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);                bh[mi][i]=ju; /* At least one step */
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){              /*  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);*/
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);            }
           nhstepm = nhstepm/hstepm;          } /* end if mle */
                  }
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      } /* end wave */
           oldm=oldms;savm=savms;    }
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      jmean=sum/k;
           for (h=0; h<=nhstepm; h++){    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);
             if (h==(int) (calagedate+YEARM*cpt)) {    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);
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);   }
             }  
             for(j=1; j<=nlstate+ndeath;j++) {  /*********** Tricode ****************************/
               kk1=0.;kk2=0;  void tricode(int *Tvar, int **nbcode, int imx)
               for(i=1; i<=nlstate;i++) {                {
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];        
               }    /*      Tvar[i]=atoi(stre); /* find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 */
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);  
             }    int Ndum[20],ij=1, k=0, j=0, i=0, maxncov=19;
           }    int cptcode=0;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    cptcoveff=0; 
         }   
       }    for (k=0; k<maxncov; k++) Ndum[k]=0;
    }    for (k=1; k<=7; k++) ncodemax[k]=0;
   }  
      for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
                                  modality*/ 
   if (popforecast==1) {        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
     free_ivector(popage,0,AGESUP);        Ndum[ij]++; /*store the modality */
     free_vector(popeffectif,0,AGESUP);        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
     free_vector(popcount,0,AGESUP);        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
   }                                         Tvar[j]. If V=sex and male is 0 and 
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);                                         female is 1, then  cptcode=1.*/
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      }
   fclose(ficrespop);  
 }      for (i=0; i<=cptcode; i++) {
         if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */
 /***********************************************/      }
 /**************** Main Program *****************/  
 /***********************************************/      ij=1; 
       for (i=1; i<=ncodemax[j]; i++) {
 int main(int argc, char *argv[])        for (k=0; k<= maxncov; k++) {
 {          if (Ndum[k] != 0) {
             nbcode[Tvar[j]][ij]=k; 
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;            /* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
   double agedeb, agefin,hf;            
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;            ij++;
           }
   double fret;          if (ij > ncodemax[j]) break; 
   double **xi,tmp,delta;        }  
       } 
   double dum; /* Dummy variable */    }  
   double ***p3mat;  
   int *indx;   for (k=0; k< maxncov; k++) Ndum[k]=0;
   char line[MAXLINE], linepar[MAXLINE];  
   char title[MAXLINE];   for (i=1; i<=ncovmodel-2; i++) { 
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];     ij=Tvar[i];
       Ndum[ij]++;
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];   }
   
   char filerest[FILENAMELENGTH];   ij=1;
   char fileregp[FILENAMELENGTH];   for (i=1; i<= maxncov; i++) {
   char popfile[FILENAMELENGTH];     if((Ndum[i]!=0) && (i<=ncovcol)){
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];       Tvaraff[ij]=i; /*For printing */
   int firstobs=1, lastobs=10;       ij++;
   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;   cptcoveff=ij-1; /*Number of simple covariates*/
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;  }
   int mobilav=0,popforecast=0;  
   int hstepm, nhstepm;  /*********** Health Expectancies ****************/
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1;  
   void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
   double bage, fage, age, agelim, agebase;  
   double ftolpl=FTOL;  {
   double **prlim;    /* Health expectancies, no variances */
   double *severity;    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
   double ***param; /* Matrix of parameters */    int nhstepma, nstepma; /* Decreasing with age */
   double  *p;    double age, agelim, hf;
   double **matcov; /* Matrix of covariance */    double ***p3mat;
   double ***delti3; /* Scale */    double eip;
   double *delti; /* Scale */  
   double ***eij, ***vareij;    pstamp(ficreseij);
   double **varpl; /* Variances of prevalence limits by age */    fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
   double *epj, vepp;    fprintf(ficreseij,"# Age");
   double kk1, kk2;    for(i=1; i<=nlstate;i++){
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;      for(j=1; j<=nlstate;j++){
          fprintf(ficreseij," e%1d%1d ",i,j);
       }
   char version[80]="Imach version 0.8a, March 2002, INED-EUROREVES ";      fprintf(ficreseij," e%1d. ",i);
   char *alph[]={"a","a","b","c","d","e"}, str[4];    }
     fprintf(ficreseij,"\n");
   
   char z[1]="c", occ;    
 #include <sys/time.h>    if(estepm < stepm){
 #include <time.h>      printf ("Problem %d lower than %d\n",estepm, stepm);
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];    }
      else  hstepm=estepm;   
   /* long total_usecs;    /* We compute the life expectancy from trapezoids spaced every estepm months
   struct timeval start_time, end_time;     * 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
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */     * we are calculating an estimate of the Life Expectancy assuming a linear 
   getcwd(pathcd, size);     * progression in between and thus overestimating or underestimating according
      * to the curvature of the survival function. If, for the same date, we 
   printf("\n%s",version);     * estimate the model with stepm=1 month, we can keep estepm to 24 months
   if(argc <=1){     * to compare the new estimate of Life expectancy with the same linear 
     printf("\nEnter the parameter file name: ");     * hypothesis. A more precise result, taking into account a more precise
     scanf("%s",pathtot);     * curvature will be obtained if estepm is as small as stepm. */
   }  
   else{    /* For example we decided to compute the life expectancy with the smallest unit */
     strcpy(pathtot,argv[1]);    /* 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 
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/       nstepm is the number of stepm from age to agelin. 
   /*cygwin_split_path(pathtot,path,optionfile);       Look at hpijx to understand the reason of that which relies in memory size
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/       and note for a fixed period like estepm months */
   /* cutv(path,optionfile,pathtot,'\\');*/    /* 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
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);       means that if the survival funtion is printed only each two years of age and if
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   chdir(path);       results. So we changed our mind and took the option of the best precision.
   replace(pathc,path);    */
     hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
 /*-------- arguments in the command line --------*/  
     agelim=AGESUP;
   strcpy(fileres,"r");    /* If stepm=6 months */
   strcat(fileres, optionfilefiname);      /* Computed by stepm unit matrices, product of hstepm matrices, stored
   strcat(fileres,".txt");    /* Other files have txt extension */         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
       
   /*---------arguments file --------*/  /* nhstepm age range expressed in number of stepm */
     nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
   if((ficpar=fopen(optionfile,"r"))==NULL)    {    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     printf("Problem with optionfile %s\n",optionfile);    /* if (stepm >= YEARM) hstepm=1;*/
     goto end;    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   }    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   
   strcpy(filereso,"o");    for (age=bage; age<=fage; age ++){ 
   strcat(filereso,fileres);      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
   if((ficparo=fopen(filereso,"w"))==NULL) {      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     printf("Problem with Output resultfile: %s\n", filereso);goto end;      /* if (stepm >= YEARM) hstepm=1;*/
   }      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
   
   /* Reads comments: lines beginning with '#' */      /* If stepm=6 months */
   while((c=getc(ficpar))=='#' && c!= EOF){      /* Computed by stepm unit matrices, product of hstepma matrices, stored
     ungetc(c,ficpar);         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
     fgets(line, MAXLINE, ficpar);      
     puts(line);      hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
     fputs(line,ficparo);      
   }      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   ungetc(c,ficpar);      
       printf("%d|",(int)age);fflush(stdout);
   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);      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
   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);      /* Computing expectancies */
 while((c=getc(ficpar))=='#' && c!= EOF){      for(i=1; i<=nlstate;i++)
     ungetc(c,ficpar);        for(j=1; j<=nlstate;j++)
     fgets(line, MAXLINE, ficpar);          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
     puts(line);            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
     fputs(line,ficparo);            
   }            /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
   ungetc(c,ficpar);  
            }
      
   covar=matrix(0,NCOVMAX,1,n);      fprintf(ficreseij,"%3.0f",age );
   cptcovn=0;      for(i=1; i<=nlstate;i++){
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;        eip=0;
         for(j=1; j<=nlstate;j++){
   ncovmodel=2+cptcovn;          eip +=eij[i][j][(int)age];
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */          fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
          }
   /* Read guess parameters */        fprintf(ficreseij,"%9.4f", eip );
   /* Reads comments: lines beginning with '#' */      }
   while((c=getc(ficpar))=='#' && c!= EOF){      fprintf(ficreseij,"\n");
     ungetc(c,ficpar);      
     fgets(line, MAXLINE, ficpar);    }
     puts(line);    free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     fputs(line,ficparo);    printf("\n");
   }    fprintf(ficlog,"\n");
   ungetc(c,ficpar);    
    }
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);  
     for(i=1; i <=nlstate; i++)  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[] )
     for(j=1; j <=nlstate+ndeath-1; j++){  
       fscanf(ficpar,"%1d%1d",&i1,&j1);  {
       fprintf(ficparo,"%1d%1d",i1,j1);    /* Covariances of health expectancies eij and of total life expectancies according
       printf("%1d%1d",i,j);     to initial status i, ei. .
       for(k=1; k<=ncovmodel;k++){    */
         fscanf(ficpar," %lf",&param[i][j][k]);    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
         printf(" %lf",param[i][j][k]);    int nhstepma, nstepma; /* Decreasing with age */
         fprintf(ficparo," %lf",param[i][j][k]);    double age, agelim, hf;
       }    double ***p3matp, ***p3matm, ***varhe;
       fscanf(ficpar,"\n");    double **dnewm,**doldm;
       printf("\n");    double *xp, *xm;
       fprintf(ficparo,"\n");    double **gp, **gm;
     }    double ***gradg, ***trgradg;
      int theta;
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;  
     double eip, vip;
   p=param[1][1];  
      varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
   /* Reads comments: lines beginning with '#' */    xp=vector(1,npar);
   while((c=getc(ficpar))=='#' && c!= EOF){    xm=vector(1,npar);
     ungetc(c,ficpar);    dnewm=matrix(1,nlstate*nlstate,1,npar);
     fgets(line, MAXLINE, ficpar);    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
     puts(line);    
     fputs(line,ficparo);    pstamp(ficresstdeij);
   }    fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
   ungetc(c,ficpar);    fprintf(ficresstdeij,"# Age");
     for(i=1; i<=nlstate;i++){
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);      for(j=1; j<=nlstate;j++)
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */        fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
   for(i=1; i <=nlstate; i++){      fprintf(ficresstdeij," e%1d. ",i);
     for(j=1; j <=nlstate+ndeath-1; j++){    }
       fscanf(ficpar,"%1d%1d",&i1,&j1);    fprintf(ficresstdeij,"\n");
       printf("%1d%1d",i,j);  
       fprintf(ficparo,"%1d%1d",i1,j1);    pstamp(ficrescveij);
       for(k=1; k<=ncovmodel;k++){    fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
         fscanf(ficpar,"%le",&delti3[i][j][k]);    fprintf(ficrescveij,"# Age");
         printf(" %le",delti3[i][j][k]);    for(i=1; i<=nlstate;i++)
         fprintf(ficparo," %le",delti3[i][j][k]);      for(j=1; j<=nlstate;j++){
       }        cptj= (j-1)*nlstate+i;
       fscanf(ficpar,"\n");        for(i2=1; i2<=nlstate;i2++)
       printf("\n");          for(j2=1; j2<=nlstate;j2++){
       fprintf(ficparo,"\n");            cptj2= (j2-1)*nlstate+i2;
     }            if(cptj2 <= cptj)
   }              fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
   delti=delti3[1][1];          }
        }
   /* Reads comments: lines beginning with '#' */    fprintf(ficrescveij,"\n");
   while((c=getc(ficpar))=='#' && c!= EOF){    
     ungetc(c,ficpar);    if(estepm < stepm){
     fgets(line, MAXLINE, ficpar);      printf ("Problem %d lower than %d\n",estepm, stepm);
     puts(line);    }
     fputs(line,ficparo);    else  hstepm=estepm;   
   }    /* We compute the life expectancy from trapezoids spaced every estepm months
   ungetc(c,ficpar);     * 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
   matcov=matrix(1,npar,1,npar);     * we are calculating an estimate of the Life Expectancy assuming a linear 
   for(i=1; i <=npar; i++){     * progression in between and thus overestimating or underestimating according
     fscanf(ficpar,"%s",&str);     * to the curvature of the survival function. If, for the same date, we 
     printf("%s",str);     * estimate the model with stepm=1 month, we can keep estepm to 24 months
     fprintf(ficparo,"%s",str);     * to compare the new estimate of Life expectancy with the same linear 
     for(j=1; j <=i; j++){     * hypothesis. A more precise result, taking into account a more precise
       fscanf(ficpar," %le",&matcov[i][j]);     * curvature will be obtained if estepm is as small as stepm. */
       printf(" %.5le",matcov[i][j]);  
       fprintf(ficparo," %.5le",matcov[i][j]);    /* 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. 
     fscanf(ficpar,"\n");       nhstepm is the number of hstepm from age to agelim 
     printf("\n");       nstepm is the number of stepm from age to agelin. 
     fprintf(ficparo,"\n");       Look at hpijx to understand the reason of that which relies in memory size
   }       and note for a fixed period like estepm months */
   for(i=1; i <=npar; i++)    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
     for(j=i+1;j<=npar;j++)       survival function given by stepm (the optimization length). Unfortunately it
       matcov[i][j]=matcov[j][i];       means that if the survival funtion is printed only each two years of age and if
           you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   printf("\n");       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 */ 
     /*-------- Rewriting paramater file ----------*/  
      strcpy(rfileres,"r");    /* "Rparameterfile */    /* If stepm=6 months */
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/    /* nhstepm age range expressed in number of stepm */
      strcat(rfileres,".");    /* */    agelim=AGESUP;
      strcat(rfileres,optionfilext);    /* Other files have txt extension */    nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
     if((ficres =fopen(rfileres,"w"))==NULL) {    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       printf("Problem writing new parameter file: %s\n", fileres);goto end;    /* if (stepm >= YEARM) hstepm=1;*/
     }    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     fprintf(ficres,"#%s\n",version);    
        p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     /*-------- data file ----------*/    p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     if((fic=fopen(datafile,"r"))==NULL)    {    gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
       printf("Problem with datafile: %s\n", datafile);goto end;    trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
     }    gp=matrix(0,nhstepm,1,nlstate*nlstate);
     gm=matrix(0,nhstepm,1,nlstate*nlstate);
     n= lastobs;  
     severity = vector(1,maxwav);    for (age=bage; age<=fage; age ++){ 
     outcome=imatrix(1,maxwav+1,1,n);      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
     num=ivector(1,n);      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     moisnais=vector(1,n);      /* if (stepm >= YEARM) hstepm=1;*/
     annais=vector(1,n);      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
     moisdc=vector(1,n);  
     andc=vector(1,n);      /* If stepm=6 months */
     agedc=vector(1,n);      /* Computed by stepm unit matrices, product of hstepma matrices, stored
     cod=ivector(1,n);         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
     weight=vector(1,n);      
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     mint=matrix(1,maxwav,1,n);  
     anint=matrix(1,maxwav,1,n);      /* Computing  Variances of health expectancies */
     s=imatrix(1,maxwav+1,1,n);      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
     adl=imatrix(1,maxwav+1,1,n);             decrease memory allocation */
     tab=ivector(1,NCOVMAX);      for(theta=1; theta <=npar; theta++){
     ncodemax=ivector(1,8);        for(i=1; i<=npar; i++){ 
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
     i=1;          xm[i] = x[i] - (i==theta ?delti[theta]:0);
     while (fgets(line, MAXLINE, fic) != NULL)    {        }
       if ((i >= firstobs) && (i <=lastobs)) {        hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
                hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
         for (j=maxwav;j>=1;j--){    
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);        for(j=1; j<= nlstate; j++){
           strcpy(line,stra);          for(i=1; i<=nlstate; i++){
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);            for(h=0; h<=nhstepm-1; h++){
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);              gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
         }              gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
                    }
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);          }
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);        }
        
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);        for(ij=1; ij<= nlstate*nlstate; ij++)
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);          for(h=0; h<=nhstepm-1; h++){
             gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);          }
         for (j=ncovcol;j>=1;j--){      }/* End theta */
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);      
         }      
         num[i]=atol(stra);      for(h=0; h<=nhstepm-1; h++)
                for(j=1; j<=nlstate*nlstate;j++)
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){          for(theta=1; theta <=npar; theta++)
           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;}*/            trgradg[h][j][theta]=gradg[h][theta][j];
       
         i=i+1;  
       }       for(ij=1;ij<=nlstate*nlstate;ij++)
     }        for(ji=1;ji<=nlstate*nlstate;ji++)
     /* printf("ii=%d", ij);          varhe[ij][ji][(int)age] =0.;
        scanf("%d",i);*/  
   imx=i-1; /* Number of individuals */       printf("%d|",(int)age);fflush(stdout);
        fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
   /* for (i=1; i<=imx; i++){       for(h=0;h<=nhstepm-1;h++){
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;        for(k=0;k<=nhstepm-1;k++){
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
     }*/          for(ij=1;ij<=nlstate*nlstate;ij++)
              for(ji=1;ji<=nlstate*nlstate;ji++)
   /* for (i=1; i<=imx; i++){              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
      if (s[4][i]==9)  s[4][i]=-1;        }
      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]));}      }
   */  
        /* Computing expectancies */
   /* Calculation of the number of parameter from char model*/      hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
   Tvar=ivector(1,15);      for(i=1; i<=nlstate;i++)
   Tprod=ivector(1,15);        for(j=1; j<=nlstate;j++)
   Tvaraff=ivector(1,15);          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
   Tvard=imatrix(1,15,1,2);            eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
   Tage=ivector(1,15);                  
                /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
   if (strlen(model) >1){  
     j=0, j1=0, k1=1, k2=1;          }
     j=nbocc(model,'+');  
     j1=nbocc(model,'*');      fprintf(ficresstdeij,"%3.0f",age );
     cptcovn=j+1;      for(i=1; i<=nlstate;i++){
     cptcovprod=j1;        eip=0.;
            vip=0.;
     strcpy(modelsav,model);        for(j=1; j<=nlstate;j++){
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){          eip += eij[i][j][(int)age];
       printf("Error. Non available option model=%s ",model);          for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
       goto end;            vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
     }          fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
            }
     for(i=(j+1); i>=1;i--){        fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
       cutv(stra,strb,modelsav,'+');      }
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);      fprintf(ficresstdeij,"\n");
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/  
       /*scanf("%d",i);*/      fprintf(ficrescveij,"%3.0f",age );
       if (strchr(strb,'*')) {      for(i=1; i<=nlstate;i++)
         cutv(strd,strc,strb,'*');        for(j=1; j<=nlstate;j++){
         if (strcmp(strc,"age")==0) {          cptj= (j-1)*nlstate+i;
           cptcovprod--;          for(i2=1; i2<=nlstate;i2++)
           cutv(strb,stre,strd,'V');            for(j2=1; j2<=nlstate;j2++){
           Tvar[i]=atoi(stre);              cptj2= (j2-1)*nlstate+i2;
           cptcovage++;              if(cptj2 <= cptj)
             Tage[cptcovage]=i;                fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
             /*printf("stre=%s ", stre);*/            }
         }        }
         else if (strcmp(strd,"age")==0) {      fprintf(ficrescveij,"\n");
           cptcovprod--;     
           cutv(strb,stre,strc,'V');    }
           Tvar[i]=atoi(stre);    free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
           cptcovage++;    free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
           Tage[cptcovage]=i;    free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
         }    free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
         else {    free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           cutv(strb,stre,strc,'V');    free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           Tvar[i]=ncovcol+k1;    printf("\n");
           cutv(strb,strc,strd,'V');    fprintf(ficlog,"\n");
           Tprod[k1]=i;  
           Tvard[k1][1]=atoi(strc);    free_vector(xm,1,npar);
           Tvard[k1][2]=atoi(stre);    free_vector(xp,1,npar);
           Tvar[cptcovn+k2]=Tvard[k1][1];    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
           Tvar[cptcovn+k2+1]=Tvard[k1][2];    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
           for (k=1; k<=lastobs;k++)    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];  }
           k1++;  
           k2=k2+2;  /************ Variance ******************/
         }  void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
       }  {
       else {    /* Variance of health expectancies */
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
        /*  scanf("%d",i);*/    /* double **newm;*/
       cutv(strd,strc,strb,'V');    double **dnewm,**doldm;
       Tvar[i]=atoi(strc);    double **dnewmp,**doldmp;
       }    int i, j, nhstepm, hstepm, h, nstepm ;
       strcpy(modelsav,stra);      int k, cptcode;
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);    double *xp;
         scanf("%d",i);*/    double **gp, **gm;  /* for var eij */
     }    double ***gradg, ***trgradg; /*for var eij */
 }    double **gradgp, **trgradgp; /* for var p point j */
      double *gpp, *gmp; /* for var p point j */
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
   printf("cptcovprod=%d ", cptcovprod);    double ***p3mat;
   scanf("%d ",i);*/    double age,agelim, hf;
     fclose(fic);    double ***mobaverage;
     int theta;
     /*  if(mle==1){*/    char digit[4];
     if (weightopt != 1) { /* Maximisation without weights*/    char digitp[25];
       for(i=1;i<=n;i++) weight[i]=1.0;  
     }    char fileresprobmorprev[FILENAMELENGTH];
     /*-calculation of age at interview from date of interview and age at death -*/  
     agev=matrix(1,maxwav,1,imx);    if(popbased==1){
       if(mobilav!=0)
     for (i=1; i<=imx; i++) {        strcpy(digitp,"-populbased-mobilav-");
       for(m=2; (m<= maxwav); m++) {      else strcpy(digitp,"-populbased-nomobil-");
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){    }
          anint[m][i]=9999;    else 
          s[m][i]=-1;      strcpy(digitp,"-stablbased-");
        }  
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;    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);
     for (i=1; i<=imx; i++)  {        printf(" Error in movingaverage mobilav=%d\n",mobilav);
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);      }
       for(m=1; (m<= maxwav); m++){    }
         if(s[m][i] >0){  
           if (s[m][i] >= nlstate+1) {    strcpy(fileresprobmorprev,"prmorprev"); 
             if(agedc[i]>0)    sprintf(digit,"%-d",ij);
               if(moisdc[i]!=99 && andc[i]!=9999)    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
                 agev[m][i]=agedc[i];    strcat(fileresprobmorprev,digit); /* Tvar to be done */
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
            else {    strcat(fileresprobmorprev,fileres);
               if (andc[i]!=9999){    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
               printf("Warning negative age at death: %d line:%d\n",num[i],i);      printf("Problem with resultfile: %s\n", fileresprobmorprev);
               agev[m][i]=-1;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
               }    }
             }    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
           }   
           else if(s[m][i] !=9){ /* Should no more exist */    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);    pstamp(ficresprobmorprev);
             if(mint[m][i]==99 || anint[m][i]==9999)    fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
               agev[m][i]=1;    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
             else if(agev[m][i] <agemin){    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
               agemin=agev[m][i];      fprintf(ficresprobmorprev," p.%-d SE",j);
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/      for(i=1; i<=nlstate;i++)
             }        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
             else if(agev[m][i] >agemax){    }  
               agemax=agev[m][i];    fprintf(ficresprobmorprev,"\n");
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/    fprintf(ficgp,"\n# Routine varevsij");
             }    /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
             /*agev[m][i]=anint[m][i]-annais[i];*/    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");
             /*   agev[m][i] = age[i]+2*m;*/    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
           }  /*   } */
           else { /* =9 */    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
             agev[m][i]=1;    pstamp(ficresvij);
             s[m][i]=-1;    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
           }    if(popbased==1)
         }      fprintf(ficresvij,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d\n",mobilav);
         else /*= 0 Unknown */    else
           agev[m][i]=1;      fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
       }    fprintf(ficresvij,"# Age");
        for(i=1; i<=nlstate;i++)
     }      for(j=1; j<=nlstate;j++)
     for (i=1; i<=imx; i++)  {        fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
       for(m=1; (m<= maxwav); m++){    fprintf(ficresvij,"\n");
         if (s[m][i] > (nlstate+ndeath)) {  
           printf("Error: Wrong value in nlstate or ndeath\n");      xp=vector(1,npar);
           goto end;    dnewm=matrix(1,nlstate,1,npar);
         }    doldm=matrix(1,nlstate,1,nlstate);
       }    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
     }    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
     gpp=vector(nlstate+1,nlstate+ndeath);
     free_vector(severity,1,maxwav);    gmp=vector(nlstate+1,nlstate+ndeath);
     free_imatrix(outcome,1,maxwav+1,1,n);    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     free_vector(moisnais,1,n);    
     free_vector(annais,1,n);    if(estepm < stepm){
     /* free_matrix(mint,1,maxwav,1,n);      printf ("Problem %d lower than %d\n",estepm, stepm);
        free_matrix(anint,1,maxwav,1,n);*/    }
     free_vector(moisdc,1,n);    else  hstepm=estepm;   
     free_vector(andc,1,n);    /* 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 
     wav=ivector(1,imx);       nstepm is the number of stepm from age to agelin. 
     dh=imatrix(1,lastpass-firstpass+1,1,imx);       Look at function hpijx to understand why (it is linked to memory size questions) */
     mw=imatrix(1,lastpass-firstpass+1,1,imx);    /* 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
     /* Concatenates waves */       means that if the survival funtion is printed every two years of age and if
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
        results. So we changed our mind and took the option of the best precision.
     */
       Tcode=ivector(1,100);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);    agelim = AGESUP;
       ncodemax[1]=1;    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
            nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
    codtab=imatrix(1,100,1,10);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
    h=0;      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
    m=pow(2,cptcoveff);      gp=matrix(0,nhstepm,1,nlstate);
        gm=matrix(0,nhstepm,1,nlstate);
    for(k=1;k<=cptcoveff; k++){  
      for(i=1; i <=(m/pow(2,k));i++){  
        for(j=1; j <= ncodemax[k]; j++){      for(theta=1; theta <=npar; theta++){
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
            h++;          xp[i] = x[i] + (i==theta ?delti[theta]:0);
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;        }
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
          }        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
        }  
      }        if (popbased==1) {
    }          if(mobilav ==0){
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);            for(i=1; i<=nlstate;i++)
       codtab[1][2]=1;codtab[2][2]=2; */              prlim[i][i]=probs[(int)age][i][ij];
    /* for(i=1; i <=m ;i++){          }else{ /* mobilav */ 
       for(k=1; k <=cptcovn; k++){            for(i=1; i<=nlstate;i++)
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);              prlim[i][i]=mobaverage[(int)age][i][ij];
       }          }
       printf("\n");        }
       }    
       scanf("%d",i);*/        for(j=1; j<= nlstate; j++){
              for(h=0; h<=nhstepm; h++){
    /* Calculates basic frequencies. Computes observed prevalence at single age            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
        and prints on file fileres'p'. */              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
            }
            /* This for computing probability of death (h=1 means
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */           computed over hstepm matrices product = hstepm*stepm months) 
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */           as a weighted average of prlim.
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        */
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        for(j=nlstate+1;j<=nlstate+ndeath;j++){
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */          for(i=1,gpp[j]=0.; i<= nlstate; i++)
                  gpp[j] += prlim[i][i]*p3mat[i][j][1];
     /* 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] */        /* end probability of death */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */  
         for(i=1; i<=npar; i++) /* Computes gradient x - delta */
     if(mle==1){          xp[i] = x[i] - (i==theta ?delti[theta]:0);
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     }        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
       
     /*--------- results files --------------*/        if (popbased==1) {
     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);          if(mobilav ==0){
              for(i=1; i<=nlstate;i++)
               prlim[i][i]=probs[(int)age][i][ij];
    jk=1;          }else{ /* mobilav */ 
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");            for(i=1; i<=nlstate;i++)
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");              prlim[i][i]=mobaverage[(int)age][i][ij];
    for(i=1,jk=1; i <=nlstate; i++){          }
      for(k=1; k <=(nlstate+ndeath); k++){        }
        if (k != i)  
          {        for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
            printf("%d%d ",i,k);          for(h=0; h<=nhstepm; h++){
            fprintf(ficres,"%1d%1d ",i,k);            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
            for(j=1; j <=ncovmodel; j++){              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
              printf("%f ",p[jk]);          }
              fprintf(ficres,"%f ",p[jk]);        }
              jk++;        /* This for computing probability of death (h=1 means
            }           computed over hstepm matrices product = hstepm*stepm months) 
            printf("\n");           as a weighted average of prlim.
            fprintf(ficres,"\n");        */
          }        for(j=nlstate+1;j<=nlstate+ndeath;j++){
      }          for(i=1,gmp[j]=0.; i<= nlstate; i++)
    }           gmp[j] += prlim[i][i]*p3mat[i][j][1];
  if(mle==1){        }    
     /* Computing hessian and covariance matrix */        /* end probability of death */
     ftolhess=ftol; /* Usually correct */  
     hesscov(matcov, p, npar, delti, ftolhess, func);        for(j=1; j<= nlstate; j++) /* vareij */
  }          for(h=0; h<=nhstepm; h++){
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
     printf("# Scales (for hessian or gradient estimation)\n");          }
      for(i=1,jk=1; i <=nlstate; i++){  
       for(j=1; j <=nlstate+ndeath; j++){        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
         if (j!=i) {          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
           fprintf(ficres,"%1d%1d",i,j);        }
           printf("%1d%1d",i,j);  
           for(k=1; k<=ncovmodel;k++){      } /* End theta */
             printf(" %.5e",delti[jk]);  
             fprintf(ficres," %.5e",delti[jk]);      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
             jk++;  
           }      for(h=0; h<=nhstepm; h++) /* veij */
           printf("\n");        for(j=1; j<=nlstate;j++)
           fprintf(ficres,"\n");          for(theta=1; theta <=npar; theta++)
         }            trgradg[h][j][theta]=gradg[h][theta][j];
       }  
      }      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
            for(theta=1; theta <=npar; theta++)
     k=1;          trgradgp[j][theta]=gradgp[theta][j];
     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");    
     printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");  
     for(i=1;i<=npar;i++){      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       /*  if (k>nlstate) k=1;      for(i=1;i<=nlstate;i++)
       i1=(i-1)/(ncovmodel*nlstate)+1;        for(j=1;j<=nlstate;j++)
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);          vareij[i][j][(int)age] =0.;
       printf("%s%d%d",alph[k],i1,tab[i]);*/  
       fprintf(ficres,"%3d",i);      for(h=0;h<=nhstepm;h++){
       printf("%3d",i);        for(k=0;k<=nhstepm;k++){
       for(j=1; j<=i;j++){          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
         fprintf(ficres," %.5e",matcov[i][j]);          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
         printf(" %.5e",matcov[i][j]);          for(i=1;i<=nlstate;i++)
       }            for(j=1;j<=nlstate;j++)
       fprintf(ficres,"\n");              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
       printf("\n");        }
       k++;      }
     }    
          /* pptj */
     while((c=getc(ficpar))=='#' && c!= EOF){      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
       ungetc(c,ficpar);      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
       fgets(line, MAXLINE, ficpar);      for(j=nlstate+1;j<=nlstate+ndeath;j++)
       puts(line);        for(i=nlstate+1;i<=nlstate+ndeath;i++)
       fputs(line,ficparo);          varppt[j][i]=doldmp[j][i];
     }      /* end ppptj */
     ungetc(c,ficpar);      /*  x centered again */
     estepm=0;      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
     if (estepm==0 || estepm < stepm) estepm=stepm;   
     if (fage <= 2) {      if (popbased==1) {
       bage = ageminpar;        if(mobilav ==0){
       fage = agemaxpar;          for(i=1; i<=nlstate;i++)
     }            prlim[i][i]=probs[(int)age][i][ij];
            }else{ /* mobilav */ 
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");          for(i=1; i<=nlstate;i++)
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);            prlim[i][i]=mobaverage[(int)age][i][ij];
     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);      /* This for computing probability of death (h=1 means
     fgets(line, MAXLINE, ficpar);         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
     puts(line);         as a weighted average of prlim.
     fputs(line,ficparo);      */
   }      for(j=nlstate+1;j<=nlstate+ndeath;j++){
   ungetc(c,ficpar);        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
            gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);      }    
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);      /* end probability of death */
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);  
            fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
   while((c=getc(ficpar))=='#' && c!= EOF){      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
     ungetc(c,ficpar);        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
     fgets(line, MAXLINE, ficpar);        for(i=1; i<=nlstate;i++){
     puts(line);          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
     fputs(line,ficparo);        }
   }      } 
   ungetc(c,ficpar);      fprintf(ficresprobmorprev,"\n");
    
       fprintf(ficresvij,"%.0f ",age );
    dateprev1=anprev1+mprev1/12.+jprev1/365.;      for(i=1; i<=nlstate;i++)
    dateprev2=anprev2+mprev2/12.+jprev2/365.;        for(j=1; j<=nlstate;j++){
           fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
   fscanf(ficpar,"pop_based=%d\n",&popbased);        }
   fprintf(ficparo,"pop_based=%d\n",popbased);        fprintf(ficresvij,"\n");
   fprintf(ficres,"pop_based=%d\n",popbased);        free_matrix(gp,0,nhstepm,1,nlstate);
        free_matrix(gm,0,nhstepm,1,nlstate);
   while((c=getc(ficpar))=='#' && c!= EOF){      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
     ungetc(c,ficpar);      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
     fgets(line, MAXLINE, ficpar);      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     puts(line);    } /* End age */
     fputs(line,ficparo);    free_vector(gpp,nlstate+1,nlstate+ndeath);
   }    free_vector(gmp,nlstate+1,nlstate+ndeath);
   ungetc(c,ficpar);    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
     free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
   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(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
 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);    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
 fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
   /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
   /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
 while((c=getc(ficpar))=='#' && c!= EOF){  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
     ungetc(c,ficpar);    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
     fgets(line, MAXLINE, ficpar);    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
     puts(line);    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
     fputs(line,ficparo);    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
   }    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
   ungetc(c,ficpar);    /*  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);
   */
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);  
     free_vector(xp,1,npar);
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    free_matrix(doldm,1,nlstate,1,nlstate);
     free_matrix(dnewm,1,nlstate,1,npar);
 /*------------ gnuplot -------------*/    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, ageminpar,agemaxpar,fage, pathc,p);    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
      free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
 /*------------ free_vector  -------------*/    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
  chdir(path);    fclose(ficresprobmorprev);
      fflush(ficgp);
  free_ivector(wav,1,imx);    fflush(fichtm); 
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);  }  /* end varevsij */
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);    
  free_ivector(num,1,n);  /************ Variance of prevlim ******************/
  free_vector(agedc,1,n);  void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, char strstart[])
  /*free_matrix(covar,1,NCOVMAX,1,n);*/  {
  fclose(ficparo);    /* Variance of prevalence limit */
  fclose(ficres);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
     double **newm;
 /*--------- index.htm --------*/    double **dnewm,**doldm;
     int i, j, nhstepm, hstepm;
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres,optionfilegnuplot,version,popforecast,estepm);    int k, cptcode;
     double *xp;
      double *gp, *gm;
   /*--------------- Prevalence limit --------------*/    double **gradg, **trgradg;
      double age,agelim;
   strcpy(filerespl,"pl");    int theta;
   strcat(filerespl,fileres);    
   if((ficrespl=fopen(filerespl,"w"))==NULL) {    pstamp(ficresvpl);
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;    fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
   }    fprintf(ficresvpl,"# Age");
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);    for(i=1; i<=nlstate;i++)
   fprintf(ficrespl,"#Prevalence limit\n");        fprintf(ficresvpl," %1d-%1d",i,i);
   fprintf(ficrespl,"#Age ");    fprintf(ficresvpl,"\n");
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);  
   fprintf(ficrespl,"\n");    xp=vector(1,npar);
      dnewm=matrix(1,nlstate,1,npar);
   prlim=matrix(1,nlstate,1,nlstate);    doldm=matrix(1,nlstate,1,nlstate);
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    hstepm=1*YEARM; /* Every year of age */
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    agelim = AGESUP;
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   k=0;      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
   agebase=ageminpar;      if (stepm >= YEARM) hstepm=1;
   agelim=agemaxpar;      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   ftolpl=1.e-10;      gradg=matrix(1,npar,1,nlstate);
   i1=cptcoveff;      gp=vector(1,nlstate);
   if (cptcovn < 1){i1=1;}      gm=vector(1,nlstate);
   
   for(cptcov=1;cptcov<=i1;cptcov++){      for(theta=1; theta <=npar; theta++){
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        for(i=1; i<=npar; i++){ /* Computes gradient */
         k=k+1;          xp[i] = x[i] + (i==theta ?delti[theta]:0);
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/        }
         fprintf(ficrespl,"\n#******");        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(j=1;j<=cptcoveff;j++)        for(i=1;i<=nlstate;i++)
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          gp[i] = prlim[i][i];
         fprintf(ficrespl,"******\n");      
                for(i=1; i<=npar; i++) /* Computes gradient */
         for (age=agebase; age<=agelim; age++){          xp[i] = x[i] - (i==theta ?delti[theta]:0);
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
           fprintf(ficrespl,"%.0f",age );        for(i=1;i<=nlstate;i++)
           for(i=1; i<=nlstate;i++)          gm[i] = prlim[i][i];
           fprintf(ficrespl," %.5f", prlim[i][i]);  
           fprintf(ficrespl,"\n");        for(i=1;i<=nlstate;i++)
         }          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
       }      } /* End theta */
     }  
   fclose(ficrespl);      trgradg =matrix(1,nlstate,1,npar);
   
   /*------------- h Pij x at various ages ------------*/      for(j=1; j<=nlstate;j++)
          for(theta=1; theta <=npar; theta++)
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);          trgradg[j][theta]=gradg[theta][j];
   if((ficrespij=fopen(filerespij,"w"))==NULL) {  
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;      for(i=1;i<=nlstate;i++)
   }        varpl[i][(int)age] =0.;
   printf("Computing pij: result on file '%s' \n", filerespij);      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
        matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
   stepsize=(int) (stepm+YEARM-1)/YEARM;      for(i=1;i<=nlstate;i++)
   /*if (stepm<=24) stepsize=2;*/        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   
   agelim=AGESUP;      fprintf(ficresvpl,"%.0f ",age );
   hstepm=stepsize*YEARM; /* Every year of age */      for(i=1; i<=nlstate;i++)
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
        fprintf(ficresvpl,"\n");
   k=0;      free_vector(gp,1,nlstate);
   for(cptcov=1;cptcov<=i1;cptcov++){      free_vector(gm,1,nlstate);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      free_matrix(gradg,1,npar,1,nlstate);
       k=k+1;      free_matrix(trgradg,1,nlstate,1,npar);
         fprintf(ficrespij,"\n#****** ");    } /* End age */
         for(j=1;j<=cptcoveff;j++)  
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    free_vector(xp,1,npar);
         fprintf(ficrespij,"******\n");    free_matrix(doldm,1,nlstate,1,npar);
            free_matrix(dnewm,1,nlstate,1,nlstate);
         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 */  
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  /************ Variance of one-step probabilities  ******************/
           oldm=oldms;savm=savms;  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[])
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);    {
           fprintf(ficrespij,"# Age");    int i, j=0,  i1, k1, l1, t, tj;
           for(i=1; i<=nlstate;i++)    int k2, l2, j1,  z1;
             for(j=1; j<=nlstate+ndeath;j++)    int k=0,l, cptcode;
               fprintf(ficrespij," %1d-%1d",i,j);    int first=1, first1;
           fprintf(ficrespij,"\n");    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
           for (h=0; h<=nhstepm; h++){    double **dnewm,**doldm;
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );    double *xp;
             for(i=1; i<=nlstate;i++)    double *gp, *gm;
               for(j=1; j<=nlstate+ndeath;j++)    double **gradg, **trgradg;
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);    double **mu;
             fprintf(ficrespij,"\n");    double age,agelim, cov[NCOVMAX];
           }    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    int theta;
           fprintf(ficrespij,"\n");    char fileresprob[FILENAMELENGTH];
         }    char fileresprobcov[FILENAMELENGTH];
     }    char fileresprobcor[FILENAMELENGTH];
   }  
     double ***varpij;
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/  
     strcpy(fileresprob,"prob"); 
   fclose(ficrespij);    strcat(fileresprob,fileres);
     if((ficresprob=fopen(fileresprob,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprob);
   /*---------- Forecasting ------------------*/      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
   if((stepm == 1) && (strcmp(model,".")==0)){    }
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);    strcpy(fileresprobcov,"probcov"); 
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);    strcat(fileresprobcov,fileres);
     free_matrix(mint,1,maxwav,1,n);    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);      printf("Problem with resultfile: %s\n", fileresprobcov);
     free_vector(weight,1,n);}      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
   else{    }
     erreur=108;    strcpy(fileresprobcor,"probcor"); 
     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);    strcat(fileresprobcor,fileres);
   }    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
        printf("Problem with resultfile: %s\n", fileresprobcor);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
   /*---------- Health expectancies and variances ------------*/    }
     printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
   strcpy(filerest,"t");    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
   strcat(filerest,fileres);    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
   if((ficrest=fopen(filerest,"w"))==NULL) {    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   }    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   printf("Computing Total LEs with variances: file '%s' \n", filerest);    pstamp(ficresprob);
     fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
     fprintf(ficresprob,"# Age");
   strcpy(filerese,"e");    pstamp(ficresprobcov);
   strcat(filerese,fileres);    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
   if((ficreseij=fopen(filerese,"w"))==NULL) {    fprintf(ficresprobcov,"# Age");
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);    pstamp(ficresprobcor);
   }    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);    fprintf(ficresprobcor,"# Age");
   
  strcpy(fileresv,"v");  
   strcat(fileresv,fileres);    for(i=1; i<=nlstate;i++)
   if((ficresvij=fopen(fileresv,"w"))==NULL) {      for(j=1; j<=(nlstate+ndeath);j++){
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
   }        fprintf(ficresprobcov," p%1d-%1d ",i,j);
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);        fprintf(ficresprobcor," p%1d-%1d ",i,j);
       }  
   k=0;   /* 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;   */
       fprintf(ficrest,"\n#****** ");   xp=vector(1,npar);
       for(j=1;j<=cptcoveff;j++)    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
       fprintf(ficrest,"******\n");    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
     varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
       fprintf(ficreseij,"\n#****** ");    first=1;
       for(j=1;j<=cptcoveff;j++)    fprintf(ficgp,"\n# Routine varprob");
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
       fprintf(ficreseij,"******\n");    fprintf(fichtm,"\n");
   
       fprintf(ficresvij,"\n#****** ");    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
       for(j=1;j<=cptcoveff;j++)    fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    file %s<br>\n",optionfilehtmcov);
       fprintf(ficresvij,"******\n");    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.\
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);   They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
       oldm=oldms;savm=savms;    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. \
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm);    It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);  would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
       oldm=oldms;savm=savms;  standard deviations wide on each axis. <br>\
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);   Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
       and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
   To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
    
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");    cov[1]=1;
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);    tj=cptcoveff;
       fprintf(ficrest,"\n");    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
     j1=0;
       epj=vector(1,nlstate+1);    for(t=1; t<=tj;t++){
       for(age=bage; age <=fage ;age++){      for(i1=1; i1<=ncodemax[t];i1++){ 
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);        j1++;
         if (popbased==1) {        if  (cptcovn>0) {
           for(i=1; i<=nlstate;i++)          fprintf(ficresprob, "\n#********** Variable "); 
             prlim[i][i]=probs[(int)age][i][k];          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         }          fprintf(ficresprob, "**********\n#\n");
                  fprintf(ficresprobcov, "\n#********** Variable "); 
         fprintf(ficrest," %4.0f",age);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){          fprintf(ficresprobcov, "**********\n#\n");
           for(i=1, epj[j]=0.;i <=nlstate;i++) {          
             epj[j] += prlim[i][i]*eij[i][j][(int)age];          fprintf(ficgp, "\n#********** Variable "); 
           }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           epj[nlstate+1] +=epj[j];          fprintf(ficgp, "**********\n#\n");
         }          
         for(i=1, vepp=0.;i <=nlstate;i++)          
           for(j=1;j <=nlstate;j++)          fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
             vepp += vareij[i][j][(int)age];          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         fprintf(ficrest," %7.2f (%7.2f)", epj[nlstate+1],sqrt(vepp));          fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
         for(j=1;j <=nlstate;j++){          
           fprintf(ficrest," %7.2f (%7.2f)", epj[j],sqrt(vareij[j][j][(int)age]));          fprintf(ficresprobcor, "\n#********** Variable ");    
         }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         fprintf(ficrest,"\n");          fprintf(ficresprobcor, "**********\n#");    
       }        }
     }        
   }        for (age=bage; age<=fage; age ++){ 
           cov[2]=age;
   fclose(ficreseij);          for (k=1; k<=cptcovn;k++) {
   fclose(ficresvij);            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
   fclose(ficrest);          }
   fclose(ficpar);          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   free_vector(epj,1,nlstate+1);          for (k=1; k<=cptcovprod;k++)
              cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   /*------- Variance limit prevalence------*/            
           gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
   strcpy(fileresvpl,"vpl");          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
   strcat(fileresvpl,fileres);          gp=vector(1,(nlstate)*(nlstate+ndeath));
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {          gm=vector(1,(nlstate)*(nlstate+ndeath));
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);      
     exit(0);          for(theta=1; theta <=npar; theta++){
   }            for(i=1; i<=npar; i++)
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
             
   k=0;            pmij(pmmij,cov,ncovmodel,xp,nlstate);
   for(cptcov=1;cptcov<=i1;cptcov++){            
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){            k=0;
       k=k+1;            for(i=1; i<= (nlstate); i++){
       fprintf(ficresvpl,"\n#****** ");              for(j=1; j<=(nlstate+ndeath);j++){
       for(j=1;j<=cptcoveff;j++)                k=k+1;
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                gp[k]=pmmij[i][j];
       fprintf(ficresvpl,"******\n");              }
                  }
       varpl=matrix(1,nlstate,(int) bage, (int) fage);            
       oldm=oldms;savm=savms;            for(i=1; i<=npar; i++)
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
     }      
  }            pmij(pmmij,cov,ncovmodel,xp,nlstate);
             k=0;
   fclose(ficresvpl);            for(i=1; i<=(nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
   /*---------- End : free ----------------*/                k=k+1;
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);                gm[k]=pmmij[i][j];
                }
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);            }
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);       
              for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
                gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
   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);          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);            for(theta=1; theta <=npar; theta++)
                trgradg[j][theta]=gradg[theta][j];
   free_matrix(matcov,1,npar,1,npar);          
   free_vector(delti,1,npar);          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
   free_matrix(agev,1,maxwav,1,imx);          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
           free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
   if(erreur >0)          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
     printf("End of Imach with error or warning %d\n",erreur);          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   else   printf("End of Imach\n");  
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */          pmij(pmmij,cov,ncovmodel,x,nlstate);
            
   /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/          k=0;
   /*printf("Total time was %d uSec.\n", total_usecs);*/          for(i=1; i<=(nlstate); i++){
   /*------ End -----------*/            for(j=1; j<=(nlstate+ndeath);j++){
               k=k+1;
               mu[k][(int) age]=pmmij[i][j];
  end:            }
 #ifdef windows          }
   /* chdir(pathcd);*/          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
 #endif            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
  /*system("wgnuplot graph.plt");*/              varpij[i][j][(int)age] = doldm[i][j];
  /*system("../gp37mgw/wgnuplot graph.plt");*/  
  /*system("cd ../gp37mgw");*/          /*printf("\n%d ",(int)age);
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
  strcpy(plotcmd,GNUPLOTPROGRAM);            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
  strcat(plotcmd," ");            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
  strcat(plotcmd,optionfilegnuplot);            }*/
  system(plotcmd);  
           fprintf(ficresprob,"\n%d ",(int)age);
 #ifdef windows          fprintf(ficresprobcov,"\n%d ",(int)age);
   while (z[0] != 'q') {          fprintf(ficresprobcor,"\n%d ",(int)age);
     /* chdir(path); */  
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
     scanf("%s",z);            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
     if (z[0] == 'c') system("./imach");          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
     else if (z[0] == 'e') system(optionfilehtm);            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
     else if (z[0] == 'g') system(plotcmd);            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
     else if (z[0] == 'q') exit(0);          }
   }          i=0;
 #endif          for (k=1; k<=(nlstate);k++){
 }            for (l=1; l<=(nlstate+ndeath);l++){ 
               i=i++;
               fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
               fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
               for (j=1; j<=i;j++){
                 fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
                 fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
               }
             }
           }/* end of loop for state */
         } /* end of loop for age */
   
         /* Confidence intervalle of pij  */
         /*
           fprintf(ficgp,"\nset noparametric;unset label");
           fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
           fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
           fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
           fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
           fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
           fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
         */
   
         /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
         first1=1;
         for (k2=1; k2<=(nlstate);k2++){
           for (l2=1; l2<=(nlstate+ndeath);l2++){ 
             if(l2==k2) continue;
             j=(k2-1)*(nlstate+ndeath)+l2;
             for (k1=1; k1<=(nlstate);k1++){
               for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                 if(l1==k1) continue;
                 i=(k1-1)*(nlstate+ndeath)+l1;
                 if(i<=j) continue;
                 for (age=bage; age<=fage; age ++){ 
                   if ((int)age %5==0){
                     v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                     v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     mu1=mu[i][(int) age]/stepm*YEARM ;
                     mu2=mu[j][(int) age]/stepm*YEARM;
                     c12=cv12/sqrt(v1*v2);
                     /* Computing eigen value of matrix of covariance */
                     lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     /* Eigen vectors */
                     v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                     /*v21=sqrt(1.-v11*v11); *//* error */
                     v21=(lc1-v1)/cv12*v11;
                     v12=-v21;
                     v22=v11;
                     tnalp=v21/v11;
                     if(first1==1){
                       first1=0;
                       printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     }
                     fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     /*printf(fignu*/
                     /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                     /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                     if(first==1){
                       first=0;
                       fprintf(ficgp,"\nset parametric;unset label");
                       fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
                       fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
                       fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
    :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
   %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }else{
                       first=0;
                       fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }/* if first */
                   } /* age mod 5 */
                 } /* end loop age */
                 fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                 first=1;
               } /*l12 */
             } /* k12 */
           } /*l1 */
         }/* k1 */
       } /* loop covariates */
     }
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
     free_vector(xp,1,npar);
     fclose(ficresprob);
     fclose(ficresprobcov);
     fclose(ficresprobcor);
     fflush(ficgp);
     fflush(fichtmcov);
   }
   
   
   /******************* Printing html file ***********/
   void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                     int popforecast, int estepm ,\
                     double jprev1, double mprev1,double anprev1, \
                     double jprev2, double mprev2,double anprev2){
     int jj1, k1, i1, cpt;
   
      fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
      <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
   </ul>");
      fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
    - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
              jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
      fprintf(fichtm,"\
    - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
              stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
      fprintf(fichtm,"\
    - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
              subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
      fprintf(fichtm,"\
    - (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n",
              estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
      fprintf(fichtm,"\
    - Population projections by age and states: \
      <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
   
   fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
    m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        /* Pij */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d1.png\">%s%d1.png</a><br> \
   <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
        /* Quasi-incidences */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
    before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d2.png\">%s%d2.png</a><br> \
   <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
          /* Period (stable) prevalence in each health state */
          for(cpt=1; cpt<nlstate;cpt++){
            fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
   <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
          }
        for(cpt=1; cpt<=nlstate;cpt++) {
           fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
   <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
        }
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
   
   
    fprintf(fichtm,"\
   \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
    - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
   
    fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
    fprintf(fichtm,"\
    - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
   
    fprintf(fichtm,"\
    - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
    fprintf(fichtm,"\
    - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
            estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
    fprintf(fichtm,"\
    - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",
            estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
    fprintf(fichtm,"\
    - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
            subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   
   /*  if(popforecast==1) fprintf(fichtm,"\n */
   /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
   /*      <br>",fileres,fileres,fileres,fileres); */
   /*  else  */
   /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
    fflush(fichtm);
    fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   
    m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        for(cpt=1; cpt<=nlstate;cpt++) {
          fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
   prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
   <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
        }
        fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
   true period expectancies (those weighted with period prevalences are also\
    drawn in addition to the population based expectancies computed using\
    observed and cahotic prevalences: %s%d.png<br>\
   <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
    fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m0,cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
     int ng=0;
   /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   /*     printf("Problem with file %s",optionfilegnuplot); */
   /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   /*   } */
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
     m=pow(2,cptcoveff);
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
    /* 1eme*/
     for (cpt=1; cpt<= nlstate ; cpt ++) {
      for (k1=1; k1<= m ; k1 ++) {
        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
        fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
        fprintf(ficgp,"set xlabel \"Age\" \n\
   set ylabel \"Probability\" \n\
   set ter png small\n\
   set size 0.65,0.65\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }
        fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        } 
        fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }  
        fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
      }
     }
     /*2 eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
       fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
       
       for (i=1; i<= nlstate+1 ; i ++) {
         k=2*i;
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         fprintf(ficgp,"\" t\"\" w l 0,");
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
         else fprintf(ficgp,"\" t\"\" w l 0,");
       }
     }
     
     /*3eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<= nlstate ; cpt ++) {
         /*       k=2+nlstate*(2*cpt-2); */
         k=2+(nlstate+1)*(cpt-1);
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
         fprintf(ficgp,"set ter png small\n\
   set size 0.65,0.65\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           
         */
         for (i=1; i< nlstate ; i ++) {
           fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1);
           /*      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
           
         } 
         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
       }
     }
     
     /* CV preval stable (period) */
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<=nlstate ; cpt ++) {
         k=3;
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   set ter png small\nset size 0.65,0.65\n\
   unset log y\n\
   plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
         
         for (i=1; i< nlstate ; i ++)
           fprintf(ficgp,"+$%d",k+i+1);
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
         
         l=3+(nlstate+ndeath)*cpt;
         fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
         for (i=1; i< nlstate ; i ++) {
           l=3+(nlstate+ndeath)*cpt;
           fprintf(ficgp,"+$%d",l+i+1);
         }
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
       } 
     }  
     
     /* proba elementaires */
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             jk++; 
             fprintf(ficgp,"\n");
           }
         }
       }
      }
   
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        for(jk=1; jk <=m; jk++) {
          fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
          if (ng==2)
            fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
          else
            fprintf(ficgp,"\nset title \"Probability\"\n");
          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
          for(k2=1; k2<=nlstate; k2++) {
            k3=i;
            for(k=1; k<=(nlstate+ndeath); k++) {
              if (k != k2){
                if(ng==2)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                else
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;
                for(j=3; j <=ncovmodel; j++) {
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                    fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                    ij++;
                  }
                  else
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
                fprintf(ficgp,")/(1");
                
                for(k1=1; k1 <=nlstate; k1++){   
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
                  for(j=3; j <=ncovmodel; j++){
                    if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                      fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                      ij++;
                    }
                    else
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                  }
                  fprintf(ficgp,")");
                }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
              }
            } /* end k */
          } /* end k2 */
        } /* end jk */
      } /* end ng */
      fflush(ficgp); 
   }  /* end gnuplot */
   
   
   /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
     int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
     double age;
   
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          we use a 5 terms etc. until the borders are no more concerned. 
       */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
           }
         }/* end age */
       }/* end mob */
     }else return -1;
     return 0;
   }/* End movingaverage */
   
   
   /************** Forecasting ******************/
   prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
     int *popage;
     double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   
   
   /**************** function prwizard **********************/
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     /* Wizard to print covariance matrix template */
   
     char ca[32], cb[32], cc[32];
     int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
   } /* end of prwizard */
   /******************* Gompertz Likelihood ******************************/
   double gompertz(double x[])
   { 
     double A,B,L=0.0,sump=0.,num=0.;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
   
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
                +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           L=L+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
    
     return -2*L*num/sump;
   }
   
   /******************* Printing html file ***********/
   void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,  double p[],double **matcov,double agemortsup){
     int i,k;
   
     fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
     fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
     for (i=1;i<=2;i++) 
       fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
     fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
     fprintf(fichtm,"</ul>");
   
   fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
   
    fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
   
    for (k=agegomp;k<(agemortsup-2);k++) 
      fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
   
    
     fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
     fprintf(ficgp,"set out \"graphmort.png\"\n "); 
     fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
     fprintf(ficgp, "set ter png small\n set log y\n"); 
     fprintf(ficgp, "set size 0.65,0.65\n");
     fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
   
   } 
   
   
   
   
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
     int linei, month, year,iout;
     int jj, ll, li, lj, lk, imk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int itimes;
     int NDIM=2;
     int vpopbased=0;
   
     char ca[32], cb[32], cc[32];
     char dummy[]="                         ";
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     struct stat info;
     double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE], pathimach[MAXLINE]; 
     char **bp, *tok, *val; /* pathtot */
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     int agemortsup;
     float  sumlpop=0.;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double *severity;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
     double **ximort;
     char *alph[]={"a","a","b","c","d","e"}, str[4];
     int *dcwave;
   
     char z[1]="c", occ;
   
     char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
     char  *strt, strtend[80];
     char *stratrunc;
     int lstra;
   
     long total_usecs;
    
   /*   setlocale (LC_ALL, ""); */
   /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   /*   textdomain (PACKAGE); */
   /*   setlocale (LC_CTYPE, ""); */
   /*   setlocale (LC_MESSAGES, ""); */
   
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     (void) gettimeofday(&start_time,&tzp);
     curr_time=start_time;
     tm = *localtime(&start_time.tv_sec);
     tmg = *gmtime(&start_time.tv_sec);
     strcpy(strstart,asctime(&tm));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tv_sec = tp.tv_sec +86400; */
   /*  tm = *localtime(&start_time.tv_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tv_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     nberr=0; /* Number of errors and warnings */
     nbwarn=0;
     getcwd(pathcd, size);
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       fgets(pathr,FILENAMELENGTH,stdin);
       i=strlen(pathr);
       if(pathr[i-1]=='\n')
         pathr[i-1]='\0';
      for (tok = pathr; tok != NULL; ){
         printf("Pathr |%s|\n",pathr);
         while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
         printf("val= |%s| pathr=%s\n",val,pathr);
         strcpy (pathtot, val);
         if(pathr[0] == '\0') break; /* Dirty */
       }
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     /* Split argv[0], imach program to get pathimach */
     printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
     split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
     printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
    /*   strcpy(pathimach,argv[0]); */
     /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path); /* Can be a relative path */
     if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
       printf("Current directory %s!\n",pathcd);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s\n%s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: \n");
     fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     printf("Local time (at start):%s",strstart);
     fprintf(ficlog,"Local time (at start): %s",strstart);
     fflush(ficlog);
   /*   (void) gettimeofday(&curr_time,&tzp); */
   /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile %s\n",optionfile);
       fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       fflush(ficlog);
       goto end;
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n); 
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
     if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
   
     ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
   
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     delti=delti3[1][1];
     /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
     if(mle==-1){ /* Print a wizard for help writing covariance matrix */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       fclose (ficparo);
       fclose (ficlog);
       goto end;
       exit(0);
     }
     else if(mle==-3) {
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       matcov=matrix(1,npar,1,npar);
     }
     else{
       /* Read guess parameters */
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
       
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       for(i=1; i <=nlstate; i++){
         j=0;
         for(jj=1; jj <=nlstate+ndeath; jj++){
           if(jj==i) continue;
           j++;
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1 != i) && (j1 != j)){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
   It might be a problem of design; if ncovcol and the model are correct\n \
   run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           fprintf(ficparo,"%1d%1d",i1,j1);
           if(mle==1)
             printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar," %lf",&param[i][j][k]);
             if(mle==1){
               printf(" %lf",param[i][j][k]);
               fprintf(ficlog," %lf",param[i][j][k]);
             }
             else
               fprintf(ficlog," %lf",param[i][j][k]);
             fprintf(ficparo," %lf",param[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           if(mle==1)
             printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficparo,"\n");
         }
       }  
       fflush(ficlog);
   
       p=param[1][1];
       
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
   
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath-1; j++){
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1-i)*(j1-j)!=0){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           printf("%1d%1d",i,j);
           fprintf(ficparo,"%1d%1d",i1,j1);
           fprintf(ficlog,"%1d%1d",i1,j1);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar,"%le",&delti3[i][j][k]);
             printf(" %le",delti3[i][j][k]);
             fprintf(ficparo," %le",delti3[i][j][k]);
             fprintf(ficlog," %le",delti3[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           printf("\n");
           fprintf(ficparo,"\n");
           fprintf(ficlog,"\n");
         }
       }
       fflush(ficlog);
   
       delti=delti3[1][1];
   
   
       /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
     
       matcov=matrix(1,npar,1,npar);
       for(i=1; i <=npar; i++){
         fscanf(ficpar,"%s",&str);
         if(mle==1)
           printf("%s",str);
         fprintf(ficlog,"%s",str);
         fprintf(ficparo,"%s",str);
         for(j=1; j <=i; j++){
           fscanf(ficpar," %le",&matcov[i][j]);
           if(mle==1){
             printf(" %.5le",matcov[i][j]);
           }
           fprintf(ficlog," %.5le",matcov[i][j]);
           fprintf(ficparo," %.5le",matcov[i][j]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
       for(i=1; i <=npar; i++)
         for(j=i+1;j<=npar;j++)
           matcov[i][j]=matcov[j][i];
       
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       
       fflush(ficlog);
       
       /*-------- Rewriting parameter file ----------*/
       strcpy(rfileres,"r");    /* "Rparameterfile */
       strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
       strcat(rfileres,".");    /* */
       strcat(rfileres,optionfilext);    /* Other files have txt extension */
       if((ficres =fopen(rfileres,"w"))==NULL) {
         printf("Problem writing new parameter file: %s\n", fileres);goto end;
         fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
       }
       fprintf(ficres,"#%s\n",version);
     }    /* End of mle != -3 */
   
     /*-------- data file ----------*/
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem while opening datafile: %s\n", datafile);goto end;
       fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);goto end;
     }
   
     n= lastobs;
     severity = vector(1,maxwav);
     outcome=imatrix(1,maxwav+1,1,n);
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n);
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,8);
   
     i=1;
     linei=0;
     while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
       linei=linei+1;
       for(j=strlen(line); j>=0;j--){  /* Untabifies line */
         if(line[j] == '\t')
           line[j] = ' ';
       }
       for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
         ;
       };
       line[j+1]=0;  /* Trims blanks at end of line */
       if(line[0]=='#'){
         fprintf(ficlog,"Comment line\n%s\n",line);
         printf("Comment line\n%s\n",line);
         continue;
       }
   
       for (j=maxwav;j>=1;j--){
         cutv(stra, strb,line,' '); 
         errno=0;
         lval=strtol(strb,&endptr,10); 
         /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
         if( strb[0]=='\0' || (*endptr != '\0')){
           printf("Error reading data around '%d' at line number %d %s for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
           exit(1);
         }
         s[j][i]=lval;
         
         strcpy(line,stra);
         cutv(stra, strb,line,' ');
         if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
         }
         else  if(iout=sscanf(strb,"%s.") != 0){
           month=99;
           year=9999;
         }else{
           printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
           exit(1);
         }
         anint[j][i]= (double) year; 
         mint[j][i]= (double)month; 
         strcpy(line,stra);
       } /* ENd Waves */
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.",dummy) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
         exit(1);
       }
       andc[i]=(double) year; 
       moisdc[i]=(double) month; 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.") != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line,j);
         exit(1);
       }
       annais[i]=(double)(year);
       moisnais[i]=(double)(month); 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       errno=0;
       dval=strtod(strb,&endptr); 
       if( strb[0]=='\0' || (*endptr != '\0')){
         printf("Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         exit(1);
       }
       weight[i]=dval; 
       strcpy(line,stra);
       
       for (j=ncovcol;j>=1;j--){
         cutv(stra, strb,line,' '); 
         errno=0;
         lval=strtol(strb,&endptr,10); 
         if( strb[0]=='\0' || (*endptr != '\0')){
           printf("Error reading data around '%d' at line number %ld %s for individual %d, '%s'\nShould be a covar (meaning 0 for the reference or 1).  Exiting.\n",lval, linei,i, line);
           exit(1);
         }
         if(lval <-1 || lval >1){
           printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);
           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(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
     Tprod=ivector(1,15); 
     Tvaraff=ivector(1,15); 
     Tvard=imatrix(1,15,1,2);
     Tage=ivector(1,15);      
      
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=1, k2=1;
       j=nbocc(model,'+'); /* j=Number of '+' */
       j1=nbocc(model,'*'); /* j1=Number of '*' */
       cptcovn=j+1; /* 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);
         goto end;
       }
       
       /* This loop fills the array Tvar from the string 'model'.*/
       /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
       for(i=(j+1); i>=1;i--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' 
                                        modelsav=V2+V3*age+V1+V4 strb=V3*age+V1+V4 
                                        stra=V2
                                       */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /* Model includes a product V1+V3*age+V2 strb=V3*age*/
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn: V3*age strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
           if (strcmp(strc,"age")==0) { /* Vn*age */
             cptcovprod--;
             cutv(strb,stre,strd,'V');
             Tvar[i]=atoi(stre);  /* V1+V3*age+V2 Tvar[2]=3 */
             cptcovage++; /* Sum the number of covariates including ages as a product */
             Tage[cptcovage]=i;  /* Tage[1] =2 */
             /*printf("stre=%s ", stre);*/
           }
           else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutv(strb,stre,strc,'V');
             Tvar[i]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=i;
           }
           else {  /* Age is not in the model V1+V3*V2+V2  strb=V3*V2*/
             cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
             Tvar[i]=ncovcol+k1;  /* find 'n' in Vn and stores in Tvar. 
                                     If already ncovcol=2 and model=V2*V1 Tvar[1]=2+1 and Tvar[2]=2+2 etc */
             cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=i;  /* Tprod[1]  */
             Tvard[k1][1]=atoi(strc); /* m*/
             Tvard[k1][2]=atoi(stre); /* n */
             Tvar[cptcovn+k2]=Tvard[k1][1];
             Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
             for (k=1; k<=lastobs;k++) 
               covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
             k1++;
             k2=k2+2;
           }
         }
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
         cutv(strd,strc,strb,'V');
         Tvar[i]=atoi(strc);
         }
         strcpy(modelsav,stra);  /* modelsav=V2+V3*age+V1+V4 strb=V3*age+V1+V4 */ 
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);*/
   
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights*/
       for(i=1;i<=n;i++) weight[i]=1.0;
     }
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           nberr++;
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           nberr++;
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if ((int)andc[i]!=9999){
                   nbwarn++;
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] <agemin){ 
               agemin=agev[m][i];
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
             }
             else if(agev[m][i] >agemax){
               agemax=agev[m][i];
               /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           nberr++;
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           goto end;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
   
     agegomp=(int)agemin;
     free_vector(severity,1,maxwav);
     free_imatrix(outcome,1,maxwav+1,1,n);
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
   
      
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     Tcode=ivector(1,100);
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     if (cptcovn > 0) tricode(Tvar,nbcode,imx);
         
     codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
                                    the estimations*/
     h=0;
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){
       for(i=1; i <=(m/pow(2,k));i++){
         for(j=1; j <= ncodemax[k]; j++){
           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
             h++;
             if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
             printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d 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 */
     
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       globpr=1; /* to print the contributions */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       if(mle>=1){ /* Could be 1 or 2 */
         mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
       }
       
       /*--------- results files --------------*/
       fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
       
       
       fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(k=1; k <=(nlstate+ndeath); k++){
           if (k != i) {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%lf ",p[jk]);
               fprintf(ficlog,"%lf ",p[jk]);
               fprintf(ficres,"%lf ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       if(mle!=0){
         /* Computing hessian and covariance matrix */
         ftolhess=ftol; /* Usually correct */
         hesscov(matcov, p, npar, delti, ftolhess, func);
       }
       fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
       printf("# Scales (for hessian or gradient estimation)\n");
       fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if (j!=i) {
             fprintf(ficres,"%1d%1d",i,j);
             printf("%1d%1d",i,j);
             fprintf(ficlog,"%1d%1d",i,j);
             for(k=1; k<=ncovmodel;k++){
               printf(" %.5e",delti[jk]);
               fprintf(ficlog," %.5e",delti[jk]);
               fprintf(ficres," %.5e",delti[jk]);
               jk++;
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       
       fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       if(mle>=1)
         printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       /* # 121 Var(a12)\n\ */
       /* # 122 Cov(b12,a12) Var(b12)\n\ */
       /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
       /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
       /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
       /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
       /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
       /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
       
       
       /* Just to have a covariance matrix which will be more understandable
          even is we still don't want to manage dictionary of variables
       */
       for(itimes=1;itimes<=2;itimes++){
         jj=0;
         for(i=1; i <=nlstate; i++){
           for(j=1; j <=nlstate+ndeath; j++){
             if(j==i) continue;
             for(k=1; k<=ncovmodel;k++){
               jj++;
               ca[0]= k+'a'-1;ca[1]='\0';
               if(itimes==1){
                 if(mle>=1)
                   printf("#%1d%1d%d",i,j,k);
                 fprintf(ficlog,"#%1d%1d%d",i,j,k);
                 fprintf(ficres,"#%1d%1d%d",i,j,k);
               }else{
                 if(mle>=1)
                   printf("%1d%1d%d",i,j,k);
                 fprintf(ficlog,"%1d%1d%d",i,j,k);
                 fprintf(ficres,"%1d%1d%d",i,j,k);
               }
               ll=0;
               for(li=1;li <=nlstate; li++){
                 for(lj=1;lj <=nlstate+ndeath; lj++){
                   if(lj==li) continue;
                   for(lk=1;lk<=ncovmodel;lk++){
                     ll++;
                     if(ll<=jj){
                       cb[0]= lk +'a'-1;cb[1]='\0';
                       if(ll<jj){
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }else{
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }
                     }
                   } /* end lk */
                 } /* end lj */
               } /* end li */
               if(mle>=1)
                 printf("\n");
               fprintf(ficlog,"\n");
               fprintf(ficres,"\n");
               numlinepar++;
             } /* end k*/
           } /*end j */
         } /* end i */
       } /* end itimes */
       
       fflush(ficlog);
       fflush(ficres);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       estepm=0;
       fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
       if (estepm==0 || estepm < stepm) estepm=stepm;
       if (fage <= 2) {
         bage = ageminpar;
         fage = agemaxpar;
       }
       
       fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
       fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
       fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       
       dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
       dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
       
       fscanf(ficpar,"pop_based=%d\n",&popbased);
       fprintf(ficparo,"pop_based=%d\n",popbased);   
       fprintf(ficres,"pop_based=%d\n",popbased);   
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
       fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       /* day and month of proj2 are not used but only year anproj2.*/
       
       
       
       /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
       /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                    model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                    jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
         
      /*------------ free_vector  -------------*/
      /*  chdir(path); */
    
       free_ivector(wav,1,imx);
       free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
       free_lvector(num,1,n);
       free_vector(agedc,1,n);
       /*free_matrix(covar,0,NCOVMAX,1,n);*/
       /*free_matrix(covar,1,NCOVMAX,1,n);*/
       fclose(ficparo);
       fclose(ficres);
   
   
       /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
     
       strcpy(filerespl,"pl");
       strcat(filerespl,fileres);
       if((ficrespl=fopen(filerespl,"w"))==NULL) {
         printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
         fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
       }
       printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
       fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
       pstamp(ficrespl);
       fprintf(ficrespl,"# Period (stable) prevalence \n");
       fprintf(ficrespl,"#Age ");
       for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
       fprintf(ficrespl,"\n");
     
       prlim=matrix(1,nlstate,1,nlstate);
   
       agebase=ageminpar;
       agelim=agemaxpar;
       ftolpl=1.e-10;
       i1=cptcoveff;
       if (cptcovn < 1){i1=1;}
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
           fprintf(ficrespl,"\n#******");
           printf("\n#******");
           fprintf(ficlog,"\n#******");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficrespl,"******\n");
           printf("******\n");
           fprintf(ficlog,"******\n");
           
           for (age=agebase; age<=agelim; age++){
             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
             fprintf(ficrespl,"%.0f ",age );
             for(j=1;j<=cptcoveff;j++)
               fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             for(i=1; i<=nlstate;i++)
               fprintf(ficrespl," %.5f", prlim[i][i]);
             fprintf(ficrespl,"\n");
           }
         }
       }
       fclose(ficrespl);
   
       /*------------- h Pij x at various ages ------------*/
     
       strcpy(filerespij,"pij");  strcat(filerespij,fileres);
       if((ficrespij=fopen(filerespij,"w"))==NULL) {
         printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
         fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
       }
       printf("Computing pij: result on file '%s' \n", filerespij);
       fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
       stepsize=(int) (stepm+YEARM-1)/YEARM;
       /*if (stepm<=24) stepsize=2;*/
   
       agelim=AGESUP;
       hstepm=stepsize*YEARM; /* Every year of age */
       hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
       /* hstepm=1;   aff par mois*/
       pstamp(ficrespij);
       fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           fprintf(ficrespij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrespij,"******\n");
           
           for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
             nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   
             /*      nhstepm=nhstepm*YEARM; aff par mois*/
   
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %1d-%1d",i,j);
             fprintf(ficrespij,"\n");
             for (h=0; h<=nhstepm; h++){
               fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
               for(i=1; i<=nlstate;i++)
                 for(j=1; j<=nlstate+ndeath;j++)
                   fprintf(ficrespij," %.5f", p3mat[i][j][h]);
               fprintf(ficrespij,"\n");
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             fprintf(ficrespij,"\n");
           }
         }
       }
   
       varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
   
       fclose(ficrespij);
   
       probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for(i=1;i<=AGESUP;i++)
         for(j=1;j<=NCOVMAX;j++)
           for(k=1;k<=NCOVMAX;k++)
             probs[i][j][k]=0.;
   
       /*---------- Forecasting ------------------*/
       /*if((stepm == 1) && (strcmp(model,".")==0)){*/
       if(prevfcast==1){
         /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
         /*      }  */
         /*      else{ */
         /*        erreur=108; */
         /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*      } */
       }
     
   
       /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
   
       prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
       /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
           ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
       */
   
       if (mobilav!=0) {
         mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
           fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
           printf(" Error in movingaverage mobilav=%d\n",mobilav);
         }
       }
   
   
       /*---------- Health expectancies, no variances ------------*/
   
       strcpy(filerese,"e");
       strcat(filerese,fileres);
       if((ficreseij=fopen(filerese,"w"))==NULL) {
         printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
         fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       }
       printf("Computing Health Expectancies: result on file '%s' \n", filerese);
       fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1; 
           fprintf(ficreseij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficreseij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);  
         
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         }
       }
       fclose(ficreseij);
   
   
       /*---------- Health expectancies and variances ------------*/
   
   
       strcpy(filerest,"t");
       strcat(filerest,fileres);
       if((ficrest=fopen(filerest,"w"))==NULL) {
         printf("Problem with total LE resultfile: %s\n", filerest);goto end;
         fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
       }
       printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
       fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
   
   
       strcpy(fileresstde,"stde");
       strcat(fileresstde,fileres);
       if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
         printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
         fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
       }
       printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
       fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
   
       strcpy(filerescve,"cve");
       strcat(filerescve,fileres);
       if((ficrescveij=fopen(filerescve,"w"))==NULL) {
         printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
         fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
       }
       printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
       fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
   
       strcpy(fileresv,"v");
       strcat(fileresv,fileres);
       if((ficresvij=fopen(fileresv,"w"))==NULL) {
         printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
         fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
       }
       printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
       fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1; 
           fprintf(ficrest,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrest,"******\n");
   
           fprintf(ficresstdeij,"\n#****** ");
           fprintf(ficrescveij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficresstdeij,"******\n");
           fprintf(ficrescveij,"******\n");
   
           fprintf(ficresvij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);  
    
           vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           pstamp(ficrest);
           for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
             oldm=oldms;savm=savms;
             varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart);   fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");
             if(vpopbased==1)
               fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
             else
               fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
             fprintf(ficrest,"# Age e.. (std) ");
             for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
             fprintf(ficrest,"\n");
   
             epj=vector(1,nlstate+1);
             for(age=bage; age <=fage ;age++){
               prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
               if (vpopbased==1) {
                 if(mobilav ==0){
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=probs[(int)age][i][k];
                 }else{ /* mobilav */ 
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=mobaverage[(int)age][i][k];
                 }
               }
           
               fprintf(ficrest," %4.0f",age);
               for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
                 for(i=1, epj[j]=0.;i <=nlstate;i++) {
                   epj[j] += prlim[i][i]*eij[i][j][(int)age];
                   /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
                 }
                 epj[nlstate+1] +=epj[j];
               }
   
               for(i=1, vepp=0.;i <=nlstate;i++)
                 for(j=1;j <=nlstate;j++)
                   vepp += vareij[i][j][(int)age];
               fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
               for(j=1;j <=nlstate;j++){
                 fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
               }
               fprintf(ficrest,"\n");
             }
           }
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_vector(epj,1,nlstate+1);
         }
       }
       free_vector(weight,1,n);
       free_imatrix(Tvard,1,15,1,2);
       free_imatrix(s,1,maxwav+1,1,n);
       free_matrix(anint,1,maxwav,1,n); 
       free_matrix(mint,1,maxwav,1,n);
       free_ivector(cod,1,n);
       free_ivector(tab,1,NCOVMAX);
       fclose(ficresstdeij);
       fclose(ficrescveij);
       fclose(ficresvij);
       fclose(ficrest);
       fclose(ficpar);
     
       /*------- Variance of period (stable) prevalence------*/   
   
       strcpy(fileresvpl,"vpl");
       strcat(fileresvpl,fileres);
       if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
         printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
         exit(0);
       }
       printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           fprintf(ficresvpl,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvpl,"******\n");
         
           varpl=matrix(1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
           free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
         }
       }
   
       fclose(ficresvpl);
   
       /*---------- End : free ----------------*/
       if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     }  /* mle==-3 arrives here for freeing */
     free_matrix(prlim,1,nlstate,1,nlstate);
       free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(covar,0,NCOVMAX,1,n);
       free_matrix(matcov,1,npar,1,npar);
       /*free_vector(delti,1,npar);*/
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       free_matrix(agev,1,maxwav,1,imx);
       free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   
       free_ivector(ncodemax,1,8);
       free_ivector(Tvar,1,15);
       free_ivector(Tprod,1,15);
       free_ivector(Tvaraff,1,15);
       free_ivector(Tage,1,15);
       free_ivector(Tcode,1,100);
   
       free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
       free_imatrix(codtab,1,100,1,10);
     fflush(fichtm);
     fflush(ficgp);
     
   
     if((nberr >0) || (nbwarn>0)){
       printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
       fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
     }else{
       printf("End of Imach\n");
       fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     (void) gettimeofday(&end_time,&tzp);
     tm = *localtime(&end_time.tv_sec);
     tmg = *gmtime(&end_time.tv_sec);
     strcpy(strtend,asctime(&tm));
     printf("Local time at start %s\nLocal time at end   %s",strstart, strtend); 
     fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
     printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
   
     printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
     fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
     fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
     /*  printf("Total time was %d uSec.\n", total_usecs);*/
   /*   if(fileappend(fichtm,optionfilehtm)){ */
     fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtm);
     fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtmcov);
     fclose(ficgp);
     fclose(ficlog);
     /*------ End -----------*/
   
   
      printf("Before Current directory %s!\n",pathcd);
      if(chdir(pathcd) != 0)
       printf("Can't move to directory %s!\n",path);
     if(getcwd(pathcd,MAXLINE) > 0)
       printf("Current directory %s!\n",pathcd);
     /*strcat(plotcmd,CHARSEPARATOR);*/
     sprintf(plotcmd,"gnuplot");
   #ifndef UNIX
     sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
   #endif
     if(!stat(plotcmd,&info)){
       printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
       if(!stat(getenv("GNUPLOTBIN"),&info)){
         printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #ifdef UNIX
       strcpy(plotcmd,GNUPLOTPROGRAM);
       if(!stat(plotcmd,&info)){
         printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #endif
     }else
       strcpy(pplotcmd,plotcmd);
     
     sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
     printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
   
     if((outcmd=system(plotcmd)) != 0){
       printf("\n Problem with gnuplot\n");
     }
     printf(" Wait...");
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again and q for exiting: ");
       scanf("%s",z);
   /*     if (z[0] == 'c') system("./imach"); */
       if (z[0] == 'e') {
         printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
         system(optionfilehtm);
       }
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     end:
     while (z[0] != 'q') {
       printf("\nType  q for exiting: ");
       scanf("%s",z);
     }
   }
   
   
   

Removed from v.1.36  
changed lines
  Added in v.1.130


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