Diff for /imach/src/imach.c between versions 1.33 and 1.143

version 1.33, 2002/03/12 22:13:38 version 1.143, 2014/01/26 09:45:38
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.143  2014/01/26 09:45:38  brouard
      Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
   This program computes Healthy Life Expectancies from  
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
   first survey ("cross") where individuals from different ages are    (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
   interviewed on their health status or degree of disability (in the  
   case of a health survey which is our main interest) -2- at least a    Revision 1.142  2014/01/26 03:57:36  brouard
   second wave of interviews ("longitudinal") which measure each change    Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
   (if any) in individual health status.  Health expectancies are  
   computed from the time spent in each health state according to a    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
   model. More health states you consider, more time is necessary to reach the  
   Maximum Likelihood of the parameters involved in the model.  The    Revision 1.141  2014/01/26 02:42:01  brouard
   simplest model is the multinomial logistic model where pij is the    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
   probabibility to be observed in state j at the second wave  
   conditional to be observed in state i at the first wave. Therefore    Revision 1.140  2011/09/02 10:37:54  brouard
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    Summary: times.h is ok with mingw32 now.
   'age' is age and 'sex' is a covariate. If you want to have a more  
   complex model than "constant and age", you should modify the program    Revision 1.139  2010/06/14 07:50:17  brouard
   where the markup *Covariates have to be included here again* invites    After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
   you to do it.  More covariates you add, slower the    I remember having already fixed agemin agemax which are pointers now but not cvs saved.
   convergence.  
     Revision 1.138  2010/04/30 18:19:40  brouard
   The advantage of this computer programme, compared to a simple    *** empty log message ***
   multinomial logistic model, is clear when the delay between waves is not  
   identical for each individual. Also, if a individual missed an    Revision 1.137  2010/04/29 18:11:38  brouard
   intermediate interview, the information is lost, but taken into    (Module): Checking covariates for more complex models
   account using an interpolation or extrapolation.      than V1+V2. A lot of change to be done. Unstable.
   
   hPijx is the probability to be observed in state i at age x+h    Revision 1.136  2010/04/26 20:30:53  brouard
   conditional to the observed state i at age x. The delay 'h' can be    (Module): merging some libgsl code. Fixing computation
   split into an exact number (nh*stepm) of unobserved intermediate    of likelione (using inter/intrapolation if mle = 0) in order to
   states. This elementary transition (by month or quarter trimester,    get same likelihood as if mle=1.
   semester or year) is model as a multinomial logistic.  The hPx    Some cleaning of code and comments added.
   matrix is simply the matrix product of nh*stepm elementary matrices  
   and the contribution of each individual to the likelihood is simply    Revision 1.135  2009/10/29 15:33:14  brouard
   hPijx.    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
   
   Also this programme outputs the covariance matrix of the parameters but also    Revision 1.134  2009/10/29 13:18:53  brouard
   of the life expectancies. It also computes the prevalence limits.    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
    
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    Revision 1.133  2009/07/06 10:21:25  brouard
            Institut national d'études démographiques, Paris.    just nforces
   This software have been partly granted by Euro-REVES, a concerted action  
   from the European Union.    Revision 1.132  2009/07/06 08:22:05  brouard
   It is copyrighted identically to a GNU software product, ie programme and    Many tings
   software can be distributed freely for non commercial use. Latest version  
   can be accessed at http://euroreves.ined.fr/imach .    Revision 1.131  2009/06/20 16:22:47  brouard
   **********************************************************************/    Some dimensions resccaled
    
 #include <math.h>    Revision 1.130  2009/05/26 06:44:34  brouard
 #include <stdio.h>    (Module): Max Covariate is now set to 20 instead of 8. A
 #include <stdlib.h>    lot of cleaning with variables initialized to 0. Trying to make
 #include <unistd.h>    V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
   
 #define MAXLINE 256    Revision 1.129  2007/08/31 13:49:27  lievre
 #define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"    Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
 #define FILENAMELENGTH 80  
 /*#define DEBUG*/    Revision 1.128  2006/06/30 13:02:05  brouard
 #define windows    (Module): Clarifications on computing e.j
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */  
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    Revision 1.127  2006/04/28 18:11:50  brouard
     (Module): Yes the sum of survivors was wrong since
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    imach-114 because nhstepm was no more computed in the age
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    loop. Now we define nhstepma in the age loop.
     (Module): In order to speed up (in case of numerous covariates) we
 #define NINTERVMAX 8    compute health expectancies (without variances) in a first step
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    and then all the health expectancies with variances or standard
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    deviation (needs data from the Hessian matrices) which slows the
 #define NCOVMAX 8 /* Maximum number of covariates */    computation.
 #define MAXN 20000    In the future we should be able to stop the program is only health
 #define YEARM 12. /* Number of months per year */    expectancies and graph are needed without standard deviations.
 #define AGESUP 130  
 #define AGEBASE 40    Revision 1.126  2006/04/28 17:23:28  brouard
     (Module): Yes the sum of survivors was wrong since
     imach-114 because nhstepm was no more computed in the age
 int erreur; /* Error number */    loop. Now we define nhstepma in the age loop.
 int nvar;    Version 0.98h
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;  
 int npar=NPARMAX;    Revision 1.125  2006/04/04 15:20:31  lievre
 int nlstate=2; /* Number of live states */    Errors in calculation of health expectancies. Age was not initialized.
 int ndeath=1; /* Number of dead states */    Forecasting file added.
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  
 int popbased=0;    Revision 1.124  2006/03/22 17:13:53  lievre
     Parameters are printed with %lf instead of %f (more numbers after the comma).
 int *wav; /* Number of waves for this individuual 0 is possible */    The log-likelihood is printed in the log file
 int maxwav; /* Maxim number of waves */  
 int jmin, jmax; /* min, max spacing between 2 waves */    Revision 1.123  2006/03/20 10:52:43  brouard
 int mle, weightopt;    * imach.c (Module): <title> changed, corresponds to .htm file
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    name. <head> headers where missing.
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */  
 double jmean; /* Mean space between 2 waves */    * imach.c (Module): Weights can have a decimal point as for
 double **oldm, **newm, **savm; /* Working pointers to matrices */    English (a comma might work with a correct LC_NUMERIC environment,
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    otherwise the weight is truncated).
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    Modification of warning when the covariates values are not 0 or
 FILE *ficgp,*ficresprob,*ficpop;    1.
 FILE *ficreseij;    Version 0.98g
   char filerese[FILENAMELENGTH];  
  FILE  *ficresvij;    Revision 1.122  2006/03/20 09:45:41  brouard
   char fileresv[FILENAMELENGTH];    (Module): Weights can have a decimal point as for
  FILE  *ficresvpl;    English (a comma might work with a correct LC_NUMERIC environment,
   char fileresvpl[FILENAMELENGTH];    otherwise the weight is truncated).
     Modification of warning when the covariates values are not 0 or
 #define NR_END 1    1.
 #define FREE_ARG char*    Version 0.98g
 #define FTOL 1.0e-10  
     Revision 1.121  2006/03/16 17:45:01  lievre
 #define NRANSI    * imach.c (Module): Comments concerning covariates added
 #define ITMAX 200  
     * imach.c (Module): refinements in the computation of lli if
 #define TOL 2.0e-4    status=-2 in order to have more reliable computation if stepm is
     not 1 month. Version 0.98f
 #define CGOLD 0.3819660  
 #define ZEPS 1.0e-10    Revision 1.120  2006/03/16 15:10:38  lievre
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    (Module): refinements in the computation of lli if
     status=-2 in order to have more reliable computation if stepm is
 #define GOLD 1.618034    not 1 month. Version 0.98f
 #define GLIMIT 100.0  
 #define TINY 1.0e-20    Revision 1.119  2006/03/15 17:42:26  brouard
     (Module): Bug if status = -2, the loglikelihood was
 static double maxarg1,maxarg2;    computed as likelihood omitting the logarithm. Version O.98e
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    Revision 1.118  2006/03/14 18:20:07  brouard
      (Module): varevsij Comments added explaining the second
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    table of variances if popbased=1 .
 #define rint(a) floor(a+0.5)    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
     (Module): Function pstamp added
 static double sqrarg;    (Module): Version 0.98d
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    Revision 1.117  2006/03/14 17:16:22  brouard
     (Module): varevsij Comments added explaining the second
 int imx;    table of variances if popbased=1 .
 int stepm;    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 /* Stepm, step in month: minimum step interpolation*/    (Module): Function pstamp added
     (Module): Version 0.98d
 int m,nb;  
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    Revision 1.116  2006/03/06 10:29:27  brouard
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    (Module): Variance-covariance wrong links and
 double **pmmij, ***probs, ***mobaverage;    varian-covariance of ej. is needed (Saito).
 double dateintmean=0;  
     Revision 1.115  2006/02/27 12:17:45  brouard
 double *weight;    (Module): One freematrix added in mlikeli! 0.98c
 int **s; /* Status */  
 double *agedc, **covar, idx;    Revision 1.114  2006/02/26 12:57:58  brouard
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    (Module): Some improvements in processing parameter
     filename with strsep.
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  
 double ftolhess; /* Tolerance for computing hessian */    Revision 1.113  2006/02/24 14:20:24  brouard
     (Module): Memory leaks checks with valgrind and:
 /**************** split *************************/    datafile was not closed, some imatrix were not freed and on matrix
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    allocation too.
 {  
    char *s;                             /* pointer */    Revision 1.112  2006/01/30 09:55:26  brouard
    int  l1, l2;                         /* length counters */    (Module): Back to gnuplot.exe instead of wgnuplot.exe
   
    l1 = strlen( path );                 /* length of path */    Revision 1.111  2006/01/25 20:38:18  brouard
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    (Module): Lots of cleaning and bugs added (Gompertz)
 #ifdef windows    (Module): Comments can be added in data file. Missing date values
    s = strrchr( path, '\\' );           /* find last / */    can be a simple dot '.'.
 #else  
    s = strrchr( path, '/' );            /* find last / */    Revision 1.110  2006/01/25 00:51:50  brouard
 #endif    (Module): Lots of cleaning and bugs added (Gompertz)
    if ( s == NULL ) {                   /* no directory, so use current */  
 #if     defined(__bsd__)                /* get current working directory */    Revision 1.109  2006/01/24 19:37:15  brouard
       extern char       *getwd( );    (Module): Comments (lines starting with a #) are allowed in data.
   
       if ( getwd( dirc ) == NULL ) {    Revision 1.108  2006/01/19 18:05:42  lievre
 #else    Gnuplot problem appeared...
       extern char       *getcwd( );    To be fixed
   
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    Revision 1.107  2006/01/19 16:20:37  brouard
 #endif    Test existence of gnuplot in imach path
          return( GLOCK_ERROR_GETCWD );  
       }    Revision 1.106  2006/01/19 13:24:36  brouard
       strcpy( name, path );             /* we've got it */    Some cleaning and links added in html output
    } else {                             /* strip direcotry from path */  
       s++;                              /* after this, the filename */    Revision 1.105  2006/01/05 20:23:19  lievre
       l2 = strlen( s );                 /* length of filename */    *** empty log message ***
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  
       strcpy( name, s );                /* save file name */    Revision 1.104  2005/09/30 16:11:43  lievre
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    (Module): sump fixed, loop imx fixed, and simplifications.
       dirc[l1-l2] = 0;                  /* add zero */    (Module): If the status is missing at the last wave but we know
    }    that the person is alive, then we can code his/her status as -2
    l1 = strlen( dirc );                 /* length of directory */    (instead of missing=-1 in earlier versions) and his/her
 #ifdef windows    contributions to the likelihood is 1 - Prob of dying from last
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    health status (= 1-p13= p11+p12 in the easiest case of somebody in
 #else    the healthy state at last known wave). Version is 0.98
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }  
 #endif    Revision 1.103  2005/09/30 15:54:49  lievre
    s = strrchr( name, '.' );            /* find last / */    (Module): sump fixed, loop imx fixed, and simplifications.
    s++;  
    strcpy(ext,s);                       /* save extension */    Revision 1.102  2004/09/15 17:31:30  brouard
    l1= strlen( name);    Add the possibility to read data file including tab characters.
    l2= strlen( s)+1;  
    strncpy( finame, name, l1-l2);    Revision 1.101  2004/09/15 10:38:38  brouard
    finame[l1-l2]= 0;    Fix on curr_time
    return( 0 );                         /* we're done */  
 }    Revision 1.100  2004/07/12 18:29:06  brouard
     Add version for Mac OS X. Just define UNIX in Makefile
   
 /******************************************/    Revision 1.99  2004/06/05 08:57:40  brouard
     *** empty log message ***
 void replace(char *s, char*t)  
 {    Revision 1.98  2004/05/16 15:05:56  brouard
   int i;    New version 0.97 . First attempt to estimate force of mortality
   int lg=20;    directly from the data i.e. without the need of knowing the health
   i=0;    state at each age, but using a Gompertz model: log u =a + b*age .
   lg=strlen(t);    This is the basic analysis of mortality and should be done before any
   for(i=0; i<= lg; i++) {    other analysis, in order to test if the mortality estimated from the
     (s[i] = t[i]);    cross-longitudinal survey is different from the mortality estimated
     if (t[i]== '\\') s[i]='/';    from other sources like vital statistic data.
   }  
 }    The same imach parameter file can be used but the option for mle should be -3.
   
 int nbocc(char *s, char occ)    Agnès, who wrote this part of the code, tried to keep most of the
 {    former routines in order to include the new code within the former code.
   int i,j=0;  
   int lg=20;    The output is very simple: only an estimate of the intercept and of
   i=0;    the slope with 95% confident intervals.
   lg=strlen(s);  
   for(i=0; i<= lg; i++) {    Current limitations:
   if  (s[i] == occ ) j++;    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.
   return j;    B) There is no computation of Life Expectancy nor Life Table.
 }  
     Revision 1.97  2004/02/20 13:25:42  lievre
 void cutv(char *u,char *v, char*t, char occ)    Version 0.96d. Population forecasting command line is (temporarily)
 {    suppressed.
   int i,lg,j,p=0;  
   i=0;    Revision 1.96  2003/07/15 15:38:55  brouard
   for(j=0; j<=strlen(t)-1; j++) {    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    rewritten within the same printf. Workaround: many printfs.
   }  
     Revision 1.95  2003/07/08 07:54:34  brouard
   lg=strlen(t);    * imach.c (Repository):
   for(j=0; j<p; j++) {    (Repository): Using imachwizard code to output a more meaningful covariance
     (u[j] = t[j]);    matrix (cov(a12,c31) instead of numbers.
   }  
      u[p]='\0';    Revision 1.94  2003/06/27 13:00:02  brouard
     Just cleaning
    for(j=0; j<= lg; j++) {  
     if (j>=(p+1))(v[j-p-1] = t[j]);    Revision 1.93  2003/06/25 16:33:55  brouard
   }    (Module): On windows (cygwin) function asctime_r doesn't
 }    exist so I changed back to asctime which exists.
     (Module): Version 0.96b
 /********************** nrerror ********************/  
     Revision 1.92  2003/06/25 16:30:45  brouard
 void nrerror(char error_text[])    (Module): On windows (cygwin) function asctime_r doesn't
 {    exist so I changed back to asctime which exists.
   fprintf(stderr,"ERREUR ...\n");  
   fprintf(stderr,"%s\n",error_text);    Revision 1.91  2003/06/25 15:30:29  brouard
   exit(1);    * imach.c (Repository): Duplicated warning errors corrected.
 }    (Repository): Elapsed time after each iteration is now output. It
 /*********************** vector *******************/    helps to forecast when convergence will be reached. Elapsed time
 double *vector(int nl, int nh)    is stamped in powell.  We created a new html file for the graphs
 {    concerning matrix of covariance. It has extension -cov.htm.
   double *v;  
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    Revision 1.90  2003/06/24 12:34:15  brouard
   if (!v) nrerror("allocation failure in vector");    (Module): Some bugs corrected for windows. Also, when
   return v-nl+NR_END;    mle=-1 a template is output in file "or"mypar.txt with the design
 }    of the covariance matrix to be input.
   
 /************************ free vector ******************/    Revision 1.89  2003/06/24 12:30:52  brouard
 void free_vector(double*v, int nl, int nh)    (Module): Some bugs corrected for windows. Also, when
 {    mle=-1 a template is output in file "or"mypar.txt with the design
   free((FREE_ARG)(v+nl-NR_END));    of the covariance matrix to be input.
 }  
     Revision 1.88  2003/06/23 17:54:56  brouard
 /************************ivector *******************************/    * 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 *ivector(long nl,long nh)  
 {    Revision 1.87  2003/06/18 12:26:01  brouard
   int *v;    Version 0.96
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  
   if (!v) nrerror("allocation failure in ivector");    Revision 1.86  2003/06/17 20:04:08  brouard
   return v-nl+NR_END;    (Module): Change position of html and gnuplot routines and added
 }    routine fileappend.
   
 /******************free ivector **************************/    Revision 1.85  2003/06/17 13:12:43  brouard
 void free_ivector(int *v, long nl, long nh)    * imach.c (Repository): Check when date of death was earlier that
 {    current date of interview. It may happen when the death was just
   free((FREE_ARG)(v+nl-NR_END));    prior to the death. In this case, dh was negative and likelihood
 }    was wrong (infinity). We still send an "Error" but patch by
     assuming that the date of death was just one stepm after the
 /******************* imatrix *******************************/    interview.
 int **imatrix(long nrl, long nrh, long ncl, long nch)    (Repository): Because some people have very long ID (first column)
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    we changed int to long in num[] and we added a new lvector for
 {    memory allocation. But we also truncated to 8 characters (left
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    truncation)
   int **m;    (Repository): No more line truncation errors.
    
   /* allocate pointers to rows */    Revision 1.84  2003/06/13 21:44:43  brouard
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    * imach.c (Repository): Replace "freqsummary" at a correct
   if (!m) nrerror("allocation failure 1 in matrix()");    place. It differs from routine "prevalence" which may be called
   m += NR_END;    many times. Probs is memory consuming and must be used with
   m -= nrl;    parcimony.
      Version 0.95a3 (should output exactly the same maximization than 0.8a2)
    
   /* allocate rows and set pointers to them */    Revision 1.83  2003/06/10 13:39:11  lievre
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    *** empty log message ***
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;    Revision 1.82  2003/06/05 15:57:20  brouard
   m[nrl] -= ncl;    Add log in  imach.c and  fullversion number is now printed.
    
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  */
    /*
   /* return pointer to array of pointers to rows */     Interpolated Markov Chain
   return m;  
 }    Short summary of the programme:
     
 /****************** free_imatrix *************************/    This program computes Healthy Life Expectancies from
 void free_imatrix(m,nrl,nrh,ncl,nch)    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
       int **m;    first survey ("cross") where individuals from different ages are
       long nch,ncl,nrh,nrl;    interviewed on their health status or degree of disability (in the
      /* free an int matrix allocated by imatrix() */    case of a health survey which is our main interest) -2- at least a
 {    second wave of interviews ("longitudinal") which measure each change
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    (if any) in individual health status.  Health expectancies are
   free((FREE_ARG) (m+nrl-NR_END));    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
     Maximum Likelihood of the parameters involved in the model.  The
 /******************* matrix *******************************/    simplest model is the multinomial logistic model where pij is the
 double **matrix(long nrl, long nrh, long ncl, long nch)    probability to be observed in state j at the second wave
 {    conditional to be observed in state i at the first wave. Therefore
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
   double **m;    'age' is age and 'sex' is a covariate. If you want to have a more
     complex model than "constant and age", you should modify the program
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    where the markup *Covariates have to be included here again* invites
   if (!m) nrerror("allocation failure 1 in matrix()");    you to do it.  More covariates you add, slower the
   m += NR_END;    convergence.
   m -= nrl;  
     The advantage of this computer programme, compared to a simple
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    multinomial logistic model, is clear when the delay between waves is not
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    identical for each individual. Also, if a individual missed an
   m[nrl] += NR_END;    intermediate interview, the information is lost, but taken into
   m[nrl] -= ncl;    account using an interpolation or extrapolation.  
   
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    hPijx is the probability to be observed in state i at age x+h
   return m;    conditional to the observed state i at age x. The delay 'h' can be
 }    split into an exact number (nh*stepm) of unobserved intermediate
     states. This elementary transition (by month, quarter,
 /*************************free matrix ************************/    semester or year) is modelled as a multinomial logistic.  The hPx
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    matrix is simply the matrix product of nh*stepm elementary matrices
 {    and the contribution of each individual to the likelihood is simply
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    hPijx.
   free((FREE_ARG)(m+nrl-NR_END));  
 }    Also this programme outputs the covariance matrix of the parameters but also
     of the life expectancies. It also computes the period (stable) prevalence. 
 /******************* ma3x *******************************/    
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
 {             Institut national d'études démographiques, Paris.
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    This software have been partly granted by Euro-REVES, a concerted action
   double ***m;    from the European Union.
     It is copyrighted identically to a GNU software product, ie programme and
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    software can be distributed freely for non commercial use. Latest version
   if (!m) nrerror("allocation failure 1 in matrix()");    can be accessed at http://euroreves.ined.fr/imach .
   m += NR_END;  
   m -= nrl;    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
     or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    **********************************************************************/
   m[nrl] += NR_END;  /*
   m[nrl] -= ncl;    main
     read parameterfile
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    read datafile
     concatwav
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    freqsummary
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    if (mle >= 1)
   m[nrl][ncl] += NR_END;      mlikeli
   m[nrl][ncl] -= nll;    print results files
   for (j=ncl+1; j<=nch; j++)    if mle==1 
     m[nrl][j]=m[nrl][j-1]+nlay;       computes hessian
      read end of parameter file: agemin, agemax, bage, fage, estepm
   for (i=nrl+1; i<=nrh; i++) {        begin-prev-date,...
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;    open gnuplot file
     for (j=ncl+1; j<=nch; j++)    open html file
       m[i][j]=m[i][j-1]+nlay;    period (stable) prevalence
   }     for age prevalim()
   return m;    h Pij x
 }    variance of p varprob
     forecasting if prevfcast==1 prevforecast call prevalence()
 /*************************free ma3x ************************/    health expectancies
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    Variance-covariance of DFLE
 {    prevalence()
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));     movingaverage()
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    varevsij() 
   free((FREE_ARG)(m+nrl-NR_END));    if popbased==1 varevsij(,popbased)
 }    total life expectancies
     Variance of period (stable) prevalence
 /***************** f1dim *************************/   end
 extern int ncom;  */
 extern double *pcom,*xicom;  
 extern double (*nrfunc)(double []);  
    
 double f1dim(double x)   
 {  #include <math.h>
   int j;  #include <stdio.h>
   double f;  #include <stdlib.h>
   double *xt;  #include <string.h>
    #include <unistd.h>
   xt=vector(1,ncom);  
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  #include <limits.h>
   f=(*nrfunc)(xt);  #include <sys/types.h>
   free_vector(xt,1,ncom);  #include <sys/stat.h>
   return f;  #include <errno.h>
 }  extern int errno;
   
 /*****************brent *************************/  #ifdef LINUX
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  #include <time.h>
 {  #include "timeval.h"
   int iter;  #else
   double a,b,d,etemp;  #include <sys/time.h>
   double fu,fv,fw,fx;  #endif
   double ftemp;  
   double p,q,r,tol1,tol2,u,v,w,x,xm;  #ifdef GSL
   double e=0.0;  #include <gsl/gsl_errno.h>
    #include <gsl/gsl_multimin.h>
   a=(ax < cx ? ax : cx);  #endif
   b=(ax > cx ? ax : cx);  
   x=w=v=bx;  /* #include <libintl.h> */
   fw=fv=fx=(*f)(x);  /* #define _(String) gettext (String) */
   for (iter=1;iter<=ITMAX;iter++) {  
     xm=0.5*(a+b);  #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  #define GNUPLOTPROGRAM "gnuplot"
     printf(".");fflush(stdout);  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 #ifdef DEBUG  #define FILENAMELENGTH 132
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);  
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 #endif  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  
       *xmin=x;  #define MAXPARM 128 /* Maximum number of parameters for the optimization */
       return fx;  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
     }  
     ftemp=fu;  #define NINTERVMAX 8
     if (fabs(e) > tol1) {  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
       r=(x-w)*(fx-fv);  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
       q=(x-v)*(fx-fw);  #define NCOVMAX 20 /* Maximum number of covariates */
       p=(x-v)*q-(x-w)*r;  #define MAXN 20000
       q=2.0*(q-r);  #define YEARM 12. /* Number of months per year */
       if (q > 0.0) p = -p;  #define AGESUP 130
       q=fabs(q);  #define AGEBASE 40
       etemp=e;  #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
       e=d;  #ifdef UNIX
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  #define DIRSEPARATOR '/'
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  #define CHARSEPARATOR "/"
       else {  #define ODIRSEPARATOR '\\'
         d=p/q;  #else
         u=x+d;  #define DIRSEPARATOR '\\'
         if (u-a < tol2 || b-u < tol2)  #define CHARSEPARATOR "\\"
           d=SIGN(tol1,xm-x);  #define ODIRSEPARATOR '/'
       }  #endif
     } else {  
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  /* $Id$ */
     }  /* $State$ */
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  
     fu=(*f)(u);  char version[]="Imach version 0.98nR2, January 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121)";
     if (fu <= fx) {  char fullversion[]="$Revision$ $Date$"; 
       if (u >= x) a=x; else b=x;  char strstart[80];
       SHFT(v,w,x,u)  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
         SHFT(fv,fw,fx,fu)  int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
         } else {  int nvar=0, nforce=0; /* Number of variables, number of forces */
           if (u < x) a=u; else b=u;  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov=0; /* Number of covariates, of covariates with '*age' */
           if (fu <= fw || w == x) {  int npar=NPARMAX;
             v=w;  int nlstate=2; /* Number of live states */
             w=u;  int ndeath=1; /* Number of dead states */
             fv=fw;  int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
             fw=fu;  int popbased=0;
           } else if (fu <= fv || v == x || v == w) {  
             v=u;  int *wav; /* Number of waves for this individuual 0 is possible */
             fv=fu;  int maxwav=0; /* Maxim number of waves */
           }  int jmin=0, jmax=0; /* min, max spacing between 2 waves */
         }  int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
   }  int gipmx=0, gsw=0; /* Global variables on the number of contributions 
   nrerror("Too many iterations in brent");                     to the likelihood and the sum of weights (done by funcone)*/
   *xmin=x;  int mle=1, weightopt=0;
   return fx;  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 */
   int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
 /****************** mnbrak ***********************/             * wave mi and wave mi+1 is not an exact multiple of stepm. */
   double jmean=1; /* Mean space between 2 waves */
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  double **oldm, **newm, **savm; /* Working pointers to matrices */
             double (*func)(double))  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
 {  /*FILE *fic ; */ /* Used in readdata only */
   double ulim,u,r,q, dum;  FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   double fu;  FILE *ficlog, *ficrespow;
    int globpr=0; /* Global variable for printing or not */
   *fa=(*func)(*ax);  double fretone; /* Only one call to likelihood */
   *fb=(*func)(*bx);  long ipmx=0; /* Number of contributions */
   if (*fb > *fa) {  double sw; /* Sum of weights */
     SHFT(dum,*ax,*bx,dum)  char filerespow[FILENAMELENGTH];
       SHFT(dum,*fb,*fa,dum)  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
       }  FILE *ficresilk;
   *cx=(*bx)+GOLD*(*bx-*ax);  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   *fc=(*func)(*cx);  FILE *ficresprobmorprev;
   while (*fb > *fc) {  FILE *fichtm, *fichtmcov; /* Html File */
     r=(*bx-*ax)*(*fb-*fc);  FILE *ficreseij;
     q=(*bx-*cx)*(*fb-*fa);  char filerese[FILENAMELENGTH];
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  FILE *ficresstdeij;
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  char fileresstde[FILENAMELENGTH];
     ulim=(*bx)+GLIMIT*(*cx-*bx);  FILE *ficrescveij;
     if ((*bx-u)*(u-*cx) > 0.0) {  char filerescve[FILENAMELENGTH];
       fu=(*func)(u);  FILE  *ficresvij;
     } else if ((*cx-u)*(u-ulim) > 0.0) {  char fileresv[FILENAMELENGTH];
       fu=(*func)(u);  FILE  *ficresvpl;
       if (fu < *fc) {  char fileresvpl[FILENAMELENGTH];
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  char title[MAXLINE];
           SHFT(*fb,*fc,fu,(*func)(u))  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
           }  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
       u=ulim;  char command[FILENAMELENGTH];
       fu=(*func)(u);  int  outcmd=0;
     } else {  
       u=(*cx)+GOLD*(*cx-*bx);  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
       fu=(*func)(u);  
     }  char filelog[FILENAMELENGTH]; /* Log file */
     SHFT(*ax,*bx,*cx,u)  char filerest[FILENAMELENGTH];
       SHFT(*fa,*fb,*fc,fu)  char fileregp[FILENAMELENGTH];
       }  char popfile[FILENAMELENGTH];
 }  
   char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
 /*************** linmin ************************/  
   struct timeval start_time, end_time, curr_time, last_time, forecast_time;
 int ncom;  struct timezone tzp;
 double *pcom,*xicom;  extern int gettimeofday();
 double (*nrfunc)(double []);  struct tm tmg, tm, tmf, *gmtime(), *localtime();
    long time_value;
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  extern long time();
 {  char strcurr[80], strfor[80];
   double brent(double ax, double bx, double cx,  
                double (*f)(double), double tol, double *xmin);  char *endptr;
   double f1dim(double x);  long lval;
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  double dval;
               double *fc, double (*func)(double));  
   int j;  #define NR_END 1
   double xx,xmin,bx,ax;  #define FREE_ARG char*
   double fx,fb,fa;  #define FTOL 1.0e-10
    
   ncom=n;  #define NRANSI 
   pcom=vector(1,n);  #define ITMAX 200 
   xicom=vector(1,n);  
   nrfunc=func;  #define TOL 2.0e-4 
   for (j=1;j<=n;j++) {  
     pcom[j]=p[j];  #define CGOLD 0.3819660 
     xicom[j]=xi[j];  #define ZEPS 1.0e-10 
   }  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
   ax=0.0;  
   xx=1.0;  #define GOLD 1.618034 
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  #define GLIMIT 100.0 
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  #define TINY 1.0e-20 
 #ifdef DEBUG  
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  static double maxarg1,maxarg2;
 #endif  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
   for (j=1;j<=n;j++) {  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
     xi[j] *= xmin;    
     p[j] += xi[j];  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   }  #define rint(a) floor(a+0.5)
   free_vector(xicom,1,n);  
   free_vector(pcom,1,n);  static double sqrarg;
 }  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
   #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
 /*************** powell ************************/  int agegomp= AGEGOMP;
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  
             double (*func)(double []))  int imx; 
 {  int stepm=1;
   void linmin(double p[], double xi[], int n, double *fret,  /* Stepm, step in month: minimum step interpolation*/
               double (*func)(double []));  
   int i,ibig,j;  int estepm;
   double del,t,*pt,*ptt,*xit;  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
   double fp,fptt;  
   double *xits;  int m,nb;
   pt=vector(1,n);  long *num;
   ptt=vector(1,n);  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
   xit=vector(1,n);  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
   xits=vector(1,n);  double **pmmij, ***probs;
   *fret=(*func)(p);  double *ageexmed,*agecens;
   for (j=1;j<=n;j++) pt[j]=p[j];  double dateintmean=0;
   for (*iter=1;;++(*iter)) {  
     fp=(*fret);  double *weight;
     ibig=0;  int **s; /* Status */
     del=0.0;  double *agedc;
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  double  **covar; /**< covar[i,j], value of jth covariate for individual i,
     for (i=1;i<=n;i++)                    * covar=matrix(0,NCOVMAX,1,n); 
       printf(" %d %.12f",i, p[i]);                    * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
     printf("\n");  double  idx; 
     for (i=1;i<=n;i++) {  int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  int **codtab; /**< codtab=imatrix(1,100,1,10); */
       fptt=(*fret);  int **Tvard, *Tprod, cptcovprod, *Tvaraff;
 #ifdef DEBUG  double *lsurv, *lpop, *tpop;
       printf("fret=%lf \n",*fret);  
 #endif  double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
       printf("%d",i);fflush(stdout);  double ftolhess; /**< Tolerance for computing hessian */
       linmin(p,xit,n,fret,func);  
       if (fabs(fptt-(*fret)) > del) {  /**************** split *************************/
         del=fabs(fptt-(*fret));  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
         ibig=i;  {
       }    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
 #ifdef DEBUG       the name of the file (name), its extension only (ext) and its first part of the name (finame)
       printf("%d %.12e",i,(*fret));    */ 
       for (j=1;j<=n;j++) {    char  *ss;                            /* pointer */
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);    int   l1, l2;                         /* length counters */
         printf(" x(%d)=%.12e",j,xit[j]);  
       }    l1 = strlen(path );                   /* length of path */
       for(j=1;j<=n;j++)    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
         printf(" p=%.12e",p[j]);    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
       printf("\n");    if ( ss == NULL ) {                   /* no directory, so determine current directory */
 #endif      strcpy( name, path );               /* we got the fullname name because no directory */
     }      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
 #ifdef DEBUG      /* get current working directory */
       int k[2],l;      /*    extern  char* getcwd ( char *buf , int len);*/
       k[0]=1;      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
       k[1]=-1;        return( GLOCK_ERROR_GETCWD );
       printf("Max: %.12e",(*func)(p));      }
       for (j=1;j<=n;j++)      /* got dirc from getcwd*/
         printf(" %.12e",p[j]);      printf(" DIRC = %s \n",dirc);
       printf("\n");    } else {                              /* strip direcotry from path */
       for(l=0;l<=1;l++) {      ss++;                               /* after this, the filename */
         for (j=1;j<=n;j++) {      l2 = strlen( ss );                  /* length of filename */
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);      strcpy( name, ss );         /* save file name */
         }      strncpy( dirc, path, l1 - l2 );     /* now the directory */
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));      dirc[l1-l2] = 0;                    /* add zero */
       }      printf(" DIRC2 = %s \n",dirc);
 #endif    }
     /* We add a separator at the end of dirc if not exists */
     l1 = strlen( dirc );                  /* length of directory */
       free_vector(xit,1,n);    if( dirc[l1-1] != DIRSEPARATOR ){
       free_vector(xits,1,n);      dirc[l1] =  DIRSEPARATOR;
       free_vector(ptt,1,n);      dirc[l1+1] = 0; 
       free_vector(pt,1,n);      printf(" DIRC3 = %s \n",dirc);
       return;    }
     }    ss = strrchr( name, '.' );            /* find last / */
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    if (ss >0){
     for (j=1;j<=n;j++) {      ss++;
       ptt[j]=2.0*p[j]-pt[j];      strcpy(ext,ss);                     /* save extension */
       xit[j]=p[j]-pt[j];      l1= strlen( name);
       pt[j]=p[j];      l2= strlen(ss)+1;
     }      strncpy( finame, name, l1-l2);
     fptt=(*func)(ptt);      finame[l1-l2]= 0;
     if (fptt < fp) {    }
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  
       if (t < 0.0) {    return( 0 );                          /* we're done */
         linmin(p,xit,n,fret,func);  }
         for (j=1;j<=n;j++) {  
           xi[j][ibig]=xi[j][n];  
           xi[j][n]=xit[j];  /******************************************/
         }  
 #ifdef DEBUG  void replace_back_to_slash(char *s, char*t)
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  {
         for(j=1;j<=n;j++)    int i;
           printf(" %.12e",xit[j]);    int lg=0;
         printf("\n");    i=0;
 #endif    lg=strlen(t);
       }    for(i=0; i<= lg; i++) {
     }      (s[i] = t[i]);
   }      if (t[i]== '\\') s[i]='/';
 }    }
   }
 /**** Prevalence limit ****************/  
   char *trimbb(char *out, char *in)
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
 {    char *s;
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit    s=out;
      matrix by transitions matrix until convergence is reached */    while (*in != '\0'){
       while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
   int i, ii,j,k;        in++;
   double min, max, maxmin, maxmax,sumnew=0.;      }
   double **matprod2();      *out++ = *in++;
   double **out, cov[NCOVMAX], **pmij();    }
   double **newm;    *out='\0';
   double agefin, delaymax=50 ; /* Max number of years to converge */    return s;
   }
   for (ii=1;ii<=nlstate+ndeath;ii++)  
     for (j=1;j<=nlstate+ndeath;j++){  char *cutv(char *blocc, char *alocc, char *in, char occ)
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);  {
     }    /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ' 
        and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
    cov[1]=1.;       gives blocc="abcdef2ghi" and alocc="j".
         If occ is not found blocc is null and alocc is equal to in. Returns alocc
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */    */
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){    char *s, *t;
     newm=savm;    t=in;s=in;
     /* Covariates have to be included here again */    while (*in != '\0'){
      cov[2]=agefin;      while( *in == occ){
          *blocc++ = *in++;
       for (k=1; k<=cptcovn;k++) {        s=in;
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];      }
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/      *blocc++ = *in++;
       }    }
       for (k=1; k<=cptcovage;k++)    if (s == t) /* occ not found */
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];      *(blocc-(in-s))='\0';
       for (k=1; k<=cptcovprod;k++)    else
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];      *(blocc-(in-s)-1)='\0';
     in=s;
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/    while ( *in != '\0'){
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/      *alocc++ = *in++;
     }
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  
     *alocc='\0';
     savm=oldm;    return s;
     oldm=newm;  }
     maxmax=0.;  
     for(j=1;j<=nlstate;j++){  int nbocc(char *s, char occ)
       min=1.;  {
       max=0.;    int i,j=0;
       for(i=1; i<=nlstate; i++) {    int lg=20;
         sumnew=0;    i=0;
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];    lg=strlen(s);
         prlim[i][j]= newm[i][j]/(1-sumnew);    for(i=0; i<= lg; i++) {
         max=FMAX(max,prlim[i][j]);    if  (s[i] == occ ) j++;
         min=FMIN(min,prlim[i][j]);    }
       }    return j;
       maxmin=max-min;  }
       maxmax=FMAX(maxmax,maxmin);  
     }  /* void cutv(char *u,char *v, char*t, char occ) */
     if(maxmax < ftolpl){  /* { */
       return prlim;  /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
     }  /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
   }  /*      gives u="abcdef2ghi" and v="j" *\/ */
 }  /*   int i,lg,j,p=0; */
   /*   i=0; */
 /*************** transition probabilities ***************/  /*   lg=strlen(t); */
   /*   for(j=0; j<=lg-1; j++) { */
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
 {  /*   } */
   double s1, s2;  
   /*double t34;*/  /*   for(j=0; j<p; j++) { */
   int i,j,j1, nc, ii, jj;  /*     (u[j] = t[j]); */
   /*   } */
     for(i=1; i<= nlstate; i++){  /*      u[p]='\0'; */
     for(j=1; j<i;j++){  
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  /*    for(j=0; j<= lg; j++) { */
         /*s2 += param[i][j][nc]*cov[nc];*/  /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
         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;  /********************** nrerror ********************/
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/  
     }  void nrerror(char error_text[])
     for(j=i+1; j<=nlstate+ndeath;j++){  {
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    fprintf(stderr,"ERREUR ...\n");
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    fprintf(stderr,"%s\n",error_text);
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/    exit(EXIT_FAILURE);
       }  }
       ps[i][j]=s2;  /*********************** vector *******************/
     }  double *vector(int nl, int nh)
   }  {
     /*ps[3][2]=1;*/    double *v;
     v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
   for(i=1; i<= nlstate; i++){    if (!v) nrerror("allocation failure in vector");
      s1=0;    return v-nl+NR_END;
     for(j=1; j<i; j++)  }
       s1+=exp(ps[i][j]);  
     for(j=i+1; j<=nlstate+ndeath; j++)  /************************ free vector ******************/
       s1+=exp(ps[i][j]);  void free_vector(double*v, int nl, int nh)
     ps[i][i]=1./(s1+1.);  {
     for(j=1; j<i; j++)    free((FREE_ARG)(v+nl-NR_END));
       ps[i][j]= exp(ps[i][j])*ps[i][i];  }
     for(j=i+1; j<=nlstate+ndeath; j++)  
       ps[i][j]= exp(ps[i][j])*ps[i][i];  /************************ivector *******************************/
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */  int *ivector(long nl,long nh)
   } /* end i */  {
     int *v;
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
     for(jj=1; jj<= nlstate+ndeath; jj++){    if (!v) nrerror("allocation failure in ivector");
       ps[ii][jj]=0;    return v-nl+NR_END;
       ps[ii][ii]=1;  }
     }  
   }  /******************free ivector **************************/
   void free_ivector(int *v, long nl, long nh)
   {
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){    free((FREE_ARG)(v+nl-NR_END));
     for(jj=1; jj<= nlstate+ndeath; jj++){  }
      printf("%lf ",ps[ii][jj]);  
    }  /************************lvector *******************************/
     printf("\n ");  long *lvector(long nl,long nh)
     }  {
     printf("\n ");printf("%lf ",cov[2]);*/    long *v;
 /*    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
   for(i=1; i<= npar; i++) printf("%f ",x[i]);    if (!v) nrerror("allocation failure in ivector");
   goto end;*/    return v-nl+NR_END;
     return ps;  }
 }  
   /******************free lvector **************************/
 /**************** Product of 2 matrices ******************/  void free_lvector(long *v, long nl, long nh)
   {
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)    free((FREE_ARG)(v+nl-NR_END));
 {  }
   /* 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(...) */  /******************* imatrix *******************************/
   /* in, b, out are matrice of pointers which should have been initialized  int **imatrix(long nrl, long nrh, long ncl, long nch) 
      before: only the contents of out is modified. The function returns       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
      a pointer to pointers identical to out */  { 
   long i, j, k;    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
   for(i=nrl; i<= nrh; i++)    int **m; 
     for(k=ncolol; k<=ncoloh; k++)    
       for(j=ncl,out[i][k]=0.; j<=nch; j++)    /* allocate pointers to rows */ 
         out[i][k] +=in[i][j]*b[j][k];    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
     if (!m) nrerror("allocation failure 1 in matrix()"); 
   return out;    m += NR_END; 
 }    m -= nrl; 
     
     
 /************* Higher Matrix Product ***************/    /* allocate rows and set pointers to them */ 
     m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
 {    m[nrl] += NR_END; 
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month    m[nrl] -= ncl; 
      duration (i.e. until    
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step    
      (typically every 2 years instead of every month which is too big).    /* return pointer to array of pointers to rows */ 
      Model is determined by parameters x and covariates have to be    return m; 
      included manually here.  } 
   
      */  /****************** free_imatrix *************************/
   void free_imatrix(m,nrl,nrh,ncl,nch)
   int i, j, d, h, k;        int **m;
   double **out, cov[NCOVMAX];        long nch,ncl,nrh,nrl; 
   double **newm;       /* free an int matrix allocated by imatrix() */ 
   { 
   /* Hstepm could be zero and should return the unit matrix */    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
   for (i=1;i<=nlstate+ndeath;i++)    free((FREE_ARG) (m+nrl-NR_END)); 
     for (j=1;j<=nlstate+ndeath;j++){  } 
       oldm[i][j]=(i==j ? 1.0 : 0.0);  
       po[i][j][0]=(i==j ? 1.0 : 0.0);  /******************* matrix *******************************/
     }  double **matrix(long nrl, long nrh, long ncl, long nch)
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */  {
   for(h=1; h <=nhstepm; h++){    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
     for(d=1; d <=hstepm; d++){    double **m;
       newm=savm;  
       /* Covariates have to be included here again */    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       cov[1]=1.;    if (!m) nrerror("allocation failure 1 in matrix()");
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;    m += NR_END;
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    m -= nrl;
       for (k=1; k<=cptcovage;k++)  
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       for (k=1; k<=cptcovprod;k++)    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    m[nrl] += NR_END;
     m[nrl] -= ncl;
   
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/    return m;
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
                    pmij(pmmij,cov,ncovmodel,x,nlstate));     */
       savm=oldm;  }
       oldm=newm;  
     }  /*************************free matrix ************************/
     for(i=1; i<=nlstate+ndeath; i++)  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
       for(j=1;j<=nlstate+ndeath;j++) {  {
         po[i][j][h]=newm[i][j];    free((FREE_ARG)(m[nrl]+ncl-NR_END));
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);    free((FREE_ARG)(m+nrl-NR_END));
          */  }
       }  
   } /* end h */  /******************* ma3x *******************************/
   return po;  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
 }  {
     long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
     double ***m;
 /*************** log-likelihood *************/  
 double func( double *x)    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
 {    if (!m) nrerror("allocation failure 1 in matrix()");
   int i, ii, j, k, mi, d, kk;    m += NR_END;
   double l, ll[NLSTATEMAX], cov[NCOVMAX];    m -= nrl;
   double **out;  
   double sw; /* Sum of weights */    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   double lli; /* Individual log likelihood */    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   long ipmx;    m[nrl] += NR_END;
   /*extern weight */    m[nrl] -= ncl;
   /* We are differentiating ll according to initial status */  
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   /*for(i=1;i<imx;i++)  
     printf(" %d\n",s[4][i]);    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
   */    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
   cov[1]=1.;    m[nrl][ncl] += NR_END;
     m[nrl][ncl] -= nll;
   for(k=1; k<=nlstate; k++) ll[k]=0.;    for (j=ncl+1; j<=nch; j++) 
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){      m[nrl][j]=m[nrl][j-1]+nlay;
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];    
     for(mi=1; mi<= wav[i]-1; mi++){    for (i=nrl+1; i<=nrh; i++) {
       for (ii=1;ii<=nlstate+ndeath;ii++)      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);      for (j=ncl+1; j<=nch; j++) 
       for(d=0; d<dh[mi][i]; d++){        m[i][j]=m[i][j-1]+nlay;
         newm=savm;    }
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;    return m; 
         for (kk=1; kk<=cptcovage;kk++) {    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
         }    */
          }
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,  
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));  /*************************free ma3x ************************/
         savm=oldm;  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
         oldm=newm;  {
            free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
            free((FREE_ARG)(m[nrl]+ncl-NR_END));
       } /* end mult */    free((FREE_ARG)(m+nrl-NR_END));
        }
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);  
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/  /*************** function subdirf ***********/
       ipmx +=1;  char *subdirf(char fileres[])
       sw += weight[i];  {
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;    /* Caution optionfilefiname is hidden */
     } /* end of wave */    strcpy(tmpout,optionfilefiname);
   } /* end of individual */    strcat(tmpout,"/"); /* Add to the right */
     strcat(tmpout,fileres);
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];    return tmpout;
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */  }
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */  
   return -l;  /*************** function subdirf2 ***********/
 }  char *subdirf2(char fileres[], char *preop)
   {
     
 /*********** Maximum Likelihood Estimation ***************/    /* Caution optionfilefiname is hidden */
     strcpy(tmpout,optionfilefiname);
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))    strcat(tmpout,"/");
 {    strcat(tmpout,preop);
   int i,j, iter;    strcat(tmpout,fileres);
   double **xi,*delti;    return tmpout;
   double fret;  }
   xi=matrix(1,npar,1,npar);  
   for (i=1;i<=npar;i++)  /*************** function subdirf3 ***********/
     for (j=1;j<=npar;j++)  char *subdirf3(char fileres[], char *preop, char *preop2)
       xi[i][j]=(i==j ? 1.0 : 0.0);  {
   printf("Powell\n");    
   powell(p,xi,npar,ftol,&iter,&fret,func);    /* Caution optionfilefiname is hidden */
     strcpy(tmpout,optionfilefiname);
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));    strcat(tmpout,"/");
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));    strcat(tmpout,preop);
     strcat(tmpout,preop2);
 }    strcat(tmpout,fileres);
     return tmpout;
 /**** Computes Hessian and covariance matrix ***/  }
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))  
 {  /***************** f1dim *************************/
   double  **a,**y,*x,pd;  extern int ncom; 
   double **hess;  extern double *pcom,*xicom;
   int i, j,jk;  extern double (*nrfunc)(double []); 
   int *indx;   
   double f1dim(double x) 
   double hessii(double p[], double delta, int theta, double delti[]);  { 
   double hessij(double p[], double delti[], int i, int j);    int j; 
   void lubksb(double **a, int npar, int *indx, double b[]) ;    double f;
   void ludcmp(double **a, int npar, int *indx, double *d) ;    double *xt; 
    
   hess=matrix(1,npar,1,npar);    xt=vector(1,ncom); 
     for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
   printf("\nCalculation of the hessian matrix. Wait...\n");    f=(*nrfunc)(xt); 
   for (i=1;i<=npar;i++){    free_vector(xt,1,ncom); 
     printf("%d",i);fflush(stdout);    return f; 
     hess[i][i]=hessii(p,ftolhess,i,delti);  } 
     /*printf(" %f ",p[i]);*/  
     /*printf(" %lf ",hess[i][i]);*/  /*****************brent *************************/
   }  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
    { 
   for (i=1;i<=npar;i++) {    int iter; 
     for (j=1;j<=npar;j++)  {    double a,b,d,etemp;
       if (j>i) {    double fu,fv,fw,fx;
         printf(".%d%d",i,j);fflush(stdout);    double ftemp;
         hess[i][j]=hessij(p,delti,i,j);    double p,q,r,tol1,tol2,u,v,w,x,xm; 
         hess[j][i]=hess[i][j];        double e=0.0; 
         /*printf(" %lf ",hess[i][j]);*/   
       }    a=(ax < cx ? ax : cx); 
     }    b=(ax > cx ? ax : cx); 
   }    x=w=v=bx; 
   printf("\n");    fw=fv=fx=(*f)(x); 
     for (iter=1;iter<=ITMAX;iter++) { 
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");      xm=0.5*(a+b); 
        tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
   a=matrix(1,npar,1,npar);      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
   y=matrix(1,npar,1,npar);      printf(".");fflush(stdout);
   x=vector(1,npar);      fprintf(ficlog,".");fflush(ficlog);
   indx=ivector(1,npar);  #ifdef DEBUG
   for (i=1;i<=npar;i++)      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);
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];      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);
   ludcmp(a,npar,indx,&pd);      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
   #endif
   for (j=1;j<=npar;j++) {      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
     for (i=1;i<=npar;i++) x[i]=0;        *xmin=x; 
     x[j]=1;        return fx; 
     lubksb(a,npar,indx,x);      } 
     for (i=1;i<=npar;i++){      ftemp=fu;
       matcov[i][j]=x[i];      if (fabs(e) > tol1) { 
     }        r=(x-w)*(fx-fv); 
   }        q=(x-v)*(fx-fw); 
         p=(x-v)*q-(x-w)*r; 
   printf("\n#Hessian matrix#\n");        q=2.0*(q-r); 
   for (i=1;i<=npar;i++) {        if (q > 0.0) p = -p; 
     for (j=1;j<=npar;j++) {        q=fabs(q); 
       printf("%.3e ",hess[i][j]);        etemp=e; 
     }        e=d; 
     printf("\n");        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
   }          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
         else { 
   /* Recompute Inverse */          d=p/q; 
   for (i=1;i<=npar;i++)          u=x+d; 
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];          if (u-a < tol2 || b-u < tol2) 
   ludcmp(a,npar,indx,&pd);            d=SIGN(tol1,xm-x); 
         } 
   /*  printf("\n#Hessian matrix recomputed#\n");      } else { 
         d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   for (j=1;j<=npar;j++) {      } 
     for (i=1;i<=npar;i++) x[i]=0;      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
     x[j]=1;      fu=(*f)(u); 
     lubksb(a,npar,indx,x);      if (fu <= fx) { 
     for (i=1;i<=npar;i++){        if (u >= x) a=x; else b=x; 
       y[i][j]=x[i];        SHFT(v,w,x,u) 
       printf("%.3e ",y[i][j]);          SHFT(fv,fw,fx,fu) 
     }          } else { 
     printf("\n");            if (u < x) a=u; else b=u; 
   }            if (fu <= fw || w == x) { 
   */              v=w; 
               w=u; 
   free_matrix(a,1,npar,1,npar);              fv=fw; 
   free_matrix(y,1,npar,1,npar);              fw=fu; 
   free_vector(x,1,npar);            } else if (fu <= fv || v == x || v == w) { 
   free_ivector(indx,1,npar);              v=u; 
   free_matrix(hess,1,npar,1,npar);              fv=fu; 
             } 
           } 
 }    } 
     nrerror("Too many iterations in brent"); 
 /*************** hessian matrix ****************/    *xmin=x; 
 double hessii( double x[], double delta, int theta, double delti[])    return fx; 
 {  } 
   int i;  
   int l=1, lmax=20;  /****************** mnbrak ***********************/
   double k1,k2;  
   double p2[NPARMAX+1];  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
   double res;              double (*func)(double)) 
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;  { 
   double fx;    double ulim,u,r,q, dum;
   int k=0,kmax=10;    double fu; 
   double l1;   
     *fa=(*func)(*ax); 
   fx=func(x);    *fb=(*func)(*bx); 
   for (i=1;i<=npar;i++) p2[i]=x[i];    if (*fb > *fa) { 
   for(l=0 ; l <=lmax; l++){      SHFT(dum,*ax,*bx,dum) 
     l1=pow(10,l);        SHFT(dum,*fb,*fa,dum) 
     delts=delt;        } 
     for(k=1 ; k <kmax; k=k+1){    *cx=(*bx)+GOLD*(*bx-*ax); 
       delt = delta*(l1*k);    *fc=(*func)(*cx); 
       p2[theta]=x[theta] +delt;    while (*fb > *fc) { 
       k1=func(p2)-fx;      r=(*bx-*ax)*(*fb-*fc); 
       p2[theta]=x[theta]-delt;      q=(*bx-*cx)*(*fb-*fa); 
       k2=func(p2)-fx;      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
       /*res= (k1-2.0*fx+k2)/delt/delt; */        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */      ulim=(*bx)+GLIMIT*(*cx-*bx); 
            if ((*bx-u)*(u-*cx) > 0.0) { 
 #ifdef DEBUG        fu=(*func)(u); 
       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);      } else if ((*cx-u)*(u-ulim) > 0.0) { 
 #endif        fu=(*func)(u); 
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */        if (fu < *fc) { 
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
         k=kmax;            SHFT(*fb,*fc,fu,(*func)(u)) 
       }            } 
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
         k=kmax; l=lmax*10.;        u=ulim; 
       }        fu=(*func)(u); 
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){      } else { 
         delts=delt;        u=(*cx)+GOLD*(*cx-*bx); 
       }        fu=(*func)(u); 
     }      } 
   }      SHFT(*ax,*bx,*cx,u) 
   delti[theta]=delts;        SHFT(*fa,*fb,*fc,fu) 
   return res;        } 
    } 
 }  
   /*************** linmin ************************/
 double hessij( double x[], double delti[], int thetai,int thetaj)  
 {  int ncom; 
   int i;  double *pcom,*xicom;
   int l=1, l1, lmax=20;  double (*nrfunc)(double []); 
   double k1,k2,k3,k4,res,fx;   
   double p2[NPARMAX+1];  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
   int k;  { 
     double brent(double ax, double bx, double cx, 
   fx=func(x);                 double (*f)(double), double tol, double *xmin); 
   for (k=1; k<=2; k++) {    double f1dim(double x); 
     for (i=1;i<=npar;i++) p2[i]=x[i];    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
     p2[thetai]=x[thetai]+delti[thetai]/k;                double *fc, double (*func)(double)); 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    int j; 
     k1=func(p2)-fx;    double xx,xmin,bx,ax; 
      double fx,fb,fa;
     p2[thetai]=x[thetai]+delti[thetai]/k;   
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    ncom=n; 
     k2=func(p2)-fx;    pcom=vector(1,n); 
      xicom=vector(1,n); 
     p2[thetai]=x[thetai]-delti[thetai]/k;    nrfunc=func; 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    for (j=1;j<=n;j++) { 
     k3=func(p2)-fx;      pcom[j]=p[j]; 
        xicom[j]=xi[j]; 
     p2[thetai]=x[thetai]-delti[thetai]/k;    } 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    ax=0.0; 
     k4=func(p2)-fx;    xx=1.0; 
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
 #ifdef DEBUG    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);  #ifdef DEBUG
 #endif    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   }    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   return res;  #endif
 }    for (j=1;j<=n;j++) { 
       xi[j] *= xmin; 
 /************** Inverse of matrix **************/      p[j] += xi[j]; 
 void ludcmp(double **a, int n, int *indx, double *d)    } 
 {    free_vector(xicom,1,n); 
   int i,imax,j,k;    free_vector(pcom,1,n); 
   double big,dum,sum,temp;  } 
   double *vv;  
    char *asc_diff_time(long time_sec, char ascdiff[])
   vv=vector(1,n);  {
   *d=1.0;    long sec_left, days, hours, minutes;
   for (i=1;i<=n;i++) {    days = (time_sec) / (60*60*24);
     big=0.0;    sec_left = (time_sec) % (60*60*24);
     for (j=1;j<=n;j++)    hours = (sec_left) / (60*60) ;
       if ((temp=fabs(a[i][j])) > big) big=temp;    sec_left = (sec_left) %(60*60);
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");    minutes = (sec_left) /60;
     vv[i]=1.0/big;    sec_left = (sec_left) % (60);
   }    sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);  
   for (j=1;j<=n;j++) {    return ascdiff;
     for (i=1;i<j;i++) {  }
       sum=a[i][j];  
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];  /*************** powell ************************/
       a[i][j]=sum;  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
     }              double (*func)(double [])) 
     big=0.0;  { 
     for (i=j;i<=n;i++) {    void linmin(double p[], double xi[], int n, double *fret, 
       sum=a[i][j];                double (*func)(double [])); 
       for (k=1;k<j;k++)    int i,ibig,j; 
         sum -= a[i][k]*a[k][j];    double del,t,*pt,*ptt,*xit;
       a[i][j]=sum;    double fp,fptt;
       if ( (dum=vv[i]*fabs(sum)) >= big) {    double *xits;
         big=dum;    int niterf, itmp;
         imax=i;  
       }    pt=vector(1,n); 
     }    ptt=vector(1,n); 
     if (j != imax) {    xit=vector(1,n); 
       for (k=1;k<=n;k++) {    xits=vector(1,n); 
         dum=a[imax][k];    *fret=(*func)(p); 
         a[imax][k]=a[j][k];    for (j=1;j<=n;j++) pt[j]=p[j]; 
         a[j][k]=dum;    for (*iter=1;;++(*iter)) { 
       }      fp=(*fret); 
       *d = -(*d);      ibig=0; 
       vv[imax]=vv[j];      del=0.0; 
     }      last_time=curr_time;
     indx[j]=imax;      (void) gettimeofday(&curr_time,&tzp);
     if (a[j][j] == 0.0) a[j][j]=TINY;      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);
     if (j != n) {      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);
       dum=1.0/(a[j][j]);  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
       for (i=j+1;i<=n;i++) a[i][j] *= dum;     for (i=1;i<=n;i++) {
     }        printf(" %d %.12f",i, p[i]);
   }        fprintf(ficlog," %d %.12lf",i, p[i]);
   free_vector(vv,1,n);  /* Doesn't work */        fprintf(ficrespow," %.12lf", p[i]);
 ;      }
 }      printf("\n");
       fprintf(ficlog,"\n");
 void lubksb(double **a, int n, int *indx, double b[])      fprintf(ficrespow,"\n");fflush(ficrespow);
 {      if(*iter <=3){
   int i,ii=0,ip,j;        tm = *localtime(&curr_time.tv_sec);
   double sum;        strcpy(strcurr,asctime(&tm));
    /*       asctime_r(&tm,strcurr); */
   for (i=1;i<=n;i++) {        forecast_time=curr_time; 
     ip=indx[i];        itmp = strlen(strcurr);
     sum=b[ip];        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
     b[ip]=b[i];          strcurr[itmp-1]='\0';
     if (ii)        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
     else if (sum) ii=i;        for(niterf=10;niterf<=30;niterf+=10){
     b[i]=sum;          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
   }          tmf = *localtime(&forecast_time.tv_sec);
   for (i=n;i>=1;i--) {  /*      asctime_r(&tmf,strfor); */
     sum=b[i];          strcpy(strfor,asctime(&tmf));
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];          itmp = strlen(strfor);
     b[i]=sum/a[i][i];          if(strfor[itmp-1]=='\n')
   }          strfor[itmp-1]='\0';
 }          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);
 /************ 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 */      for (i=1;i<=n;i++) { 
          for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;        fptt=(*fret); 
   double ***freq; /* Frequencies */  #ifdef DEBUG
   double *pp;        printf("fret=%lf \n",*fret);
   double pos, k2, dateintsum=0,k2cpt=0;        fprintf(ficlog,"fret=%lf \n",*fret);
   FILE *ficresp;  #endif
   char fileresp[FILENAMELENGTH];        printf("%d",i);fflush(stdout);
          fprintf(ficlog,"%d",i);fflush(ficlog);
   pp=vector(1,nlstate);        linmin(p,xit,n,fret,func); 
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);        if (fabs(fptt-(*fret)) > del) { 
   strcpy(fileresp,"p");          del=fabs(fptt-(*fret)); 
   strcat(fileresp,fileres);          ibig=i; 
   if((ficresp=fopen(fileresp,"w"))==NULL) {        } 
     printf("Problem with prevalence resultfile: %s\n", fileresp);  #ifdef DEBUG
     exit(0);        printf("%d %.12e",i,(*fret));
   }        fprintf(ficlog,"%d %.12e",i,(*fret));
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);        for (j=1;j<=n;j++) {
   j1=0;          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
           printf(" x(%d)=%.12e",j,xit[j]);
   j=cptcoveff;          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
   if (cptcovn<1) {j=1;ncodemax[1]=1;}        }
         for(j=1;j<=n;j++) {
   for(k1=1; k1<=j;k1++){          printf(" p=%.12e",p[j]);
    for(i1=1; i1<=ncodemax[k1];i1++){          fprintf(ficlog," p=%.12e",p[j]);
        j1++;        }
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);        printf("\n");
          scanf("%d", i);*/        fprintf(ficlog,"\n");
         for (i=-1; i<=nlstate+ndeath; i++)    #endif
          for (jk=-1; jk<=nlstate+ndeath; jk++)        } 
            for(m=agemin; m <= agemax+3; m++)      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
              freq[i][jk][m]=0;  #ifdef DEBUG
         int k[2],l;
         dateintsum=0;        k[0]=1;
         k2cpt=0;        k[1]=-1;
        for (i=1; i<=imx; i++) {        printf("Max: %.12e",(*func)(p));
          bool=1;        fprintf(ficlog,"Max: %.12e",(*func)(p));
          if  (cptcovn>0) {        for (j=1;j<=n;j++) {
            for (z1=1; z1<=cptcoveff; z1++)          printf(" %.12e",p[j]);
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])          fprintf(ficlog," %.12e",p[j]);
                bool=0;        }
          }        printf("\n");
          if (bool==1) {        fprintf(ficlog,"\n");
            for(m=firstpass; m<=lastpass; m++){        for(l=0;l<=1;l++) {
              k2=anint[m][i]+(mint[m][i]/12.);          for (j=1;j<=n;j++) {
              if ((k2>=dateprev1) && (k2<=dateprev2)) {            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
                if(agev[m][i]==0) agev[m][i]=agemax+1;            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
                if(agev[m][i]==1) agev[m][i]=agemax+2;            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];          }
                freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
                  dateintsum=dateintsum+k2;        }
                  k2cpt++;  #endif
                }  
   
              }        free_vector(xit,1,n); 
            }        free_vector(xits,1,n); 
          }        free_vector(ptt,1,n); 
        }        free_vector(pt,1,n); 
                return; 
        fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);      } 
       if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
         if  (cptcovn>0) {      for (j=1;j<=n;j++) { 
          fprintf(ficresp, "\n#********** Variable ");        ptt[j]=2.0*p[j]-pt[j]; 
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);        xit[j]=p[j]-pt[j]; 
        fprintf(ficresp, "**********\n#");        pt[j]=p[j]; 
         }      } 
        for(i=1; i<=nlstate;i++)      fptt=(*func)(ptt); 
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);      if (fptt < fp) { 
        fprintf(ficresp, "\n");        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
                if (t < 0.0) { 
   for(i=(int)agemin; i <= (int)agemax+3; i++){          linmin(p,xit,n,fret,func); 
     if(i==(int)agemax+3)          for (j=1;j<=n;j++) { 
       printf("Total");            xi[j][ibig]=xi[j][n]; 
     else            xi[j][n]=xit[j]; 
       printf("Age %d", i);          }
     for(jk=1; jk <=nlstate ; jk++){  #ifdef DEBUG
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
         pp[jk] += freq[jk][m][i];          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
     }          for(j=1;j<=n;j++){
     for(jk=1; jk <=nlstate ; jk++){            printf(" %.12e",xit[j]);
       for(m=-1, pos=0; m <=0 ; m++)            fprintf(ficlog," %.12e",xit[j]);
         pos += freq[jk][m][i];          }
       if(pp[jk]>=1.e-10)          printf("\n");
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);          fprintf(ficlog,"\n");
       else  #endif
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);        }
     }      } 
     } 
      for(jk=1; jk <=nlstate ; jk++){  } 
       for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)  
         pp[jk] += freq[jk][m][i];  /**** Prevalence limit (stable or period prevalence)  ****************/
      }  
   double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
     for(jk=1,pos=0; jk <=nlstate ; jk++)  {
       pos += pp[jk];    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
     for(jk=1; jk <=nlstate ; jk++){       matrix by transitions matrix until convergence is reached */
       if(pos>=1.e-5)  
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);    int i, ii,j,k;
       else    double min, max, maxmin, maxmax,sumnew=0.;
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);    double **matprod2();
       if( i <= (int) agemax){    double **out, cov[NCOVMAX+1], **pmij();
         if(pos>=1.e-5){    double **newm;
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);    double agefin, delaymax=50 ; /* Max number of years to converge */
           probs[i][jk][j1]= pp[jk]/pos;  
           /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/    for (ii=1;ii<=nlstate+ndeath;ii++)
         }      for (j=1;j<=nlstate+ndeath;j++){
       else        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);      }
       }  
     }     cov[1]=1.;
     for(jk=-1; jk <=nlstate+ndeath; jk++)   
       for(m=-1; m <=nlstate+ndeath; m++)   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
     if(i <= (int) agemax)      newm=savm;
       fprintf(ficresp,"\n");      /* Covariates have to be included here again */
     printf("\n");      cov[2]=agefin;
     }      
     }      for (k=1; k<=cptcovn;k++) {
  }        cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   dateintmean=dateintsum/k2cpt;        /*        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]]);*/
        }
   fclose(ficresp);      for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);      for (k=1; k<=cptcovprod;k++)
   free_vector(pp,1,nlstate);        cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
       
   /* End of Freq */      /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
 }      /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
 /************ Prevalence ********************/      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
 void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)      
 {  /* Some frequencies */      savm=oldm;
        oldm=newm;
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;      maxmax=0.;
   double ***freq; /* Frequencies */      for(j=1;j<=nlstate;j++){
   double *pp;        min=1.;
   double pos, k2;        max=0.;
         for(i=1; i<=nlstate; i++) {
   pp=vector(1,nlstate);          sumnew=0;
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
            prlim[i][j]= newm[i][j]/(1-sumnew);
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);          max=FMAX(max,prlim[i][j]);
   j1=0;          min=FMIN(min,prlim[i][j]);
          }
   j=cptcoveff;        maxmin=max-min;
   if (cptcovn<1) {j=1;ncodemax[1]=1;}        maxmax=FMAX(maxmax,maxmin);
        }
  for(k1=1; k1<=j;k1++){      if(maxmax < ftolpl){
     for(i1=1; i1<=ncodemax[k1];i1++){        return prlim;
       j1++;      }
      }
       for (i=-1; i<=nlstate+ndeath; i++)    }
         for (jk=-1; jk<=nlstate+ndeath; jk++)    
           for(m=agemin; m <= agemax+3; m++)  /*************** transition probabilities ***************/ 
             freq[i][jk][m]=0;  
        double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
       for (i=1; i<=imx; i++) {  {
         bool=1;    /* According to parameters values stored in x and the covariate's values stored in cov,
         if  (cptcovn>0) {       computes the probability to be observed in state j being in state i by appying the
           for (z1=1; z1<=cptcoveff; z1++)       model to the ncovmodel covariates (including constant and age).
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])       lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
               bool=0;       and, according on how parameters are entered, the position of the coefficient xij(nc) of the
         }       ncth covariate in the global vector x is given by the formula:
         if (bool==1) {       j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
           for(m=firstpass; m<=lastpass; m++){       j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
             k2=anint[m][i]+(mint[m][i]/12.);       Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
             if ((k2>=dateprev1) && (k2<=dateprev2)) {       sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
               if(agev[m][i]==0) agev[m][i]=agemax+1;       Outputs ps[i][j] the probability to be observed in j being in j according to
               if(agev[m][i]==1) agev[m][i]=agemax+2;       the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
               freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];    */
               /* freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];  */    double s1, lnpijopii;
             }    /*double t34;*/
           }    int i,j,j1, nc, ii, jj;
         }  
       }      for(i=1; i<= nlstate; i++){
         for(i=(int)agemin; i <= (int)agemax+3; i++){        for(j=1; j<i;j++){
           for(jk=1; jk <=nlstate ; jk++){          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)            /*lnpijopii += param[i][j][nc]*cov[nc];*/
               pp[jk] += freq[jk][m][i];            lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
           }  /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
           for(jk=1; jk <=nlstate ; jk++){          }
             for(m=-1, pos=0; m <=0 ; m++)          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
             pos += freq[jk][m][i];  /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
         }        }
                for(j=i+1; j<=nlstate+ndeath;j++){
          for(jk=1; jk <=nlstate ; jk++){          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)            /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
              pp[jk] += freq[jk][m][i];            lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
          }  /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
                    }
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
         }
          for(jk=1; jk <=nlstate ; jk++){                }
            if( i <= (int) agemax){      
              if(pos>=1.e-5){      for(i=1; i<= nlstate; i++){
                probs[i][jk][j1]= pp[jk]/pos;        s1=0;
              }        for(j=1; j<i; j++){
            }          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
          }          /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
                  }
         }        for(j=i+1; j<=nlstate+ndeath; j++){
     }          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
   }          /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
          }
          /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);        ps[i][i]=1./(s1+1.);
   free_vector(pp,1,nlstate);        /* Computing other pijs */
          for(j=1; j<i; j++)
 }  /* End of Freq */          ps[i][j]= exp(ps[i][j])*ps[i][i];
         for(j=i+1; j<=nlstate+ndeath; j++)
 /************* Waves Concatenation ***************/          ps[i][j]= exp(ps[i][j])*ps[i][i];
         /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)      } /* end i */
 {      
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
      Death is a valid wave (if date is known).        for(jj=1; jj<= nlstate+ndeath; jj++){
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i          ps[ii][jj]=0;
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]          ps[ii][ii]=1;
      and mw[mi+1][i]. dh depends on stepm.        }
      */      }
       
   int i, mi, m;  
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;  /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
      double sum=0., jmean=0.;*/  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
   /*         printf("ddd %lf ",ps[ii][jj]); */
   int j, k=0,jk, ju, jl;  /*       } */
   double sum=0.;  /*       printf("\n "); */
   jmin=1e+5;  /*        } */
   jmax=-1;  /*        printf("\n ");printf("%lf ",cov[2]); */
   jmean=0.;         /*
   for(i=1; i<=imx; i++){        for(i=1; i<= npar; i++) printf("%f ",x[i]);
     mi=0;        goto end;*/
     m=firstpass;      return ps;
     while(s[m][i] <= nlstate){  }
       if(s[m][i]>=1)  
         mw[++mi][i]=m;  /**************** Product of 2 matrices ******************/
       if(m >=lastpass)  
         break;  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
       else  {
         m++;    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
     }/* end while */       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
     if (s[m][i] > nlstate){    /* in, b, out are matrice of pointers which should have been initialized 
       mi++;     /* Death is another wave */       before: only the contents of out is modified. The function returns
       /* if(mi==0)  never been interviewed correctly before death */       a pointer to pointers identical to out */
          /* Only death is a correct wave */    long i, j, k;
       mw[mi][i]=m;    for(i=nrl; i<= nrh; i++)
     }      for(k=ncolol; k<=ncoloh; k++)
         for(j=ncl,out[i][k]=0.; j<=nch; j++)
     wav[i]=mi;          out[i][k] +=in[i][j]*b[j][k];
     if(mi==0)  
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);    return out;
   }  }
   
   for(i=1; i<=imx; i++){  
     for(mi=1; mi<wav[i];mi++){  /************* Higher Matrix Product ***************/
       if (stepm <=0)  
         dh[mi][i]=1;  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
       else{  {
         if (s[mw[mi+1][i]][i] > nlstate) {    /* Computes the transition matrix starting at age 'age' over 
           if (agedc[i] < 2*AGESUP) {       'nhstepm*hstepm*stepm' months (i.e. until
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
           if(j==0) j=1;  /* Survives at least one month after exam */       nhstepm*hstepm matrices. 
           k=k+1;       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
           if (j >= jmax) jmax=j;       (typically every 2 years instead of every month which is too big 
           if (j <= jmin) jmin=j;       for the memory).
           sum=sum+j;       Model is determined by parameters x and covariates have to be 
           /*if (j<0) printf("j=%d num=%d \n",j,i); */       included manually here. 
           }  
         }       */
         else{  
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));    int i, j, d, h, k;
           k=k+1;    double **out, cov[NCOVMAX+1];
           if (j >= jmax) jmax=j;    double **newm;
           else if (j <= jmin)jmin=j;  
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */    /* Hstepm could be zero and should return the unit matrix */
           sum=sum+j;    for (i=1;i<=nlstate+ndeath;i++)
         }      for (j=1;j<=nlstate+ndeath;j++){
         jk= j/stepm;        oldm[i][j]=(i==j ? 1.0 : 0.0);
         jl= j -jk*stepm;        po[i][j][0]=(i==j ? 1.0 : 0.0);
         ju= j -(jk+1)*stepm;      }
         if(jl <= -ju)    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
           dh[mi][i]=jk;    for(h=1; h <=nhstepm; h++){
         else      for(d=1; d <=hstepm; d++){
           dh[mi][i]=jk+1;        newm=savm;
         if(dh[mi][i]==0)        /* Covariates have to be included here again */
           dh[mi][i]=1; /* At least one step */        cov[1]=1.;
       }        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
     }        for (k=1; k<=cptcovn;k++) 
   }          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   jmean=sum/k;        for (k=1; k<=cptcovage;k++)
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
  }        for (k=1; k<=cptcovprod;k++)
 /*********** Tricode ****************************/          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
 void tricode(int *Tvar, int **nbcode, int imx)  
 {  
   int Ndum[20],ij=1, k, j, i;        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
   int cptcode=0;        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
   cptcoveff=0;        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
                       pmij(pmmij,cov,ncovmodel,x,nlstate));
   for (k=0; k<19; k++) Ndum[k]=0;        savm=oldm;
   for (k=1; k<=7; k++) ncodemax[k]=0;        oldm=newm;
       }
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {      for(i=1; i<=nlstate+ndeath; i++)
     for (i=1; i<=imx; i++) {        for(j=1;j<=nlstate+ndeath;j++) {
       ij=(int)(covar[Tvar[j]][i]);          po[i][j][h]=newm[i][j];
       Ndum[ij]++;          /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/        }
       if (ij > cptcode) cptcode=ij;      /*printf("h=%d ",h);*/
     }    } /* end h */
   /*     printf("\n H=%d \n",h); */
     for (i=0; i<=cptcode; i++) {    return po;
       if(Ndum[i]!=0) ncodemax[j]++;  }
     }  
     ij=1;  
   /*************** log-likelihood *************/
   double func( double *x)
     for (i=1; i<=ncodemax[j]; i++) {  {
       for (k=0; k<=19; k++) {    int i, ii, j, k, mi, d, kk;
         if (Ndum[k] != 0) {    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
           nbcode[Tvar[j]][ij]=k;    double **out;
           ij++;    double sw; /* Sum of weights */
         }    double lli; /* Individual log likelihood */
         if (ij > ncodemax[j]) break;    int s1, s2;
       }      double bbh, survp;
     }    long ipmx;
   }      /*extern weight */
     /* We are differentiating ll according to initial status */
  for (k=0; k<19; k++) Ndum[k]=0;    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     /*for(i=1;i<imx;i++) 
  for (i=1; i<=ncovmodel-2; i++) {      printf(" %d\n",s[4][i]);
       ij=Tvar[i];    */
       Ndum[ij]++;    cov[1]=1.;
     }  
     for(k=1; k<=nlstate; k++) ll[k]=0.;
  ij=1;  
  for (i=1; i<=10; i++) {    if(mle==1){
    if((Ndum[i]!=0) && (i<=ncov)){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
      Tvaraff[ij]=i;        /* Computes the values of the ncovmodel covariates of the model
      ij++;           depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
    }           Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
  }           to be observed in j being in i according to the model.
           */
     cptcoveff=ij-1;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
 }        /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 
            is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] 
 /*********** Health Expectancies ****************/           has been calculated etc */
         for(mi=1; mi<= wav[i]-1; mi++){
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)          for (ii=1;ii<=nlstate+ndeath;ii++)
 {            for (j=1;j<=nlstate+ndeath;j++){
   /* Health expectancies */              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   int i, j, nhstepm, hstepm, h, nstepm, k;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   double age, agelim,hf;            }
   double ***p3mat;          for(d=0; d<dh[mi][i]; d++){
              newm=savm;
   fprintf(ficreseij,"# Health expectancies\n");            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   fprintf(ficreseij,"# Age");            for (kk=1; kk<=cptcovage;kk++) {
   for(i=1; i<=nlstate;i++)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
     for(j=1; j<=nlstate;j++)            }
       fprintf(ficreseij," %1d-%1d",i,j);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   fprintf(ficreseij,"\n");                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
   k=1;             /* For example stepm=6 months */            oldm=newm;
   hstepm=k*YEARM; /* (a) Every k years of age (in months), for example every k=2 years 24 m */          } /* end mult */
   hstepm=stepm;   /* or (b) 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.          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
      nhstepm is the number of hstepm from age to agelim          /* But now since version 0.9 we anticipate for bias at large stepm.
      nstepm is the number of stepm from age to agelin.           * If stepm is larger than one month (smallest stepm) and if the exact delay 
      Look at hpijx to understand the reason of that which relies in memory size           * (in months) between two waves is not a multiple of stepm, we rounded to 
      and note for a fixed period like k years */           * the nearest (and in case of equal distance, to the lowest) interval but now
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the           * we keep into memory the bias bh[mi][i] and also the previous matrix product
      survival function given by stepm (the optimization length). Unfortunately it           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
      means that if the survival funtion is printed only each two years of age and if           * probability in order to take into account the bias as a fraction of the way
      you sum them up and add 1 year (area under the trapezoids) you won't get the same           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
      results. So we changed our mind and took the option of the best precision.           * -stepm/2 to stepm/2 .
   */           * For stepm=1 the results are the same as for previous versions of Imach.
   hstepm=hstepm/stepm; /* Typically in stepm units, if k= 2 years, = 2/6 months = 4 */           * For stepm > 1 the results are less biased than in previous versions. 
            */
   agelim=AGESUP;          s1=s[mw[mi][i]][i];
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          s2=s[mw[mi+1][i]][i];
     /* nhstepm age range expressed in number of stepm */          bbh=(double)bh[mi][i]/(double)stepm; 
     nstepm=(int) rint((agelim-age)*YEARM/stepm);          /* bias bh is positive if real duration
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */           * is higher than the multiple of stepm and negative otherwise.
     /* if (stepm >= YEARM) hstepm=1;*/           */
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          if( s2 > nlstate){ 
     /* Computed by stepm unit matrices, product of hstepm matrices, stored            /* i.e. if s2 is a death state and if the date of death is known 
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */               then the contribution to the likelihood is the probability to 
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);                 die between last step unit time and current  step unit time, 
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */               which is also equal to probability to die before dh 
     for(i=1; i<=nlstate;i++)               minus probability to die before dh-stepm . 
       for(j=1; j<=nlstate;j++)               In version up to 0.92 likelihood was computed
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){          as if date of death was unknown. Death was treated as any other
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;          health state: the date of the interview describes the actual state
           /* 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]);*/          and not the date of a change in health state. The former idea was
         }          to consider that at each interview the state was recorded
     fprintf(ficreseij,"%3.0f",age );          (healthy, disable or death) and IMaCh was corrected; but when we
     for(i=1; i<=nlstate;i++)          introduced the exact date of death then we should have modified
       for(j=1; j<=nlstate;j++){          the contribution of an exact death to the likelihood. This new
         fprintf(ficreseij," %9.4f", eij[i][j][(int)age]);          contribution is smaller and very dependent of the step unit
       }          stepm. It is no more the probability to die between last interview
     fprintf(ficreseij,"\n");          and month of death but the probability to survive from last
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          interview up to one month before death multiplied by the
   }          probability to die within a month. Thanks to Chris
 }          Jackson for correcting this bug.  Former versions increased
           mortality artificially. The bad side is that we add another loop
 /************ Variance ******************/          which slows down the processing. The difference can be up to 10%
 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)          lower mortality.
 {            */
   /* Variance of health expectancies */            lli=log(out[s1][s2] - savm[s1][s2]);
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/  
   double **newm;  
   double **dnewm,**doldm;          } else if  (s2==-2) {
   int i, j, nhstepm, hstepm, h;            for (j=1,survp=0. ; j<=nlstate; j++) 
   int k, cptcode;              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   double *xp;            /*survp += out[s1][j]; */
   double **gp, **gm;            lli= log(survp);
   double ***gradg, ***trgradg;          }
   double ***p3mat;          
   double age,agelim;          else if  (s2==-4) { 
   int theta;            for (j=3,survp=0. ; j<=nlstate; j++)  
               survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
    fprintf(ficresvij,"# Covariances of life expectancies\n");            lli= log(survp); 
   fprintf(ficresvij,"# Age");          } 
   for(i=1; i<=nlstate;i++)  
     for(j=1; j<=nlstate;j++)          else if  (s2==-5) { 
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);            for (j=1,survp=0. ; j<=2; j++)  
   fprintf(ficresvij,"\n");              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
             lli= log(survp); 
   xp=vector(1,npar);          } 
   dnewm=matrix(1,nlstate,1,npar);          
   doldm=matrix(1,nlstate,1,nlstate);          else{
              lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   hstepm=1*YEARM; /* Every year of age */            /*  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 */
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */          } 
   agelim = AGESUP;          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          /*if(lli ==000.0)*/
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          /*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); */
     if (stepm >= YEARM) hstepm=1;          ipmx +=1;
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */          sw += weight[i];
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);        } /* end of wave */
     gp=matrix(0,nhstepm,1,nlstate);      } /* end of individual */
     gm=matrix(0,nhstepm,1,nlstate);    }  else if(mle==2){
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     for(theta=1; theta <=npar; theta++){        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       for(i=1; i<=npar; i++){ /* Computes gradient */        for(mi=1; mi<= wav[i]-1; mi++){
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          for (ii=1;ii<=nlstate+ndeath;ii++)
       }            for (j=1;j<=nlstate+ndeath;j++){
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);                oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             }
       if (popbased==1) {          for(d=0; d<=dh[mi][i]; d++){
         for(i=1; i<=nlstate;i++)            newm=savm;
           prlim[i][i]=probs[(int)age][i][ij];            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       }            for (kk=1; kk<=cptcovage;kk++) {
                cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       for(j=1; j<= nlstate; j++){            }
         for(h=0; h<=nhstepm; h++){            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];            savm=oldm;
         }            oldm=newm;
       }          } /* end mult */
            
       for(i=1; i<=npar; i++) /* Computes gradient */          s1=s[mw[mi][i]][i];
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          s2=s[mw[mi+1][i]][i];
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            bbh=(double)bh[mi][i]/(double)stepm; 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          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;
       if (popbased==1) {          sw += weight[i];
         for(i=1; i<=nlstate;i++)          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           prlim[i][i]=probs[(int)age][i][ij];        } /* end of wave */
       }      } /* end of individual */
     }  else if(mle==3){  /* exponential inter-extrapolation */
       for(j=1; j<= nlstate; j++){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for(h=0; h<=nhstepm; h++){        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)        for(mi=1; mi<= wav[i]-1; mi++){
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];          for (ii=1;ii<=nlstate+ndeath;ii++)
         }            for (j=1;j<=nlstate+ndeath;j++){
       }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               savm[ii][j]=(ii==j ? 1.0 : 0.0);
       for(j=1; j<= nlstate; j++)            }
         for(h=0; h<=nhstepm; h++){          for(d=0; d<dh[mi][i]; d++){
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];            newm=savm;
         }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     } /* End theta */            for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);            }
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     for(h=0; h<=nhstepm; h++)                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       for(j=1; j<=nlstate;j++)            savm=oldm;
         for(theta=1; theta <=npar; theta++)            oldm=newm;
           trgradg[h][j][theta]=gradg[h][theta][j];          } /* end mult */
         
     for(i=1;i<=nlstate;i++)          s1=s[mw[mi][i]][i];
       for(j=1;j<=nlstate;j++)          s2=s[mw[mi+1][i]][i];
         vareij[i][j][(int)age] =0.;          bbh=(double)bh[mi][i]/(double)stepm; 
     for(h=0;h<=nhstepm;h++){          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 */
       for(k=0;k<=nhstepm;k++){          ipmx +=1;
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);          sw += weight[i];
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         for(i=1;i<=nlstate;i++)        } /* end of wave */
           for(j=1;j<=nlstate;j++)      } /* end of individual */
             vareij[i][j][(int)age] += doldm[i][j];    }else if (mle==4){  /* ml=4 no inter-extrapolation */
       }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     h=1;        for(mi=1; mi<= wav[i]-1; mi++){
     if (stepm >= YEARM) h=stepm/YEARM;          for (ii=1;ii<=nlstate+ndeath;ii++)
     fprintf(ficresvij,"%.0f ",age );            for (j=1;j<=nlstate+ndeath;j++){
     for(i=1; i<=nlstate;i++)              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       for(j=1; j<=nlstate;j++){              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);            }
       }          for(d=0; d<dh[mi][i]; d++){
     fprintf(ficresvij,"\n");            newm=savm;
     free_matrix(gp,0,nhstepm,1,nlstate);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     free_matrix(gm,0,nhstepm,1,nlstate);            for (kk=1; kk<=cptcovage;kk++) {
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);            }
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          
   } /* End age */            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   free_vector(xp,1,npar);            savm=oldm;
   free_matrix(doldm,1,nlstate,1,npar);            oldm=newm;
   free_matrix(dnewm,1,nlstate,1,nlstate);          } /* end mult */
         
 }          s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
 /************ Variance of prevlim ******************/          if( s2 > nlstate){ 
 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)            lli=log(out[s1][s2] - savm[s1][s2]);
 {          }else{
   /* Variance of prevalence limit */            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/          }
   double **newm;          ipmx +=1;
   double **dnewm,**doldm;          sw += weight[i];
   int i, j, nhstepm, hstepm;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   int k, cptcode;  /*      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 *xp;        } /* end of wave */
   double *gp, *gm;      } /* end of individual */
   double **gradg, **trgradg;    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
   double age,agelim;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   int theta;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
            for(mi=1; mi<= wav[i]-1; mi++){
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");          for (ii=1;ii<=nlstate+ndeath;ii++)
   fprintf(ficresvpl,"# Age");            for (j=1;j<=nlstate+ndeath;j++){
   for(i=1; i<=nlstate;i++)              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       fprintf(ficresvpl," %1d-%1d",i,i);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   fprintf(ficresvpl,"\n");            }
           for(d=0; d<dh[mi][i]; d++){
   xp=vector(1,npar);            newm=savm;
   dnewm=matrix(1,nlstate,1,npar);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   doldm=matrix(1,nlstate,1,nlstate);            for (kk=1; kk<=cptcovage;kk++) {
                cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   hstepm=1*YEARM; /* Every year of age */            }
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */          
   agelim = AGESUP;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */            savm=oldm;
     if (stepm >= YEARM) hstepm=1;            oldm=newm;
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */          } /* end mult */
     gradg=matrix(1,npar,1,nlstate);        
     gp=vector(1,nlstate);          s1=s[mw[mi][i]][i];
     gm=vector(1,nlstate);          s2=s[mw[mi+1][i]][i];
           lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
     for(theta=1; theta <=npar; theta++){          ipmx +=1;
       for(i=1; i<=npar; i++){ /* Computes gradient */          sw += weight[i];
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       }          /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        } /* end of wave */
       for(i=1;i<=nlstate;i++)      } /* end of individual */
         gp[i] = prlim[i][i];    } /* End of if */
        for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
       for(i=1; i<=npar; i++) /* Computes gradient */    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    return -l;
       for(i=1;i<=nlstate;i++)  }
         gm[i] = prlim[i][i];  
   /*************** log-likelihood *************/
       for(i=1;i<=nlstate;i++)  double funcone( double *x)
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];  {
     } /* End theta */    /* Same as likeli but slower because of a lot of printf and if */
     int i, ii, j, k, mi, d, kk;
     trgradg =matrix(1,nlstate,1,npar);    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
     double **out;
     for(j=1; j<=nlstate;j++)    double lli; /* Individual log likelihood */
       for(theta=1; theta <=npar; theta++)    double llt;
         trgradg[j][theta]=gradg[theta][j];    int s1, s2;
     double bbh, survp;
     for(i=1;i<=nlstate;i++)    /*extern weight */
       varpl[i][(int)age] =0.;    /* We are differentiating ll according to initial status */
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);    /*for(i=1;i<imx;i++) 
     for(i=1;i<=nlstate;i++)      printf(" %d\n",s[4][i]);
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */    */
     cov[1]=1.;
     fprintf(ficresvpl,"%.0f ",age );  
     for(i=1; i<=nlstate;i++)    for(k=1; k<=nlstate; k++) ll[k]=0.;
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));  
     fprintf(ficresvpl,"\n");    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     free_vector(gp,1,nlstate);      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     free_vector(gm,1,nlstate);      for(mi=1; mi<= wav[i]-1; mi++){
     free_matrix(gradg,1,npar,1,nlstate);        for (ii=1;ii<=nlstate+ndeath;ii++)
     free_matrix(trgradg,1,nlstate,1,npar);          for (j=1;j<=nlstate+ndeath;j++){
   } /* End age */            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
             savm[ii][j]=(ii==j ? 1.0 : 0.0);
   free_vector(xp,1,npar);          }
   free_matrix(doldm,1,nlstate,1,npar);        for(d=0; d<dh[mi][i]; d++){
   free_matrix(dnewm,1,nlstate,1,nlstate);          newm=savm;
           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
 }          for (kk=1; kk<=cptcovage;kk++) {
             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
 /************ Variance of one-step probabilities  ******************/          }
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 {                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   int i, j;          savm=oldm;
   int k=0, cptcode;          oldm=newm;
   double **dnewm,**doldm;        } /* end mult */
   double *xp;        
   double *gp, *gm;        s1=s[mw[mi][i]][i];
   double **gradg, **trgradg;        s2=s[mw[mi+1][i]][i];
   double age,agelim, cov[NCOVMAX];        bbh=(double)bh[mi][i]/(double)stepm; 
   int theta;        /* bias is positive if real duration
   char fileresprob[FILENAMELENGTH];         * is higher than the multiple of stepm and negative otherwise.
          */
   strcpy(fileresprob,"prob");        if( s2 > nlstate && (mle <5) ){  /* Jackson */
   strcat(fileresprob,fileres);          lli=log(out[s1][s2] - savm[s1][s2]);
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {        } else if  (s2==-2) {
     printf("Problem with resultfile: %s\n", fileresprob);          for (j=1,survp=0. ; j<=nlstate; j++) 
   }            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);          lli= log(survp);
          }else if (mle==1){
           lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   xp=vector(1,npar);        } else if(mle==2){
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);          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 */
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));        } else if(mle==3){  /* exponential inter-extrapolation */
            lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
   cov[1]=1;        } else if (mle==4){  /* mle=4 no inter-extrapolation */
   for (age=bage; age<=fage; age ++){          lli=log(out[s1][s2]); /* Original formula */
     cov[2]=age;        } else{  /* mle=0 back to 1 */
     gradg=matrix(1,npar,1,9);          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
     trgradg=matrix(1,9,1,npar);          /*lli=log(out[s1][s2]); */ /* Original formula */
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));        } /* End of if */
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));        ipmx +=1;
            sw += weight[i];
     for(theta=1; theta <=npar; theta++){        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       for(i=1; i<=npar; i++)        /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        if(globpr){
                fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
       pmij(pmmij,cov,ncovmodel,xp,nlstate);   %11.6f %11.6f %11.6f ", \
                      num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
       k=0;                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
       for(i=1; i<= (nlstate+ndeath); i++){          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
         for(j=1; j<=(nlstate+ndeath);j++){            llt +=ll[k]*gipmx/gsw;
            k=k+1;            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
           gp[k]=pmmij[i][j];          }
         }          fprintf(ficresilk," %10.6f\n", -llt);
       }        }
       } /* end of wave */
       for(i=1; i<=npar; i++)    } /* end of individual */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
        /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
       pmij(pmmij,cov,ncovmodel,xp,nlstate);    if(globpr==0){ /* First time we count the contributions and weights */
       k=0;      gipmx=ipmx;
       for(i=1; i<=(nlstate+ndeath); i++){      gsw=sw;
         for(j=1; j<=(nlstate+ndeath);j++){    }
           k=k+1;    return -l;
           gm[k]=pmmij[i][j];  }
         }  
       }  
        /*************** function likelione ***********/
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];    {
     }    /* This routine should help understanding what is done with 
        the selection of individuals/waves and
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)       to check the exact contribution to the likelihood.
       for(theta=1; theta <=npar; theta++)       Plotting could be done.
       trgradg[j][theta]=gradg[theta][j];     */
      int k;
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);  
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);    if(*globpri !=0){ /* Just counts and sums, no printings */
       strcpy(fileresilk,"ilk"); 
      pmij(pmmij,cov,ncovmodel,x,nlstate);      strcat(fileresilk,fileres);
       if((ficresilk=fopen(fileresilk,"w"))==NULL) {
      k=0;        printf("Problem with resultfile: %s\n", fileresilk);
      for(i=1; i<=(nlstate+ndeath); i++){        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
        for(j=1; j<=(nlstate+ndeath);j++){      }
          k=k+1;      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");
          gm[k]=pmmij[i][j];      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
         }      /*  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; k<=nlstate; k++) 
              fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
      /*printf("\n%d ",(int)age);      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){    }
          
     *fretone=(*funcone)(p);
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));    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));
   fprintf(ficresprob,"\n%d ",(int)age);      fflush(fichtm); 
     } 
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){    return;
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);  }
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);  
   }  
   /*********** Maximum Likelihood Estimation ***************/
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));  
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);  {
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    int i,j, iter;
 }    double **xi;
  free_vector(xp,1,npar);    double fret;
 fclose(ficresprob);    double fretone; /* Only one call to likelihood */
     /*  char filerespow[FILENAMELENGTH];*/
 }    xi=matrix(1,npar,1,npar);
     for (i=1;i<=npar;i++)
 /******************* Printing html file ***********/      for (j=1;j<=npar;j++)
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, int lastpass, int stepm, int weightopt, char model[],int imx,int jmin, int jmax, double jmeanint,char optionfile[],char optionfilehtm[],char rfileres[] ){        xi[i][j]=(i==j ? 1.0 : 0.0);
   int jj1, k1, i1, cpt;    printf("Powell\n");  fprintf(ficlog,"Powell\n");
   FILE *fichtm;    strcpy(filerespow,"pow"); 
   /*char optionfilehtm[FILENAMELENGTH];*/    strcat(filerespow,fileres);
     if((ficrespow=fopen(filerespow,"w"))==NULL) {
   strcpy(optionfilehtm,optionfile);      printf("Problem with resultfile: %s\n", filerespow);
   strcat(optionfilehtm,".htm");      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {    }
     printf("Problem with %s \n",optionfilehtm), exit(0);    fprintf(ficrespow,"# Powell\n# iter -2*LL");
   }    for (i=1;i<=nlstate;i++)
       for(j=1;j<=nlstate+ndeath;j++)
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.71e </font> <hr size=\"2\" color=\"#EC5E5E\">        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>    fprintf(ficrespow,"\n");
   
 Total number of observations=%d <br>    powell(p,xi,npar,ftol,&iter,&fret,func);
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>  
 <hr  size=\"2\" color=\"#EC5E5E\">    free_matrix(xi,1,npar,1,npar);
 <li>Outputs files<br><br>\n    fclose(ficrespow);
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>  
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>  }
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>  
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>  /**** Computes Hessian and covariance matrix ***/
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>  {
         - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>    double  **a,**y,*x,pd;
         - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>    double **hess;
         <br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);    int i, j,jk;
      int *indx;
 fprintf(fichtm," <li>Graphs</li><p>");  
     double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
  m=cptcoveff;    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}    void lubksb(double **a, int npar, int *indx, double b[]) ;
     void ludcmp(double **a, int npar, int *indx, double *d) ;
  jj1=0;    double gompertz(double p[]);
  for(k1=1; k1<=m;k1++){    hess=matrix(1,npar,1,npar);
    for(i1=1; i1<=ncodemax[k1];i1++){  
        jj1++;    printf("\nCalculation of the hessian matrix. Wait...\n");
        if (cptcovn > 0) {    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");    for (i=1;i<=npar;i++){
          for (cpt=1; cpt<=cptcoveff;cpt++)      printf("%d",i);fflush(stdout);
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);      fprintf(ficlog,"%d",i);fflush(ficlog);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");     
        }       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>      
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);          /*  printf(" %f ",p[i]);
        for(cpt=1; cpt<nlstate;cpt++){          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>    }
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    
        }    for (i=1;i<=npar;i++) {
     for(cpt=1; cpt<=nlstate;cpt++) {      for (j=1;j<=npar;j++)  {
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident        if (j>i) { 
 interval) in state (%d): v%s%d%d.gif <br>          printf(".%d%d",i,j);fflush(stdout);
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);            fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
      }          hess[i][j]=hessij(p,delti,i,j,func,npar);
      for(cpt=1; cpt<=nlstate;cpt++) {          
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>          hess[j][i]=hess[i][j];    
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);          /*printf(" %lf ",hess[i][j]);*/
      }        }
      fprintf(fichtm,"\n<br>- Total life expectancy by age and      }
 health expectancies in states (1) and (2): e%s%d.gif<br>    }
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);    printf("\n");
 fprintf(fichtm,"\n</body>");    fprintf(ficlog,"\n");
    }  
    }    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
 fclose(fichtm);    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
 }    
     a=matrix(1,npar,1,npar);
 /******************* Gnuplot file **************/    y=matrix(1,npar,1,npar);
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double agemin, double agemaxpar, double fage , char pathc[], double p[]){    x=vector(1,npar);
     indx=ivector(1,npar);
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;    for (i=1;i<=npar;i++)
       for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
   strcpy(optionfilegnuplot,optionfilefiname);    ludcmp(a,npar,indx,&pd);
   strcat(optionfilegnuplot,".plt");  
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {    for (j=1;j<=npar;j++) {
     printf("Problem with file %s",optionfilegnuplot);      for (i=1;i<=npar;i++) x[i]=0;
   }      x[j]=1;
       lubksb(a,npar,indx,x);
 #ifdef windows      for (i=1;i<=npar;i++){ 
     fprintf(ficgp,"cd \"%s\" \n",pathc);        matcov[i][j]=x[i];
 #endif      }
 m=pow(2,cptcoveff);    }
    
  /* 1eme*/    printf("\n#Hessian matrix#\n");
   for (cpt=1; cpt<= nlstate ; cpt ++) {    fprintf(ficlog,"\n#Hessian matrix#\n");
    for (k1=1; k1<= m ; k1 ++) {    for (i=1;i<=npar;i++) { 
       for (j=1;j<=npar;j++) { 
 #ifdef windows        printf("%.3e ",hess[i][j]);
     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",agemin,fage,fileres,k1-1,k1-1);        fprintf(ficlog,"%.3e ",hess[i][j]);
 #endif      }
 #ifdef unix      printf("\n");
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);      fprintf(ficlog,"\n");
 #endif    }
   
 for (i=1; i<= nlstate ; i ++) {    /* Recompute Inverse */
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    for (i=1;i<=npar;i++)
   else fprintf(ficgp," \%%*lf (\%%*lf)");      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
 }    ludcmp(a,npar,indx,&pd);
     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 ++) {    /*  printf("\n#Hessian matrix recomputed#\n");
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");    for (j=1;j<=npar;j++) {
 }      for (i=1;i<=npar;i++) x[i]=0;
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);      x[j]=1;
      for (i=1; i<= nlstate ; i ++) {      lubksb(a,npar,indx,x);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      for (i=1;i<=npar;i++){ 
   else fprintf(ficgp," \%%*lf (\%%*lf)");        y[i][j]=x[i];
 }          printf("%.3e ",y[i][j]);
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));        fprintf(ficlog,"%.3e ",y[i][j]);
 #ifdef unix      }
 fprintf(ficgp,"\nset ter gif small size 400,300");      printf("\n");
 #endif      fprintf(ficlog,"\n");
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    }
    }    */
   }  
   /*2 eme*/    free_matrix(a,1,npar,1,npar);
     free_matrix(y,1,npar,1,npar);
   for (k1=1; k1<= m ; k1 ++) {    free_vector(x,1,npar);
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);    free_ivector(indx,1,npar);
        free_matrix(hess,1,npar,1,npar);
     for (i=1; i<= nlstate+1 ; i ++) {  
       k=2*i;  
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);  }
       for (j=1; j<= nlstate+1 ; j ++) {  
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");  /*************** hessian matrix ****************/
   else fprintf(ficgp," \%%*lf (\%%*lf)");  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
 }    {
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");    int i;
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);    int l=1, lmax=20;
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);    double k1,k2;
       for (j=1; j<= nlstate+1 ; j ++) {    double p2[MAXPARM+1]; /* identical to x */
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    double res;
         else fprintf(ficgp," \%%*lf (\%%*lf)");    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
 }      double fx;
       fprintf(ficgp,"\" t\"\" w l 0,");    int k=0,kmax=10;
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);    double l1;
       for (j=1; j<= nlstate+1 ; j ++) {  
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    fx=func(x);
   else fprintf(ficgp," \%%*lf (\%%*lf)");    for (i=1;i<=npar;i++) p2[i]=x[i];
 }      for(l=0 ; l <=lmax; l++){
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");      l1=pow(10,l);
       else fprintf(ficgp,"\" t\"\" w l 0,");      delts=delt;
     }      for(k=1 ; k <kmax; k=k+1){
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);        delt = delta*(l1*k);
   }        p2[theta]=x[theta] +delt;
          k1=func(p2)-fx;
   /*3eme*/        p2[theta]=x[theta]-delt;
         k2=func(p2)-fx;
   for (k1=1; k1<= m ; k1 ++) {        /*res= (k1-2.0*fx+k2)/delt/delt; */
     for (cpt=1; cpt<= nlstate ; cpt ++) {        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
       k=2+nlstate*(cpt-1);        
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k1-1,k1-1,k,cpt);  #ifdef DEBUGHESS
       for (i=1; i< nlstate ; 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);
         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);        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
       }  #endif
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
     }        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
     }          k=kmax;
          }
   /* CV preval stat */        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
     for (k1=1; k1<= m ; k1 ++) {          k=kmax; l=lmax*10.;
     for (cpt=1; cpt<nlstate ; cpt ++) {        }
       k=3;        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",agemin,agemaxpar,fileres,k1,k+cpt+1,k+1);          delts=delt;
         }
       for (i=1; i< nlstate ; i ++)      }
         fprintf(ficgp,"+$%d",k+i+1);    }
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);    delti[theta]=delts;
          return res; 
       l=3+(nlstate+ndeath)*cpt;    
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);  }
       for (i=1; i< nlstate ; i ++) {  
         l=3+(nlstate+ndeath)*cpt;  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
         fprintf(ficgp,"+$%d",l+i+1);  {
       }    int i;
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);      int l=1, l1, lmax=20;
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    double k1,k2,k3,k4,res,fx;
     }    double p2[MAXPARM+1];
   }      int k;
    
   /* proba elementaires */    fx=func(x);
    for(i=1,jk=1; i <=nlstate; i++){    for (k=1; k<=2; k++) {
     for(k=1; k <=(nlstate+ndeath); k++){      for (i=1;i<=npar;i++) p2[i]=x[i];
       if (k != i) {      p2[thetai]=x[thetai]+delti[thetai]/k;
         for(j=1; j <=ncovmodel; j++){      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
              k1=func(p2)-fx;
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);    
           jk++;      p2[thetai]=x[thetai]+delti[thetai]/k;
           fprintf(ficgp,"\n");      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
         }      k2=func(p2)-fx;
       }    
     }      p2[thetai]=x[thetai]-delti[thetai]/k;
     }      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       k3=func(p2)-fx;
     for(jk=1; jk <=m; jk++) {    
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemaxpar);      p2[thetai]=x[thetai]-delti[thetai]/k;
    i=1;      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
    for(k2=1; k2<=nlstate; k2++) {      k4=func(p2)-fx;
      k3=i;      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
      for(k=1; k<=(nlstate+ndeath); k++) {  #ifdef DEBUG
        if (k != k2){      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);      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);
 ij=1;  #endif
         for(j=3; j <=ncovmodel; j++) {    }
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    return res;
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);  }
             ij++;  
           }  /************** Inverse of matrix **************/
           else  void ludcmp(double **a, int n, int *indx, double *d) 
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);  { 
         }    int i,imax,j,k; 
           fprintf(ficgp,")/(1");    double big,dum,sum,temp; 
            double *vv; 
         for(k1=1; k1 <=nlstate; k1++){     
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);    vv=vector(1,n); 
 ij=1;    *d=1.0; 
           for(j=3; j <=ncovmodel; j++){    for (i=1;i<=n;i++) { 
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {      big=0.0; 
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);      for (j=1;j<=n;j++) 
             ij++;        if ((temp=fabs(a[i][j])) > big) big=temp; 
           }      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
           else      vv[i]=1.0/big; 
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    } 
           }    for (j=1;j<=n;j++) { 
           fprintf(ficgp,")");      for (i=1;i<j;i++) { 
         }        sum=a[i][j]; 
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");        a[i][j]=sum; 
         i=i+ncovmodel;      } 
        }      big=0.0; 
      }      for (i=j;i<=n;i++) { 
    }        sum=a[i][j]; 
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);        for (k=1;k<j;k++) 
    }          sum -= a[i][k]*a[k][j]; 
            a[i][j]=sum; 
   fclose(ficgp);        if ( (dum=vv[i]*fabs(sum)) >= big) { 
 }  /* end gnuplot */          big=dum; 
           imax=i; 
         } 
 /*************** Moving average **************/      } 
 void movingaverage(double agedeb, double fage,double agemin, double ***mobaverage){      if (j != imax) { 
         for (k=1;k<=n;k++) { 
   int i, cpt, cptcod;          dum=a[imax][k]; 
     for (agedeb=agemin; agedeb<=fage; agedeb++)          a[imax][k]=a[j][k]; 
       for (i=1; i<=nlstate;i++)          a[j][k]=dum; 
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)        } 
           mobaverage[(int)agedeb][i][cptcod]=0.;        *d = -(*d); 
            vv[imax]=vv[j]; 
     for (agedeb=agemin+4; agedeb<=fage; agedeb++){      } 
       for (i=1; i<=nlstate;i++){      indx[j]=imax; 
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      if (a[j][j] == 0.0) a[j][j]=TINY; 
           for (cpt=0;cpt<=4;cpt++){      if (j != n) { 
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];        dum=1.0/(a[j][j]); 
           }        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;      } 
         }    } 
       }    free_vector(vv,1,n);  /* Doesn't work */
     }  ;
      } 
 }  
   void lubksb(double **a, int n, int *indx, double b[]) 
   { 
 /************** Forecasting ******************/    int i,ii=0,ip,j; 
 prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double agemin, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){    double sum; 
     
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;    for (i=1;i<=n;i++) { 
   int *popage;      ip=indx[i]; 
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;      sum=b[ip]; 
   double *popeffectif,*popcount;      b[ip]=b[i]; 
   double ***p3mat;      if (ii) 
   char fileresf[FILENAMELENGTH];        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
       else if (sum) ii=i; 
  agelim=AGESUP;      b[i]=sum; 
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;    } 
     for (i=n;i>=1;i--) { 
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);      sum=b[i]; 
        for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
        b[i]=sum/a[i][i]; 
   strcpy(fileresf,"f");    } 
   strcat(fileresf,fileres);  } 
   if((ficresf=fopen(fileresf,"w"))==NULL) {  
     printf("Problem with forecast resultfile: %s\n", fileresf);  void pstamp(FILE *fichier)
   }  {
   printf("Computing forecasting: result on file '%s' \n", fileresf);    fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
   }
   if (cptcoveff==0) ncodemax[cptcoveff]=1;  
   /************ Frequencies ********************/
   if (mobilav==1) {  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[])
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  {  /* Some frequencies */
     movingaverage(agedeb, fage, agemin, mobaverage);    
   }    int i, m, jk, k1,i1, j1, bool, z1,j;
     int first;
   stepsize=(int) (stepm+YEARM-1)/YEARM;    double ***freq; /* Frequencies */
   if (stepm<=12) stepsize=1;    double *pp, **prop;
      double pos,posprop, k2, dateintsum=0,k2cpt=0;
   agelim=AGESUP;    char fileresp[FILENAMELENGTH];
      
   hstepm=1;    pp=vector(1,nlstate);
   hstepm=hstepm/stepm;    prop=matrix(1,nlstate,iagemin,iagemax+3);
   yp1=modf(dateintmean,&yp);    strcpy(fileresp,"p");
   anprojmean=yp;    strcat(fileresp,fileres);
   yp2=modf((yp1*12),&yp);    if((ficresp=fopen(fileresp,"w"))==NULL) {
   mprojmean=yp;      printf("Problem with prevalence resultfile: %s\n", fileresp);
   yp1=modf((yp2*30.5),&yp);      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
   jprojmean=yp;      exit(0);
   if(jprojmean==0) jprojmean=1;    }
   if(mprojmean==0) jprojmean=1;    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
      j1=0;
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);    
      j=cptcoveff;
   for(cptcov=1;cptcov<=i2;cptcov++){    if (cptcovn<1) {j=1;ncodemax[1]=1;}
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){  
       k=k+1;    first=1;
       fprintf(ficresf,"\n#******");  
       for(j=1;j<=cptcoveff;j++) {    for(k1=1; k1<=j;k1++){   /* Loop on covariates */
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      for(i1=1; i1<=ncodemax[k1];i1++){ /* Now it is 2 */
       }        j1++;
       fprintf(ficresf,"******\n");        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
       fprintf(ficresf,"# StartingAge FinalAge");          scanf("%d", i);*/
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);        for (i=-5; i<=nlstate+ndeath; i++)  
                for (jk=-5; jk<=nlstate+ndeath; jk++)  
                  for(m=iagemin; m <= iagemax+3; m++)
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {              freq[i][jk][m]=0;
         fprintf(ficresf,"\n");        
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);          for (i=1; i<=nlstate; i++)  
           for(m=iagemin; m <= iagemax+3; m++)
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){            prop[i][m]=0;
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);        
           nhstepm = nhstepm/hstepm;        dateintsum=0;
                  k2cpt=0;
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        for (i=1; i<=imx; i++) {
           oldm=oldms;savm=savms;          bool=1;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            if  (cptcovn>0) {
                    for (z1=1; z1<=cptcoveff; z1++) 
           for (h=0; h<=nhstepm; h++){              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
             if (h==(int) (calagedate+YEARM*cpt)) {                bool=0;
               fprintf(ficresf,"\n %.f ",agedeb+h*hstepm/YEARM*stepm);          }
             }          if (bool==1){
             for(j=1; j<=nlstate+ndeath;j++) {            for(m=firstpass; m<=lastpass; m++){
               kk1=0.;kk2=0;              k2=anint[m][i]+(mint[m][i]/12.);
               for(i=1; i<=nlstate;i++) {                            /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
                 if (mobilav==1)                if(agev[m][i]==0) agev[m][i]=iagemax+1;
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];                if(agev[m][i]==1) agev[m][i]=iagemax+2;
                 else {                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];                if (m<lastpass) {
                 }                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
                                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
               }                }
               if (h==(int)(calagedate+12*cpt)){                
                 fprintf(ficresf," %.3f", kk1);                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
                                          dateintsum=dateintsum+k2;
               }                  k2cpt++;
             }                }
           }                /*}*/
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            }
         }          }
       }        }
     }         
   }        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
                pstamp(ficresp);
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        if  (cptcovn>0) {
           fprintf(ficresp, "\n#********** Variable "); 
   fclose(ficresf);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
 }          fprintf(ficresp, "**********\n#");
 /************** Forecasting ******************/          fprintf(ficlog, "\n#********** Variable "); 
 populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double agemin, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
            fprintf(ficlog, "**********\n#");
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;        }
   int *popage;        for(i=1; i<=nlstate;i++) 
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
   double *popeffectif,*popcount;        fprintf(ficresp, "\n");
   double ***p3mat,***tabpop,***tabpopprev;        
   char filerespop[FILENAMELENGTH];        for(i=iagemin; i <= iagemax+3; i++){
           if(i==iagemax+3){
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            fprintf(ficlog,"Total");
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          }else{
   agelim=AGESUP;            if(first==1){
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;              first=0;
                printf("See log file for details...\n");
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);            }
              fprintf(ficlog,"Age %d", i);
            }
   strcpy(filerespop,"pop");          for(jk=1; jk <=nlstate ; jk++){
   strcat(filerespop,fileres);            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
   if((ficrespop=fopen(filerespop,"w"))==NULL) {              pp[jk] += freq[jk][m][i]; 
     printf("Problem with forecast resultfile: %s\n", filerespop);          }
   }          for(jk=1; jk <=nlstate ; jk++){
   printf("Computing forecasting: result on file '%s' \n", filerespop);            for(m=-1, pos=0; m <=0 ; m++)
               pos += freq[jk][m][i];
   if (cptcoveff==0) ncodemax[cptcoveff]=1;            if(pp[jk]>=1.e-10){
               if(first==1){
   if (mobilav==1) {                printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);              }
     movingaverage(agedeb, fage, agemin, mobaverage);              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   }            }else{
               if(first==1)
   stepsize=(int) (stepm+YEARM-1)/YEARM;                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   if (stepm<=12) stepsize=1;              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
              }
   agelim=AGESUP;          }
    
   hstepm=1;          for(jk=1; jk <=nlstate ; jk++){
   hstepm=hstepm/stepm;            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
                pp[jk] += freq[jk][m][i];
   if (popforecast==1) {          }       
     if((ficpop=fopen(popfile,"r"))==NULL) {          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
       printf("Problem with population file : %s\n",popfile);exit(0);            pos += pp[jk];
     }            posprop += prop[jk][i];
     popage=ivector(0,AGESUP);          }
     popeffectif=vector(0,AGESUP);          for(jk=1; jk <=nlstate ; jk++){
     popcount=vector(0,AGESUP);            if(pos>=1.e-5){
                  if(first==1)
     i=1;                  printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
                }else{
     imx=i;              if(first==1)
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   }              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
             }
   for(cptcov=1;cptcov<=i2;cptcov++){            if( i <= iagemax){
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){              if(pos>=1.e-5){
       k=k+1;                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
       fprintf(ficrespop,"\n#******");                /*probs[i][jk][j1]= pp[jk]/pos;*/
       for(j=1;j<=cptcoveff;j++) {                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);              }
       }              else
       fprintf(ficrespop,"******\n");                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
       fprintf(ficrespop,"# Age");            }
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);          }
       if (popforecast==1)  fprintf(ficrespop," [Population]");          
                for(jk=-1; jk <=nlstate+ndeath; jk++)
       for (cpt=0; cpt<=0;cpt++) {            for(m=-1; m <=nlstate+ndeath; m++)
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);                if(freq[jk][m][i] !=0 ) {
                      if(first==1)
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
           nhstepm = nhstepm/hstepm;              }
                    if(i <= iagemax)
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            fprintf(ficresp,"\n");
           oldm=oldms;savm=savms;          if(first==1)
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);              printf("Others in log...\n");
                  fprintf(ficlog,"\n");
           for (h=0; h<=nhstepm; h++){        }
             if (h==(int) (calagedate+YEARM*cpt)) {      }
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);    }
             }    dateintmean=dateintsum/k2cpt; 
             for(j=1; j<=nlstate+ndeath;j++) {   
               kk1=0.;kk2=0;    fclose(ficresp);
               for(i=1; i<=nlstate;i++) {                  free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
                 if (mobilav==1)    free_vector(pp,1,nlstate);
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
                 else {    /* End of Freq */
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];  }
                 }  
               }  /************ Prevalence ********************/
               if (h==(int)(calagedate+12*cpt)){  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)
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;  {  
                   /*fprintf(ficrespop," %.3f", kk1);    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/       in each health status at the date of interview (if between dateprev1 and dateprev2).
               }       We still use firstpass and lastpass as another selection.
             }    */
             for(i=1; i<=nlstate;i++){   
               kk1=0.;    int i, m, jk, k1, i1, j1, bool, z1,j;
                 for(j=1; j<=nlstate;j++){    double ***freq; /* Frequencies */
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];    double *pp, **prop;
                 }    double pos,posprop; 
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];    double  y2; /* in fractional years */
             }    int iagemin, iagemax;
   
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)    iagemin= (int) agemin;
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);    iagemax= (int) agemax;
           }    /*pp=vector(1,nlstate);*/
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    prop=matrix(1,nlstate,iagemin,iagemax+3); 
         }    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
       }    j1=0;
      
   /******/    j=cptcoveff;
     if (cptcovn<1) {j=1;ncodemax[1]=1;}
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {    
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);      for(k1=1; k1<=j;k1++){
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){      for(i1=1; i1<=ncodemax[k1];i1++){
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);        j1++;
           nhstepm = nhstepm/hstepm;        
                  for (i=1; i<=nlstate; i++)  
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          for(m=iagemin; m <= iagemax+3; m++)
           oldm=oldms;savm=savms;            prop[i][m]=0.0;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);         
           for (h=0; h<=nhstepm; h++){        for (i=1; i<=imx; i++) { /* Each individual */
             if (h==(int) (calagedate+YEARM*cpt)) {          bool=1;
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);          if  (cptcovn>0) {
             }            for (z1=1; z1<=cptcoveff; z1++) 
             for(j=1; j<=nlstate+ndeath;j++) {              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
               kk1=0.;kk2=0;                bool=0;
               for(i=1; i<=nlstate;i++) {                        } 
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];              if (bool==1) { 
               }            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
             }              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
           }                if(agev[m][i]==0) agev[m][i]=iagemax+1;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
         }                if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
       }                if (s[m][i]>0 && s[m][i]<=nlstate) { 
    }                  /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
   }                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
                    prop[s[m][i]][iagemax+3] += weight[i]; 
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);                } 
               }
   if (popforecast==1) {            } /* end selection of waves */
     free_ivector(popage,0,AGESUP);          }
     free_vector(popeffectif,0,AGESUP);        }
     free_vector(popcount,0,AGESUP);        for(i=iagemin; i <= iagemax+3; i++){  
   }          
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            posprop += prop[jk][i]; 
   fclose(ficrespop);          } 
 }  
           for(jk=1; jk <=nlstate ; jk++){     
 /***********************************************/            if( i <=  iagemax){ 
 /**************** Main Program *****************/              if(posprop>=1.e-5){ 
 /***********************************************/                probs[i][jk][j1]= prop[jk][i]/posprop;
               } else
 int main(int argc, char *argv[])                printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\n",jk,i,j1,probs[i][jk][j1]);
 {            } 
           }/* end jk */ 
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;        }/* end i */ 
   double agedeb, agefin,hf;      } /* end i1 */
   double agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;    } /* end k1 */
     
   double fret;    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
   double **xi,tmp,delta;    /*free_vector(pp,1,nlstate);*/
     free_matrix(prop,1,nlstate, iagemin,iagemax+3);
   double dum; /* Dummy variable */  }  /* End of prevalence */
   double ***p3mat;  
   int *indx;  /************* Waves Concatenation ***************/
   char line[MAXLINE], linepar[MAXLINE];  
   char title[MAXLINE];  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)
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];  {
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
         Death is a valid wave (if date is known).
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];       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]
   char filerest[FILENAMELENGTH];       and mw[mi+1][i]. dh depends on stepm.
   char fileregp[FILENAMELENGTH];       */
   char popfile[FILENAMELENGTH];  
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];    int i, mi, m;
   int firstobs=1, lastobs=10;    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
   int sdeb, sfin; /* Status at beginning and end */       double sum=0., jmean=0.;*/
   int c,  h , cpt,l;    int first;
   int ju,jl, mi;    int j, k=0,jk, ju, jl;
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;    double sum=0.;
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;    first=0;
   int mobilav=0,popforecast=0;    jmin=1e+5;
   int hstepm, nhstepm;    jmax=-1;
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1;    jmean=0.;
     for(i=1; i<=imx; i++){
   double bage, fage, age, agelim, agebase;      mi=0;
   double ftolpl=FTOL;      m=firstpass;
   double **prlim;      while(s[m][i] <= nlstate){
   double *severity;        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
   double ***param; /* Matrix of parameters */          mw[++mi][i]=m;
   double  *p;        if(m >=lastpass)
   double **matcov; /* Matrix of covariance */          break;
   double ***delti3; /* Scale */        else
   double *delti; /* Scale */          m++;
   double ***eij, ***vareij;      }/* end while */
   double **varpl; /* Variances of prevalence limits by age */      if (s[m][i] > nlstate){
   double *epj, vepp;        mi++;     /* Death is another wave */
   double kk1, kk2;        /* if(mi==0)  never been interviewed correctly before death */
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;           /* Only death is a correct wave */
          mw[mi][i]=m;
       }
   char version[80]="Imach version 0.71e, March 2002, INED-EUROREVES ";  
   char *alph[]={"a","a","b","c","d","e"}, str[4];      wav[i]=mi;
       if(mi==0){
         nbwarn++;
   char z[1]="c", occ;        if(first==0){
 #include <sys/time.h>          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
 #include <time.h>          first=1;
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];        }
          if(first==1){
   /* long total_usecs;          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
   struct timeval start_time, end_time;        }
        } /* end mi==0 */
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */    } /* End individuals */
   
     for(i=1; i<=imx; i++){
   printf("\n%s",version);      for(mi=1; mi<wav[i];mi++){
   if(argc <=1){        if (stepm <=0)
     printf("\nEnter the parameter file name: ");          dh[mi][i]=1;
     scanf("%s",pathtot);        else{
   }          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
   else{            if (agedc[i] < 2*AGESUP) {
     strcpy(pathtot,argv[1]);              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
   }              if(j==0) j=1;  /* Survives at least one month after exam */
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/              else if(j<0){
   /*cygwin_split_path(pathtot,path,optionfile);                nberr++;
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/                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]);
   /* cutv(path,optionfile,pathtot,'\\');*/                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);
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);                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]);
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);                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);
   chdir(path);              }
   replace(pathc,path);              k=k+1;
               if (j >= jmax){
 /*-------- arguments in the command line --------*/                jmax=j;
                 ijmax=i;
   strcpy(fileres,"r");              }
   strcat(fileres, optionfilefiname);              if (j <= jmin){
   strcat(fileres,".txt");    /* Other files have txt extension */                jmin=j;
                 ijmin=i;
   /*---------arguments file --------*/              }
               sum=sum+j;
   if((ficpar=fopen(optionfile,"r"))==NULL)    {              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
     printf("Problem with optionfile %s\n",optionfile);              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
     goto end;            }
   }          }
           else{
   strcpy(filereso,"o");            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
   strcat(filereso,fileres);  /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
   if((ficparo=fopen(filereso,"w"))==NULL) {  
     printf("Problem with Output resultfile: %s\n", filereso);goto end;            k=k+1;
   }            if (j >= jmax) {
               jmax=j;
   /* Reads comments: lines beginning with '#' */              ijmax=i;
   while((c=getc(ficpar))=='#' && c!= EOF){            }
     ungetc(c,ficpar);            else if (j <= jmin){
     fgets(line, MAXLINE, ficpar);              jmin=j;
     puts(line);              ijmin=i;
     fputs(line,ficparo);            }
   }            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
   ungetc(c,ficpar);            /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
             if(j<0){
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncov, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);              nberr++;
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate,ndeath, maxwav, mle, weightopt,model);              printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncov,nlstate,ndeath,maxwav, mle, weightopt,model);              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]);
 while((c=getc(ficpar))=='#' && c!= EOF){            }
     ungetc(c,ficpar);            sum=sum+j;
     fgets(line, MAXLINE, ficpar);          }
     puts(line);          jk= j/stepm;
     fputs(line,ficparo);          jl= j -jk*stepm;
   }          ju= j -(jk+1)*stepm;
   ungetc(c,ficpar);          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
              if(jl==0){
                  dh[mi][i]=jk;
   covar=matrix(0,NCOVMAX,1,n);              bh[mi][i]=0;
   cptcovn=0;            }else{ /* We want a negative bias in order to only have interpolation ie
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;                    * to avoid the price of an extra matrix product in likelihood */
               dh[mi][i]=jk+1;
   ncovmodel=2+cptcovn;              bh[mi][i]=ju;
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */            }
            }else{
   /* Read guess parameters */            if(jl <= -ju){
   /* Reads comments: lines beginning with '#' */              dh[mi][i]=jk;
   while((c=getc(ficpar))=='#' && c!= EOF){              bh[mi][i]=jl;       /* bias is positive if real duration
     ungetc(c,ficpar);                                   * is higher than the multiple of stepm and negative otherwise.
     fgets(line, MAXLINE, ficpar);                                   */
     puts(line);            }
     fputs(line,ficparo);            else{
   }              dh[mi][i]=jk+1;
   ungetc(c,ficpar);              bh[mi][i]=ju;
              }
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);            if(dh[mi][i]==0){
     for(i=1; i <=nlstate; i++)              dh[mi][i]=1; /* At least one step */
     for(j=1; j <=nlstate+ndeath-1; j++){              bh[mi][i]=ju; /* At least one step */
       fscanf(ficpar,"%1d%1d",&i1,&j1);              /*  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);*/
       fprintf(ficparo,"%1d%1d",i1,j1);            }
       printf("%1d%1d",i,j);          } /* end if mle */
       for(k=1; k<=ncovmodel;k++){        }
         fscanf(ficpar," %lf",&param[i][j][k]);      } /* end wave */
         printf(" %lf",param[i][j][k]);    }
         fprintf(ficparo," %lf",param[i][j][k]);    jmean=sum/k;
       }    printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
       fscanf(ficpar,"\n");    fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %d) Max=%d (%d) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
       printf("\n");   }
       fprintf(ficparo,"\n");  
     }  /*********** Tricode ****************************/
    void tricode(int *Tvar, int **nbcode, int imx)
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;  {
     /* Uses cptcovn+2*cptcovprod as the number of covariates */
   p=param[1][1];    /*      Tvar[i]=atoi(stre); /* find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 */
    
   /* Reads comments: lines beginning with '#' */    int Ndum[20],ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
   while((c=getc(ficpar))=='#' && c!= EOF){    int modmaxcovj=0; /* Modality max of covariates j */
     ungetc(c,ficpar);    cptcoveff=0; 
     fgets(line, MAXLINE, ficpar);   
     puts(line);    for (k=0; k<maxncov; k++) Ndum[k]=0;
     fputs(line,ficparo);    for (k=1; k<=7; k++) ncodemax[k]=0; /* Horrible constant again */
   }  
   ungetc(c,ficpar);    for (j=1; j<=(cptcovn+2*cptcovprod); j++) { /* For each covariate j */
       for (i=1; i<=imx; i++) { /*reads the data file to get the maximum value of the 
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);                                 modality of this covariate Vj*/ 
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */        ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Finds for covariate j, n=Tvar[j] of Vn . ij is the
   for(i=1; i <=nlstate; i++){                                        modality of the nth covariate of individual i. */
     for(j=1; j <=nlstate+ndeath-1; j++){        Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
       fscanf(ficpar,"%1d%1d",&i1,&j1);        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
       printf("%1d%1d",i,j);        if (ij > modmaxcovj) modmaxcovj=ij; 
       fprintf(ficparo,"%1d%1d",i1,j1);        /* getting the maximum value of the modality of the covariate
       for(k=1; k<=ncovmodel;k++){           (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
         fscanf(ficpar,"%le",&delti3[i][j][k]);           female is 1, then modmaxcovj=1.*/
         printf(" %le",delti3[i][j][k]);      }
         fprintf(ficparo," %le",delti3[i][j][k]);      /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
       }      for (i=0; i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each modality of model-cov j */
       fscanf(ficpar,"\n");        if( Ndum[i] != 0 )
       printf("\n");          ncodemax[j]++; 
       fprintf(ficparo,"\n");        /* Number of modalities of the j th covariate. In fact
     }           ncodemax[j]=2 (dichotom. variables only) but it could be more for
   }           historical reasons */
   delti=delti3[1][1];      } /* Ndum[-1] number of undefined modalities */
    
   /* Reads comments: lines beginning with '#' */      /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
   while((c=getc(ficpar))=='#' && c!= EOF){      ij=1; 
     ungetc(c,ficpar);      for (i=1; i<=ncodemax[j]; i++) { /* i= 1 to 2 for dichotomous */
     fgets(line, MAXLINE, ficpar);        for (k=0; k<= modmaxcovj; k++) { /* k=-1 ? NCOVMAX*//* maxncov or modmaxcovj */
     puts(line);          if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
     fputs(line,ficparo);            nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode. 
   }                                       k is a modality. If we have model=V1+V1*sex 
   ungetc(c,ficpar);                                       then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
              ij++;
   matcov=matrix(1,npar,1,npar);          }
   for(i=1; i <=npar; i++){          if (ij > ncodemax[j]) break; 
     fscanf(ficpar,"%s",&str);        }  /* end of loop on */
     printf("%s",str);      } /* end of loop on modality */ 
     fprintf(ficparo,"%s",str);    } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/  
     for(j=1; j <=i; j++){    
       fscanf(ficpar," %le",&matcov[i][j]);    for (k=0; k< maxncov; k++) Ndum[k]=0;
       printf(" %.5le",matcov[i][j]);    
       fprintf(ficparo," %.5le",matcov[i][j]);    for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */
     }     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
     fscanf(ficpar,"\n");     ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
     printf("\n");     Ndum[ij]++;
     fprintf(ficparo,"\n");   }
   }  
   for(i=1; i <=npar; i++)   ij=1;
     for(j=i+1;j<=npar;j++)   for (i=1; i<= maxncov; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
       matcov[i][j]=matcov[j][i];     if((Ndum[i]!=0) && (i<=ncovcol)){
           Tvaraff[ij]=i; /*For printing */
   printf("\n");       ij++;
      }
    }
     /*-------- Rewriting paramater file ----------*/   ij--;
      strcpy(rfileres,"r");    /* "Rparameterfile */   cptcoveff=ij; /*Number of simple covariates*/
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/  }
      strcat(rfileres,".");    /* */  
      strcat(rfileres,optionfilext);    /* Other files have txt extension */  /*********** Health Expectancies ****************/
     if((ficres =fopen(rfileres,"w"))==NULL) {  
       printf("Problem writing new parameter file: %s\n", fileres);goto end;  void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
     }  
     fprintf(ficres,"#%s\n",version);  {
        /* Health expectancies, no variances */
     /*-------- data file ----------*/    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
     if((fic=fopen(datafile,"r"))==NULL)    {    int nhstepma, nstepma; /* Decreasing with age */
       printf("Problem with datafile: %s\n", datafile);goto end;    double age, agelim, hf;
     }    double ***p3mat;
     double eip;
     n= lastobs;  
     severity = vector(1,maxwav);    pstamp(ficreseij);
     outcome=imatrix(1,maxwav+1,1,n);    fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
     num=ivector(1,n);    fprintf(ficreseij,"# Age");
     moisnais=vector(1,n);    for(i=1; i<=nlstate;i++){
     annais=vector(1,n);      for(j=1; j<=nlstate;j++){
     moisdc=vector(1,n);        fprintf(ficreseij," e%1d%1d ",i,j);
     andc=vector(1,n);      }
     agedc=vector(1,n);      fprintf(ficreseij," e%1d. ",i);
     cod=ivector(1,n);    }
     weight=vector(1,n);    fprintf(ficreseij,"\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);    if(estepm < stepm){
     s=imatrix(1,maxwav+1,1,n);      printf ("Problem %d lower than %d\n",estepm, stepm);
     adl=imatrix(1,maxwav+1,1,n);        }
     tab=ivector(1,NCOVMAX);    else  hstepm=estepm;   
     ncodemax=ivector(1,8);    /* We compute the life expectancy from trapezoids spaced every estepm months
      * This is mainly to measure the difference between two models: for example
     i=1;     * if stepm=24 months pijx are given only every 2 years and by summing them
     while (fgets(line, MAXLINE, fic) != NULL)    {     * we are calculating an estimate of the Life Expectancy assuming a linear 
       if ((i >= firstobs) && (i <=lastobs)) {     * progression in between and thus overestimating or underestimating according
             * to the curvature of the survival function. If, for the same date, we 
         for (j=maxwav;j>=1;j--){     * estimate the model with stepm=1 month, we can keep estepm to 24 months
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);     * to compare the new estimate of Life expectancy with the same linear 
           strcpy(line,stra);     * hypothesis. A more precise result, taking into account a more precise
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);     * curvature will be obtained if estepm is as small as stepm. */
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);  
         }    /* 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. 
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);       nhstepm is the number of hstepm from age to agelim 
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);       nstepm is the number of stepm from age to agelin. 
        Look at hpijx to understand the reason of that which relies in memory size
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);       and note for a fixed period like estepm months */
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);    /* 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
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);       means that if the survival funtion is printed only each two years of age and if
         for (j=ncov;j>=1;j--){       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);       results. So we changed our mind and took the option of the best precision.
         }    */
         num[i]=atol(stra);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
          
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){    agelim=AGESUP;
           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;}*/    /* If stepm=6 months */
       /* Computed by stepm unit matrices, product of hstepm matrices, stored
         i=i+1;         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
       }      
     }  /* nhstepm age range expressed in number of stepm */
     /* printf("ii=%d", ij);    nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
        scanf("%d",i);*/    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   imx=i-1; /* Number of individuals */    /* if (stepm >= YEARM) hstepm=1;*/
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   /* for (i=1; i<=imx; i++){    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     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;    for (age=bage; age<=fage; age ++){ 
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
     }      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       /* if (stepm >= YEARM) hstepm=1;*/
     for (i=1; i<=imx; i++)      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
     if (covar[1][i]==0) printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));*/  
       /* If stepm=6 months */
   /* Calculation of the number of parameter from char model*/      /* Computed by stepm unit matrices, product of hstepma matrices, stored
   Tvar=ivector(1,15);         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
   Tprod=ivector(1,15);      
   Tvaraff=ivector(1,15);      hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
   Tvard=imatrix(1,15,1,2);      
   Tage=ivector(1,15);            hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
          
   if (strlen(model) >1){      printf("%d|",(int)age);fflush(stdout);
     j=0, j1=0, k1=1, k2=1;      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
     j=nbocc(model,'+');      
     j1=nbocc(model,'*');      /* Computing expectancies */
     cptcovn=j+1;      for(i=1; i<=nlstate;i++)
     cptcovprod=j1;        for(j=1; j<=nlstate;j++)
              for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
                eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
     strcpy(modelsav,model);            
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){            /* 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]);*/
       printf("Error. Non available option model=%s ",model);  
       goto end;          }
     }  
          fprintf(ficreseij,"%3.0f",age );
     for(i=(j+1); i>=1;i--){      for(i=1; i<=nlstate;i++){
       cutv(stra,strb,modelsav,'+');        eip=0;
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);        for(j=1; j<=nlstate;j++){
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/          eip +=eij[i][j][(int)age];
       /*scanf("%d",i);*/          fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
       if (strchr(strb,'*')) {        }
         cutv(strd,strc,strb,'*');        fprintf(ficreseij,"%9.4f", eip );
         if (strcmp(strc,"age")==0) {      }
           cptcovprod--;      fprintf(ficreseij,"\n");
           cutv(strb,stre,strd,'V');      
           Tvar[i]=atoi(stre);    }
           cptcovage++;    free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             Tage[cptcovage]=i;    printf("\n");
             /*printf("stre=%s ", stre);*/    fprintf(ficlog,"\n");
         }    
         else if (strcmp(strd,"age")==0) {  }
           cptcovprod--;  
           cutv(strb,stre,strc,'V');  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[] )
           Tvar[i]=atoi(stre);  
           cptcovage++;  {
           Tage[cptcovage]=i;    /* Covariances of health expectancies eij and of total life expectancies according
         }     to initial status i, ei. .
         else {    */
           cutv(strb,stre,strc,'V');    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
           Tvar[i]=ncov+k1;    int nhstepma, nstepma; /* Decreasing with age */
           cutv(strb,strc,strd,'V');    double age, agelim, hf;
           Tprod[k1]=i;    double ***p3matp, ***p3matm, ***varhe;
           Tvard[k1][1]=atoi(strc);    double **dnewm,**doldm;
           Tvard[k1][2]=atoi(stre);    double *xp, *xm;
           Tvar[cptcovn+k2]=Tvard[k1][1];    double **gp, **gm;
           Tvar[cptcovn+k2+1]=Tvard[k1][2];    double ***gradg, ***trgradg;
           for (k=1; k<=lastobs;k++)    int theta;
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];  
           k1++;    double eip, vip;
           k2=k2+2;  
         }    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
       }    xp=vector(1,npar);
       else {    xm=vector(1,npar);
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/    dnewm=matrix(1,nlstate*nlstate,1,npar);
        /*  scanf("%d",i);*/    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
       cutv(strd,strc,strb,'V');    
       Tvar[i]=atoi(strc);    pstamp(ficresstdeij);
       }    fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
       strcpy(modelsav,stra);      fprintf(ficresstdeij,"# Age");
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);    for(i=1; i<=nlstate;i++){
         scanf("%d",i);*/      for(j=1; j<=nlstate;j++)
     }        fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
 }      fprintf(ficresstdeij," e%1d. ",i);
      }
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);    fprintf(ficresstdeij,"\n");
   printf("cptcovprod=%d ", cptcovprod);  
   scanf("%d ",i);*/    pstamp(ficrescveij);
     fclose(fic);    fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
     fprintf(ficrescveij,"# Age");
     /*  if(mle==1){*/    for(i=1; i<=nlstate;i++)
     if (weightopt != 1) { /* Maximisation without weights*/      for(j=1; j<=nlstate;j++){
       for(i=1;i<=n;i++) weight[i]=1.0;        cptj= (j-1)*nlstate+i;
     }        for(i2=1; i2<=nlstate;i2++)
     /*-calculation of age at interview from date of interview and age at death -*/          for(j2=1; j2<=nlstate;j2++){
     agev=matrix(1,maxwav,1,imx);            cptj2= (j2-1)*nlstate+i2;
             if(cptj2 <= cptj)
    for (i=1; i<=imx; i++)              fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
      for(m=2; (m<= maxwav); m++)          }
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){      }
          anint[m][i]=9999;    fprintf(ficrescveij,"\n");
          s[m][i]=-1;    
        }    if(estepm < stepm){
          printf ("Problem %d lower than %d\n",estepm, stepm);
     for (i=1; i<=imx; i++)  {    }
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);    else  hstepm=estepm;   
       for(m=1; (m<= maxwav); m++){    /* We compute the life expectancy from trapezoids spaced every estepm months
         if(s[m][i] >0){     * This is mainly to measure the difference between two models: for example
           if (s[m][i] == nlstate+1) {     * if stepm=24 months pijx are given only every 2 years and by summing them
             if(agedc[i]>0)     * we are calculating an estimate of the Life Expectancy assuming a linear 
               if(moisdc[i]!=99 && andc[i]!=9999)     * progression in between and thus overestimating or underestimating according
               agev[m][i]=agedc[i];     * to the curvature of the survival function. If, for the same date, we 
             else {     * estimate the model with stepm=1 month, we can keep estepm to 24 months
               if (andc[i]!=9999){     * to compare the new estimate of Life expectancy with the same linear 
               printf("Warning negative age at death: %d line:%d\n",num[i],i);     * hypothesis. A more precise result, taking into account a more precise
               agev[m][i]=-1;     * curvature will be obtained if estepm is as small as stepm. */
               }  
             }    /* 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. 
           else if(s[m][i] !=9){ /* Should no more exist */       nhstepm is the number of hstepm from age to agelim 
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);       nstepm is the number of stepm from age to agelin. 
             if(mint[m][i]==99 || anint[m][i]==9999)       Look at hpijx to understand the reason of that which relies in memory size
               agev[m][i]=1;       and note for a fixed period like estepm months */
             else if(agev[m][i] <agemin){    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
               agemin=agev[m][i];       survival function given by stepm (the optimization length). Unfortunately it
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/       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 
             else if(agev[m][i] >agemax){       results. So we changed our mind and took the option of the best precision.
               agemax=agev[m][i];    */
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
             }  
             /*agev[m][i]=anint[m][i]-annais[i];*/    /* If stepm=6 months */
             /*   agev[m][i] = age[i]+2*m;*/    /* nhstepm age range expressed in number of stepm */
           }    agelim=AGESUP;
           else { /* =9 */    nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
             agev[m][i]=1;    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
             s[m][i]=-1;    /* if (stepm >= YEARM) hstepm=1;*/
           }    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
         }    
         else /*= 0 Unknown */    p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           agev[m][i]=1;    p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       }    gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
        trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
     }    gp=matrix(0,nhstepm,1,nlstate*nlstate);
     for (i=1; i<=imx; i++)  {    gm=matrix(0,nhstepm,1,nlstate*nlstate);
       for(m=1; (m<= maxwav); m++){  
         if (s[m][i] > (nlstate+ndeath)) {    for (age=bage; age<=fage; age ++){ 
           printf("Error: Wrong value in nlstate or ndeath\n");        nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
           goto end;      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
         }      /* if (stepm >= YEARM) hstepm=1;*/
       }      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
     }  
       /* If stepm=6 months */
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);      /* Computed by stepm unit matrices, product of hstepma matrices, stored
          in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
     free_vector(severity,1,maxwav);      
     free_imatrix(outcome,1,maxwav+1,1,n);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     free_vector(moisnais,1,n);  
     free_vector(annais,1,n);      /* Computing  Variances of health expectancies */
     /* free_matrix(mint,1,maxwav,1,n);      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
        free_matrix(anint,1,maxwav,1,n);*/         decrease memory allocation */
     free_vector(moisdc,1,n);      for(theta=1; theta <=npar; theta++){
     free_vector(andc,1,n);        for(i=1; i<=npar; i++){ 
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
              xm[i] = x[i] - (i==theta ?delti[theta]:0);
     wav=ivector(1,imx);        }
     dh=imatrix(1,lastpass-firstpass+1,1,imx);        hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
     mw=imatrix(1,lastpass-firstpass+1,1,imx);        hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
        
     /* Concatenates waves */        for(j=1; j<= nlstate; j++){
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);          for(i=1; i<=nlstate; i++){
             for(h=0; h<=nhstepm-1; h++){
               gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
       Tcode=ivector(1,100);              gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);            }
       ncodemax[1]=1;          }
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);        }
             
    codtab=imatrix(1,100,1,10);        for(ij=1; ij<= nlstate*nlstate; ij++)
    h=0;          for(h=0; h<=nhstepm-1; h++){
    m=pow(2,cptcoveff);            gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
            }
    for(k=1;k<=cptcoveff; k++){      }/* End theta */
      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++){      for(h=0; h<=nhstepm-1; h++)
            h++;        for(j=1; j<=nlstate*nlstate;j++)
            if (h>m) h=1;codtab[h][k]=j;          for(theta=1; theta <=npar; theta++)
          }            trgradg[h][j][theta]=gradg[h][theta][j];
        }      
      }  
    }       for(ij=1;ij<=nlstate*nlstate;ij++)
         for(ji=1;ji<=nlstate*nlstate;ji++)
           varhe[ij][ji][(int)age] =0.;
    /*for(i=1; i <=m ;i++){  
      for(k=1; k <=cptcovn; k++){       printf("%d|",(int)age);fflush(stdout);
        printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
      }       for(h=0;h<=nhstepm-1;h++){
      printf("\n");        for(k=0;k<=nhstepm-1;k++){
    }          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
    scanf("%d",i);*/          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
              for(ij=1;ij<=nlstate*nlstate;ij++)
    /* Calculates basic frequencies. Computes observed prevalence at single age            for(ji=1;ji<=nlstate*nlstate;ji++)
        and prints on file fileres'p'. */              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
         }
          }
      
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      /* Computing expectancies */
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      for(i=1; i<=nlstate;i++)
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        for(j=1; j<=nlstate;j++)
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
                  eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
     /* 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] */            /* 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]);*/
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */  
           }
     if(mle==1){  
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);      fprintf(ficresstdeij,"%3.0f",age );
     }      for(i=1; i<=nlstate;i++){
            eip=0.;
     /*--------- results files --------------*/        vip=0.;
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, weightopt,model);        for(j=1; j<=nlstate;j++){
            eip += eij[i][j][(int)age];
           for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
    jk=1;            vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
    fprintf(ficres,"# Parameters\n");          fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
    printf("# Parameters\n");        }
    for(i=1,jk=1; i <=nlstate; i++){        fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
      for(k=1; k <=(nlstate+ndeath); k++){      }
        if (k != i)      fprintf(ficresstdeij,"\n");
          {  
            printf("%d%d ",i,k);      fprintf(ficrescveij,"%3.0f",age );
            fprintf(ficres,"%1d%1d ",i,k);      for(i=1; i<=nlstate;i++)
            for(j=1; j <=ncovmodel; j++){        for(j=1; j<=nlstate;j++){
              printf("%f ",p[jk]);          cptj= (j-1)*nlstate+i;
              fprintf(ficres,"%f ",p[jk]);          for(i2=1; i2<=nlstate;i2++)
              jk++;            for(j2=1; j2<=nlstate;j2++){
            }              cptj2= (j2-1)*nlstate+i2;
            printf("\n");              if(cptj2 <= cptj)
            fprintf(ficres,"\n");                fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
          }            }
      }        }
    }      fprintf(ficrescveij,"\n");
  if(mle==1){     
     /* Computing hessian and covariance matrix */    }
     ftolhess=ftol; /* Usually correct */    free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
     hesscov(matcov, p, npar, delti, ftolhess, func);    free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
  }    free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
     fprintf(ficres,"# Scales\n");    free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
     printf("# Scales\n");    free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
      for(i=1,jk=1; i <=nlstate; i++){    free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       for(j=1; j <=nlstate+ndeath; j++){    printf("\n");
         if (j!=i) {    fprintf(ficlog,"\n");
           fprintf(ficres,"%1d%1d",i,j);  
           printf("%1d%1d",i,j);    free_vector(xm,1,npar);
           for(k=1; k<=ncovmodel;k++){    free_vector(xp,1,npar);
             printf(" %.5e",delti[jk]);    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
             fprintf(ficres," %.5e",delti[jk]);    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
             jk++;    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
           }  }
           printf("\n");  
           fprintf(ficres,"\n");  /************ 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[])
       }  {
      }    /* Variance of health expectancies */
        /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
     k=1;    /* double **newm;*/
     fprintf(ficres,"# Covariance\n");    double **dnewm,**doldm;
     printf("# Covariance\n");    double **dnewmp,**doldmp;
     for(i=1;i<=npar;i++){    int i, j, nhstepm, hstepm, h, nstepm ;
       /*  if (k>nlstate) k=1;    int k, cptcode;
       i1=(i-1)/(ncovmodel*nlstate)+1;    double *xp;
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);    double **gp, **gm;  /* for var eij */
       printf("%s%d%d",alph[k],i1,tab[i]);*/    double ***gradg, ***trgradg; /*for var eij */
       fprintf(ficres,"%3d",i);    double **gradgp, **trgradgp; /* for var p point j */
       printf("%3d",i);    double *gpp, *gmp; /* for var p point j */
       for(j=1; j<=i;j++){    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
         fprintf(ficres," %.5e",matcov[i][j]);    double ***p3mat;
         printf(" %.5e",matcov[i][j]);    double age,agelim, hf;
       }    double ***mobaverage;
       fprintf(ficres,"\n");    int theta;
       printf("\n");    char digit[4];
       k++;    char digitp[25];
     }  
        char fileresprobmorprev[FILENAMELENGTH];
     while((c=getc(ficpar))=='#' && c!= EOF){  
       ungetc(c,ficpar);    if(popbased==1){
       fgets(line, MAXLINE, ficpar);      if(mobilav!=0)
       puts(line);        strcpy(digitp,"-populbased-mobilav-");
       fputs(line,ficparo);      else strcpy(digitp,"-populbased-nomobil-");
     }    }
     ungetc(c,ficpar);    else 
        strcpy(digitp,"-stablbased-");
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemaxpar, &bage, &fage);  
        if (mobilav!=0) {
     if (fage <= 2) {      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       bage = agemin;      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
       fage = agemaxpar;        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
     }        printf(" Error in movingaverage mobilav=%d\n",mobilav);
          }
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");    }
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemaxpar,bage,fage);  
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemaxpar,bage,fage);    strcpy(fileresprobmorprev,"prmorprev"); 
      sprintf(digit,"%-d",ij);
     while((c=getc(ficpar))=='#' && c!= EOF){    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
     ungetc(c,ficpar);    strcat(fileresprobmorprev,digit); /* Tvar to be done */
     fgets(line, MAXLINE, ficpar);    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
     puts(line);    strcat(fileresprobmorprev,fileres);
     fputs(line,ficparo);    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
   }      printf("Problem with resultfile: %s\n", fileresprobmorprev);
   ungetc(c,ficpar);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
      }
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);   
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
          pstamp(ficresprobmorprev);
   while((c=getc(ficpar))=='#' && c!= EOF){    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);
     ungetc(c,ficpar);    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
     fgets(line, MAXLINE, ficpar);    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
     puts(line);      fprintf(ficresprobmorprev," p.%-d SE",j);
     fputs(line,ficparo);      for(i=1; i<=nlstate;i++)
   }        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
   ungetc(c,ficpar);    }  
      fprintf(ficresprobmorprev,"\n");
     fprintf(ficgp,"\n# Routine varevsij");
    dateprev1=anprev1+mprev1/12.+jprev1/365.;    /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
    dateprev2=anprev2+mprev2/12.+jprev2/365.;    fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
     fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
   fscanf(ficpar,"pop_based=%d\n",&popbased);  /*   } */
   fprintf(ficparo,"pop_based=%d\n",popbased);      varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   fprintf(ficres,"pop_based=%d\n",popbased);      pstamp(ficresvij);
      fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
   while((c=getc(ficpar))=='#' && c!= EOF){    if(popbased==1)
     ungetc(c,ficpar);      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);
     fgets(line, MAXLINE, ficpar);    else
     puts(line);      fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
     fputs(line,ficparo);    fprintf(ficresvij,"# Age");
   }    for(i=1; i<=nlstate;i++)
   ungetc(c,ficpar);      for(j=1; j<=nlstate;j++)
         fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,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(ficresvij,"\n");
 fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);  
 fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);    xp=vector(1,npar);
     dnewm=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
 while((c=getc(ficpar))=='#' && c!= EOF){    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
     ungetc(c,ficpar);    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     fgets(line, MAXLINE, ficpar);  
     puts(line);    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
     fputs(line,ficparo);    gpp=vector(nlstate+1,nlstate+ndeath);
   }    gmp=vector(nlstate+1,nlstate+ndeath);
   ungetc(c,ficpar);    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);    if(estepm < stepm){
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);      printf ("Problem %d lower than %d\n",estepm, stepm);
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);    }
     else  hstepm=estepm;   
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    /* 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. 
 /*------------ gnuplot -------------*/       nhstepm is the number of hstepm from age to agelim 
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, agemin,agemaxpar,fage, pathc,p);       nstepm is the number of stepm from age to agelin. 
         Look at function hpijx to understand why (it is linked to memory size questions) */
 /*------------ free_vector  -------------*/    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
  chdir(path);       survival function given by stepm (the optimization length). Unfortunately it
         means that if the survival funtion is printed every two years of age and if
  free_ivector(wav,1,imx);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);       results. So we changed our mind and took the option of the best precision.
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);      */
  free_ivector(num,1,n);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
  free_vector(agedc,1,n);    agelim = AGESUP;
  /*free_matrix(covar,1,NCOVMAX,1,n);*/    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
  fclose(ficparo);      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
  fclose(ficres);      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 /*--------- index.htm --------*/      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
       gp=matrix(0,nhstepm,1,nlstate);
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres);      gm=matrix(0,nhstepm,1,nlstate);
   
    
   /*--------------- Prevalence limit --------------*/      for(theta=1; theta <=npar; theta++){
          for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
   strcpy(filerespl,"pl");          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   strcat(filerespl,fileres);        }
   if((ficrespl=fopen(filerespl,"w"))==NULL) {        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   }  
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);        if (popbased==1) {
   fprintf(ficrespl,"#Prevalence limit\n");          if(mobilav ==0){
   fprintf(ficrespl,"#Age ");            for(i=1; i<=nlstate;i++)
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);              prlim[i][i]=probs[(int)age][i][ij];
   fprintf(ficrespl,"\n");          }else{ /* mobilav */ 
              for(i=1; i<=nlstate;i++)
   prlim=matrix(1,nlstate,1,nlstate);              prlim[i][i]=mobaverage[(int)age][i][ij];
   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 */        for(j=1; j<= nlstate; j++){
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */          for(h=0; h<=nhstepm; h++){
   k=0;            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
   agebase=agemin;              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
   agelim=agemaxpar;          }
   ftolpl=1.e-10;        }
   i1=cptcoveff;        /* This for computing probability of death (h=1 means
   if (cptcovn < 1){i1=1;}           computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
   for(cptcov=1;cptcov<=i1;cptcov++){        */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        for(j=nlstate+1;j<=nlstate+ndeath;j++){
         k=k+1;          for(i=1,gpp[j]=0.; i<= nlstate; i++)
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/            gpp[j] += prlim[i][i]*p3mat[i][j][1];
         fprintf(ficrespl,"\n#******");        }    
         for(j=1;j<=cptcoveff;j++)        /* end probability of death */
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
         fprintf(ficrespl,"******\n");        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
                  xp[i] = x[i] - (i==theta ?delti[theta]:0);
         for (age=agebase; age<=agelim; age++){        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
           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++)        if (popbased==1) {
           fprintf(ficrespl," %.5f", prlim[i][i]);          if(mobilav ==0){
           fprintf(ficrespl,"\n");            for(i=1; i<=nlstate;i++)
         }              prlim[i][i]=probs[(int)age][i][ij];
       }          }else{ /* mobilav */ 
     }            for(i=1; i<=nlstate;i++)
   fclose(ficrespl);              prlim[i][i]=mobaverage[(int)age][i][ij];
           }
   /*------------- h Pij x at various ages ------------*/        }
    
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);        for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
   if((ficrespij=fopen(filerespij,"w"))==NULL) {          for(h=0; h<=nhstepm; h++){
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
   }              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
   printf("Computing pij: result on file '%s' \n", filerespij);          }
          }
   stepsize=(int) (stepm+YEARM-1)/YEARM;        /* This for computing probability of death (h=1 means
   /*if (stepm<=24) stepsize=2;*/           computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
   agelim=AGESUP;        */
   hstepm=stepsize*YEARM; /* Every year of age */        for(j=nlstate+1;j<=nlstate+ndeath;j++){
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */          for(i=1,gmp[j]=0.; i<= nlstate; i++)
             gmp[j] += prlim[i][i]*p3mat[i][j][1];
   k=0;        }    
   for(cptcov=1;cptcov<=i1;cptcov++){        /* end probability of death */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  
       k=k+1;        for(j=1; j<= nlstate; j++) /* vareij */
         fprintf(ficrespij,"\n#****** ");          for(h=0; h<=nhstepm; h++){
         for(j=1;j<=cptcoveff;j++)            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          }
         fprintf(ficrespij,"******\n");  
                for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
           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);      } /* End theta */
           oldm=oldms;savm=savms;  
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
           fprintf(ficrespij,"# Age");  
           for(i=1; i<=nlstate;i++)      for(h=0; h<=nhstepm; h++) /* veij */
             for(j=1; j<=nlstate+ndeath;j++)        for(j=1; j<=nlstate;j++)
               fprintf(ficrespij," %1d-%1d",i,j);          for(theta=1; theta <=npar; theta++)
           fprintf(ficrespij,"\n");            trgradg[h][j][theta]=gradg[h][theta][j];
           for (h=0; h<=nhstepm; h++){  
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
             for(i=1; i<=nlstate;i++)        for(theta=1; theta <=npar; theta++)
               for(j=1; j<=nlstate+ndeath;j++)          trgradgp[j][theta]=gradgp[theta][j];
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);    
             fprintf(ficrespij,"\n");  
           }      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      for(i=1;i<=nlstate;i++)
           fprintf(ficrespij,"\n");        for(j=1;j<=nlstate;j++)
         }          vareij[i][j][(int)age] =0.;
     }  
   }      for(h=0;h<=nhstepm;h++){
         for(k=0;k<=nhstepm;k++){
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
           matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
   fclose(ficrespij);          for(i=1;i<=nlstate;i++)
             for(j=1;j<=nlstate;j++)
               vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
   /*---------- Forecasting ------------------*/        }
   if((stepm == 1) && (strcmp(model,".")==0)){      }
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);    
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);      /* pptj */
     free_matrix(mint,1,maxwav,1,n);      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
     free_vector(weight,1,n);}      for(j=nlstate+1;j<=nlstate+ndeath;j++)
   else{        for(i=nlstate+1;i<=nlstate+ndeath;i++)
     erreur=108;          varppt[j][i]=doldmp[j][i];
     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);      /* end ppptj */
   }      /*  x centered again */
        hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
       prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
   /*---------- Health expectancies and variances ------------*/   
       if (popbased==1) {
   strcpy(filerest,"t");        if(mobilav ==0){
   strcat(filerest,fileres);          for(i=1; i<=nlstate;i++)
   if((ficrest=fopen(filerest,"w"))==NULL) {            prlim[i][i]=probs[(int)age][i][ij];
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;        }else{ /* mobilav */ 
   }          for(i=1; i<=nlstate;i++)
   printf("Computing Total LEs with variances: file '%s' \n", filerest);            prlim[i][i]=mobaverage[(int)age][i][ij];
         }
       }
   strcpy(filerese,"e");               
   strcat(filerese,fileres);      /* This for computing probability of death (h=1 means
   if((ficreseij=fopen(filerese,"w"))==NULL) {         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);         as a weighted average of prlim.
   }      */
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);      for(j=nlstate+1;j<=nlstate+ndeath;j++){
         for(i=1,gmp[j]=0.;i<= nlstate; i++) 
  strcpy(fileresv,"v");          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
   strcat(fileresv,fileres);      }    
   if((ficresvij=fopen(fileresv,"w"))==NULL) {      /* end probability of death */
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);  
   }      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
   k=0;        for(i=1; i<=nlstate;i++){
   for(cptcov=1;cptcov<=i1;cptcov++){          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        }
       k=k+1;      } 
       fprintf(ficrest,"\n#****** ");      fprintf(ficresprobmorprev,"\n");
       for(j=1;j<=cptcoveff;j++)  
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      fprintf(ficresvij,"%.0f ",age );
       fprintf(ficrest,"******\n");      for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
       fprintf(ficreseij,"\n#****** ");          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
       for(j=1;j<=cptcoveff;j++)        }
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);      fprintf(ficresvij,"\n");
       fprintf(ficreseij,"******\n");      free_matrix(gp,0,nhstepm,1,nlstate);
       free_matrix(gm,0,nhstepm,1,nlstate);
       fprintf(ficresvij,"\n#****** ");      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
       for(j=1;j<=cptcoveff;j++)      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       fprintf(ficresvij,"******\n");    } /* End age */
     free_vector(gpp,nlstate+1,nlstate+ndeath);
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    free_vector(gmp,nlstate+1,nlstate+ndeath);
       oldm=oldms;savm=savms;    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);      free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    fprintf(ficgp,"\nunset parametric;unset label; set ter png small;set size 0.65, 0.65");
       oldm=oldms;savm=savms;    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);    fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
      /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
   /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
    /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l lt 2 ",subdirf(fileresprobmorprev));
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l lt 3 ",subdirf(fileresprobmorprev));
       fprintf(ficrest,"\n");    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l lt 3 ",subdirf(fileresprobmorprev));
     fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
       epj=vector(1,nlstate+1);    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);
       for(age=bage; age <=fage ;age++){    /*  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);
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);  */
         if (popbased==1) {  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
           for(i=1; i<=nlstate;i++)    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
             prlim[i][i]=probs[(int)age][i][k];  
         }    free_vector(xp,1,npar);
            free_matrix(doldm,1,nlstate,1,nlstate);
         fprintf(ficrest," %4.0f",age);    free_matrix(dnewm,1,nlstate,1,npar);
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
           for(i=1, epj[j]=0.;i <=nlstate;i++) {    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
             epj[j] += prlim[i][i]*eij[i][j][(int)age];    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
           }    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
           epj[nlstate+1] +=epj[j];    fclose(ficresprobmorprev);
         }    fflush(ficgp);
         for(i=1, vepp=0.;i <=nlstate;i++)    fflush(fichtm); 
           for(j=1;j <=nlstate;j++)  }  /* end varevsij */
             vepp += vareij[i][j][(int)age];  
         fprintf(ficrest," %7.2f (%7.2f)", epj[nlstate+1],sqrt(vepp));  /************ Variance of prevlim ******************/
         for(j=1;j <=nlstate;j++){  void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, char strstart[])
           fprintf(ficrest," %7.2f (%7.2f)", epj[j],sqrt(vareij[j][j][(int)age]));  {
         }    /* Variance of prevalence limit */
         fprintf(ficrest,"\n");    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
       }    double **newm;
     }    double **dnewm,**doldm;
   }    int i, j, nhstepm, hstepm;
     int k, cptcode;
   fclose(ficreseij);    double *xp;
   fclose(ficresvij);    double *gp, *gm;
   fclose(ficrest);    double **gradg, **trgradg;
   fclose(ficpar);    double age,agelim;
   free_vector(epj,1,nlstate+1);    int theta;
      
   /*------- Variance limit prevalence------*/      pstamp(ficresvpl);
     fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
   strcpy(fileresvpl,"vpl");    fprintf(ficresvpl,"# Age");
   strcat(fileresvpl,fileres);    for(i=1; i<=nlstate;i++)
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {        fprintf(ficresvpl," %1d-%1d",i,i);
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);    fprintf(ficresvpl,"\n");
     exit(0);  
   }    xp=vector(1,npar);
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);    dnewm=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
   k=0;    
   for(cptcov=1;cptcov<=i1;cptcov++){    hstepm=1*YEARM; /* Every year of age */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
       k=k+1;    agelim = AGESUP;
       fprintf(ficresvpl,"\n#****** ");    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       for(j=1;j<=cptcoveff;j++)      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      if (stepm >= YEARM) hstepm=1;
       fprintf(ficresvpl,"******\n");      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
            gradg=matrix(1,npar,1,nlstate);
       varpl=matrix(1,nlstate,(int) bage, (int) fage);      gp=vector(1,nlstate);
       oldm=oldms;savm=savms;      gm=vector(1,nlstate);
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);  
     }      for(theta=1; theta <=npar; theta++){
  }        for(i=1; i<=npar; i++){ /* Computes gradient */
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
   fclose(ficresvpl);        }
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   /*---------- End : free ----------------*/        for(i=1;i<=nlstate;i++)
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);          gp[i] = prlim[i][i];
        
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);        for(i=1; i<=npar; i++) /* Computes gradient */
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
          prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
          for(i=1;i<=nlstate;i++)
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);          gm[i] = prlim[i][i];
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);  
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);        for(i=1;i<=nlstate;i++)
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
        } /* End theta */
   free_matrix(matcov,1,npar,1,npar);  
   free_vector(delti,1,npar);      trgradg =matrix(1,nlstate,1,npar);
   free_matrix(agev,1,maxwav,1,imx);  
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);      for(j=1; j<=nlstate;j++)
         for(theta=1; theta <=npar; theta++)
   if(erreur >0)          trgradg[j][theta]=gradg[theta][j];
     printf("End of Imach with error %d\n",erreur);  
   else   printf("End of Imach\n");      for(i=1;i<=nlstate;i++)
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */        varpl[i][(int)age] =0.;
        matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
   /* 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);*/      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
   /*printf("Total time was %d uSec.\n", total_usecs);*/      for(i=1;i<=nlstate;i++)
   /*------ End -----------*/        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   
       fprintf(ficresvpl,"%.0f ",age );
  end:      for(i=1; i<=nlstate;i++)
 #ifdef windows        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
   /* chdir(pathcd);*/      fprintf(ficresvpl,"\n");
 #endif      free_vector(gp,1,nlstate);
  /*system("wgnuplot graph.plt");*/      free_vector(gm,1,nlstate);
  /*system("../gp37mgw/wgnuplot graph.plt");*/      free_matrix(gradg,1,npar,1,nlstate);
  /*system("cd ../gp37mgw");*/      free_matrix(trgradg,1,nlstate,1,npar);
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/    } /* End age */
  strcpy(plotcmd,GNUPLOTPROGRAM);  
  strcat(plotcmd," ");    free_vector(xp,1,npar);
  strcat(plotcmd,optionfilegnuplot);    free_matrix(doldm,1,nlstate,1,npar);
  system(plotcmd);    free_matrix(dnewm,1,nlstate,1,nlstate);
   
 #ifdef windows  }
   while (z[0] != 'q') {  
     chdir(path);  /************ Variance of one-step probabilities  ******************/
     printf("\nType e to edit output files, c to start again, and q for exiting: ");  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[])
     scanf("%s",z);  {
     if (z[0] == 'c') system("./imach");    int i, j=0,  i1, k1, l1, t, tj;
     else if (z[0] == 'e') {    int k2, l2, j1,  z1;
       chdir(path);    int k=0,l, cptcode;
       system(optionfilehtm);    int first=1, first1;
     }    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
     else if (z[0] == 'q') exit(0);    double **dnewm,**doldm;
   }    double *xp;
 #endif    double *gp, *gm;
 }    double **gradg, **trgradg;
     double **mu;
     double age,agelim, cov[NCOVMAX];
     double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
     int theta;
     char fileresprob[FILENAMELENGTH];
     char fileresprobcov[FILENAMELENGTH];
     char fileresprobcor[FILENAMELENGTH];
   
     double ***varpij;
   
     strcpy(fileresprob,"prob"); 
     strcat(fileresprob,fileres);
     if((ficresprob=fopen(fileresprob,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprob);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
     }
     strcpy(fileresprobcov,"probcov"); 
     strcat(fileresprobcov,fileres);
     if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcov);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
     }
     strcpy(fileresprobcor,"probcor"); 
     strcat(fileresprobcor,fileres);
     if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcor);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
     }
     printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     pstamp(ficresprob);
     fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
     fprintf(ficresprob,"# Age");
     pstamp(ficresprobcov);
     fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
     fprintf(ficresprobcov,"# Age");
     pstamp(ficresprobcor);
     fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
     fprintf(ficresprobcor,"# Age");
   
   
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprob," p%1d-%1d (SE)",i,j);
         fprintf(ficresprobcov," p%1d-%1d ",i,j);
         fprintf(ficresprobcor," p%1d-%1d ",i,j);
       }  
    /* fprintf(ficresprob,"\n");
     fprintf(ficresprobcov,"\n");
     fprintf(ficresprobcor,"\n");
    */
     xp=vector(1,npar);
     dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
     varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
     first=1;
     fprintf(ficgp,"\n# Routine varprob");
     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
     fprintf(fichtm,"\n");
   
     fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
     fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
     file %s<br>\n",optionfilehtmcov);
     fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
   and drawn. It helps understanding how is the covariance between two incidences.\
    They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
     fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
   It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
   would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
   standard deviations wide on each axis. <br>\
    Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
    and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
   To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
   
     cov[1]=1;
     tj=cptcoveff;
     if (cptcovn<1) {tj=1;ncodemax[1]=1;}
     j1=0;
     for(t=1; t<=tj;t++){
       for(i1=1; i1<=ncodemax[t];i1++){ 
         j1++;
         if  (cptcovn>0) {
           fprintf(ficresprob, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprob, "**********\n#\n");
           fprintf(ficresprobcov, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcov, "**********\n#\n");
           
           fprintf(ficgp, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficgp, "**********\n#\n");
           
           
           fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
           
           fprintf(ficresprobcor, "\n#********** Variable ");    
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcor, "**********\n#");    
         }
         
         for (age=bage; age<=fage; age ++){ 
           cov[2]=age;
           for (k=1; k<=cptcovn;k++) {
             cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
           }
           for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
           for (k=1; k<=cptcovprod;k++)
             cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
           
           gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
           trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
           gp=vector(1,(nlstate)*(nlstate+ndeath));
           gm=vector(1,(nlstate)*(nlstate+ndeath));
       
           for(theta=1; theta <=npar; theta++){
             for(i=1; i<=npar; i++)
               xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
             
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             
             k=0;
             for(i=1; i<= (nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gp[k]=pmmij[i][j];
               }
             }
             
             for(i=1; i<=npar; i++)
               xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
       
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             k=0;
             for(i=1; i<=(nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gm[k]=pmmij[i][j];
               }
             }
        
             for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
               gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
           }
   
           for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
             for(theta=1; theta <=npar; theta++)
               trgradg[j][theta]=gradg[theta][j];
           
           matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
           matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
           free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
           free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
           free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
           free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   
           pmij(pmmij,cov,ncovmodel,x,nlstate);
           
           k=0;
           for(i=1; i<=(nlstate); i++){
             for(j=1; j<=(nlstate+ndeath);j++){
               k=k+1;
               mu[k][(int) age]=pmmij[i][j];
             }
           }
           for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
             for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
               varpij[i][j][(int)age] = doldm[i][j];
   
           /*printf("\n%d ",(int)age);
             for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             }*/
   
           fprintf(ficresprob,"\n%d ",(int)age);
           fprintf(ficresprobcov,"\n%d ",(int)age);
           fprintf(ficresprobcor,"\n%d ",(int)age);
   
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
             fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
             fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
           }
           i=0;
           for (k=1; k<=(nlstate);k++){
             for (l=1; l<=(nlstate+ndeath);l++){ 
               i=i++;
               fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
               fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
               for (j=1; j<=i;j++){
                 fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
                 fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
               }
             }
           }/* end of loop for state */
         } /* end of loop for age */
   
         /* Confidence intervalle of pij  */
         /*
           fprintf(ficgp,"\nunset parametric;unset label");
           fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
           fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
           fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
           fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
           fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
           fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
         */
   
         /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
         first1=1;
         for (k2=1; k2<=(nlstate);k2++){
           for (l2=1; l2<=(nlstate+ndeath);l2++){ 
             if(l2==k2) continue;
             j=(k2-1)*(nlstate+ndeath)+l2;
             for (k1=1; k1<=(nlstate);k1++){
               for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                 if(l1==k1) continue;
                 i=(k1-1)*(nlstate+ndeath)+l1;
                 if(i<=j) continue;
                 for (age=bage; age<=fage; age ++){ 
                   if ((int)age %5==0){
                     v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                     v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     mu1=mu[i][(int) age]/stepm*YEARM ;
                     mu2=mu[j][(int) age]/stepm*YEARM;
                     c12=cv12/sqrt(v1*v2);
                     /* Computing eigen value of matrix of covariance */
                     lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     if ((lc2 <0) || (lc1 <0) ){
                       printf("Error: One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Continuing by making them positive: WRONG RESULTS.\n", lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);
                       fprintf(ficlog,"Error: One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e\n", lc1, lc2, v1, v2, cv12);fflush(ficlog);
                       lc1=fabs(lc1);
                       lc2=fabs(lc2);
                     }
   
                     /* Eigen vectors */
                     v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                     /*v21=sqrt(1.-v11*v11); *//* error */
                     v21=(lc1-v1)/cv12*v11;
                     v12=-v21;
                     v22=v11;
                     tnalp=v21/v11;
                     if(first1==1){
                       first1=0;
                       printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     }
                     fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     /*printf(fignu*/
                     /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                     /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                     if(first==1){
                       first=0;
                       fprintf(ficgp,"\nset parametric;unset label");
                       fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
                       fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
                       fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
    :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
   %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }else{
                       first=0;
                       fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }/* if first */
                   } /* age mod 5 */
                 } /* end loop age */
                 fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                 first=1;
               } /*l12 */
             } /* k12 */
           } /*l1 */
         }/* k1 */
       } /* loop covariates */
     }
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
     free_vector(xp,1,npar);
     fclose(ficresprob);
     fclose(ficresprobcov);
     fclose(ficresprobcor);
     fflush(ficgp);
     fflush(fichtmcov);
   }
   
   
   /******************* Printing html file ***********/
   void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                     int popforecast, int estepm ,\
                     double jprev1, double mprev1,double anprev1, \
                     double jprev2, double mprev2,double anprev2){
     int jj1, k1, i1, cpt;
   
      fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
      <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
   </ul>");
      fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
    - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
              jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
      fprintf(fichtm,"\
    - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
              stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
      fprintf(fichtm,"\
    - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
              subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
      fprintf(fichtm,"\
    - (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n",
              estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
      fprintf(fichtm,"\
    - Population projections by age and states: \
      <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
   
   fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
    m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        /* Pij */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d1.png\">%s%d1.png</a><br> \
   <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
        /* Quasi-incidences */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
    before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d2.png\">%s%d2.png</a><br> \
   <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
          /* Period (stable) prevalence in each health state */
          for(cpt=1; cpt<nlstate;cpt++){
            fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
   <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
          }
        for(cpt=1; cpt<=nlstate;cpt++) {
           fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
   <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
        }
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
   
   
    fprintf(fichtm,"\
   \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
    - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
   
    fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
    fprintf(fichtm,"\
    - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
   
    fprintf(fichtm,"\
    - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
    fprintf(fichtm,"\
    - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
            estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
    fprintf(fichtm,"\
    - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",
            estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
    fprintf(fichtm,"\
    - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
            subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   
   /*  if(popforecast==1) fprintf(fichtm,"\n */
   /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
   /*      <br>",fileres,fileres,fileres,fileres); */
   /*  else  */
   /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
    fflush(fichtm);
    fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   
    m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        for(cpt=1; cpt<=nlstate;cpt++) {
          fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
   prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
   <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
        }
        fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
   true period expectancies (those weighted with period prevalences are also\
    drawn in addition to the population based expectancies computed using\
    observed and cahotic prevalences: %s%d.png<br>\
   <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
    fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m0,cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
     int ng=0;
   /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   /*     printf("Problem with file %s",optionfilegnuplot); */
   /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   /*   } */
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
     m=pow(2,cptcoveff);
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
    /* 1eme*/
     for (cpt=1; cpt<= nlstate ; cpt ++) {
      for (k1=1; k1<= m ; k1 ++) {
        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
        fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
        fprintf(ficgp,"set xlabel \"Age\" \n\
   set ylabel \"Probability\" \n\
   set ter png small\n\
   set size 0.65,0.65\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else        fprintf(ficgp," \%%*lf (\%%*lf)");
        }
        fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 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\"95\%% CI\" w l lt 2,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }  
        fprintf(ficgp,"\" t\"\" w l lt 2,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 3",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 lt 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)");
         }   
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 1");
         else fprintf(ficgp,"\" t\"\" w l lt 1,");
       }
     }
     
     /*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;/* To be checked else nbcode[0][0] wrong */
                for(j=3; j <=ncovmodel; j++) {
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /* Bug valgrind */
                    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;
   }
   
   #ifdef GSL
   /******************* Gompertz_f Likelihood ******************************/
   double gompertz_f(const gsl_vector *v, void *params)
   { 
     double A,B,LL=0.0,sump=0.,num=0.;
     double *x= (double *) v->data;
     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]);*/
     printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
                +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           LL=LL+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);*/
     printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
    
     return -2*LL*num/sump;
   }
   #endif
   
   /******************* 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);
   
   } 
   
   int readdata(char datafile[], int firstobs, int lastobs, int *imax)
   {
   
     /*-------- data file ----------*/
     FILE *fic;
     char dummy[]="                         ";
     int i, j, n;
     int linei, month, year,iout;
     char line[MAXLINE], linetmp[MAXLINE];
     char stra[80], strb[80];
     char *stratrunc;
     int lstra;
   
   
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem while opening datafile: %s\n", datafile);return 1;
       fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
     }
   
     i=1;
     linei=0;
     while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
       linei=linei+1;
       for(j=strlen(line); j>=0;j--){  /* Untabifies line */
         if(line[j] == '\t')
           line[j] = ' ';
       }
       for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
         ;
       };
       line[j+1]=0;  /* Trims blanks at end of line */
       if(line[0]=='#'){
         fprintf(ficlog,"Comment line\n%s\n",line);
         printf("Comment line\n%s\n",line);
         continue;
       }
       trimbb(linetmp,line); /* Trims multiple blanks in line */
       for (j=0; line[j]!='\0';j++){
         line[j]=linetmp[j];
       }
     
   
       for (j=maxwav;j>=1;j--){
         cutv(stra, strb, line, ' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
         /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
             fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);
             return 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 %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);fflush(ficlog);
           return 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 %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 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 %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
       }
       if (year==9999) {
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given.  Exiting.\n",strb, linei,i,line);
         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 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 %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fprintf(ficlog,"Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fflush(ficlog);
         return 1;
       }
       weight[i]=dval; 
       strcpy(line,stra);
       
       for (j=ncovcol;j>=1;j--){
         cutv(stra, strb,line,' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);
             fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);fflush(ficlog);
             return 1;
           }
         }
         if(lval <-1 || lval >1){
           printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);
           fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
           return 1;
         }
         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 */
   
     *imax=i-1; /* Number of individuals */
     fclose(fic);
    
     return (0);
     endread:
       printf("Exiting readdata: ");
       fclose(fic);
       return (1);
   
   
   
   }
   
   int decodemodel ( char model[], int lastobs)
   {
     int i, j, k;
     int i1, j1, k1, k2;
     char modelsav[80];
      char stra[80], strb[80], strc[80], strd[80],stre[80];
   
     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*age+V3 =>(2 plus signs) + 1=3 
                     but the covariates which are product must be computed and stored. */
       cptcovprod=j1; /*Number of products  V1*V2 +v3*age = 2 */
       
       strcpy(modelsav,model); 
       if (strstr(model,"AGE") !=0){
         printf("Error. AGE must be in lower case 'age' model=%s ",model);
         fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
         return 1;
       }
       if (strstr(model,"v") !=0){
         printf("Error. 'v' must be in upper case 'V' model=%s ",model);
         fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
         return 1;
       }
       
       /* 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 */
       /*   modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4  */
       /*  k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
       /*  k=3 V4 Tvar[k=3]= 4 (from V4) */
       /*  k=2 V1 Tvar[k=2]= 1 (from V1) */
       /*  k=1 Tvar[1]=2 (from V2) */
       /*  k=5 Tvar[5] */
       /* for (k=1; k<=cptcovn;k++) { */
       /*  cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
       /*  } */
       /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
       for(k=cptcovn; k>=1;k--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' 
                                        modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 
                                       */ 
         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 V2+V1+V4+V3*age strb=V3*age */
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn: strb=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'); /* stre="V3" */
             Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=2 ; V1+V2*age Tvar[2]=2 */
             cptcovage++; /* Sums the number of covariates which include age as a product */
             Tage[cptcovage]=k;  /* Tage[1] = 4 */
             /*printf("stre=%s ", stre);*/
           } else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutv(strb,stre,strc,'V');
             Tvar[k]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=k;
           } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/
             /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
             cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
             Tvar[k]=ncovcol+k1;  /* For model-covariate k tells which data-covariate to use but
                                     because this model-covariate is a construction we invent a new column
                                     ncovcol + k1
                                     If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
                                     Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
             cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */
             Tvard[k1][1]=atoi(strc); /* m 1 for V1*/
             Tvard[k1][2]=atoi(stre); /* n 4 for V4*/
             Tvar[cptcovn+k2]=Tvard[k1][1]; /* Tvar[(cptcovn=4+k2=1)=5]= 1 (V1) */
             Tvar[cptcovn+k2+1]=Tvard[k1][2];  /* Tvar[(cptcovn=4+(k2=1)+1)=6]= 4 (V4) */
             for (i=1; i<=lastobs;i++){
               /* Computes the new covariate which is a product of
                  covar[n][i]* covar[m][i] and stores it at ncovol+k1 */
               covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
             }
             k1++;
             k2=k2+2;
           } /* End age is not in the model */
         } /* End if model includes a product */
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
           cutv(strd,strc,strb,'V');
           Tvar[k]=atoi(strc);
         }
         strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+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);*/
   
   
     return (0); /* with covar[new additional covariate if product] and Tage if age */ 
     endread:
       printf("Exiting decodemodel: ");
       return (1);
   }
   
   calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
   {
     int i, m;
   
     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(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\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);     
           return 1;
         }
       }
     }
   
     /*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); 
   
     return (0);
     endread:
       printf("Exiting calandcheckages: ");
       return (1);
   }
   
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
   #ifdef GSL
     const gsl_multimin_fminimizer_type *T;
     size_t iteri = 0, it;
     int rval = GSL_CONTINUE;
     int status = GSL_SUCCESS;
     double ssval;
   #endif
     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];
     /*  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, jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,*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 ***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  *strt;*/
     char strtend[80];
   
     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++;
       fputs(line,stdout);
       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++;
       fputs(line, stdout);
       //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 plus one, indepently of n in Vn*/
     /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
        v1+v2*age+v2*v3 makes cptcovn = 3
     */
     if (strlen(model)>1) 
       cptcovn=nbocc(model,'+')+1;
     /* ncovprod */
     ncovmodel=2+cptcovn; /*Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7*/
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
     npar= nforce*ncovmodel; /* Number of parameters like aij*/
     if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
       printf("Too complex model for current IMaCh: npar=(nlstate+ndeath-1)*nlstate*ncovmodel=%d >= %d(MAXPARM) or nlstate=%d >= %d(NLSTATEMAX) or ndeath=%d >= %d(NDEATHMAX) or ncovmodel=(k+age+#of+signs)=%d(NCOVMAX) >= %d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fprintf(ficlog,"Too complex model for current IMaCh: %d >=%d(MAXPARM) or %d >=%d(NLSTATEMAX) or %d >=%d(NDEATHMAX) or %d(NCOVMAX) >=%d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fflush(stdout);
       fclose (ficlog);
       goto end;
     }
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     delti=delti3[1][1];
     /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
     if(mle==-1){ /* Print a wizard for help writing covariance matrix */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       fclose (ficparo);
       fclose (ficlog);
       goto end;
       exit(0);
     }
     else if(mle==-3) {
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       matcov=matrix(1,npar,1,npar);
     }
     else{
       /* Read guess parameters */
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         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++;
         fputs(line,stdout);
         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++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
     
       matcov=matrix(1,npar,1,npar);
       for(i=1; i <=npar; i++)
         for(j=1; j <=npar; j++) matcov[i][j]=0.;
         
       for(i=1; i <=npar; i++){
         fscanf(ficpar,"%s",&str);
         if(mle==1)
           printf("%s",str);
         fprintf(ficlog,"%s",str);
         fprintf(ficparo,"%s",str);
         for(j=1; j <=i; j++){
           fscanf(ficpar," %le",&matcov[i][j]);
           if(mle==1){
             printf(" %.5le",matcov[i][j]);
           }
           fprintf(ficlog," %.5le",matcov[i][j]);
           fprintf(ficparo," %.5le",matcov[i][j]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
       for(i=1; i <=npar; i++)
         for(j=i+1;j<=npar;j++)
           matcov[i][j]=matcov[j][i];
       
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       
       fflush(ficlog);
       
       /*-------- Rewriting parameter file ----------*/
       strcpy(rfileres,"r");    /* "Rparameterfile */
       strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
       strcat(rfileres,".");    /* */
       strcat(rfileres,optionfilext);    /* Other files have txt extension */
       if((ficres =fopen(rfileres,"w"))==NULL) {
         printf("Problem writing new parameter file: %s\n", fileres);goto end;
         fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
       }
       fprintf(ficres,"#%s\n",version);
     }    /* End of mle != -3 */
   
   
     n= lastobs;
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */ 
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,8); /* hard coded ? */
   
     /* Reads data from file datafile */
     if (readdata(datafile, firstobs, lastobs, &imx)==1)
       goto end;
   
     /* Calculation of the number of parameters from char model */
       /*    modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 
           k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
           k=3 V4 Tvar[k=3]= 4 (from V4)
           k=2 V1 Tvar[k=2]= 1 (from V1)
           k=1 Tvar[1]=2 (from V2)
       */
     Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
     /*  V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs). 
         For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4, 
         Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
     */
     /* For model-covariate k tells which data-covariate to use but
       because this model-covariate is a construction we invent a new column
       ncovcol + k1
       If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
       Tvar[3=V1*V4]=4+1 etc */
     Tprod=ivector(1,15); /* Gives the position of a product */
     /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
        if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2)
     */
     Tvaraff=ivector(1,15); 
     Tvard=imatrix(1,15,1,2); /* n=Tvard[k1][1]  and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm
                               * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd. 
                               * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
     Tage=ivector(1,15); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
                            4 covariates (3 plus signs)
                            Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
                         */  
   
     if(decodemodel(model, lastobs) == 1)
       goto end;
   
     if((double)(lastobs-imx)/(double)imx > 1.10){
       nbwarn++;
       printf("Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
       fprintf(ficlog,"Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
     }
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
       for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
     }
   
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
       goto end;
   
   
     agegomp=(int)agemin;
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
   
      
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     if (cptcovn > 0) tricode(Tvar,nbcode,imx);
         
     codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
                                    the estimations*/
     h=0;
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
       for(i=1; i <=pow(2,cptcoveff-k);i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */ 
         for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
           for(cpt=1; cpt <=pow(2,k-1); cpt++){  /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */ 
             h++;
             if (h>m) 
               h=1;
             /**< codtab(h,k)  k
              *     h     1     2     3     4
              *______________________________  
              *     1 i=1 1 i=1 1 i=1 1 i=1 1
              *     2     2     1     1     1
              *     3 i=2 1     2     1     1
              *     4     2     2     1     1
              *     5 i=3 1 i=2 1     2     1
              *     6     2     1     2     1
              *     7 i=4 1     2     2     1
              *     8     2     2     2     1
              *     9 i=5 1 i=3 1 i=2 1     1
              *    10     2     1     1     1
              *    11 i=6 1     2     1     1
              *    12     2     2     1     1
              *    13 i=7 1 i=4 1     2     1    
              *    14     2     1     2     1
              *    15 i=8 1     2     2     1
              *    16     2     2     2     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");
       fprintf(ficgp,"set datafile 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); 
   /*     ximort=gsl_matrix_alloc(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]);*/
       
       
   #ifdef GSL
       printf("GSL optimization\n");  fprintf(ficlog,"Powell\n");
   #elsedef
       printf("Powell\n");  fprintf(ficlog,"Powell\n");
   #endif
       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);
       }
   #ifdef GSL
       fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
   #elsedef
       fprintf(ficrespow,"# Powell\n# iter -2*LL");
   #endif
       /*  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");
   #ifdef GSL
       /* gsl starts here */ 
       T = gsl_multimin_fminimizer_nmsimplex;
       gsl_multimin_fminimizer *sfm = NULL;
       gsl_vector *ss, *x;
       gsl_multimin_function minex_func;
   
       /* Initial vertex size vector */
       ss = gsl_vector_alloc (NDIM);
       
       if (ss == NULL){
         GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
       }
       /* Set all step sizes to 1 */
       gsl_vector_set_all (ss, 0.001);
   
       /* Starting point */
       
       x = gsl_vector_alloc (NDIM);
       
       if (x == NULL){
         gsl_vector_free(ss);
         GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
       }
     
       /* Initialize method and iterate */
       /*     p[1]=0.0268; p[NDIM]=0.083; */
   /*     gsl_vector_set(x, 0, 0.0268); */
   /*     gsl_vector_set(x, 1, 0.083); */
       gsl_vector_set(x, 0, p[1]);
       gsl_vector_set(x, 1, p[2]);
   
       minex_func.f = &gompertz_f;
       minex_func.n = NDIM;
       minex_func.params = (void *)&p; /* ??? */
       
       sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
       gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
       
       printf("Iterations beginning .....\n\n");
       printf("Iter. #    Intercept       Slope     -Log Likelihood     Simplex size\n");
   
       iteri=0;
       while (rval == GSL_CONTINUE){
         iteri++;
         status = gsl_multimin_fminimizer_iterate(sfm);
         
         if (status) printf("error: %s\n", gsl_strerror (status));
         fflush(0);
         
         if (status) 
           break;
         
         rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
         ssval = gsl_multimin_fminimizer_size (sfm);
         
         if (rval == GSL_SUCCESS)
           printf ("converged to a local maximum at\n");
         
         printf("%5d ", iteri);
         for (it = 0; it < NDIM; it++){
           printf ("%10.5f ", gsl_vector_get (sfm->x, it));
         }
         printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
       }
       
       printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
       
       gsl_vector_free(x); /* initial values */
       gsl_vector_free(ss); /* inital step size */
       for (it=0; it<NDIM; it++){
         p[it+1]=gsl_vector_get(sfm->x,it);
         fprintf(ficrespow," %.12lf", p[it]);
       }
       gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1)  */
   #endif
   #ifdef POWELL
        powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
   #endif  
       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);
   #ifdef GSL
       free_ivector(cens,1,n);
       free_vector(agecens,1,n);
       free_ivector(dcwave,1,n);
       free_matrix(ximort,1,NDIM,1,NDIM);
   #endif
     } /* Endof if mle==-3 */
     
     else{ /* For mle >=1 */
       globpr=0;/* debug */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       globpr=1; /* to print the contributions */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       if(mle>=1){ /* Could be 1 or 2 */
         mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
       }
       
       /*--------- results files --------------*/
       fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
       
       
       fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(k=1; k <=(nlstate+ndeath); k++){
           if (k != i) {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%lf ",p[jk]);
               fprintf(ficlog,"%lf ",p[jk]);
               fprintf(ficres,"%lf ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       if(mle!=0){
         /* Computing hessian and covariance matrix */
         ftolhess=ftol; /* Usually correct */
         hesscov(matcov, p, npar, delti, ftolhess, func);
       }
       fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
       printf("# Scales (for hessian or gradient estimation)\n");
       fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if (j!=i) {
             fprintf(ficres,"%1d%1d",i,j);
             printf("%1d%1d",i,j);
             fprintf(ficlog,"%1d%1d",i,j);
             for(k=1; k<=ncovmodel;k++){
               printf(" %.5e",delti[jk]);
               fprintf(ficlog," %.5e",delti[jk]);
               fprintf(ficres," %.5e",delti[jk]);
               jk++;
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       
       fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       if(mle>=1)
         printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       /* # 121 Var(a12)\n\ */
       /* # 122 Cov(b12,a12) Var(b12)\n\ */
       /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
       /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
       /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
       /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
       /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
       /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
       
       
       /* Just to have a covariance matrix which will be more understandable
          even is we still don't want to manage dictionary of variables
       */
       for(itimes=1;itimes<=2;itimes++){
         jj=0;
         for(i=1; i <=nlstate; i++){
           for(j=1; j <=nlstate+ndeath; j++){
             if(j==i) continue;
             for(k=1; k<=ncovmodel;k++){
               jj++;
               ca[0]= k+'a'-1;ca[1]='\0';
               if(itimes==1){
                 if(mle>=1)
                   printf("#%1d%1d%d",i,j,k);
                 fprintf(ficlog,"#%1d%1d%d",i,j,k);
                 fprintf(ficres,"#%1d%1d%d",i,j,k);
               }else{
                 if(mle>=1)
                   printf("%1d%1d%d",i,j,k);
                 fprintf(ficlog,"%1d%1d%d",i,j,k);
                 fprintf(ficres,"%1d%1d%d",i,j,k);
               }
               ll=0;
               for(li=1;li <=nlstate; li++){
                 for(lj=1;lj <=nlstate+ndeath; lj++){
                   if(lj==li) continue;
                   for(lk=1;lk<=ncovmodel;lk++){
                     ll++;
                     if(ll<=jj){
                       cb[0]= lk +'a'-1;cb[1]='\0';
                       if(ll<jj){
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }else{
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }
                     }
                   } /* end lk */
                 } /* end lj */
               } /* end li */
               if(mle>=1)
                 printf("\n");
               fprintf(ficlog,"\n");
               fprintf(ficres,"\n");
               numlinepar++;
             } /* end k*/
           } /*end j */
         } /* end i */
       } /* end itimes */
       
       fflush(ficlog);
       fflush(ficres);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         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);
         fputs(line,stdout);
         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);
         fputs(line,stdout);
         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);
         fputs(line,stdout);
         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=pow(2,cptcoveff);
       if (cptcovn < 1){i1=1;}
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           /* to clean */
           //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,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");
           } /* Age */
           /* was end of cptcod */
       } /* cptcov */
       fclose(ficrespl);
   
       /*------------- h Pij x at various ages ------------*/
     
       strcpy(filerespij,"pij");  strcat(filerespij,fileres);
       if((ficrespij=fopen(filerespij,"w"))==NULL) {
         printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
         fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
       }
       printf("Computing pij: result on file '%s' \n", filerespij);
       fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
       stepsize=(int) (stepm+YEARM-1)/YEARM;
       /*if (stepm<=24) stepsize=2;*/
   
       agelim=AGESUP;
       hstepm=stepsize*YEARM; /* Every year of age */
       hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
       /* hstepm=1;   aff par mois*/
       pstamp(ficrespij);
       fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           fprintf(ficrespij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrespij,"******\n");
           
           for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
             nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   
             /*      nhstepm=nhstepm*YEARM; aff par mois*/
   
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %1d-%1d",i,j);
             fprintf(ficrespij,"\n");
             for (h=0; h<=nhstepm; h++){
               fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
               for(i=1; i<=nlstate;i++)
                 for(j=1; j<=nlstate+ndeath;j++)
                   fprintf(ficrespij," %.5f", p3mat[i][j][h]);
               fprintf(ficrespij,"\n");
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             fprintf(ficrespij,"\n");
           }
         }
       }
   
       varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
   
       fclose(ficrespij);
   
       probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for(i=1;i<=AGESUP;i++)
         for(j=1;j<=NCOVMAX;j++)
           for(k=1;k<=NCOVMAX;k++)
             probs[i][j][k]=0.;
   
       /*---------- Forecasting ------------------*/
       /*if((stepm == 1) && (strcmp(model,".")==0)){*/
       if(prevfcast==1){
         /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
         /*      }  */
         /*      else{ */
         /*        erreur=108; */
         /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*      } */
       }
     
   
       /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
   
       prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
       /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
           ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
       */
   
       if (mobilav!=0) {
         mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
           fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
           printf(" Error in movingaverage mobilav=%d\n",mobilav);
         }
       }
   
   
       /*---------- Health expectancies, no variances ------------*/
   
       strcpy(filerese,"e");
       strcat(filerese,fileres);
       if((ficreseij=fopen(filerese,"w"))==NULL) {
         printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
         fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       }
       printf("Computing Health Expectancies: result on file '%s' \n", filerese);
       fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1; 
           fprintf(ficreseij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficreseij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);  
         
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         }
       }
       fclose(ficreseij);
   
   
       /*---------- Health expectancies and variances ------------*/
   
   
       strcpy(filerest,"t");
       strcat(filerest,fileres);
       if((ficrest=fopen(filerest,"w"))==NULL) {
         printf("Problem with total LE resultfile: %s\n", filerest);goto end;
         fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
       }
       printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
       fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
   
   
       strcpy(fileresstde,"stde");
       strcat(fileresstde,fileres);
       if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
         printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
         fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
       }
       printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
       fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
   
       strcpy(filerescve,"cve");
       strcat(filerescve,fileres);
       if((ficrescveij=fopen(filerescve,"w"))==NULL) {
         printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
         fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
       }
       printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
       fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
   
       strcpy(fileresv,"v");
       strcat(fileresv,fileres);
       if((ficresvij=fopen(fileresv,"w"))==NULL) {
         printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
         fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
       }
       printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
       fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1; 
           fprintf(ficrest,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrest,"******\n");
   
           fprintf(ficresstdeij,"\n#****** ");
           fprintf(ficrescveij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficresstdeij,"******\n");
           fprintf(ficrescveij,"******\n");
   
           fprintf(ficresvij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);  
    
           vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           pstamp(ficrest);
           for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
             oldm=oldms;savm=savms;
             varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart);   fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");
             if(vpopbased==1)
               fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
             else
               fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
             fprintf(ficrest,"# Age e.. (std) ");
             for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
             fprintf(ficrest,"\n");
   
             epj=vector(1,nlstate+1);
             for(age=bage; age <=fage ;age++){
               prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
               if (vpopbased==1) {
                 if(mobilav ==0){
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=probs[(int)age][i][k];
                 }else{ /* mobilav */ 
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=mobaverage[(int)age][i][k];
                 }
               }
           
               fprintf(ficrest," %4.0f",age);
               for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
                 for(i=1, epj[j]=0.;i <=nlstate;i++) {
                   epj[j] += prlim[i][i]*eij[i][j][(int)age];
                   /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
                 }
                 epj[nlstate+1] +=epj[j];
               }
   
               for(i=1, vepp=0.;i <=nlstate;i++)
                 for(j=1;j <=nlstate;j++)
                   vepp += vareij[i][j][(int)age];
               fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
               for(j=1;j <=nlstate;j++){
                 fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
               }
               fprintf(ficrest,"\n");
             }
           }
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_vector(epj,1,nlstate+1);
         }
       }
       free_vector(weight,1,n);
       free_imatrix(Tvard,1,15,1,2);
       free_imatrix(s,1,maxwav+1,1,n);
       free_matrix(anint,1,maxwav,1,n); 
       free_matrix(mint,1,maxwav,1,n);
       free_ivector(cod,1,n);
       free_ivector(tab,1,NCOVMAX);
       fclose(ficresstdeij);
       fclose(ficrescveij);
       fclose(ficresvij);
       fclose(ficrest);
       fclose(ficpar);
     
       /*------- Variance of period (stable) prevalence------*/   
   
       strcpy(fileresvpl,"vpl");
       strcat(fileresvpl,fileres);
       if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
         printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
         exit(0);
       }
       printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           fprintf(ficresvpl,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvpl,"******\n");
         
           varpl=matrix(1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
           free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
         }
       }
   
       fclose(ficresvpl);
   
       /*---------- End : free ----------------*/
       if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
     }  /* mle==-3 arrives here for freeing */
    endfree:
       free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
       free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(covar,0,NCOVMAX,1,n);
       free_matrix(matcov,1,npar,1,npar);
       /*free_vector(delti,1,npar);*/
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       free_matrix(agev,1,maxwav,1,imx);
       free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   
       free_ivector(ncodemax,1,8);
       free_ivector(Tvar,1,15);
       free_ivector(Tprod,1,15);
       free_ivector(Tvaraff,1,15);
       free_ivector(Tage,1,15);
   
       free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
       free_imatrix(codtab,1,100,1,10);
     fflush(fichtm);
     fflush(ficgp);
     
   
     if((nberr >0) || (nbwarn>0)){
       printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
       fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
     }else{
       printf("End of Imach\n");
       fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     (void) gettimeofday(&end_time,&tzp);
     tm = *localtime(&end_time.tv_sec);
     tmg = *gmtime(&end_time.tv_sec);
     strcpy(strtend,asctime(&tm));
     printf("Local time at start %s\nLocal time at end   %s",strstart, strtend); 
     fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
     printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
   
     printf("Total time was %ld 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 %ld 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.1.33  
changed lines
  Added in v.1.143


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