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version 1.7, 2001/05/02 17:50:24 version 1.132, 2009/07/06 08:22:05
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      /* $Id$
 /*********************** Imach **************************************            $State$
   This program computes Healthy Life Expectancies from cross-longitudinal    $Log$
   data. Cross-longitudinal consist in a first survey ("cross") where    Revision 1.132  2009/07/06 08:22:05  brouard
   individuals from different ages are interviewed on their health status    Many tings
   or degree of  disability. At least a second wave of interviews  
   ("longitudinal") should  measure each new individual health status.    Revision 1.131  2009/06/20 16:22:47  brouard
   Health expectancies are computed from the transistions observed between    Some dimensions resccaled
   waves and are computed for each degree of severity of disability (number  
   of life states). More degrees you consider, more time is necessary to    Revision 1.130  2009/05/26 06:44:34  brouard
   reach the Maximum Likelihood of the parameters involved in the model.    (Module): Max Covariate is now set to 20 instead of 8. A
   The simplest model is the multinomial logistic model where pij is    lot of cleaning with variables initialized to 0. Trying to make
   the probabibility to be observed in state j at the second wave conditional    V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
   to be observed in state i at the first wave. Therefore the model is:  
   log(pij/pii)= aij + bij*age+ cij*sex + etc , where 'age' is age and 'sex'    Revision 1.129  2007/08/31 13:49:27  lievre
   is a covariate. If you want to have a more complex model than "constant and    Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
   age", you should modify the program where the markup  
     *Covariates have to be included here again* invites you to do it.    Revision 1.128  2006/06/30 13:02:05  brouard
   More covariates you add, less is the speed of the convergence.    (Module): Clarifications on computing e.j
   
   The advantage that this computer programme claims, comes from that if the    Revision 1.127  2006/04/28 18:11:50  brouard
   delay between waves is not identical for each individual, or if some    (Module): Yes the sum of survivors was wrong since
   individual missed an interview, the information is not rounded or lost, but    imach-114 because nhstepm was no more computed in the age
   taken into account using an interpolation or extrapolation.    loop. Now we define nhstepma in the age loop.
   hPijx is the probability to be    (Module): In order to speed up (in case of numerous covariates) we
   observed in state i at age x+h conditional to the observed state i at age    compute health expectancies (without variances) in a first step
   x. The delay 'h' can be split into an exact number (nh*stepm) of    and then all the health expectancies with variances or standard
   unobserved intermediate  states. This elementary transition (by month or    deviation (needs data from the Hessian matrices) which slows the
   quarter trimester, semester or year) is model as a multinomial logistic.    computation.
   The hPx matrix is simply the matrix product of nh*stepm elementary matrices    In the future we should be able to stop the program is only health
   and the contribution of each individual to the likelihood is simply hPijx.    expectancies and graph are needed without standard deviations.
   
   Also this programme outputs the covariance matrix of the parameters but also    Revision 1.126  2006/04/28 17:23:28  brouard
   of the life expectancies. It also computes the prevalence limits.    (Module): Yes the sum of survivors was wrong since
      imach-114 because nhstepm was no more computed in the age
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    loop. Now we define nhstepma in the age loop.
            Institut national d'études démographiques, Paris.    Version 0.98h
   This software have been partly granted by Euro-REVES, a concerted action  
   from the European Union.    Revision 1.125  2006/04/04 15:20:31  lievre
   It is copyrighted identically to a GNU software product, ie programme and    Errors in calculation of health expectancies. Age was not initialized.
   software can be distributed freely for non commercial use. Latest version    Forecasting file added.
   can be accessed at http://euroreves.ined.fr/imach .  
   **********************************************************************/    Revision 1.124  2006/03/22 17:13:53  lievre
      Parameters are printed with %lf instead of %f (more numbers after the comma).
 #include <math.h>    The log-likelihood is printed in the log file
 #include <stdio.h>  
 #include <stdlib.h>    Revision 1.123  2006/03/20 10:52:43  brouard
 #include <unistd.h>    * imach.c (Module): <title> changed, corresponds to .htm file
     name. <head> headers where missing.
 #define MAXLINE 256  
 #define FILENAMELENGTH 80    * imach.c (Module): Weights can have a decimal point as for
 /*#define DEBUG*/    English (a comma might work with a correct LC_NUMERIC environment,
 #define windows    otherwise the weight is truncated).
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    Modification of warning when the covariates values are not 0 or
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    1.
     Version 0.98g
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */  
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    Revision 1.122  2006/03/20 09:45:41  brouard
     (Module): Weights can have a decimal point as for
 #define NINTERVMAX 8    English (a comma might work with a correct LC_NUMERIC environment,
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    otherwise the weight is truncated).
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    Modification of warning when the covariates values are not 0 or
 #define NCOVMAX 8 /* Maximum number of covariates */    1.
 #define MAXN 20000    Version 0.98g
 #define YEARM 12. /* Number of months per year */  
 #define AGESUP 130    Revision 1.121  2006/03/16 17:45:01  lievre
 #define AGEBASE 40    * imach.c (Module): Comments concerning covariates added
   
     * imach.c (Module): refinements in the computation of lli if
 int nvar;    status=-2 in order to have more reliable computation if stepm is
 static int cptcov;    not 1 month. Version 0.98f
 int cptcovn, cptcovage=0, cptcoveff=0;  
 int npar=NPARMAX;    Revision 1.120  2006/03/16 15:10:38  lievre
 int nlstate=2; /* Number of live states */    (Module): refinements in the computation of lli if
 int ndeath=1; /* Number of dead states */    status=-2 in order to have more reliable computation if stepm is
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    not 1 month. Version 0.98f
   
 int *wav; /* Number of waves for this individuual 0 is possible */    Revision 1.119  2006/03/15 17:42:26  brouard
 int maxwav; /* Maxim number of waves */    (Module): Bug if status = -2, the loglikelihood was
 int mle, weightopt;    computed as likelihood omitting the logarithm. Version O.98e
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */  
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    Revision 1.118  2006/03/14 18:20:07  brouard
 double **oldm, **newm, **savm; /* Working pointers to matrices */    (Module): varevsij Comments added explaining the second
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    table of variances if popbased=1 .
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest;    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 FILE *ficgp, *fichtm;    (Module): Function pstamp added
 FILE *ficreseij;    (Module): Version 0.98d
   char filerese[FILENAMELENGTH];  
  FILE  *ficresvij;    Revision 1.117  2006/03/14 17:16:22  brouard
   char fileresv[FILENAMELENGTH];    (Module): varevsij Comments added explaining the second
  FILE  *ficresvpl;    table of variances if popbased=1 .
   char fileresvpl[FILENAMELENGTH];    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
     (Module): Function pstamp added
 #define NR_END 1    (Module): Version 0.98d
 #define FREE_ARG char*  
 #define FTOL 1.0e-10    Revision 1.116  2006/03/06 10:29:27  brouard
     (Module): Variance-covariance wrong links and
 #define NRANSI    varian-covariance of ej. is needed (Saito).
 #define ITMAX 200  
     Revision 1.115  2006/02/27 12:17:45  brouard
 #define TOL 2.0e-4    (Module): One freematrix added in mlikeli! 0.98c
   
 #define CGOLD 0.3819660    Revision 1.114  2006/02/26 12:57:58  brouard
 #define ZEPS 1.0e-10    (Module): Some improvements in processing parameter
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    filename with strsep.
   
 #define GOLD 1.618034    Revision 1.113  2006/02/24 14:20:24  brouard
 #define GLIMIT 100.0    (Module): Memory leaks checks with valgrind and:
 #define TINY 1.0e-20    datafile was not closed, some imatrix were not freed and on matrix
     allocation too.
 static double maxarg1,maxarg2;  
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    Revision 1.112  2006/01/30 09:55:26  brouard
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    (Module): Back to gnuplot.exe instead of wgnuplot.exe
    
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    Revision 1.111  2006/01/25 20:38:18  brouard
 #define rint(a) floor(a+0.5)    (Module): Lots of cleaning and bugs added (Gompertz)
     (Module): Comments can be added in data file. Missing date values
 static double sqrarg;    can be a simple dot '.'.
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    Revision 1.110  2006/01/25 00:51:50  brouard
     (Module): Lots of cleaning and bugs added (Gompertz)
 int imx;  
 int stepm;    Revision 1.109  2006/01/24 19:37:15  brouard
 /* Stepm, step in month: minimum step interpolation*/    (Module): Comments (lines starting with a #) are allowed in data.
   
 int m,nb;    Revision 1.108  2006/01/19 18:05:42  lievre
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    Gnuplot problem appeared...
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    To be fixed
 double **pmmij;  
     Revision 1.107  2006/01/19 16:20:37  brouard
 double *weight;    Test existence of gnuplot in imach path
 int **s; /* Status */  
 double *agedc, **covar, idx;    Revision 1.106  2006/01/19 13:24:36  brouard
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    Some cleaning and links added in html output
   
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    Revision 1.105  2006/01/05 20:23:19  lievre
 double ftolhess; /* Tolerance for computing hessian */    *** empty log message ***
   
 /**************** split *************************/    Revision 1.104  2005/09/30 16:11:43  lievre
 static  int split( char *path, char *dirc, char *name )    (Module): sump fixed, loop imx fixed, and simplifications.
 {    (Module): If the status is missing at the last wave but we know
    char *s;                             /* pointer */    that the person is alive, then we can code his/her status as -2
    int  l1, l2;                         /* length counters */    (instead of missing=-1 in earlier versions) and his/her
     contributions to the likelihood is 1 - Prob of dying from last
    l1 = strlen( path );                 /* length of path */    health status (= 1-p13= p11+p12 in the easiest case of somebody in
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    the healthy state at last known wave). Version is 0.98
    s = strrchr( path, '\\' );           /* find last / */  
    if ( s == NULL ) {                   /* no directory, so use current */    Revision 1.103  2005/09/30 15:54:49  lievre
 #if     defined(__bsd__)                /* get current working directory */    (Module): sump fixed, loop imx fixed, and simplifications.
       extern char       *getwd( );  
     Revision 1.102  2004/09/15 17:31:30  brouard
       if ( getwd( dirc ) == NULL ) {    Add the possibility to read data file including tab characters.
 #else  
       extern char       *getcwd( );    Revision 1.101  2004/09/15 10:38:38  brouard
     Fix on curr_time
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  
 #endif    Revision 1.100  2004/07/12 18:29:06  brouard
          return( GLOCK_ERROR_GETCWD );    Add version for Mac OS X. Just define UNIX in Makefile
       }  
       strcpy( name, path );             /* we've got it */    Revision 1.99  2004/06/05 08:57:40  brouard
    } else {                             /* strip direcotry from path */    *** empty log message ***
       s++;                              /* after this, the filename */  
       l2 = strlen( s );                 /* length of filename */    Revision 1.98  2004/05/16 15:05:56  brouard
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    New version 0.97 . First attempt to estimate force of mortality
       strcpy( name, s );                /* save file name */    directly from the data i.e. without the need of knowing the health
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    state at each age, but using a Gompertz model: log u =a + b*age .
       dirc[l1-l2] = 0;                  /* add zero */    This is the basic analysis of mortality and should be done before any
    }    other analysis, in order to test if the mortality estimated from the
    l1 = strlen( dirc );                 /* length of directory */    cross-longitudinal survey is different from the mortality estimated
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    from other sources like vital statistic data.
    return( 0 );                         /* we're done */  
 }    The same imach parameter file can be used but the option for mle should be -3.
   
     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.
   
 void replace(char *s, char*t)    The output is very simple: only an estimate of the intercept and of
 {    the slope with 95% confident intervals.
   int i;  
   int lg=20;    Current limitations:
   i=0;    A) Even if you enter covariates, i.e. with the
   lg=strlen(t);    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
   for(i=0; i<= lg; i++) {    B) There is no computation of Life Expectancy nor Life Table.
     (s[i] = t[i]);  
     if (t[i]== '\\') s[i]='/';    Revision 1.97  2004/02/20 13:25:42  lievre
   }    Version 0.96d. Population forecasting command line is (temporarily)
 }    suppressed.
   
 int nbocc(char *s, char occ)    Revision 1.96  2003/07/15 15:38:55  brouard
 {    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
   int i,j=0;    rewritten within the same printf. Workaround: many printfs.
   int lg=20;  
   i=0;    Revision 1.95  2003/07/08 07:54:34  brouard
   lg=strlen(s);    * imach.c (Repository):
   for(i=0; i<= lg; i++) {    (Repository): Using imachwizard code to output a more meaningful covariance
   if  (s[i] == occ ) j++;    matrix (cov(a12,c31) instead of numbers.
   }  
   return j;    Revision 1.94  2003/06/27 13:00:02  brouard
 }    Just cleaning
   
 void cutv(char *u,char *v, char*t, char occ)    Revision 1.93  2003/06/25 16:33:55  brouard
 {    (Module): On windows (cygwin) function asctime_r doesn't
   int i,lg,j,p=0;    exist so I changed back to asctime which exists.
   i=0;    (Module): Version 0.96b
   for(j=0; j<=strlen(t)-1; j++) {  
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    Revision 1.92  2003/06/25 16:30:45  brouard
   }    (Module): On windows (cygwin) function asctime_r doesn't
     exist so I changed back to asctime which exists.
   lg=strlen(t);  
   for(j=0; j<p; j++) {    Revision 1.91  2003/06/25 15:30:29  brouard
     (u[j] = t[j]);    * imach.c (Repository): Duplicated warning errors corrected.
   }    (Repository): Elapsed time after each iteration is now output. It
      u[p]='\0';    helps to forecast when convergence will be reached. Elapsed time
     is stamped in powell.  We created a new html file for the graphs
    for(j=0; j<= lg; j++) {    concerning matrix of covariance. It has extension -cov.htm.
     if (j>=(p+1))(v[j-p-1] = t[j]);  
   }    Revision 1.90  2003/06/24 12:34:15  brouard
 }    (Module): Some bugs corrected for windows. Also, when
     mle=-1 a template is output in file "or"mypar.txt with the design
 /********************** nrerror ********************/    of the covariance matrix to be input.
   
 void nrerror(char error_text[])    Revision 1.89  2003/06/24 12:30:52  brouard
 {    (Module): Some bugs corrected for windows. Also, when
   fprintf(stderr,"ERREUR ...\n");    mle=-1 a template is output in file "or"mypar.txt with the design
   fprintf(stderr,"%s\n",error_text);    of the covariance matrix to be input.
   exit(1);  
 }    Revision 1.88  2003/06/23 17:54:56  brouard
 /*********************** vector *******************/    * 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.
 double *vector(int nl, int nh)  
 {    Revision 1.87  2003/06/18 12:26:01  brouard
   double *v;    Version 0.96
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  
   if (!v) nrerror("allocation failure in vector");    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 vector ******************/    Revision 1.85  2003/06/17 13:12:43  brouard
 void free_vector(double*v, int nl, int 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
 /************************ivector *******************************/    interview.
 int *ivector(long nl,long nh)    (Repository): Because some people have very long ID (first column)
 {    we changed int to long in num[] and we added a new lvector for
   int *v;    memory allocation. But we also truncated to 8 characters (left
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    truncation)
   if (!v) nrerror("allocation failure in ivector");    (Repository): No more line truncation errors.
   return v-nl+NR_END;  
 }    Revision 1.84  2003/06/13 21:44:43  brouard
     * imach.c (Repository): Replace "freqsummary" at a correct
 /******************free ivector **************************/    place. It differs from routine "prevalence" which may be called
 void free_ivector(int *v, long nl, long nh)    many times. Probs is memory consuming and must be used with
 {    parcimony.
   free((FREE_ARG)(v+nl-NR_END));    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
 }  
     Revision 1.83  2003/06/10 13:39:11  lievre
 /******************* imatrix *******************************/    *** empty log message ***
 int **imatrix(long nrl, long nrh, long ncl, long nch)  
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    Revision 1.82  2003/06/05 15:57:20  brouard
 {    Add log in  imach.c and  fullversion number is now printed.
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  
   int **m;  */
    /*
   /* allocate pointers to rows */     Interpolated Markov Chain
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");    Short summary of the programme:
   m += NR_END;    
   m -= nrl;    This program computes Healthy Life Expectancies from
      cross-longitudinal data. Cross-longitudinal data consist in: -1- a
      first survey ("cross") where individuals from different ages are
   /* allocate rows and set pointers to them */    interviewed on their health status or degree of disability (in the
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    case of a health survey which is our main interest) -2- at least a
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    second wave of interviews ("longitudinal") which measure each change
   m[nrl] += NR_END;    (if any) in individual health status.  Health expectancies are
   m[nrl] -= ncl;    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
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    Maximum Likelihood of the parameters involved in the model.  The
      simplest model is the multinomial logistic model where pij is the
   /* return pointer to array of pointers to rows */    probability to be observed in state j at the second wave
   return m;    conditional to be observed in state i at the first wave. Therefore
 }    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
     'age' is age and 'sex' is a covariate. If you want to have a more
 /****************** free_imatrix *************************/    complex model than "constant and age", you should modify the program
 void free_imatrix(m,nrl,nrh,ncl,nch)    where the markup *Covariates have to be included here again* invites
       int **m;    you to do it.  More covariates you add, slower the
       long nch,ncl,nrh,nrl;    convergence.
      /* free an int matrix allocated by imatrix() */  
 {    The advantage of this computer programme, compared to a simple
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    multinomial logistic model, is clear when the delay between waves is not
   free((FREE_ARG) (m+nrl-NR_END));    identical for each individual. Also, if a individual missed an
 }    intermediate interview, the information is lost, but taken into
     account using an interpolation or extrapolation.  
 /******************* matrix *******************************/  
 double **matrix(long nrl, long nrh, long ncl, long nch)    hPijx is the probability to be observed in state i at age x+h
 {    conditional to the observed state i at age x. The delay 'h' can be
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    split into an exact number (nh*stepm) of unobserved intermediate
   double **m;    states. This elementary transition (by month, quarter,
     semester or year) is modelled as a multinomial logistic.  The hPx
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    matrix is simply the matrix product of nh*stepm elementary matrices
   if (!m) nrerror("allocation failure 1 in matrix()");    and the contribution of each individual to the likelihood is simply
   m += NR_END;    hPijx.
   m -= nrl;  
     Also this programme outputs the covariance matrix of the parameters but also
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    of the life expectancies. It also computes the period (stable) prevalence. 
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    
   m[nrl] += NR_END;    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
   m[nrl] -= ncl;             Institut national d'études démographiques, Paris.
     This software have been partly granted by Euro-REVES, a concerted action
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    from the European Union.
   return m;    It is copyrighted identically to a GNU software product, ie programme and
 }    software can be distributed freely for non commercial use. Latest version
     can be accessed at http://euroreves.ined.fr/imach .
 /*************************free matrix ************************/  
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    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
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    
   free((FREE_ARG)(m+nrl-NR_END));    **********************************************************************/
 }  /*
     main
 /******************* ma3x *******************************/    read parameterfile
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    read datafile
 {    concatwav
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    freqsummary
   double ***m;    if (mle >= 1)
       mlikeli
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    print results files
   if (!m) nrerror("allocation failure 1 in matrix()");    if mle==1 
   m += NR_END;       computes hessian
   m -= nrl;    read end of parameter file: agemin, agemax, bage, fage, estepm
         begin-prev-date,...
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    open gnuplot file
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    open html file
   m[nrl] += NR_END;    period (stable) prevalence
   m[nrl] -= ncl;     for age prevalim()
     h Pij x
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    variance of p varprob
     forecasting if prevfcast==1 prevforecast call prevalence()
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    health expectancies
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    Variance-covariance of DFLE
   m[nrl][ncl] += NR_END;    prevalence()
   m[nrl][ncl] -= nll;     movingaverage()
   for (j=ncl+1; j<=nch; j++)    varevsij() 
     m[nrl][j]=m[nrl][j-1]+nlay;    if popbased==1 varevsij(,popbased)
      total life expectancies
   for (i=nrl+1; i<=nrh; i++) {    Variance of period (stable) prevalence
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;   end
     for (j=ncl+1; j<=nch; j++)  */
       m[i][j]=m[i][j-1]+nlay;  
   }  
   return m;  
 }   
   #include <math.h>
 /*************************free ma3x ************************/  #include <stdio.h>
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  #include <stdlib.h>
 {  #include <string.h>
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  #include <unistd.h>
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  
   free((FREE_ARG)(m+nrl-NR_END));  #include <limits.h>
 }  #include <sys/types.h>
   #include <sys/stat.h>
 /***************** f1dim *************************/  #include <errno.h>
 extern int ncom;  extern int errno;
 extern double *pcom,*xicom;  
 extern double (*nrfunc)(double []);  /* #include <sys/time.h> */
    #include <time.h>
 double f1dim(double x)  #include "timeval.h"
 {  
   int j;  /* #include <libintl.h> */
   double f;  /* #define _(String) gettext (String) */
   double *xt;  
    #define MAXLINE 256
   xt=vector(1,ncom);  
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  #define GNUPLOTPROGRAM "gnuplot"
   f=(*nrfunc)(xt);  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
   free_vector(xt,1,ncom);  #define FILENAMELENGTH 132
   return f;  
 }  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
   #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
 /*****************brent *************************/  
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  #define MAXPARM 128 /* Maximum number of parameters for the optimization */
 {  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
   int iter;  
   double a,b,d,etemp;  #define NINTERVMAX 8
   double fu,fv,fw,fx;  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
   double ftemp;  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
   double p,q,r,tol1,tol2,u,v,w,x,xm;  #define NCOVMAX 20 /* Maximum number of covariates */
   double e=0.0;  #define MAXN 20000
    #define YEARM 12. /* Number of months per year */
   a=(ax < cx ? ax : cx);  #define AGESUP 130
   b=(ax > cx ? ax : cx);  #define AGEBASE 40
   x=w=v=bx;  #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
   fw=fv=fx=(*f)(x);  #ifdef UNIX
   for (iter=1;iter<=ITMAX;iter++) {  #define DIRSEPARATOR '/'
     xm=0.5*(a+b);  #define CHARSEPARATOR "/"
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  #define ODIRSEPARATOR '\\'
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  #else
     printf(".");fflush(stdout);  #define DIRSEPARATOR '\\'
 #ifdef DEBUG  #define CHARSEPARATOR "\\"
     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);  #define ODIRSEPARATOR '/'
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  #endif
 #endif  
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  /* $Id$ */
       *xmin=x;  /* $State$ */
       return fx;  
     }  char version[]="Imach version 0.98k, June 2006, INED-EUROREVES-Institut de longevite ";
     ftemp=fu;  char fullversion[]="$Revision$ $Date$"; 
     if (fabs(e) > tol1) {  char strstart[80];
       r=(x-w)*(fx-fv);  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
       q=(x-v)*(fx-fw);  int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
       p=(x-v)*q-(x-w)*r;  int nvar=0;
       q=2.0*(q-r);  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov=0; /* Number of covariates, of covariates with '*age' */
       if (q > 0.0) p = -p;  int npar=NPARMAX;
       q=fabs(q);  int nlstate=2; /* Number of live states */
       etemp=e;  int ndeath=1; /* Number of dead states */
       e=d;  int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  int popbased=0;
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  
       else {  int *wav; /* Number of waves for this individuual 0 is possible */
         d=p/q;  int maxwav=0; /* Maxim number of waves */
         u=x+d;  int jmin=0, jmax=0; /* min, max spacing between 2 waves */
         if (u-a < tol2 || b-u < tol2)  int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
           d=SIGN(tol1,xm-x);  int gipmx=0, gsw=0; /* Global variables on the number of contributions 
       }                     to the likelihood and the sum of weights (done by funcone)*/
     } else {  int mle=1, weightopt=0;
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  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 */
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
     fu=(*f)(u);             * wave mi and wave mi+1 is not an exact multiple of stepm. */
     if (fu <= fx) {  double jmean=1; /* Mean space between 2 waves */
       if (u >= x) a=x; else b=x;  double **oldm, **newm, **savm; /* Working pointers to matrices */
       SHFT(v,w,x,u)  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
         SHFT(fv,fw,fx,fu)  FILE *fic,*ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
         } else {  FILE *ficlog, *ficrespow;
           if (u < x) a=u; else b=u;  int globpr=0; /* Global variable for printing or not */
           if (fu <= fw || w == x) {  double fretone; /* Only one call to likelihood */
             v=w;  long ipmx=0; /* Number of contributions */
             w=u;  double sw; /* Sum of weights */
             fv=fw;  char filerespow[FILENAMELENGTH];
             fw=fu;  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
           } else if (fu <= fv || v == x || v == w) {  FILE *ficresilk;
             v=u;  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
             fv=fu;  FILE *ficresprobmorprev;
           }  FILE *fichtm, *fichtmcov; /* Html File */
         }  FILE *ficreseij;
   }  char filerese[FILENAMELENGTH];
   nrerror("Too many iterations in brent");  FILE *ficresstdeij;
   *xmin=x;  char fileresstde[FILENAMELENGTH];
   return fx;  FILE *ficrescveij;
 }  char filerescve[FILENAMELENGTH];
   FILE  *ficresvij;
 /****************** mnbrak ***********************/  char fileresv[FILENAMELENGTH];
   FILE  *ficresvpl;
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  char fileresvpl[FILENAMELENGTH];
             double (*func)(double))  char title[MAXLINE];
 {  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   double ulim,u,r,q, dum;  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
   double fu;  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
    char command[FILENAMELENGTH];
   *fa=(*func)(*ax);  int  outcmd=0;
   *fb=(*func)(*bx);  
   if (*fb > *fa) {  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
     SHFT(dum,*ax,*bx,dum)  
       SHFT(dum,*fb,*fa,dum)  char filelog[FILENAMELENGTH]; /* Log file */
       }  char filerest[FILENAMELENGTH];
   *cx=(*bx)+GOLD*(*bx-*ax);  char fileregp[FILENAMELENGTH];
   *fc=(*func)(*cx);  char popfile[FILENAMELENGTH];
   while (*fb > *fc) {  
     r=(*bx-*ax)*(*fb-*fc);  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
     q=(*bx-*cx)*(*fb-*fa);  
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  struct timezone tzp;
     ulim=(*bx)+GLIMIT*(*cx-*bx);  extern int gettimeofday();
     if ((*bx-u)*(u-*cx) > 0.0) {  struct tm tmg, tm, tmf, *gmtime(), *localtime();
       fu=(*func)(u);  long time_value;
     } else if ((*cx-u)*(u-ulim) > 0.0) {  extern long time();
       fu=(*func)(u);  char strcurr[80], strfor[80];
       if (fu < *fc) {  
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  char *endptr;
           SHFT(*fb,*fc,fu,(*func)(u))  long lval;
           }  double dval;
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  
       u=ulim;  #define NR_END 1
       fu=(*func)(u);  #define FREE_ARG char*
     } else {  #define FTOL 1.0e-10
       u=(*cx)+GOLD*(*cx-*bx);  
       fu=(*func)(u);  #define NRANSI 
     }  #define ITMAX 200 
     SHFT(*ax,*bx,*cx,u)  
       SHFT(*fa,*fb,*fc,fu)  #define TOL 2.0e-4 
       }  
 }  #define CGOLD 0.3819660 
   #define ZEPS 1.0e-10 
 /*************** linmin ************************/  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
   
 int ncom;  #define GOLD 1.618034 
 double *pcom,*xicom;  #define GLIMIT 100.0 
 double (*nrfunc)(double []);  #define TINY 1.0e-20 
    
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  static double maxarg1,maxarg2;
 {  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
   double brent(double ax, double bx, double cx,  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
                double (*f)(double), double tol, double *xmin);    
   double f1dim(double x);  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  #define rint(a) floor(a+0.5)
               double *fc, double (*func)(double));  
   int j;  static double sqrarg;
   double xx,xmin,bx,ax;  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
   double fx,fb,fa;  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
    int agegomp= AGEGOMP;
   ncom=n;  
   pcom=vector(1,n);  int imx; 
   xicom=vector(1,n);  int stepm=1;
   nrfunc=func;  /* Stepm, step in month: minimum step interpolation*/
   for (j=1;j<=n;j++) {  
     pcom[j]=p[j];  int estepm;
     xicom[j]=xi[j];  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
   }  
   ax=0.0;  int m,nb;
   xx=1.0;  long *num;
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
 #ifdef DEBUG  double **pmmij, ***probs;
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  double *ageexmed,*agecens;
 #endif  double dateintmean=0;
   for (j=1;j<=n;j++) {  
     xi[j] *= xmin;  double *weight;
     p[j] += xi[j];  int **s; /* Status */
   }  double *agedc, **covar, idx;
   free_vector(xicom,1,n);  int **nbcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
   free_vector(pcom,1,n);  double *lsurv, *lpop, *tpop;
 }  
   double ftol=FTOL; /* Tolerance for computing Max Likelihood */
 /*************** powell ************************/  double ftolhess; /* Tolerance for computing hessian */
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  
             double (*func)(double []))  /**************** split *************************/
 {  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   void linmin(double p[], double xi[], int n, double *fret,  {
               double (*func)(double []));    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
   int i,ibig,j;       the name of the file (name), its extension only (ext) and its first part of the name (finame)
   double del,t,*pt,*ptt,*xit;    */ 
   double fp,fptt;    char  *ss;                            /* pointer */
   double *xits;    int   l1, l2;                         /* length counters */
   pt=vector(1,n);  
   ptt=vector(1,n);    l1 = strlen(path );                   /* length of path */
   xit=vector(1,n);    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   xits=vector(1,n);    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
   *fret=(*func)(p);    if ( ss == NULL ) {                   /* no directory, so determine current directory */
   for (j=1;j<=n;j++) pt[j]=p[j];      strcpy( name, path );               /* we got the fullname name because no directory */
   for (*iter=1;;++(*iter)) {      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
     fp=(*fret);        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
     ibig=0;      /* get current working directory */
     del=0.0;      /*    extern  char* getcwd ( char *buf , int len);*/
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
     for (i=1;i<=n;i++)        return( GLOCK_ERROR_GETCWD );
       printf(" %d %.12f",i, p[i]);      }
     printf("\n");      /* got dirc from getcwd*/
     for (i=1;i<=n;i++) {      printf(" DIRC = %s \n",dirc);
       for (j=1;j<=n;j++) xit[j]=xi[j][i];    } else {                              /* strip direcotry from path */
       fptt=(*fret);      ss++;                               /* after this, the filename */
 #ifdef DEBUG      l2 = strlen( ss );                  /* length of filename */
       printf("fret=%lf \n",*fret);      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
 #endif      strcpy( name, ss );         /* save file name */
       printf("%d",i);fflush(stdout);      strncpy( dirc, path, l1 - l2 );     /* now the directory */
       linmin(p,xit,n,fret,func);      dirc[l1-l2] = 0;                    /* add zero */
       if (fabs(fptt-(*fret)) > del) {      printf(" DIRC2 = %s \n",dirc);
         del=fabs(fptt-(*fret));    }
         ibig=i;    /* We add a separator at the end of dirc if not exists */
       }    l1 = strlen( dirc );                  /* length of directory */
 #ifdef DEBUG    if( dirc[l1-1] != DIRSEPARATOR ){
       printf("%d %.12e",i,(*fret));      dirc[l1] =  DIRSEPARATOR;
       for (j=1;j<=n;j++) {      dirc[l1+1] = 0; 
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);      printf(" DIRC3 = %s \n",dirc);
         printf(" x(%d)=%.12e",j,xit[j]);    }
       }    ss = strrchr( name, '.' );            /* find last / */
       for(j=1;j<=n;j++)    if (ss >0){
         printf(" p=%.12e",p[j]);      ss++;
       printf("\n");      strcpy(ext,ss);                     /* save extension */
 #endif      l1= strlen( name);
     }      l2= strlen(ss)+1;
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {      strncpy( finame, name, l1-l2);
 #ifdef DEBUG      finame[l1-l2]= 0;
       int k[2],l;    }
       k[0]=1;  
       k[1]=-1;    return( 0 );                          /* we're done */
       printf("Max: %.12e",(*func)(p));  }
       for (j=1;j<=n;j++)  
         printf(" %.12e",p[j]);  
       printf("\n");  /******************************************/
       for(l=0;l<=1;l++) {  
         for (j=1;j<=n;j++) {  void replace_back_to_slash(char *s, char*t)
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  {
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);    int i;
         }    int lg=0;
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    i=0;
       }    lg=strlen(t);
 #endif    for(i=0; i<= lg; i++) {
       (s[i] = t[i]);
       if (t[i]== '\\') s[i]='/';
       free_vector(xit,1,n);    }
       free_vector(xits,1,n);  }
       free_vector(ptt,1,n);  
       free_vector(pt,1,n);  char *trimbb(char *out, char *in)
       return;  { /* Trim multiple blanks in line */
     }    char *s;
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    s=out;
     for (j=1;j<=n;j++) {    while (*in != '\0'){
       ptt[j]=2.0*p[j]-pt[j];      while( *in == ' ' && *(in+1) == ' ' && *(in+1) != '\0'){
       xit[j]=p[j]-pt[j];        in++;
       pt[j]=p[j];      }
     }      *out++ = *in++;
     fptt=(*func)(ptt);    }
     if (fptt < fp) {    *out='\0';
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);    return s;
       if (t < 0.0) {  }
         linmin(p,xit,n,fret,func);  
         for (j=1;j<=n;j++) {  int nbocc(char *s, char occ)
           xi[j][ibig]=xi[j][n];  {
           xi[j][n]=xit[j];    int i,j=0;
         }    int lg=20;
 #ifdef DEBUG    i=0;
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);    lg=strlen(s);
         for(j=1;j<=n;j++)    for(i=0; i<= lg; i++) {
           printf(" %.12e",xit[j]);    if  (s[i] == occ ) j++;
         printf("\n");    }
 #endif    return j;
       }  }
     }  
   }  void cutv(char *u,char *v, char*t, char occ)
 }  {
     /* cuts string t into u and v where u ends before first occurence of char 'occ' 
 /**** Prevalence limit ****************/       and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
        gives u="abcedf" and v="ghi2j" */
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)    int i,lg,j,p=0;
 {    i=0;
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit    for(j=0; j<=strlen(t)-1; j++) {
      matrix by transitions matrix until convergence is reached */      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
     }
   int i, ii,j,k;  
   double min, max, maxmin, maxmax,sumnew=0.;    lg=strlen(t);
   double **matprod2();    for(j=0; j<p; j++) {
   double **out, cov[NCOVMAX], **pmij();      (u[j] = t[j]);
   double **newm;    }
   double agefin, delaymax=50 ; /* Max number of years to converge */       u[p]='\0';
   
   for (ii=1;ii<=nlstate+ndeath;ii++)     for(j=0; j<= lg; j++) {
     for (j=1;j<=nlstate+ndeath;j++){      if (j>=(p+1))(v[j-p-1] = t[j]);
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);    }
     }  }
   
    cov[1]=1.;  /********************** nrerror ********************/
    
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */  void nrerror(char error_text[])
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){  {
     newm=savm;    fprintf(stderr,"ERREUR ...\n");
     /* Covariates have to be included here again */    fprintf(stderr,"%s\n",error_text);
      cov[2]=agefin;    exit(EXIT_FAILURE);
    }
       for (k=1; k<=cptcovn;k++) {  /*********************** vector *******************/
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  double *vector(int nl, int nh)
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/  {
       }    double *v;
       for (k=1; k<=cptcovage;k++)    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    if (!v) nrerror("allocation failure in vector");
       for (k=1; k<=cptcovprod;k++)    return v-nl+NR_END;
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  }
   
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/  /************************ free vector ******************/
   void free_vector(double*v, int nl, int nh)
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/  {
     free((FREE_ARG)(v+nl-NR_END));
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  }
   
     savm=oldm;  /************************ivector *******************************/
     oldm=newm;  int *ivector(long nl,long nh)
     maxmax=0.;  {
     for(j=1;j<=nlstate;j++){    int *v;
       min=1.;    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
       max=0.;    if (!v) nrerror("allocation failure in ivector");
       for(i=1; i<=nlstate; i++) {    return v-nl+NR_END;
         sumnew=0;  }
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  
         prlim[i][j]= newm[i][j]/(1-sumnew);  /******************free ivector **************************/
         max=FMAX(max,prlim[i][j]);  void free_ivector(int *v, long nl, long nh)
         min=FMIN(min,prlim[i][j]);  {
       }    free((FREE_ARG)(v+nl-NR_END));
       maxmin=max-min;  }
       maxmax=FMAX(maxmax,maxmin);  
     }  /************************lvector *******************************/
     if(maxmax < ftolpl){  long *lvector(long nl,long nh)
       return prlim;  {
     }    long *v;
   }    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
 }    if (!v) nrerror("allocation failure in ivector");
     return v-nl+NR_END;
 /*************** transition probabilities **********/  }
   
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  /******************free lvector **************************/
 {  void free_lvector(long *v, long nl, long nh)
   double s1, s2;  {
   /*double t34;*/    free((FREE_ARG)(v+nl-NR_END));
   int i,j,j1, nc, ii, jj;  }
   
     for(i=1; i<= nlstate; i++){  /******************* imatrix *******************************/
     for(j=1; j<i;j++){  int **imatrix(long nrl, long nrh, long ncl, long nch) 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
         /*s2 += param[i][j][nc]*cov[nc];*/  { 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/    int **m; 
       }    
       ps[i][j]=s2;    /* allocate pointers to rows */ 
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
     }    if (!m) nrerror("allocation failure 1 in matrix()"); 
     for(j=i+1; j<=nlstate+ndeath;j++){    m += NR_END; 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    m -= nrl; 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/    
       }    /* allocate rows and set pointers to them */ 
       ps[i][j]=s2;    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
     }    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
   }    m[nrl] += NR_END; 
   for(i=1; i<= nlstate; i++){    m[nrl] -= ncl; 
      s1=0;    
     for(j=1; j<i; j++)    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
       s1+=exp(ps[i][j]);    
     for(j=i+1; j<=nlstate+ndeath; j++)    /* return pointer to array of pointers to rows */ 
       s1+=exp(ps[i][j]);    return m; 
     ps[i][i]=1./(s1+1.);  } 
     for(j=1; j<i; j++)  
       ps[i][j]= exp(ps[i][j])*ps[i][i];  /****************** free_imatrix *************************/
     for(j=i+1; j<=nlstate+ndeath; j++)  void free_imatrix(m,nrl,nrh,ncl,nch)
       ps[i][j]= exp(ps[i][j])*ps[i][i];        int **m;
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */        long nch,ncl,nrh,nrl; 
   } /* end i */       /* free an int matrix allocated by imatrix() */ 
   { 
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
     for(jj=1; jj<= nlstate+ndeath; jj++){    free((FREE_ARG) (m+nrl-NR_END)); 
       ps[ii][jj]=0;  } 
       ps[ii][ii]=1;  
     }  /******************* matrix *******************************/
   }  double **matrix(long nrl, long nrh, long ncl, long nch)
   {
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
     for(jj=1; jj<= nlstate+ndeath; jj++){    double **m;
      printf("%lf ",ps[ii][jj]);  
    }    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     printf("\n ");    if (!m) nrerror("allocation failure 1 in matrix()");
     }    m += NR_END;
     printf("\n ");printf("%lf ",cov[2]);*/    m -= nrl;
 /*  
   for(i=1; i<= npar; i++) printf("%f ",x[i]);    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   goto end;*/    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     return ps;    m[nrl] += NR_END;
 }    m[nrl] -= ncl;
   
 /**************** Product of 2 matrices ******************/    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     return m;
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
 {     */
   /* Computes the matric product of in(1,nrh-nrl+1)(1,nch-ncl+1) times  }
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */  
   /* in, b, out are matrice of pointers which should have been initialized  /*************************free matrix ************************/
      before: only the contents of out is modified. The function returns  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
      a pointer to pointers identical to out */  {
   long i, j, k;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   for(i=nrl; i<= nrh; i++)    free((FREE_ARG)(m+nrl-NR_END));
     for(k=ncolol; k<=ncoloh; k++)  }
       for(j=ncl,out[i][k]=0.; j<=nch; j++)  
         out[i][k] +=in[i][j]*b[j][k];  /******************* ma3x *******************************/
   double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
   return out;  {
 }    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
     double ***m;
   
 /************* Higher Matrix Product ***************/    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     if (!m) nrerror("allocation failure 1 in matrix()");
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )    m += NR_END;
 {    m -= nrl;
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month  
      duration (i.e. until    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step    m[nrl] += NR_END;
      (typically every 2 years instead of every month which is too big).    m[nrl] -= ncl;
      Model is determined by parameters x and covariates have to be  
      included manually here.    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   
      */    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
     if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
   int i, j, d, h, k;    m[nrl][ncl] += NR_END;
   double **out, cov[NCOVMAX];    m[nrl][ncl] -= nll;
   double **newm;    for (j=ncl+1; j<=nch; j++) 
       m[nrl][j]=m[nrl][j-1]+nlay;
   /* Hstepm could be zero and should return the unit matrix */    
   for (i=1;i<=nlstate+ndeath;i++)    for (i=nrl+1; i<=nrh; i++) {
     for (j=1;j<=nlstate+ndeath;j++){      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
       oldm[i][j]=(i==j ? 1.0 : 0.0);      for (j=ncl+1; j<=nch; j++) 
       po[i][j][0]=(i==j ? 1.0 : 0.0);        m[i][j]=m[i][j-1]+nlay;
     }    }
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    return m; 
   for(h=1; h <=nhstepm; h++){    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
     for(d=1; d <=hstepm; d++){             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
       newm=savm;    */
       /* Covariates have to be included here again */  }
       cov[1]=1.;  
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;  /*************************free ma3x ************************/
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
 for (k=1; k<=cptcovage;k++)  {
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
    for (k=1; k<=cptcovprod;k++)    free((FREE_ARG)(m[nrl]+ncl-NR_END));
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    free((FREE_ARG)(m+nrl-NR_END));
   }
   
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/  /*************** function subdirf ***********/
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/  char *subdirf(char fileres[])
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,  {
                    pmij(pmmij,cov,ncovmodel,x,nlstate));    /* Caution optionfilefiname is hidden */
       savm=oldm;    strcpy(tmpout,optionfilefiname);
       oldm=newm;    strcat(tmpout,"/"); /* Add to the right */
     }    strcat(tmpout,fileres);
     for(i=1; i<=nlstate+ndeath; i++)    return tmpout;
       for(j=1;j<=nlstate+ndeath;j++) {  }
         po[i][j][h]=newm[i][j];  
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);  /*************** function subdirf2 ***********/
          */  char *subdirf2(char fileres[], char *preop)
       }  {
   } /* end h */    
   return po;    /* Caution optionfilefiname is hidden */
 }    strcpy(tmpout,optionfilefiname);
     strcat(tmpout,"/");
     strcat(tmpout,preop);
 /*************** log-likelihood *************/    strcat(tmpout,fileres);
 double func( double *x)    return tmpout;
 {  }
   int i, ii, j, k, mi, d, kk;  
   double l, ll[NLSTATEMAX], cov[NCOVMAX];  /*************** function subdirf3 ***********/
   double **out;  char *subdirf3(char fileres[], char *preop, char *preop2)
   double sw; /* Sum of weights */  {
   double lli; /* Individual log likelihood */    
   long ipmx;    /* Caution optionfilefiname is hidden */
   /*extern weight */    strcpy(tmpout,optionfilefiname);
   /* We are differentiating ll according to initial status */    strcat(tmpout,"/");
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    strcat(tmpout,preop);
   /*for(i=1;i<imx;i++)    strcat(tmpout,preop2);
 printf(" %d\n",s[4][i]);    strcat(tmpout,fileres);
   */    return tmpout;
   cov[1]=1.;  }
   
   for(k=1; k<=nlstate; k++) ll[k]=0.;  /***************** f1dim *************************/
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){  extern int ncom; 
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];  extern double *pcom,*xicom;
        for(mi=1; mi<= wav[i]-1; mi++){  extern double (*nrfunc)(double []); 
       for (ii=1;ii<=nlstate+ndeath;ii++)   
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);  double f1dim(double x) 
             for(d=0; d<dh[mi][i]; d++){  { 
               newm=savm;    int j; 
               cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;    double f;
               for (kk=1; kk<=cptcovage;kk++) {    double *xt; 
                  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];   
                  /*printf("%d %d",kk,Tage[kk]);*/    xt=vector(1,ncom); 
               }    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
               /*cov[4]=covar[1][i]*cov[2];scanf("%d", i);*/    f=(*nrfunc)(xt); 
               /*cov[3]=pow(cov[2],2)/1000.;*/    free_vector(xt,1,ncom); 
     return f; 
           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,  } 
                        1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));  
           savm=oldm;  /*****************brent *************************/
           oldm=newm;  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
   { 
     int iter; 
       } /* end mult */    double a,b,d,etemp;
        double fu,fv,fw,fx;
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);    double ftemp;
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/    double p,q,r,tol1,tol2,u,v,w,x,xm; 
       ipmx +=1;    double e=0.0; 
       sw += weight[i];   
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;    a=(ax < cx ? ax : cx); 
     } /* end of wave */    b=(ax > cx ? ax : cx); 
   } /* end of individual */    x=w=v=bx; 
     fw=fv=fx=(*f)(x); 
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];    for (iter=1;iter<=ITMAX;iter++) { 
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */      xm=0.5*(a+b); 
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
   return -l;      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
 }      printf(".");fflush(stdout);
       fprintf(ficlog,".");fflush(ficlog);
   #ifdef DEBUG
 /*********** Maximum Likelihood Estimation ***************/      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);
       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);
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
 {  #endif
   int i,j, iter;      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
   double **xi,*delti;        *xmin=x; 
   double fret;        return fx; 
   xi=matrix(1,npar,1,npar);      } 
   for (i=1;i<=npar;i++)      ftemp=fu;
     for (j=1;j<=npar;j++)      if (fabs(e) > tol1) { 
       xi[i][j]=(i==j ? 1.0 : 0.0);        r=(x-w)*(fx-fv); 
   printf("Powell\n");        q=(x-v)*(fx-fw); 
   powell(p,xi,npar,ftol,&iter,&fret,func);        p=(x-v)*q-(x-w)*r; 
         q=2.0*(q-r); 
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));        if (q > 0.0) p = -p; 
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f ",iter,func(p));        q=fabs(q); 
         etemp=e; 
 }        e=d; 
         if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
 /**** Computes Hessian and covariance matrix ***/          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))        else { 
 {          d=p/q; 
   double  **a,**y,*x,pd;          u=x+d; 
   double **hess;          if (u-a < tol2 || b-u < tol2) 
   int i, j,jk;            d=SIGN(tol1,xm-x); 
   int *indx;        } 
       } else { 
   double hessii(double p[], double delta, int theta, double delti[]);        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   double hessij(double p[], double delti[], int i, int j);      } 
   void lubksb(double **a, int npar, int *indx, double b[]) ;      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
   void ludcmp(double **a, int npar, int *indx, double *d) ;      fu=(*f)(u); 
       if (fu <= fx) { 
         if (u >= x) a=x; else b=x; 
   hess=matrix(1,npar,1,npar);        SHFT(v,w,x,u) 
           SHFT(fv,fw,fx,fu) 
   printf("\nCalculation of the hessian matrix. Wait...\n");          } else { 
   for (i=1;i<=npar;i++){            if (u < x) a=u; else b=u; 
     printf("%d",i);fflush(stdout);            if (fu <= fw || w == x) { 
     hess[i][i]=hessii(p,ftolhess,i,delti);              v=w; 
     /*printf(" %f ",p[i]);*/              w=u; 
   }              fv=fw; 
               fw=fu; 
   for (i=1;i<=npar;i++) {            } else if (fu <= fv || v == x || v == w) { 
     for (j=1;j<=npar;j++)  {              v=u; 
       if (j>i) {              fv=fu; 
         printf(".%d%d",i,j);fflush(stdout);            } 
         hess[i][j]=hessij(p,delti,i,j);          } 
         hess[j][i]=hess[i][j];    } 
       }    nrerror("Too many iterations in brent"); 
     }    *xmin=x; 
   }    return fx; 
   printf("\n");  } 
   
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");  /****************** mnbrak ***********************/
    
   a=matrix(1,npar,1,npar);  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
   y=matrix(1,npar,1,npar);              double (*func)(double)) 
   x=vector(1,npar);  { 
   indx=ivector(1,npar);    double ulim,u,r,q, dum;
   for (i=1;i<=npar;i++)    double fu; 
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];   
   ludcmp(a,npar,indx,&pd);    *fa=(*func)(*ax); 
     *fb=(*func)(*bx); 
   for (j=1;j<=npar;j++) {    if (*fb > *fa) { 
     for (i=1;i<=npar;i++) x[i]=0;      SHFT(dum,*ax,*bx,dum) 
     x[j]=1;        SHFT(dum,*fb,*fa,dum) 
     lubksb(a,npar,indx,x);        } 
     for (i=1;i<=npar;i++){    *cx=(*bx)+GOLD*(*bx-*ax); 
       matcov[i][j]=x[i];    *fc=(*func)(*cx); 
     }    while (*fb > *fc) { 
   }      r=(*bx-*ax)*(*fb-*fc); 
       q=(*bx-*cx)*(*fb-*fa); 
   printf("\n#Hessian matrix#\n");      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
   for (i=1;i<=npar;i++) {        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
     for (j=1;j<=npar;j++) {      ulim=(*bx)+GLIMIT*(*cx-*bx); 
       printf("%.3e ",hess[i][j]);      if ((*bx-u)*(u-*cx) > 0.0) { 
     }        fu=(*func)(u); 
     printf("\n");      } else if ((*cx-u)*(u-ulim) > 0.0) { 
   }        fu=(*func)(u); 
         if (fu < *fc) { 
   /* Recompute Inverse */          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
   for (i=1;i<=npar;i++)            SHFT(*fb,*fc,fu,(*func)(u)) 
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];            } 
   ludcmp(a,npar,indx,&pd);      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
         u=ulim; 
   /*  printf("\n#Hessian matrix recomputed#\n");        fu=(*func)(u); 
       } else { 
   for (j=1;j<=npar;j++) {        u=(*cx)+GOLD*(*cx-*bx); 
     for (i=1;i<=npar;i++) x[i]=0;        fu=(*func)(u); 
     x[j]=1;      } 
     lubksb(a,npar,indx,x);      SHFT(*ax,*bx,*cx,u) 
     for (i=1;i<=npar;i++){        SHFT(*fa,*fb,*fc,fu) 
       y[i][j]=x[i];        } 
       printf("%.3e ",y[i][j]);  } 
     }  
     printf("\n");  /*************** linmin ************************/
   }  
   */  int ncom; 
   double *pcom,*xicom;
   free_matrix(a,1,npar,1,npar);  double (*nrfunc)(double []); 
   free_matrix(y,1,npar,1,npar);   
   free_vector(x,1,npar);  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
   free_ivector(indx,1,npar);  { 
   free_matrix(hess,1,npar,1,npar);    double brent(double ax, double bx, double cx, 
                  double (*f)(double), double tol, double *xmin); 
     double f1dim(double x); 
 }    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
                 double *fc, double (*func)(double)); 
 /*************** hessian matrix ****************/    int j; 
 double hessii( double x[], double delta, int theta, double delti[])    double xx,xmin,bx,ax; 
 {    double fx,fb,fa;
   int i;   
   int l=1, lmax=20;    ncom=n; 
   double k1,k2;    pcom=vector(1,n); 
   double p2[NPARMAX+1];    xicom=vector(1,n); 
   double res;    nrfunc=func; 
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;    for (j=1;j<=n;j++) { 
   double fx;      pcom[j]=p[j]; 
   int k=0,kmax=10;      xicom[j]=xi[j]; 
   double l1;    } 
     ax=0.0; 
   fx=func(x);    xx=1.0; 
   for (i=1;i<=npar;i++) p2[i]=x[i];    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
   for(l=0 ; l <=lmax; l++){    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
     l1=pow(10,l);  #ifdef DEBUG
     delts=delt;    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     for(k=1 ; k <kmax; k=k+1){    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
       delt = delta*(l1*k);  #endif
       p2[theta]=x[theta] +delt;    for (j=1;j<=n;j++) { 
       k1=func(p2)-fx;      xi[j] *= xmin; 
       p2[theta]=x[theta]-delt;      p[j] += xi[j]; 
       k2=func(p2)-fx;    } 
       /*res= (k1-2.0*fx+k2)/delt/delt; */    free_vector(xicom,1,n); 
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */    free_vector(pcom,1,n); 
        } 
 #ifdef DEBUG  
       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);  char *asc_diff_time(long time_sec, char ascdiff[])
 #endif  {
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */    long sec_left, days, hours, minutes;
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){    days = (time_sec) / (60*60*24);
         k=kmax;    sec_left = (time_sec) % (60*60*24);
       }    hours = (sec_left) / (60*60) ;
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */    sec_left = (sec_left) %(60*60);
         k=kmax; l=lmax*10.;    minutes = (sec_left) /60;
       }    sec_left = (sec_left) % (60);
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){    sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
         delts=delt;    return ascdiff;
       }  }
     }  
   }  /*************** powell ************************/
   delti[theta]=delts;  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
   return res;              double (*func)(double [])) 
    { 
 }    void linmin(double p[], double xi[], int n, double *fret, 
                 double (*func)(double [])); 
 double hessij( double x[], double delti[], int thetai,int thetaj)    int i,ibig,j; 
 {    double del,t,*pt,*ptt,*xit;
   int i;    double fp,fptt;
   int l=1, l1, lmax=20;    double *xits;
   double k1,k2,k3,k4,res,fx;    int niterf, itmp;
   double p2[NPARMAX+1];  
   int k;    pt=vector(1,n); 
     ptt=vector(1,n); 
   fx=func(x);    xit=vector(1,n); 
   for (k=1; k<=2; k++) {    xits=vector(1,n); 
     for (i=1;i<=npar;i++) p2[i]=x[i];    *fret=(*func)(p); 
     p2[thetai]=x[thetai]+delti[thetai]/k;    for (j=1;j<=n;j++) pt[j]=p[j]; 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    for (*iter=1;;++(*iter)) { 
     k1=func(p2)-fx;      fp=(*fret); 
        ibig=0; 
     p2[thetai]=x[thetai]+delti[thetai]/k;      del=0.0; 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;      last_time=curr_time;
     k2=func(p2)-fx;      (void) gettimeofday(&curr_time,&tzp);
        printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);
     p2[thetai]=x[thetai]-delti[thetai]/k;      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);
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
     k3=func(p2)-fx;     for (i=1;i<=n;i++) {
          printf(" %d %.12f",i, p[i]);
     p2[thetai]=x[thetai]-delti[thetai]/k;        fprintf(ficlog," %d %.12lf",i, p[i]);
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;        fprintf(ficrespow," %.12lf", p[i]);
     k4=func(p2)-fx;      }
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */      printf("\n");
 #ifdef DEBUG      fprintf(ficlog,"\n");
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);      fprintf(ficrespow,"\n");fflush(ficrespow);
 #endif      if(*iter <=3){
   }        tm = *localtime(&curr_time.tv_sec);
   return res;        strcpy(strcurr,asctime(&tm));
 }  /*       asctime_r(&tm,strcurr); */
         forecast_time=curr_time; 
 /************** Inverse of matrix **************/        itmp = strlen(strcurr);
 void ludcmp(double **a, int n, int *indx, double *d)        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
 {          strcurr[itmp-1]='\0';
   int i,imax,j,k;        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
   double big,dum,sum,temp;        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
   double *vv;        for(niterf=10;niterf<=30;niterf+=10){
            forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
   vv=vector(1,n);          tmf = *localtime(&forecast_time.tv_sec);
   *d=1.0;  /*      asctime_r(&tmf,strfor); */
   for (i=1;i<=n;i++) {          strcpy(strfor,asctime(&tmf));
     big=0.0;          itmp = strlen(strfor);
     for (j=1;j<=n;j++)          if(strfor[itmp-1]=='\n')
       if ((temp=fabs(a[i][j])) > big) big=temp;          strfor[itmp-1]='\0';
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");          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);
     vv[i]=1.0/big;          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);
   }        }
   for (j=1;j<=n;j++) {      }
     for (i=1;i<j;i++) {      for (i=1;i<=n;i++) { 
       sum=a[i][j];        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];        fptt=(*fret); 
       a[i][j]=sum;  #ifdef DEBUG
     }        printf("fret=%lf \n",*fret);
     big=0.0;        fprintf(ficlog,"fret=%lf \n",*fret);
     for (i=j;i<=n;i++) {  #endif
       sum=a[i][j];        printf("%d",i);fflush(stdout);
       for (k=1;k<j;k++)        fprintf(ficlog,"%d",i);fflush(ficlog);
         sum -= a[i][k]*a[k][j];        linmin(p,xit,n,fret,func); 
       a[i][j]=sum;        if (fabs(fptt-(*fret)) > del) { 
       if ( (dum=vv[i]*fabs(sum)) >= big) {          del=fabs(fptt-(*fret)); 
         big=dum;          ibig=i; 
         imax=i;        } 
       }  #ifdef DEBUG
     }        printf("%d %.12e",i,(*fret));
     if (j != imax) {        fprintf(ficlog,"%d %.12e",i,(*fret));
       for (k=1;k<=n;k++) {        for (j=1;j<=n;j++) {
         dum=a[imax][k];          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
         a[imax][k]=a[j][k];          printf(" x(%d)=%.12e",j,xit[j]);
         a[j][k]=dum;          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
       }        }
       *d = -(*d);        for(j=1;j<=n;j++) {
       vv[imax]=vv[j];          printf(" p=%.12e",p[j]);
     }          fprintf(ficlog," p=%.12e",p[j]);
     indx[j]=imax;        }
     if (a[j][j] == 0.0) a[j][j]=TINY;        printf("\n");
     if (j != n) {        fprintf(ficlog,"\n");
       dum=1.0/(a[j][j]);  #endif
       for (i=j+1;i<=n;i++) a[i][j] *= dum;      } 
     }      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
   }  #ifdef DEBUG
   free_vector(vv,1,n);  /* Doesn't work */        int k[2],l;
 ;        k[0]=1;
 }        k[1]=-1;
         printf("Max: %.12e",(*func)(p));
 void lubksb(double **a, int n, int *indx, double b[])        fprintf(ficlog,"Max: %.12e",(*func)(p));
 {        for (j=1;j<=n;j++) {
   int i,ii=0,ip,j;          printf(" %.12e",p[j]);
   double sum;          fprintf(ficlog," %.12e",p[j]);
          }
   for (i=1;i<=n;i++) {        printf("\n");
     ip=indx[i];        fprintf(ficlog,"\n");
     sum=b[ip];        for(l=0;l<=1;l++) {
     b[ip]=b[i];          for (j=1;j<=n;j++) {
     if (ii)            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
     else if (sum) ii=i;            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
     b[i]=sum;          }
   }          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   for (i=n;i>=1;i--) {          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     sum=b[i];        }
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];  #endif
     b[i]=sum/a[i][i];  
   }  
 }        free_vector(xit,1,n); 
         free_vector(xits,1,n); 
 /************ Frequencies ********************/        free_vector(ptt,1,n); 
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax)        free_vector(pt,1,n); 
 {  /* Some frequencies */        return; 
        } 
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
   double ***freq; /* Frequencies */      for (j=1;j<=n;j++) { 
   double *pp;        ptt[j]=2.0*p[j]-pt[j]; 
   double pos;        xit[j]=p[j]-pt[j]; 
   FILE *ficresp;        pt[j]=p[j]; 
   char fileresp[FILENAMELENGTH];      } 
       fptt=(*func)(ptt); 
   pp=vector(1,nlstate);      if (fptt < fp) { 
         t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
   strcpy(fileresp,"p");        if (t < 0.0) { 
   strcat(fileresp,fileres);          linmin(p,xit,n,fret,func); 
   if((ficresp=fopen(fileresp,"w"))==NULL) {          for (j=1;j<=n;j++) { 
     printf("Problem with prevalence resultfile: %s\n", fileresp);            xi[j][ibig]=xi[j][n]; 
     exit(0);            xi[j][n]=xit[j]; 
   }          }
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);  #ifdef DEBUG
   j1=0;          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
           fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   j=cptcoveff;          for(j=1;j<=n;j++){
   if (cptcovn<1) {j=1;ncodemax[1]=1;}            printf(" %.12e",xit[j]);
             fprintf(ficlog," %.12e",xit[j]);
   for(k1=1; k1<=j;k1++){          }
    for(i1=1; i1<=ncodemax[k1];i1++){          printf("\n");
        j1++;          fprintf(ficlog,"\n");
   #endif
         for (i=-1; i<=nlstate+ndeath; i++)          }
          for (jk=-1; jk<=nlstate+ndeath; jk++)        } 
            for(m=agemin; m <= agemax+3; m++)    } 
              freq[i][jk][m]=0;  } 
          
        for (i=1; i<=imx; i++) {  /**** Prevalence limit (stable or period prevalence)  ****************/
          bool=1;  
          if  (cptcovn>0) {  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
            for (z1=1; z1<=cptcoveff; z1++)  {
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) bool=0;    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
          }       matrix by transitions matrix until convergence is reached */
           if (bool==1) {  
            for(m=firstpass; m<=lastpass-1; m++){    int i, ii,j,k;
              if(agev[m][i]==0) agev[m][i]=agemax+1;    double min, max, maxmin, maxmax,sumnew=0.;
              if(agev[m][i]==1) agev[m][i]=agemax+2;    double **matprod2();
              freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    double **out, cov[NCOVMAX+1], **pmij();
              freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];    double **newm;
            }    double agefin, delaymax=50 ; /* Max number of years to converge */
          }  
        }    for (ii=1;ii<=nlstate+ndeath;ii++)
         if  (cptcovn>0) {      for (j=1;j<=nlstate+ndeath;j++){
          fprintf(ficresp, "\n#********** Variable ");        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);      }
        }  
        fprintf(ficresp, "**********\n#");     cov[1]=1.;
        for(i=1; i<=nlstate;i++)   
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
        fprintf(ficresp, "\n");    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
              newm=savm;
   for(i=(int)agemin; i <= (int)agemax+3; i++){      /* Covariates have to be included here again */
     if(i==(int)agemax+3)       cov[2]=agefin;
       printf("Total");    
     else        for (k=1; k<=cptcovn;k++) {
       printf("Age %d", i);          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
     for(jk=1; jk <=nlstate ; jk++){          /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        }
         pp[jk] += freq[jk][m][i];        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     }        for (k=1; k<=cptcovprod;k++)
     for(jk=1; jk <=nlstate ; jk++){          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
       for(m=-1, pos=0; m <=0 ; m++)  
         pos += freq[jk][m][i];        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
       if(pp[jk]>=1.e-10)        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
       else      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);  
     }      savm=oldm;
     for(jk=1; jk <=nlstate ; jk++){      oldm=newm;
       for(m=1, pp[jk]=0; m <=nlstate+ndeath; m++)      maxmax=0.;
         pp[jk] += freq[jk][m][i];      for(j=1;j<=nlstate;j++){
     }        min=1.;
     for(jk=1,pos=0; jk <=nlstate ; jk++)        max=0.;
       pos += pp[jk];        for(i=1; i<=nlstate; i++) {
     for(jk=1; jk <=nlstate ; jk++){          sumnew=0;
       if(pos>=1.e-5)          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);          prlim[i][j]= newm[i][j]/(1-sumnew);
       else          max=FMAX(max,prlim[i][j]);
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);          min=FMIN(min,prlim[i][j]);
       if( i <= (int) agemax){        }
         if(pos>=1.e-5)        maxmin=max-min;
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);        maxmax=FMAX(maxmax,maxmin);
       else      }
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);      if(maxmax < ftolpl){
       }        return prlim;
     }      }
     for(jk=-1; jk <=nlstate+ndeath; jk++)    }
       for(m=-1; m <=nlstate+ndeath; m++)  }
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);  
     if(i <= (int) agemax)  /*************** transition probabilities ***************/ 
       fprintf(ficresp,"\n");  
     printf("\n");  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
     }  {
     }    double s1, s2;
  }    /*double t34;*/
      int i,j,j1, nc, ii, jj;
   fclose(ficresp);  
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);      for(i=1; i<= nlstate; i++){
   free_vector(pp,1,nlstate);        for(j=1; j<i;j++){
           for (nc=1, s2=0.;nc <=ncovmodel; nc++){
 }  /* End of Freq */            /*s2 += param[i][j][nc]*cov[nc];*/
             s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
 /************* Waves Concatenation ***************/  /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
           }
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)          ps[i][j]=s2;
 {  /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.        }
      Death is a valid wave (if date is known).        for(j=i+1; j<=nlstate+ndeath;j++){
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]            s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
      and mw[mi+1][i]. dh depends on stepm.  /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
      */          }
           ps[i][j]=s2;
   int i, mi, m;        }
   int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;      }
 float sum=0.;      /*ps[3][2]=1;*/
       
   for(i=1; i<=imx; i++){      for(i=1; i<= nlstate; i++){
     mi=0;        s1=0;
     m=firstpass;        for(j=1; j<i; j++){
     while(s[m][i] <= nlstate){          s1+=exp(ps[i][j]);
       if(s[m][i]>=1)          /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
         mw[++mi][i]=m;        }
       if(m >=lastpass)        for(j=i+1; j<=nlstate+ndeath; j++){
         break;          s1+=exp(ps[i][j]);
       else          /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
         m++;        }
     }/* end while */        ps[i][i]=1./(s1+1.);
     if (s[m][i] > nlstate){        for(j=1; j<i; j++)
       mi++;     /* Death is another wave */          ps[i][j]= exp(ps[i][j])*ps[i][i];
       /* if(mi==0)  never been interviewed correctly before death */        for(j=i+1; j<=nlstate+ndeath; j++)
          /* Only death is a correct wave */          ps[i][j]= exp(ps[i][j])*ps[i][i];
       mw[mi][i]=m;        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
     }      } /* end i */
       
     wav[i]=mi;      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
     if(mi==0)        for(jj=1; jj<= nlstate+ndeath; jj++){
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);          ps[ii][jj]=0;
   }          ps[ii][ii]=1;
         }
   for(i=1; i<=imx; i++){      }
     for(mi=1; mi<wav[i];mi++){      
       if (stepm <=0)  
         dh[mi][i]=1;  /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
       else{  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
         if (s[mw[mi+1][i]][i] > nlstate) {  /*         printf("ddd %lf ",ps[ii][jj]); */
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);  /*       } */
           if(j=0) j=1;  /* Survives at least one month after exam */  /*       printf("\n "); */
         }  /*        } */
         else{  /*        printf("\n ");printf("%lf ",cov[2]); */
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));         /*
           k=k+1;        for(i=1; i<= npar; i++) printf("%f ",x[i]);
           if (j >= jmax) jmax=j;        goto end;*/
           else if (j <= jmin)jmin=j;      return ps;
           sum=sum+j;  }
         }  
         jk= j/stepm;  /**************** Product of 2 matrices ******************/
         jl= j -jk*stepm;  
         ju= j -(jk+1)*stepm;  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
         if(jl <= -ju)  {
           dh[mi][i]=jk;    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
         else       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
           dh[mi][i]=jk+1;    /* in, b, out are matrice of pointers which should have been initialized 
         if(dh[mi][i]==0)       before: only the contents of out is modified. The function returns
           dh[mi][i]=1; /* At least one step */       a pointer to pointers identical to out */
       }    long i, j, k;
     }    for(i=nrl; i<= nrh; i++)
   }      for(k=ncolol; k<=ncoloh; k++)
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,sum/k);        for(j=ncl,out[i][k]=0.; j<=nch; j++)
 }          out[i][k] +=in[i][j]*b[j][k];
 /*********** Tricode ****************************/  
 void tricode(int *Tvar, int **nbcode, int imx)    return out;
 {  }
   int Ndum[20],ij=1, k, j, i;  
   int cptcode=0;  
   cptcoveff=0;  /************* Higher Matrix Product ***************/
    
   for (k=0; k<19; k++) Ndum[k]=0;  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
   for (k=1; k<=7; k++) ncodemax[k]=0;  {
     /* Computes the transition matrix starting at age 'age' over 
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {       'nhstepm*hstepm*stepm' months (i.e. until
     for (i=1; i<=imx; i++) {       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
       ij=(int)(covar[Tvar[j]][i]);       nhstepm*hstepm matrices. 
       Ndum[ij]++;       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
       if (ij > cptcode) cptcode=ij;       (typically every 2 years instead of every month which is too big 
     }       for the memory).
        Model is determined by parameters x and covariates have to be 
     /*printf("cptcode=%d cptcovn=%d ",cptcode,cptcovn);*/       included manually here. 
     for (i=0; i<=cptcode; i++) {  
       if(Ndum[i]!=0) ncodemax[j]++;       */
     }  
     ij=1;    int i, j, d, h, k;
     double **out, cov[NCOVMAX+1];
     for (i=1; i<=ncodemax[j]; i++) {    double **newm;
       for (k=0; k<=19; k++) {  
         if (Ndum[k] != 0) {    /* Hstepm could be zero and should return the unit matrix */
           nbcode[Tvar[j]][ij]=k;    for (i=1;i<=nlstate+ndeath;i++)
           /*   printf("ij=%d ",nbcode[Tvar[2]][1]);*/      for (j=1;j<=nlstate+ndeath;j++){
           ij++;        oldm[i][j]=(i==j ? 1.0 : 0.0);
         }        po[i][j][0]=(i==j ? 1.0 : 0.0);
         if (ij > ncodemax[j]) break;      }
       }      /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     }    for(h=1; h <=nhstepm; h++){
   }        for(d=1; d <=hstepm; d++){
  for (i=1; i<=10; i++) {        newm=savm;
       ij=Tvar[i];        /* Covariates have to be included here again */
       Ndum[ij]++;        cov[1]=1.;
     }        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
  ij=1;        for (k=1; k<=cptcovn;k++) 
  for (i=1; i<=cptcovn; i++) {          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
    if((Ndum[i]!=0) && (i<=ncov)){        for (k=1; k<=cptcovage;k++)
      Tvaraff[i]=ij;          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
    ij++;        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]]];
  }  
    
  for (j=1; j<=(cptcovn+2*cptcovprod); j++) {        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
    if ((Tvar[j]>= cptcoveff) && (Tvar[j] <=ncov)) cptcoveff=Tvar[j];        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
    /*printf("j=%d %d\n",j,Tvar[j]);*/        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
  }                     pmij(pmmij,cov,ncovmodel,x,nlstate));
          savm=oldm;
  /* printf("cptcoveff=%d Tvaraff=%d %d\n",cptcoveff, Tvaraff[1],Tvaraff[2]);        oldm=newm;
     scanf("%d",i);*/      }
 }      for(i=1; i<=nlstate+ndeath; i++)
         for(j=1;j<=nlstate+ndeath;j++) {
 /*********** Health Expectancies ****************/          po[i][j][h]=newm[i][j];
           /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)        }
 {      /*printf("h=%d ",h);*/
   /* Health expectancies */    } /* end h */
   int i, j, nhstepm, hstepm, h;  /*     printf("\n H=%d \n",h); */
   double age, agelim,hf;    return po;
   double ***p3mat;  }
    
   fprintf(ficreseij,"# Health expectancies\n");  
   fprintf(ficreseij,"# Age");  /*************** log-likelihood *************/
   for(i=1; i<=nlstate;i++)  double func( double *x)
     for(j=1; j<=nlstate;j++)  {
       fprintf(ficreseij," %1d-%1d",i,j);    int i, ii, j, k, mi, d, kk;
   fprintf(ficreseij,"\n");    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
     double **out;
   hstepm=1*YEARM; /*  Every j years of age (in month) */    double sw; /* Sum of weights */
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    double lli; /* Individual log likelihood */
     int s1, s2;
   agelim=AGESUP;    double bbh, survp;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    long ipmx;
     /* nhstepm age range expressed in number of stepm */    /*extern weight */
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);    /* We are differentiating ll according to initial status */
     /* Typically if 20 years = 20*12/6=40 stepm */    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     if (stepm >= YEARM) hstepm=1;    /*for(i=1;i<imx;i++) 
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */      printf(" %d\n",s[4][i]);
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    */
     /* Computed by stepm unit matrices, product of hstepm matrices, stored    cov[1]=1.;
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */  
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);      for(k=1; k<=nlstate; k++) ll[k]=0.;
   
     if(mle==1){
     for(i=1; i<=nlstate;i++)      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       for(j=1; j<=nlstate;j++)        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){        for(mi=1; mi<= wav[i]-1; mi++){
           eij[i][j][(int)age] +=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);
     hf=1;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     if (stepm >= YEARM) hf=stepm/YEARM;            }
     fprintf(ficreseij,"%.0f",age );          for(d=0; d<dh[mi][i]; d++){
     for(i=1; i<=nlstate;i++)            newm=savm;
       for(j=1; j<=nlstate;j++){            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);            for (kk=1; kk<=cptcovage;kk++) {
       }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     fprintf(ficreseij,"\n");            }
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 }            savm=oldm;
             oldm=newm;
 /************ Variance ******************/          } /* end mult */
 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)        
 {          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
   /* Variance of health expectancies */          /* But now since version 0.9 we anticipate for bias at large stepm.
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/           * If stepm is larger than one month (smallest stepm) and if the exact delay 
   double **newm;           * (in months) between two waves is not a multiple of stepm, we rounded to 
   double **dnewm,**doldm;           * the nearest (and in case of equal distance, to the lowest) interval but now
   int i, j, nhstepm, hstepm, h;           * we keep into memory the bias bh[mi][i] and also the previous matrix product
   int k, cptcode;           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
    double *xp;           * probability in order to take into account the bias as a fraction of the way
   double **gp, **gm;           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
   double ***gradg, ***trgradg;           * -stepm/2 to stepm/2 .
   double ***p3mat;           * For stepm=1 the results are the same as for previous versions of Imach.
   double age,agelim;           * For stepm > 1 the results are less biased than in previous versions. 
   int theta;           */
           s1=s[mw[mi][i]][i];
    fprintf(ficresvij,"# Covariances of life expectancies\n");          s2=s[mw[mi+1][i]][i];
   fprintf(ficresvij,"# Age");          bbh=(double)bh[mi][i]/(double)stepm; 
   for(i=1; i<=nlstate;i++)          /* bias bh is positive if real duration
     for(j=1; j<=nlstate;j++)           * is higher than the multiple of stepm and negative otherwise.
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);           */
   fprintf(ficresvij,"\n");          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
           if( s2 > nlstate){ 
   xp=vector(1,npar);            /* i.e. if s2 is a death state and if the date of death is known 
   dnewm=matrix(1,nlstate,1,npar);               then the contribution to the likelihood is the probability to 
   doldm=matrix(1,nlstate,1,nlstate);               die between last step unit time and current  step unit time, 
                 which is also equal to probability to die before dh 
   hstepm=1*YEARM; /* Every year of age */               minus probability to die before dh-stepm . 
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */               In version up to 0.92 likelihood was computed
   agelim = AGESUP;          as if date of death was unknown. Death was treated as any other
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          health state: the date of the interview describes the actual state
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          and not the date of a change in health state. The former idea was
     if (stepm >= YEARM) hstepm=1;          to consider that at each interview the state was recorded
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */          (healthy, disable or death) and IMaCh was corrected; but when we
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          introduced the exact date of death then we should have modified
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);          the contribution of an exact death to the likelihood. This new
     gp=matrix(0,nhstepm,1,nlstate);          contribution is smaller and very dependent of the step unit
     gm=matrix(0,nhstepm,1,nlstate);          stepm. It is no more the probability to die between last interview
           and month of death but the probability to survive from last
     for(theta=1; theta <=npar; theta++){          interview up to one month before death multiplied by the
       for(i=1; i<=npar; i++){ /* Computes gradient */          probability to die within a month. Thanks to Chris
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          Jackson for correcting this bug.  Former versions increased
       }          mortality artificially. The bad side is that we add another loop
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            which slows down the processing. The difference can be up to 10%
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          lower mortality.
       for(j=1; j<= nlstate; j++){            */
         for(h=0; h<=nhstepm; h++){            lli=log(out[s1][s2] - savm[s1][s2]);
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)  
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];  
         }          } else if  (s2==-2) {
       }            for (j=1,survp=0. ; j<=nlstate; j++) 
                  survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
       for(i=1; i<=npar; i++) /* Computes gradient */            /*survp += out[s1][j]; */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);            lli= log(survp);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          
       for(j=1; j<= nlstate; j++){          else if  (s2==-4) { 
         for(h=0; h<=nhstepm; h++){            for (j=3,survp=0. ; j<=nlstate; j++)  
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];            lli= log(survp); 
         }          } 
       }  
       for(j=1; j<= nlstate; j++)          else if  (s2==-5) { 
         for(h=0; h<=nhstepm; h++){            for (j=1,survp=0. ; j<=2; j++)  
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
         }            lli= log(survp); 
     } /* End theta */          } 
           
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);          else{
             lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
     for(h=0; h<=nhstepm; h++)            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
       for(j=1; j<=nlstate;j++)          } 
         for(theta=1; theta <=npar; theta++)          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
           trgradg[h][j][theta]=gradg[h][theta][j];          /*if(lli ==000.0)*/
           /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
     for(i=1;i<=nlstate;i++)          ipmx +=1;
       for(j=1;j<=nlstate;j++)          sw += weight[i];
         vareij[i][j][(int)age] =0.;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     for(h=0;h<=nhstepm;h++){        } /* end of wave */
       for(k=0;k<=nhstepm;k++){      } /* end of individual */
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);    }  else if(mle==2){
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for(i=1;i<=nlstate;i++)        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
           for(j=1;j<=nlstate;j++)        for(mi=1; mi<= wav[i]-1; mi++){
             vareij[i][j][(int)age] += doldm[i][j];          for (ii=1;ii<=nlstate+ndeath;ii++)
       }            for (j=1;j<=nlstate+ndeath;j++){
     }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     h=1;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     if (stepm >= YEARM) h=stepm/YEARM;            }
     fprintf(ficresvij,"%.0f ",age );          for(d=0; d<=dh[mi][i]; d++){
     for(i=1; i<=nlstate;i++)            newm=savm;
       for(j=1; j<=nlstate;j++){            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);            for (kk=1; kk<=cptcovage;kk++) {
       }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     fprintf(ficresvij,"\n");            }
     free_matrix(gp,0,nhstepm,1,nlstate);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     free_matrix(gm,0,nhstepm,1,nlstate);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);            savm=oldm;
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);            oldm=newm;
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          } /* end mult */
   } /* End age */        
            s1=s[mw[mi][i]][i];
   free_vector(xp,1,npar);          s2=s[mw[mi+1][i]][i];
   free_matrix(doldm,1,nlstate,1,npar);          bbh=(double)bh[mi][i]/(double)stepm; 
   free_matrix(dnewm,1,nlstate,1,nlstate);          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
           ipmx +=1;
 }          sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
 /************ Variance of prevlim ******************/        } /* end of wave */
 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)      } /* end of individual */
 {    }  else if(mle==3){  /* exponential inter-extrapolation */
   /* Variance of prevalence limit */      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   double **newm;        for(mi=1; mi<= wav[i]-1; mi++){
   double **dnewm,**doldm;          for (ii=1;ii<=nlstate+ndeath;ii++)
   int i, j, nhstepm, hstepm;            for (j=1;j<=nlstate+ndeath;j++){
   int k, cptcode;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   double *xp;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   double *gp, *gm;            }
   double **gradg, **trgradg;          for(d=0; d<dh[mi][i]; d++){
   double age,agelim;            newm=savm;
   int theta;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
                for (kk=1; kk<=cptcovage;kk++) {
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   fprintf(ficresvpl,"# Age");            }
   for(i=1; i<=nlstate;i++)            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       fprintf(ficresvpl," %1d-%1d",i,i);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   fprintf(ficresvpl,"\n");            savm=oldm;
             oldm=newm;
   xp=vector(1,npar);          } /* end mult */
   dnewm=matrix(1,nlstate,1,npar);        
   doldm=matrix(1,nlstate,1,nlstate);          s1=s[mw[mi][i]][i];
            s2=s[mw[mi+1][i]][i];
   hstepm=1*YEARM; /* Every year of age */          bbh=(double)bh[mi][i]/(double)stepm; 
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */          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 */
   agelim = AGESUP;          ipmx +=1;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          sw += weight[i];
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     if (stepm >= YEARM) hstepm=1;        } /* end of wave */
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      } /* end of individual */
     gradg=matrix(1,npar,1,nlstate);    }else if (mle==4){  /* ml=4 no inter-extrapolation */
     gp=vector(1,nlstate);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     gm=vector(1,nlstate);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for(mi=1; mi<= wav[i]-1; mi++){
     for(theta=1; theta <=npar; theta++){          for (ii=1;ii<=nlstate+ndeath;ii++)
       for(i=1; i<=npar; i++){ /* Computes gradient */            for (j=1;j<=nlstate+ndeath;j++){
         xp[i] = x[i] + (i==theta ?delti[theta]:0);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);            }
       for(i=1;i<=nlstate;i++)          for(d=0; d<dh[mi][i]; d++){
         gp[i] = prlim[i][i];            newm=savm;
                cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       for(i=1; i<=npar; i++) /* Computes gradient */            for (kk=1; kk<=cptcovage;kk++) {
         xp[i] = x[i] - (i==theta ?delti[theta]:0);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);            }
       for(i=1;i<=nlstate;i++)          
         gm[i] = prlim[i][i];            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       for(i=1;i<=nlstate;i++)            savm=oldm;
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];            oldm=newm;
     } /* End theta */          } /* end mult */
         
     trgradg =matrix(1,nlstate,1,npar);          s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
     for(j=1; j<=nlstate;j++)          if( s2 > nlstate){ 
       for(theta=1; theta <=npar; theta++)            lli=log(out[s1][s2] - savm[s1][s2]);
         trgradg[j][theta]=gradg[theta][j];          }else{
             lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
     for(i=1;i<=nlstate;i++)          }
       varpl[i][(int)age] =0.;          ipmx +=1;
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);          sw += weight[i];
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     for(i=1;i<=nlstate;i++)  /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */        } /* end of wave */
       } /* end of individual */
     fprintf(ficresvpl,"%.0f ",age );    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
     for(i=1; i<=nlstate;i++)      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     fprintf(ficresvpl,"\n");        for(mi=1; mi<= wav[i]-1; mi++){
     free_vector(gp,1,nlstate);          for (ii=1;ii<=nlstate+ndeath;ii++)
     free_vector(gm,1,nlstate);            for (j=1;j<=nlstate+ndeath;j++){
     free_matrix(gradg,1,npar,1,nlstate);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     free_matrix(trgradg,1,nlstate,1,npar);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   } /* End age */            }
           for(d=0; d<dh[mi][i]; d++){
   free_vector(xp,1,npar);            newm=savm;
   free_matrix(doldm,1,nlstate,1,npar);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   free_matrix(dnewm,1,nlstate,1,nlstate);            for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
 }            }
           
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 /***********************************************/            savm=oldm;
 /**************** Main Program *****************/            oldm=newm;
 /***********************************************/          } /* end mult */
         
 /*int main(int argc, char *argv[])*/          s1=s[mw[mi][i]][i];
 int main()          s2=s[mw[mi+1][i]][i];
 {          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
           ipmx +=1;
   int i,j, k, n=MAXN,iter,m,size,cptcode, aaa, cptcod;          sw += weight[i];
   double agedeb, agefin,hf;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   double agemin=1.e20, agemax=-1.e20;          /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
         } /* end of wave */
   double fret;      } /* end of individual */
   double **xi,tmp,delta;    } /* End of if */
     for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   double dum; /* Dummy variable */    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   double ***p3mat;    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
   int *indx;    return -l;
   char line[MAXLINE], linepar[MAXLINE];  }
   char title[MAXLINE];  
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];  /*************** log-likelihood *************/
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH];  double funcone( double *x)
   char filerest[FILENAMELENGTH];  {
   char fileregp[FILENAMELENGTH];    /* Same as likeli but slower because of a lot of printf and if */
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];    int i, ii, j, k, mi, d, kk;
   int firstobs=1, lastobs=10;    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
   int sdeb, sfin; /* Status at beginning and end */    double **out;
   int c,  h , cpt,l;    double lli; /* Individual log likelihood */
   int ju,jl, mi;    double llt;
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;    int s1, s2;
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;    double bbh, survp;
      /*extern weight */
   int hstepm, nhstepm;    /* We are differentiating ll according to initial status */
   double bage, fage, age, agelim, agebase;    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   double ftolpl=FTOL;    /*for(i=1;i<imx;i++) 
   double **prlim;      printf(" %d\n",s[4][i]);
   double *severity;    */
   double ***param; /* Matrix of parameters */    cov[1]=1.;
   double  *p;  
   double **matcov; /* Matrix of covariance */    for(k=1; k<=nlstate; k++) ll[k]=0.;
   double ***delti3; /* Scale */  
   double *delti; /* Scale */    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   double ***eij, ***vareij;      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   double **varpl; /* Variances of prevalence limits by age */      for(mi=1; mi<= wav[i]-1; mi++){
   double *epj, vepp;        for (ii=1;ii<=nlstate+ndeath;ii++)
   char version[80]="Imach version 62c, May 1999, INED-EUROREVES ";          for (j=1;j<=nlstate+ndeath;j++){
   char *alph[]={"a","a","b","c","d","e"}, str[4];            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
             savm[ii][j]=(ii==j ? 1.0 : 0.0);
   char z[1]="c", occ;          }
 #include <sys/time.h>        for(d=0; d<dh[mi][i]; d++){
 #include <time.h>          newm=savm;
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   /* long total_usecs;          for (kk=1; kk<=cptcovage;kk++) {
   struct timeval start_time, end_time;            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
            }
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                        1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           savm=oldm;
   printf("\nIMACH, Version 0.64a");          oldm=newm;
   printf("\nEnter the parameter file name: ");        } /* end mult */
         
 #ifdef windows        s1=s[mw[mi][i]][i];
   scanf("%s",pathtot);        s2=s[mw[mi+1][i]][i];
   getcwd(pathcd, size);        bbh=(double)bh[mi][i]/(double)stepm; 
   /*cygwin_split_path(pathtot,path,optionfile);        /* bias is positive if real duration
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/         * is higher than the multiple of stepm and negative otherwise.
   /* cutv(path,optionfile,pathtot,'\\');*/         */
         if( s2 > nlstate && (mle <5) ){  /* Jackson */
 split(pathtot, path,optionfile);          lli=log(out[s1][s2] - savm[s1][s2]);
   chdir(path);        } else if  (s2==-2) {
   replace(pathc,path);          for (j=1,survp=0. ; j<=nlstate; j++) 
 #endif            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
 #ifdef unix          lli= log(survp);
   scanf("%s",optionfile);        }else if (mle==1){
 #endif          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
         } else if(mle==2){
 /*-------- arguments in the command line --------*/          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
         } else if(mle==3){  /* exponential inter-extrapolation */
   strcpy(fileres,"r");          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 */
   strcat(fileres, optionfile);        } else if (mle==4){  /* mle=4 no inter-extrapolation */
           lli=log(out[s1][s2]); /* Original formula */
   /*---------arguments file --------*/        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
           lli=log(out[s1][s2]); /* Original formula */
   if((ficpar=fopen(optionfile,"r"))==NULL)    {        } /* End of if */
     printf("Problem with optionfile %s\n",optionfile);        ipmx +=1;
     goto end;        sw += weight[i];
   }        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
   strcpy(filereso,"o");        if(globpr){
   strcat(filereso,fileres);          fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
   if((ficparo=fopen(filereso,"w"))==NULL) {   %11.6f %11.6f %11.6f ", \
     printf("Problem with Output resultfile: %s\n", filereso);goto end;                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
   }                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
           for(k=1,llt=0.,l=0.; k<=nlstate; k++){
   /* Reads comments: lines beginning with '#' */            llt +=ll[k]*gipmx/gsw;
   while((c=getc(ficpar))=='#' && c!= EOF){            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
     ungetc(c,ficpar);          }
     fgets(line, MAXLINE, ficpar);          fprintf(ficresilk," %10.6f\n", -llt);
     puts(line);        }
     fputs(line,ficparo);      } /* end of wave */
   }    } /* end of individual */
   ungetc(c,ficpar);    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   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);    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
   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);    if(globpr==0){ /* First time we count the contributions and weights */
   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);      gipmx=ipmx;
       gsw=sw;
   covar=matrix(0,NCOVMAX,1,n);        }
   if (strlen(model)<=1) cptcovn=0;    return -l;
   else {  }
     j=0;  
     j=nbocc(model,'+');  
     cptcovn=j+1;  /*************** function likelione ***********/
   }  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
   {
   ncovmodel=2+cptcovn;    /* This routine should help understanding what is done with 
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */       the selection of individuals/waves and
         to check the exact contribution to the likelihood.
   /* Read guess parameters */       Plotting could be done.
   /* Reads comments: lines beginning with '#' */     */
   while((c=getc(ficpar))=='#' && c!= EOF){    int k;
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);    if(*globpri !=0){ /* Just counts and sums, no printings */
     puts(line);      strcpy(fileresilk,"ilk"); 
     fputs(line,ficparo);      strcat(fileresilk,fileres);
   }      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
   ungetc(c,ficpar);        printf("Problem with resultfile: %s\n", fileresilk);
          fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);      }
     for(i=1; i <=nlstate; i++)      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");
     for(j=1; j <=nlstate+ndeath-1; j++){      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
       fscanf(ficpar,"%1d%1d",&i1,&j1);      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
       fprintf(ficparo,"%1d%1d",i1,j1);      for(k=1; k<=nlstate; k++) 
       printf("%1d%1d",i,j);        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
       for(k=1; k<=ncovmodel;k++){      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
         fscanf(ficpar," %lf",&param[i][j][k]);    }
         printf(" %lf",param[i][j][k]);  
         fprintf(ficparo," %lf",param[i][j][k]);    *fretone=(*funcone)(p);
       }    if(*globpri !=0){
       fscanf(ficpar,"\n");      fclose(ficresilk);
       printf("\n");      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
       fprintf(ficparo,"\n");      fflush(fichtm); 
     }    } 
      return;
   npar= (nlstate+ndeath-1)*nlstate*ncovmodel;  }
   p=param[1][1];  
    
   /* Reads comments: lines beginning with '#' */  /*********** Maximum Likelihood Estimation ***************/
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
     fgets(line, MAXLINE, ficpar);  {
     puts(line);    int i,j, iter;
     fputs(line,ficparo);    double **xi;
   }    double fret;
   ungetc(c,ficpar);    double fretone; /* Only one call to likelihood */
     /*  char filerespow[FILENAMELENGTH];*/
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    xi=matrix(1,npar,1,npar);
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */    for (i=1;i<=npar;i++)
   for(i=1; i <=nlstate; i++){      for (j=1;j<=npar;j++)
     for(j=1; j <=nlstate+ndeath-1; j++){        xi[i][j]=(i==j ? 1.0 : 0.0);
       fscanf(ficpar,"%1d%1d",&i1,&j1);    printf("Powell\n");  fprintf(ficlog,"Powell\n");
       printf("%1d%1d",i,j);    strcpy(filerespow,"pow"); 
       fprintf(ficparo,"%1d%1d",i1,j1);    strcat(filerespow,fileres);
       for(k=1; k<=ncovmodel;k++){    if((ficrespow=fopen(filerespow,"w"))==NULL) {
         fscanf(ficpar,"%le",&delti3[i][j][k]);      printf("Problem with resultfile: %s\n", filerespow);
         printf(" %le",delti3[i][j][k]);      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
         fprintf(ficparo," %le",delti3[i][j][k]);    }
       }    fprintf(ficrespow,"# Powell\n# iter -2*LL");
       fscanf(ficpar,"\n");    for (i=1;i<=nlstate;i++)
       printf("\n");      for(j=1;j<=nlstate+ndeath;j++)
       fprintf(ficparo,"\n");        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
     }    fprintf(ficrespow,"\n");
   }  
   delti=delti3[1][1];    powell(p,xi,npar,ftol,&iter,&fret,func);
    
   /* Reads comments: lines beginning with '#' */    free_matrix(xi,1,npar,1,npar);
   while((c=getc(ficpar))=='#' && c!= EOF){    fclose(ficrespow);
     ungetc(c,ficpar);    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
     fgets(line, MAXLINE, ficpar);    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     puts(line);    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     fputs(line,ficparo);  
   }  }
   ungetc(c,ficpar);  
    /**** Computes Hessian and covariance matrix ***/
   matcov=matrix(1,npar,1,npar);  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
   for(i=1; i <=npar; i++){  {
     fscanf(ficpar,"%s",&str);    double  **a,**y,*x,pd;
     printf("%s",str);    double **hess;
     fprintf(ficparo,"%s",str);    int i, j,jk;
     for(j=1; j <=i; j++){    int *indx;
       fscanf(ficpar," %le",&matcov[i][j]);  
       printf(" %.5le",matcov[i][j]);    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
       fprintf(ficparo," %.5le",matcov[i][j]);    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
     }    void lubksb(double **a, int npar, int *indx, double b[]) ;
     fscanf(ficpar,"\n");    void ludcmp(double **a, int npar, int *indx, double *d) ;
     printf("\n");    double gompertz(double p[]);
     fprintf(ficparo,"\n");    hess=matrix(1,npar,1,npar);
   }  
   for(i=1; i <=npar; i++)    printf("\nCalculation of the hessian matrix. Wait...\n");
     for(j=i+1;j<=npar;j++)    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
       matcov[i][j]=matcov[j][i];    for (i=1;i<=npar;i++){
          printf("%d",i);fflush(stdout);
   printf("\n");      fprintf(ficlog,"%d",i);fflush(ficlog);
      
        hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
     /*-------- data file ----------*/      
     if((ficres =fopen(fileres,"w"))==NULL) {      /*  printf(" %f ",p[i]);
       printf("Problem with resultfile: %s\n", fileres);goto end;          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
     }    }
     fprintf(ficres,"#%s\n",version);    
        for (i=1;i<=npar;i++) {
     if((fic=fopen(datafile,"r"))==NULL)    {      for (j=1;j<=npar;j++)  {
       printf("Problem with datafile: %s\n", datafile);goto end;        if (j>i) { 
     }          printf(".%d%d",i,j);fflush(stdout);
           fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
     n= lastobs;          hess[i][j]=hessij(p,delti,i,j,func,npar);
     severity = vector(1,maxwav);          
     outcome=imatrix(1,maxwav+1,1,n);          hess[j][i]=hess[i][j];    
     num=ivector(1,n);          /*printf(" %lf ",hess[i][j]);*/
     moisnais=vector(1,n);        }
     annais=vector(1,n);      }
     moisdc=vector(1,n);    }
     andc=vector(1,n);    printf("\n");
     agedc=vector(1,n);    fprintf(ficlog,"\n");
     cod=ivector(1,n);  
     weight=vector(1,n);    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
     mint=matrix(1,maxwav,1,n);    
     anint=matrix(1,maxwav,1,n);    a=matrix(1,npar,1,npar);
     s=imatrix(1,maxwav+1,1,n);    y=matrix(1,npar,1,npar);
     adl=imatrix(1,maxwav+1,1,n);        x=vector(1,npar);
     tab=ivector(1,NCOVMAX);    indx=ivector(1,npar);
     ncodemax=ivector(1,8);    for (i=1;i<=npar;i++)
       for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
     i=1;    ludcmp(a,npar,indx,&pd);
     while (fgets(line, MAXLINE, fic) != NULL)    {  
       if ((i >= firstobs) && (i <=lastobs)) {    for (j=1;j<=npar;j++) {
              for (i=1;i<=npar;i++) x[i]=0;
         for (j=maxwav;j>=1;j--){      x[j]=1;
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);      lubksb(a,npar,indx,x);
           strcpy(line,stra);      for (i=1;i<=npar;i++){ 
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);        matcov[i][j]=x[i];
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);      }
         }    }
          
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);    printf("\n#Hessian matrix#\n");
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);    fprintf(ficlog,"\n#Hessian matrix#\n");
     for (i=1;i<=npar;i++) { 
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);      for (j=1;j<=npar;j++) { 
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);        printf("%.3e ",hess[i][j]);
         fprintf(ficlog,"%.3e ",hess[i][j]);
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);      }
         for (j=ncov;j>=1;j--){      printf("\n");
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);      fprintf(ficlog,"\n");
         }    }
         num[i]=atol(stra);  
     /* Recompute Inverse */
         /*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]));*/    for (i=1;i<=npar;i++)
       for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
         i=i+1;    ludcmp(a,npar,indx,&pd);
       }  
     }    /*  printf("\n#Hessian matrix recomputed#\n");
   
     /*scanf("%d",i);*/    for (j=1;j<=npar;j++) {
   imx=i-1; /* Number of individuals */      for (i=1;i<=npar;i++) x[i]=0;
       x[j]=1;
   /* Calculation of the number of parameter from char model*/      lubksb(a,npar,indx,x);
   Tvar=ivector(1,15);      for (i=1;i<=npar;i++){ 
   Tprod=ivector(1,15);        y[i][j]=x[i];
   Tvaraff=ivector(1,15);        printf("%.3e ",y[i][j]);
   Tvard=imatrix(1,15,1,2);        fprintf(ficlog,"%.3e ",y[i][j]);
   Tage=ivector(1,15);            }
          printf("\n");
   if (strlen(model) >1){      fprintf(ficlog,"\n");
     j=0, j1=0, k1=1, k2=1;    }
     j=nbocc(model,'+');    */
     j1=nbocc(model,'*');  
     cptcovn=j+1;    free_matrix(a,1,npar,1,npar);
     cptcovprod=j1;    free_matrix(y,1,npar,1,npar);
        free_vector(x,1,npar);
     strcpy(modelsav,model);    free_ivector(indx,1,npar);
    if (j==0) {    free_matrix(hess,1,npar,1,npar);
       if (j1==0){  
         cutv(stra,strb,modelsav,'V');  
         Tvar[1]=atoi(strb);  }
       }  
       else if (j1==1) {  /*************** hessian matrix ****************/
         cutv(stra,strb,modelsav,'*');  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
         Tage[1]=1; cptcovage++;  {
         if (strcmp(stra,"age")==0) {    int i;
           cptcovprod--;    int l=1, lmax=20;
           cutv(strd,strc,strb,'V');    double k1,k2;
           Tvar[1]=atoi(strc);    double p2[MAXPARM+1]; /* identical to x */
         }    double res;
         else if (strcmp(strb,"age")==0) {    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
           cptcovprod--;    double fx;
           cutv(strd,strc,stra,'V');    int k=0,kmax=10;
           Tvar[1]=atoi(strc);    double l1;
         }  
         else {    fx=func(x);
           cutv(strd,strc,strb,'V');    for (i=1;i<=npar;i++) p2[i]=x[i];
           cutv(stre,strd,stra,'V');    for(l=0 ; l <=lmax; l++){
           Tvar[1]=ncov+1;      l1=pow(10,l);
           for (k=1; k<=lastobs;k++)      delts=delt;
               covar[ncov+1][k]=covar[atoi(strc)][k]*covar[atoi(strd)][k];      for(k=1 ; k <kmax; k=k+1){
         }        delt = delta*(l1*k);
         /*printf("%s %s %s\n", stra,strb,modelsav);        p2[theta]=x[theta] +delt;
 printf("%d ",Tvar[1]);        k1=func(p2)-fx;
 scanf("%d",i);*/        p2[theta]=x[theta]-delt;
       }        k2=func(p2)-fx;
     }        /*res= (k1-2.0*fx+k2)/delt/delt; */
    else {        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
       for(i=j; i>=1;i--){        
         cutv(stra,strb,modelsav,'+');  #ifdef DEBUGHESS
         /*printf("%s %s %s\n", stra,strb,modelsav);        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);
           scanf("%d",i);*/        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
         if (strchr(strb,'*')) {  #endif
           cutv(strd,strc,strb,'*');        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
           if (strcmp(strc,"age")==0) {        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
             cptcovprod--;          k=kmax;
             cutv(strb,stre,strd,'V');        }
             Tvar[i+1]=atoi(stre);        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
             cptcovage++;          k=kmax; l=lmax*10.;
             Tage[cptcovage]=i+1;        }
             printf("stre=%s ", stre);        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
           }          delts=delt;
           else if (strcmp(strd,"age")==0) {        }
             cptcovprod--;      }
             cutv(strb,stre,strc,'V');    }
             Tvar[i+1]=atoi(stre);    delti[theta]=delts;
             cptcovage++;    return res; 
             Tage[cptcovage]=i+1;    
           }  }
           else {  
             cutv(strb,stre,strc,'V');  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
             Tvar[i+1]=ncov+k1;  {
             cutv(strb,strc,strd,'V');    int i;
             Tprod[k1]=i+1;    int l=1, l1, lmax=20;
             Tvard[k1][1]=atoi(strc);    double k1,k2,k3,k4,res,fx;
             Tvard[k1][2]=atoi(stre);    double p2[MAXPARM+1];
             Tvar[cptcovn+k2]=Tvard[k1][1];    int k;
             Tvar[cptcovn+k2+1]=Tvard[k1][2];  
             for (k=1; k<=lastobs;k++)    fx=func(x);
               covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];    for (k=1; k<=2; k++) {
             k1++;      for (i=1;i<=npar;i++) p2[i]=x[i];
             k2=k2+2;      p2[thetai]=x[thetai]+delti[thetai]/k;
           }      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
         }      k1=func(p2)-fx;
         else {    
           cutv(strd,strc,strb,'V');      p2[thetai]=x[thetai]+delti[thetai]/k;
           /* printf("%s %s %s", strd,strc,strb);*/      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
           Tvar[i+1]=atoi(strc);      k2=func(p2)-fx;
         }    
         strcpy(modelsav,stra);        p2[thetai]=x[thetai]-delti[thetai]/k;
       }      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       cutv(strd,strc,stra,'V');      k3=func(p2)-fx;
       Tvar[1]=atoi(strc);    
     }      p2[thetai]=x[thetai]-delti[thetai]/k;
   }      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   /* for (i=1; i<=5; i++)      k4=func(p2)-fx;
      printf("i=%d %d ",i,Tvar[i]);*/      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
   /* printf("tvar=%d %d cptcovage=%d %d",Tvar[1],Tvar[2],cptcovage,Tage[1]);*/  #ifdef DEBUG
  /*printf("cptcovprod=%d ", cptcovprod);*/      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);
   /*  scanf("%d ",i);*/      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);
     fclose(fic);  #endif
     }
     /*  if(mle==1){*/    return res;
     if (weightopt != 1) { /* Maximisation without weights*/  }
       for(i=1;i<=n;i++) weight[i]=1.0;  
     }  /************** Inverse of matrix **************/
     /*-calculation of age at interview from date of interview and age at death -*/  void ludcmp(double **a, int n, int *indx, double *d) 
     agev=matrix(1,maxwav,1,imx);  { 
        int i,imax,j,k; 
     for (i=1; i<=imx; i++)  {    double big,dum,sum,temp; 
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);    double *vv; 
       for(m=1; (m<= maxwav); m++){   
         if(s[m][i] >0){    vv=vector(1,n); 
           if (s[m][i] == nlstate+1) {    *d=1.0; 
             if(agedc[i]>0)    for (i=1;i<=n;i++) { 
               if(moisdc[i]!=99 && andc[i]!=9999)      big=0.0; 
               agev[m][i]=agedc[i];      for (j=1;j<=n;j++) 
             else{        if ((temp=fabs(a[i][j])) > big) big=temp; 
               printf("Warning negative age at death: %d line:%d\n",num[i],i);      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
               agev[m][i]=-1;      vv[i]=1.0/big; 
             }    } 
           }    for (j=1;j<=n;j++) { 
           else if(s[m][i] !=9){ /* Should no more exist */      for (i=1;i<j;i++) { 
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);        sum=a[i][j]; 
             if(mint[m][i]==99 || anint[m][i]==9999)        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
               agev[m][i]=1;        a[i][j]=sum; 
             else if(agev[m][i] <agemin){      } 
               agemin=agev[m][i];      big=0.0; 
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/      for (i=j;i<=n;i++) { 
             }        sum=a[i][j]; 
             else if(agev[m][i] >agemax){        for (k=1;k<j;k++) 
               agemax=agev[m][i];          sum -= a[i][k]*a[k][j]; 
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/        a[i][j]=sum; 
             }        if ( (dum=vv[i]*fabs(sum)) >= big) { 
             /*agev[m][i]=anint[m][i]-annais[i];*/          big=dum; 
             /*   agev[m][i] = age[i]+2*m;*/          imax=i; 
           }        } 
           else { /* =9 */      } 
             agev[m][i]=1;      if (j != imax) { 
             s[m][i]=-1;        for (k=1;k<=n;k++) { 
           }          dum=a[imax][k]; 
         }          a[imax][k]=a[j][k]; 
         else /*= 0 Unknown */          a[j][k]=dum; 
           agev[m][i]=1;        } 
       }        *d = -(*d); 
            vv[imax]=vv[j]; 
     }      } 
     for (i=1; i<=imx; i++)  {      indx[j]=imax; 
       for(m=1; (m<= maxwav); m++){      if (a[j][j] == 0.0) a[j][j]=TINY; 
         if (s[m][i] > (nlstate+ndeath)) {      if (j != n) { 
           printf("Error: Wrong value in nlstate or ndeath\n");          dum=1.0/(a[j][j]); 
           goto end;        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
         }      } 
       }    } 
     }    free_vector(vv,1,n);  /* Doesn't work */
   ;
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);  } 
   
     free_vector(severity,1,maxwav);  void lubksb(double **a, int n, int *indx, double b[]) 
     free_imatrix(outcome,1,maxwav+1,1,n);  { 
     free_vector(moisnais,1,n);    int i,ii=0,ip,j; 
     free_vector(annais,1,n);    double sum; 
     free_matrix(mint,1,maxwav,1,n);   
     free_matrix(anint,1,maxwav,1,n);    for (i=1;i<=n;i++) { 
     free_vector(moisdc,1,n);      ip=indx[i]; 
     free_vector(andc,1,n);      sum=b[ip]; 
       b[ip]=b[i]; 
          if (ii) 
     wav=ivector(1,imx);        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
     dh=imatrix(1,lastpass-firstpass+1,1,imx);      else if (sum) ii=i; 
     mw=imatrix(1,lastpass-firstpass+1,1,imx);      b[i]=sum; 
        } 
     /* Concatenates waves */    for (i=n;i>=1;i--) { 
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);      sum=b[i]; 
       for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
       b[i]=sum/a[i][i]; 
       Tcode=ivector(1,100);    } 
       nbcode=imatrix(1,nvar,1,8);  } 
       ncodemax[1]=1;  
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);  void pstamp(FILE *fichier)
        {
    codtab=imatrix(1,100,1,10);    fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
    h=0;  }
    m=pow(2,cptcoveff);  
    /************ Frequencies ********************/
    for(k=1;k<=cptcoveff; k++){  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[])
      for(i=1; i <=(m/pow(2,k));i++){  {  /* Some frequencies */
        for(j=1; j <= ncodemax[k]; j++){    
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){    int i, m, jk, k1,i1, j1, bool, z1,j;
            h++;    int first;
            if (h>m) h=1;codtab[h][k]=j;    double ***freq; /* Frequencies */
          }    double *pp, **prop;
        }    double pos,posprop, k2, dateintsum=0,k2cpt=0;
      }    char fileresp[FILENAMELENGTH];
    }    
     pp=vector(1,nlstate);
     prop=matrix(1,nlstate,iagemin,iagemax+3);
    /*for(i=1; i <=m ;i++){    strcpy(fileresp,"p");
      for(k=1; k <=cptcovn; k++){    strcat(fileresp,fileres);
        printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);    if((ficresp=fopen(fileresp,"w"))==NULL) {
      }      printf("Problem with prevalence resultfile: %s\n", fileresp);
      printf("\n");      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
    }      exit(0);
    scanf("%d",i);*/    }
        freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
    /* Calculates basic frequencies. Computes observed prevalence at single age    j1=0;
        and prints on file fileres'p'. */    
   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax);    j=cptcoveff;
     if (cptcovn<1) {j=1;ncodemax[1]=1;}
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    first=1;
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    for(k1=1; k1<=j;k1++){
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */      for(i1=1; i1<=ncodemax[k1];i1++){
            j1++;
     /* For Powell, parameters are in a vector p[] starting at p[1]        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */          scanf("%d", i);*/
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */        for (i=-5; i<=nlstate+ndeath; i++)  
           for (jk=-5; jk<=nlstate+ndeath; jk++)  
     if(mle==1){            for(m=iagemin; m <= iagemax+3; m++)
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);              freq[i][jk][m]=0;
     }  
          for (i=1; i<=nlstate; i++)  
     /*--------- results files --------------*/        for(m=iagemin; m <= iagemax+3; m++)
     fprintf(ficres,"\ntitle=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, mle,weightopt,model);          prop[i][m]=0;
            
    jk=1;        dateintsum=0;
    fprintf(ficres,"# Parameters\n");        k2cpt=0;
    printf("# Parameters\n");        for (i=1; i<=imx; i++) {
    for(i=1,jk=1; i <=nlstate; i++){          bool=1;
      for(k=1; k <=(nlstate+ndeath); k++){          if  (cptcovn>0) {
        if (k != i)            for (z1=1; z1<=cptcoveff; z1++) 
          {              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
            printf("%d%d ",i,k);                bool=0;
            fprintf(ficres,"%1d%1d ",i,k);          }
            for(j=1; j <=ncovmodel; j++){          if (bool==1){
              printf("%f ",p[jk]);            for(m=firstpass; m<=lastpass; m++){
              fprintf(ficres,"%f ",p[jk]);              k2=anint[m][i]+(mint[m][i]/12.);
              jk++;              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
            }                if(agev[m][i]==0) agev[m][i]=iagemax+1;
            printf("\n");                if(agev[m][i]==1) agev[m][i]=iagemax+2;
            fprintf(ficres,"\n");                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
          }                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(mle==1){                }
     /* Computing hessian and covariance matrix */                
     ftolhess=ftol; /* Usually correct */                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
     hesscov(matcov, p, npar, delti, ftolhess, func);                  dateintsum=dateintsum+k2;
  }                  k2cpt++;
     fprintf(ficres,"# Scales\n");                }
     printf("# Scales\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(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
           for(k=1; k<=ncovmodel;k++){        pstamp(ficresp);
             printf(" %.5e",delti[jk]);        if  (cptcovn>0) {
             fprintf(ficres," %.5e",delti[jk]);          fprintf(ficresp, "\n#********** Variable "); 
             jk++;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           }          fprintf(ficresp, "**********\n#");
           printf("\n");        }
           fprintf(ficres,"\n");        for(i=1; i<=nlstate;i++) 
         }          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
       }        fprintf(ficresp, "\n");
       }        
            for(i=iagemin; i <= iagemax+3; i++){
     k=1;          if(i==iagemax+3){
     fprintf(ficres,"# Covariance\n");            fprintf(ficlog,"Total");
     printf("# Covariance\n");          }else{
     for(i=1;i<=npar;i++){            if(first==1){
       /*  if (k>nlstate) k=1;              first=0;
       i1=(i-1)/(ncovmodel*nlstate)+1;              printf("See log file for details...\n");
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);            }
       printf("%s%d%d",alph[k],i1,tab[i]);*/            fprintf(ficlog,"Age %d", i);
       fprintf(ficres,"%3d",i);          }
       printf("%3d",i);          for(jk=1; jk <=nlstate ; jk++){
       for(j=1; j<=i;j++){            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
         fprintf(ficres," %.5e",matcov[i][j]);              pp[jk] += freq[jk][m][i]; 
         printf(" %.5e",matcov[i][j]);          }
       }          for(jk=1; jk <=nlstate ; jk++){
       fprintf(ficres,"\n");            for(m=-1, pos=0; m <=0 ; m++)
       printf("\n");              pos += freq[jk][m][i];
       k++;            if(pp[jk]>=1.e-10){
     }              if(first==1){
                    printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
     while((c=getc(ficpar))=='#' && c!= EOF){              }
       ungetc(c,ficpar);              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
       fgets(line, MAXLINE, ficpar);            }else{
       puts(line);              if(first==1)
       fputs(line,ficparo);                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
     }              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
     ungetc(c,ficpar);            }
            }
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);  
              for(jk=1; jk <=nlstate ; jk++){
     if (fage <= 2) {            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
       bage = agemin;              pp[jk] += freq[jk][m][i];
       fage = agemax;          }       
     }          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
             pos += pp[jk];
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");            posprop += prop[jk][i];
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);          }
           for(jk=1; jk <=nlstate ; jk++){
                if(pos>=1.e-5){
 /*------------ gnuplot -------------*/              if(first==1)
 chdir(pathcd);                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   if((ficgp=fopen("graph.plt","w"))==NULL) {              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
     printf("Problem with file graph.gp");goto end;            }else{
   }              if(first==1)
 #ifdef windows                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   fprintf(ficgp,"cd \"%s\" \n",pathc);              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
 #endif            }
 m=pow(2,cptcoveff);            if( i <= iagemax){
                if(pos>=1.e-5){
  /* 1eme*/                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
   for (cpt=1; cpt<= nlstate ; cpt ++) {                /*probs[i][jk][j1]= pp[jk]/pos;*/
    for (k1=1; k1<= m ; k1 ++) {                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
               }
 #ifdef windows              else
     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(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
 #endif            }
 #ifdef unix          }
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);          
 #endif          for(jk=-1; jk <=nlstate+ndeath; jk++)
             for(m=-1; m <=nlstate+ndeath; m++)
 for (i=1; i<= nlstate ; i ++) {              if(freq[jk][m][i] !=0 ) {
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");              if(first==1)
   else fprintf(ficgp," \%%*lf (\%%*lf)");                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
 }                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);              }
     for (i=1; i<= nlstate ; i ++) {          if(i <= iagemax)
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");            fprintf(ficresp,"\n");
   else fprintf(ficgp," \%%*lf (\%%*lf)");          if(first==1)
 }            printf("Others in log...\n");
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);          fprintf(ficlog,"\n");
      for (i=1; i<= nlstate ; i ++) {        }
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      }
   else fprintf(ficgp," \%%*lf (\%%*lf)");    }
 }      dateintmean=dateintsum/k2cpt; 
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));   
 #ifdef unix    fclose(ficresp);
 fprintf(ficgp,"\nset ter gif small size 400,300");    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
 #endif    free_vector(pp,1,nlstate);
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
    }    /* End of Freq */
   }  }
   /*2 eme*/  
   /************ Prevalence ********************/
   for (k1=1; k1<= m ; k1 ++) {  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)
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);  {  
        /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
     for (i=1; i<= nlstate+1 ; i ++) {       in each health status at the date of interview (if between dateprev1 and dateprev2).
       k=2*i;       We still use firstpass and lastpass as another selection.
       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)");    int i, m, jk, k1, i1, j1, bool, z1,j;
   else fprintf(ficgp," \%%*lf (\%%*lf)");    double ***freq; /* Frequencies */
 }      double *pp, **prop;
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");    double pos,posprop; 
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);    double  y2; /* in fractional years */
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);    int iagemin, iagemax;
       for (j=1; j<= nlstate+1 ; j ++) {  
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    iagemin= (int) agemin;
         else fprintf(ficgp," \%%*lf (\%%*lf)");    iagemax= (int) agemax;
 }      /*pp=vector(1,nlstate);*/
       fprintf(ficgp,"\" t\"\" w l 0,");    prop=matrix(1,nlstate,iagemin,iagemax+3); 
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
       for (j=1; j<= nlstate+1 ; j ++) {    j1=0;
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    
   else fprintf(ficgp," \%%*lf (\%%*lf)");    j=cptcoveff;
 }      if (cptcovn<1) {j=1;ncodemax[1]=1;}
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");    
       else fprintf(ficgp,"\" t\"\" w l 0,");    for(k1=1; k1<=j;k1++){
     }      for(i1=1; i1<=ncodemax[k1];i1++){
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);        j1++;
   }        
          for (i=1; i<=nlstate; i++)  
   /*3eme*/          for(m=iagemin; m <= iagemax+3; m++)
             prop[i][m]=0.0;
   for (k1=1; k1<= m ; k1 ++) {       
     for (cpt=1; cpt<= nlstate ; cpt ++) {        for (i=1; i<=imx; i++) { /* Each individual */
       k=2+nlstate*(cpt-1);          bool=1;
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k1-1,k1-1,k,cpt);          if  (cptcovn>0) {
       for (i=1; i< nlstate ; i ++) {            for (z1=1; z1<=cptcoveff; z1++) 
         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
       }                bool=0;
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);          } 
     }          if (bool==1) { 
   }            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
                y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
   /* CV preval stat */              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
   for (k1=1; k1<= m ; k1 ++) {                if(agev[m][i]==0) agev[m][i]=iagemax+1;
     for (cpt=1; cpt<nlstate ; cpt ++) {                if(agev[m][i]==1) agev[m][i]=iagemax+2;
       k=3;                if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);                if (s[m][i]>0 && s[m][i]<=nlstate) { 
       for (i=1; i< nlstate ; i ++)                  /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
         fprintf(ficgp,"+$%d",k+i+1);                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);                  prop[s[m][i]][iagemax+3] += weight[i]; 
                      } 
       l=3+(nlstate+ndeath)*cpt;              }
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);            } /* end selection of waves */
       for (i=1; i< nlstate ; i ++) {          }
         l=3+(nlstate+ndeath)*cpt;        }
         fprintf(ficgp,"+$%d",l+i+1);        for(i=iagemin; i <= iagemax+3; i++){  
       }          
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);            for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);            posprop += prop[jk][i]; 
     }          } 
   }  
           for(jk=1; jk <=nlstate ; jk++){     
   /* proba elementaires */            if( i <=  iagemax){ 
    for(i=1,jk=1; i <=nlstate; i++){              if(posprop>=1.e-5){ 
     for(k=1; k <=(nlstate+ndeath); k++){                probs[i][jk][j1]= prop[jk][i]/posprop;
       if (k != i) {              } else
         for(j=1; j <=ncovmodel; j++){                printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\n",jk,i,j1,probs[i][jk][j1]);
           /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/            } 
           /*fprintf(ficgp,"%s",alph[1]);*/          }/* end jk */ 
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);        }/* end i */ 
           jk++;      } /* end i1 */
           fprintf(ficgp,"\n");    } /* end k1 */
         }    
       }    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
     }    /*free_vector(pp,1,nlstate);*/
     }    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
   }  /* End of prevalence */
   for(jk=1; jk <=m; jk++) {  
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);  /************* Waves Concatenation ***************/
    i=1;  
    for(k2=1; k2<=nlstate; k2++) {  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)
      k3=i;  {
      for(k=1; k<=(nlstate+ndeath); k++) {    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
        if (k != k2){       Death is a valid wave (if date is known).
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
 ij=1;       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
         for(j=3; j <=ncovmodel; j++) {       and mw[mi+1][i]. dh depends on stepm.
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {       */
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);  
             ij++;    int i, mi, m;
           }    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
           else       double sum=0., jmean=0.;*/
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    int first;
         }    int j, k=0,jk, ju, jl;
           fprintf(ficgp,")/(1");    double sum=0.;
            first=0;
         for(k1=1; k1 <=nlstate; k1++){      jmin=1e+5;
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);    jmax=-1;
 ij=1;    jmean=0.;
           for(j=3; j <=ncovmodel; j++){    for(i=1; i<=imx; i++){
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {      mi=0;
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);      m=firstpass;
             ij++;      while(s[m][i] <= nlstate){
           }        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
           else          mw[++mi][i]=m;
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);        if(m >=lastpass)
           }          break;
           fprintf(ficgp,")");        else
         }          m++;
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);      }/* end while */
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");      if (s[m][i] > nlstate){
         i=i+ncovmodel;        mi++;     /* Death is another wave */
        }        /* if(mi==0)  never been interviewed correctly before death */
      }           /* Only death is a correct wave */
    }        mw[mi][i]=m;
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);      }
   }  
          wav[i]=mi;
   fclose(ficgp);      if(mi==0){
            nbwarn++;
 chdir(path);        if(first==0){
     free_matrix(agev,1,maxwav,1,imx);          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
     free_ivector(wav,1,imx);          first=1;
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);        }
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);        if(first==1){
              fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
     free_imatrix(s,1,maxwav+1,1,n);        }
          } /* end mi==0 */
        } /* End individuals */
     free_ivector(num,1,n);  
     free_vector(agedc,1,n);    for(i=1; i<=imx; i++){
     free_vector(weight,1,n);      for(mi=1; mi<wav[i];mi++){
     /*free_matrix(covar,1,NCOVMAX,1,n);*/        if (stepm <=0)
     fclose(ficparo);          dh[mi][i]=1;
     fclose(ficres);        else{
     /*  }*/          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
                if (agedc[i] < 2*AGESUP) {
    /*________fin mle=1_________*/              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
                  if(j==0) j=1;  /* Survives at least one month after exam */
               else if(j<0){
                  nberr++;
     /* No more information from the sample is required now */                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]);
   /* Reads comments: lines beginning with '#' */                j=1; /* Temporary Dangerous patch */
   while((c=getc(ficpar))=='#' && c!= EOF){                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);
     ungetc(c,ficpar);                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]);
     fgets(line, MAXLINE, ficpar);                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);
     puts(line);              }
     fputs(line,ficparo);              k=k+1;
   }              if (j >= jmax){
   ungetc(c,ficpar);                jmax=j;
                  ijmax=i;
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);              }
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);              if (j <= jmin){
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);                jmin=j;
 /*--------- index.htm --------*/                ijmin=i;
               }
   if((fichtm=fopen("index.htm","w"))==NULL)    {              sum=sum+j;
     printf("Problem with index.htm \n");goto end;              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
   }              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
             }
  fprintf(fichtm,"<body><ul> Imach, Version 0.64a<hr> <li>Outputs files<br><br>\n          }
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n          else{
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>  /*        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]); */
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>  
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>            k=k+1;
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>            if (j >= jmax) {
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>              jmax=j;
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>              ijmax=i;
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br><br>",fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);            }
             else if (j <= jmin){
  fprintf(fichtm," <li>Graphs</li>\n<p>");              jmin=j;
               ijmin=i;
  m=cptcoveff;            }
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
             /*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]);*/
  j1=0;            if(j<0){
  for(k1=1; k1<=m;k1++){              nberr++;
    for(i1=1; i1<=ncodemax[k1];i1++){              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]);
        j1++;              fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
        if (cptcovn > 0) {            }
          fprintf(fichtm,"<hr>************ Results for covariates");            sum=sum+j;
          for (cpt=1; cpt<=cptcoveff;cpt++)          }
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[j1][cpt]]);          jk= j/stepm;
          fprintf(fichtm," ************\n<hr>");          jl= j -jk*stepm;
        }          ju= j -(jk+1)*stepm;
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);                if(jl==0){
        for(cpt=1; cpt<nlstate;cpt++){              dh[mi][i]=jk;
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>              bh[mi][i]=0;
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);            }else{ /* We want a negative bias in order to only have interpolation ie
        }                    * at the price of an extra matrix product in likelihood */
     for(cpt=1; cpt<=nlstate;cpt++) {              dh[mi][i]=jk+1;
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident              bh[mi][i]=ju;
 interval) in state (%d): v%s%d%d.gif <br>            }
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);            }else{
      }            if(jl <= -ju){
      for(cpt=1; cpt<=nlstate;cpt++) {              dh[mi][i]=jk;
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>              bh[mi][i]=jl;       /* bias is positive if real duration
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);                                   * is higher than the multiple of stepm and negative otherwise.
      }                                   */
      fprintf(fichtm,"\n<br>- Total life expectancy by age and            }
 health expectancies in states (1) and (2): e%s%d.gif<br>            else{
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);              dh[mi][i]=jk+1;
 fprintf(fichtm,"\n</body>");              bh[mi][i]=ju;
    }            }
  }            if(dh[mi][i]==0){
 fclose(fichtm);              dh[mi][i]=1; /* At least one step */
               bh[mi][i]=ju; /* At least one step */
   /*--------------- Prevalence limit --------------*/              /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
              }
   strcpy(filerespl,"pl");          } /* end if mle */
   strcat(filerespl,fileres);        }
   if((ficrespl=fopen(filerespl,"w"))==NULL) {      } /* end wave */
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;    }
   }    jmean=sum/k;
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);    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);
   fprintf(ficrespl,"#Prevalence limit\n");    fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
   fprintf(ficrespl,"#Age ");   }
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);  
   fprintf(ficrespl,"\n");  /*********** Tricode ****************************/
    void tricode(int *Tvar, int **nbcode, int imx)
   prlim=matrix(1,nlstate,1,nlstate);  {
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    /*      Tvar[i]=atoi(stre); /* find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 */
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    int Ndum[20],ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    int cptcode=0;
   k=0;    cptcoveff=0; 
   agebase=agemin;   
   agelim=agemax;    for (k=0; k<maxncov; k++) Ndum[k]=0;
   ftolpl=1.e-10;    for (k=1; k<=7; k++) ncodemax[k]=0; /* Horrible constant again */
   i1=cptcoveff;  
   if (cptcovn < 1){i1=1;}    for (j=1; j<=(cptcovn+2*cptcovprod); j++) { /* For each covariate */
       for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
   for(cptcov=1;cptcov<=i1;cptcov++){                                 modality*/ 
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual, might be -1*/
         k=k+1;        Ndum[ij]++; /*counts the occurence of this modality */
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
         fprintf(ficrespl,"\n#******");        if (ij > cptcode) cptcode=ij; /* getting the maximum value of the modality of the covariate  (should be 0 or 1 now) 
         for(j=1;j<=cptcoveff;j++)                                         Tvar[j]. If V=sex and male is 0 and 
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                                         female is 1, then  cptcode=1.*/
         fprintf(ficrespl,"******\n");      }
          
         for (age=agebase; age<=agelim; age++){      for (i=0; i<=cptcode; i++) { /* i=-1 ?*/
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);        if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j
           fprintf(ficrespl,"%.0f",age );                                         th covariate. In fact
           for(i=1; i<=nlstate;i++)                                         ncodemax[j]=2
           fprintf(ficrespl," %.5f", prlim[i][i]);                                         (dichotom. variables only) but
           fprintf(ficrespl,"\n");                                         it can be more */
         }      } /* Ndum[-1] number of undefined modalities */
       }  
     }      ij=1; 
   fclose(ficrespl);      for (i=1; i<=ncodemax[j]; i++) { /* i= 1 to 2 */
   /*------------- h Pij x at various ages ------------*/        for (k=0; k<= maxncov; k++) { /* k=-1 ?*/
            if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);            nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode. 
   if((ficrespij=fopen(filerespij,"w"))==NULL) {                                       k is a modality. If we have model=V1+V1*sex 
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;                                       then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
   }            ij++;
   printf("Computing pij: result on file '%s' \n", filerespij);          }
            if (ij > ncodemax[j]) break; 
   stepsize=(int) (stepm+YEARM-1)/YEARM;        }  
   if (stepm<=24) stepsize=2;      } 
     }  
   agelim=AGESUP;  
   hstepm=stepsize*YEARM; /* Every year of age */   for (k=0; k< maxncov; k++) Ndum[k]=0;
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */  
     for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */
   k=0;     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
   for(cptcov=1;cptcov<=i1;cptcov++){     ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){     Ndum[ij]++;
       k=k+1;   }
         fprintf(ficrespij,"\n#****** ");  
         for(j=1;j<=cptcoveff;j++)   ij=1;
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);   for (i=1; i<= maxncov; i++) {
         fprintf(ficrespij,"******\n");     if((Ndum[i]!=0) && (i<=ncovcol)){
               Tvaraff[ij]=i; /*For printing */
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */       ij++;
           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);   ij--;
           oldm=oldms;savm=savms;   cptcoveff=ij; /*Number of simple covariates*/
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);    }
           fprintf(ficrespij,"# Age");  
           for(i=1; i<=nlstate;i++)  /*********** Health Expectancies ****************/
             for(j=1; j<=nlstate+ndeath;j++)  
               fprintf(ficrespij," %1d-%1d",i,j);  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(ficrespij,"\n");  
           for (h=0; h<=nhstepm; h++){  {
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );    /* Health expectancies, no variances */
             for(i=1; i<=nlstate;i++)    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
               for(j=1; j<=nlstate+ndeath;j++)    int nhstepma, nstepma; /* Decreasing with age */
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);    double age, agelim, hf;
             fprintf(ficrespij,"\n");    double ***p3mat;
           }    double eip;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
           fprintf(ficrespij,"\n");    pstamp(ficreseij);
         }    fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
     }    fprintf(ficreseij,"# Age");
   }    for(i=1; i<=nlstate;i++){
       for(j=1; j<=nlstate;j++){
   fclose(ficrespij);        fprintf(ficreseij," e%1d%1d ",i,j);
       }
   /*---------- Health expectancies and variances ------------*/      fprintf(ficreseij," e%1d. ",i);
     }
   strcpy(filerest,"t");    fprintf(ficreseij,"\n");
   strcat(filerest,fileres);  
   if((ficrest=fopen(filerest,"w"))==NULL) {    
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;    if(estepm < stepm){
   }      printf ("Problem %d lower than %d\n",estepm, stepm);
   printf("Computing Total LEs with variances: file '%s' \n", filerest);    }
     else  hstepm=estepm;   
     /* We compute the life expectancy from trapezoids spaced every estepm months
   strcpy(filerese,"e");     * This is mainly to measure the difference between two models: for example
   strcat(filerese,fileres);     * if stepm=24 months pijx are given only every 2 years and by summing them
   if((ficreseij=fopen(filerese,"w"))==NULL) {     * we are calculating an estimate of the Life Expectancy assuming a linear 
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);     * progression in between and thus overestimating or underestimating according
   }     * to the curvature of the survival function. If, for the same date, we 
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);     * estimate the model with stepm=1 month, we can keep estepm to 24 months
      * to compare the new estimate of Life expectancy with the same linear 
  strcpy(fileresv,"v");     * hypothesis. A more precise result, taking into account a more precise
   strcat(fileresv,fileres);     * curvature will be obtained if estepm is as small as stepm. */
   if((ficresvij=fopen(fileresv,"w"))==NULL) {  
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);    /* 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. 
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);       nhstepm is the number of hstepm from age to agelim 
        nstepm is the number of stepm from age to agelin. 
   k=0;       Look at hpijx to understand the reason of that which relies in memory size
   for(cptcov=1;cptcov<=i1;cptcov++){       and note for a fixed period like estepm months */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
       k=k+1;       survival function given by stepm (the optimization length). Unfortunately it
       fprintf(ficrest,"\n#****** ");       means that if the survival funtion is printed only each two years of age and if
       for(j=1;j<=cptcoveff;j++)       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);       results. So we changed our mind and took the option of the best precision.
       fprintf(ficrest,"******\n");    */
     hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
       fprintf(ficreseij,"\n#****** ");  
       for(j=1;j<=cptcoveff;j++)    agelim=AGESUP;
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);    /* If stepm=6 months */
       fprintf(ficreseij,"******\n");      /* Computed by stepm unit matrices, product of hstepm matrices, stored
          in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
       fprintf(ficresvij,"\n#****** ");      
       for(j=1;j<=cptcoveff;j++)  /* nhstepm age range expressed in number of stepm */
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);    nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
       fprintf(ficresvij,"******\n");    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     /* if (stepm >= YEARM) hstepm=1;*/
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       oldm=oldms;savm=savms;    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);    
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    for (age=bage; age<=fage; age ++){ 
       oldm=oldms;savm=savms;      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
            /* if (stepm >= YEARM) hstepm=1;*/
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);  
       fprintf(ficrest,"\n");      /* If stepm=6 months */
              /* Computed by stepm unit matrices, product of hstepma matrices, stored
       hf=1;         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
       if (stepm >= YEARM) hf=stepm/YEARM;      
       epj=vector(1,nlstate+1);      hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
       for(age=bage; age <=fage ;age++){      
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
         fprintf(ficrest," %.0f",age);      
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){      printf("%d|",(int)age);fflush(stdout);
           for(i=1, epj[j]=0.;i <=nlstate;i++) {      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];      
           }      /* Computing expectancies */
           epj[nlstate+1] +=epj[j];      for(i=1; i<=nlstate;i++)
         }        for(j=1; j<=nlstate;j++)
         for(i=1, vepp=0.;i <=nlstate;i++)          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
           for(j=1;j <=nlstate;j++)            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
             vepp += vareij[i][j][(int)age];            
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));            /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
         for(j=1;j <=nlstate;j++){  
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));          }
         }  
         fprintf(ficrest,"\n");      fprintf(ficreseij,"%3.0f",age );
       }      for(i=1; i<=nlstate;i++){
     }        eip=0;
   }        for(j=1; j<=nlstate;j++){
                  eip +=eij[i][j][(int)age];
  fclose(ficreseij);          fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
  fclose(ficresvij);        }
   fclose(ficrest);        fprintf(ficreseij,"%9.4f", eip );
   fclose(ficpar);      }
   free_vector(epj,1,nlstate+1);      fprintf(ficreseij,"\n");
   /*  scanf("%d ",i); */      
     }
   /*------- Variance limit prevalence------*/      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     printf("\n");
 strcpy(fileresvpl,"vpl");    fprintf(ficlog,"\n");
   strcat(fileresvpl,fileres);    
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {  }
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);  
     exit(0);  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[] )
   }  
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);  {
     /* Covariances of health expectancies eij and of total life expectancies according
  k=0;     to initial status i, ei. .
  for(cptcov=1;cptcov<=i1;cptcov++){    */
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
      k=k+1;    int nhstepma, nstepma; /* Decreasing with age */
      fprintf(ficresvpl,"\n#****** ");    double age, agelim, hf;
      for(j=1;j<=cptcoveff;j++)    double ***p3matp, ***p3matm, ***varhe;
        fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    double **dnewm,**doldm;
      fprintf(ficresvpl,"******\n");    double *xp, *xm;
          double **gp, **gm;
      varpl=matrix(1,nlstate,(int) bage, (int) fage);    double ***gradg, ***trgradg;
      oldm=oldms;savm=savms;    int theta;
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);  
    }    double eip, vip;
  }  
     varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
   fclose(ficresvpl);    xp=vector(1,npar);
     xm=vector(1,npar);
   /*---------- End : free ----------------*/    dnewm=matrix(1,nlstate*nlstate,1,npar);
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
      
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);    pstamp(ficresstdeij);
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);    fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
      fprintf(ficresstdeij,"# Age");
      for(i=1; i<=nlstate;i++){
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);      for(j=1; j<=nlstate;j++)
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);        fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);      fprintf(ficresstdeij," e%1d. ",i);
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);    }
      fprintf(ficresstdeij,"\n");
   free_matrix(matcov,1,npar,1,npar);  
   free_vector(delti,1,npar);    pstamp(ficrescveij);
      fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    fprintf(ficrescveij,"# Age");
     for(i=1; i<=nlstate;i++)
   printf("End of Imach\n");      for(j=1; j<=nlstate;j++){
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */        cptj= (j-1)*nlstate+i;
          for(i2=1; i2<=nlstate;i2++)
   /* 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);*/          for(j2=1; j2<=nlstate;j2++){
   /*printf("Total time was %d uSec.\n", total_usecs);*/            cptj2= (j2-1)*nlstate+i2;
   /*------ End -----------*/            if(cptj2 <= cptj)
               fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
  end:          }
 #ifdef windows      }
  chdir(pathcd);    fprintf(ficrescveij,"\n");
 #endif    
  system("wgnuplot graph.plt");    if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
 #ifdef windows    }
   while (z[0] != 'q') {    else  hstepm=estepm;   
     chdir(pathcd);    /* We compute the life expectancy from trapezoids spaced every estepm months
     printf("\nType e to edit output files, c to start again, and q for exiting: ");     * This is mainly to measure the difference between two models: for example
     scanf("%s",z);     * if stepm=24 months pijx are given only every 2 years and by summing them
     if (z[0] == 'c') system("./imach");     * we are calculating an estimate of the Life Expectancy assuming a linear 
     else if (z[0] == 'e') {     * progression in between and thus overestimating or underestimating according
       chdir(path);     * to the curvature of the survival function. If, for the same date, we 
       system("index.htm");     * estimate the model with stepm=1 month, we can keep estepm to 24 months
     }     * to compare the new estimate of Life expectancy with the same linear 
     else if (z[0] == 'q') exit(0);     * hypothesis. A more precise result, taking into account a more precise
   }     * curvature will be obtained if estepm is as small as stepm. */
 #endif  
 }    /* For example we decided to compute the life expectancy with the smallest unit */
     /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
        nhstepm is the number of hstepm from age to agelim 
        nstepm is the number of stepm from age to agelin. 
        Look at hpijx to understand the reason of that which relies in memory size
        and note for a fixed period like estepm months */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
        survival function given by stepm (the optimization length). Unfortunately it
        means that if the survival funtion is printed only each two years of age and if
        you sum them up and add 1 year (area under the trapezoids) you won't get the same 
        results. So we changed our mind and took the option of the best precision.
     */
     hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   
     /* If stepm=6 months */
     /* nhstepm age range expressed in number of stepm */
     agelim=AGESUP;
     nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     /* if (stepm >= YEARM) hstepm=1;*/
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     
     p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     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);
     gm=matrix(0,nhstepm,1,nlstate*nlstate);
   
     for (age=bage; age<=fage; age ++){ 
       nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
       /* 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 */
       /* Computed by stepm unit matrices, product of hstepma matrices, stored
          in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
       
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   
       /* Computing  Variances of health expectancies */
       /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
          decrease memory allocation */
       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ 
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
           xm[i] = x[i] - (i==theta ?delti[theta]:0);
         }
         hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
         hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
     
         for(j=1; j<= nlstate; j++){
           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.;
               gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
             }
           }
         }
        
         for(ij=1; ij<= nlstate*nlstate; ij++)
           for(h=0; h<=nhstepm-1; h++){
             gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
           }
       }/* End theta */
       
       
       for(h=0; h<=nhstepm-1; h++)
         for(j=1; j<=nlstate*nlstate;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.;
   
        printf("%d|",(int)age);fflush(stdout);
        fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
        for(h=0;h<=nhstepm-1;h++){
         for(k=0;k<=nhstepm-1;k++){
           matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
           matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
           for(ij=1;ij<=nlstate*nlstate;ij++)
             for(ji=1;ji<=nlstate*nlstate;ji++)
               varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
         }
       }
   
       /* Computing expectancies */
       hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++)
           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;
             
             /* 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]);*/
   
           }
   
       fprintf(ficresstdeij,"%3.0f",age );
       for(i=1; i<=nlstate;i++){
         eip=0.;
         vip=0.;
         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) */
             vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
           fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
         }
         fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
       }
       fprintf(ficresstdeij,"\n");
   
       fprintf(ficrescveij,"%3.0f",age );
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
           cptj= (j-1)*nlstate+i;
           for(i2=1; i2<=nlstate;i2++)
             for(j2=1; j2<=nlstate;j2++){
               cptj2= (j2-1)*nlstate+i2;
               if(cptj2 <= cptj)
                 fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
             }
         }
       fprintf(ficrescveij,"\n");
      
     }
     free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
     free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
     free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
     free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     printf("\n");
     fprintf(ficlog,"\n");
   
     free_vector(xm,1,npar);
     free_vector(xp,1,npar);
     free_matrix(dnewm,1,nlstate*nlstate,1,npar);
     free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
     free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
   }
   
   /************ 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);*/
     /* double **newm;*/
     double **dnewm,**doldm;
     double **dnewmp,**doldmp;
     int i, j, nhstepm, hstepm, h, nstepm ;
     int k, cptcode;
     double *xp;
     double **gp, **gm;  /* for var eij */
     double ***gradg, ***trgradg; /*for var eij */
     double **gradgp, **trgradgp; /* for var p point j */
     double *gpp, *gmp; /* for var p point j */
     double **varppt; /* for var p point j nlstate to nlstate+ndeath */
     double ***p3mat;
     double age,agelim, hf;
     double ***mobaverage;
     int theta;
     char digit[4];
     char digitp[25];
   
     char fileresprobmorprev[FILENAMELENGTH];
   
     if(popbased==1){
       if(mobilav!=0)
         strcpy(digitp,"-populbased-mobilav-");
       else strcpy(digitp,"-populbased-nomobil-");
     }
     else 
       strcpy(digitp,"-stablbased-");
   
     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);
       }
     }
   
     strcpy(fileresprobmorprev,"prmorprev"); 
     sprintf(digit,"%-d",ij);
     /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
     strcat(fileresprobmorprev,digit); /* Tvar to be done */
     strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
     strcat(fileresprobmorprev,fileres);
     if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobmorprev);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
     }
     printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
    
     fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     pstamp(ficresprobmorprev);
     fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
     fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
       fprintf(ficresprobmorprev," p.%-d SE",j);
       for(i=1; i<=nlstate;i++)
         fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
     }  
     fprintf(ficresprobmorprev,"\n");
     fprintf(ficgp,"\n# Routine varevsij");
     /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
     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);
   /*   } */
     varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     pstamp(ficresvij);
     fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
     if(popbased==1)
       fprintf(ficresvij,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d\n",mobilav);
     else
       fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
     fprintf(ficresvij,"# Age");
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++)
         fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
     fprintf(ficresvij,"\n");
   
     xp=vector(1,npar);
     dnewm=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
     dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
     doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   
     gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
     gpp=vector(nlstate+1,nlstate+ndeath);
     gmp=vector(nlstate+1,nlstate+ndeath);
     trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
     /* For example we decided to compute the life expectancy with the smallest unit */
     /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
        nhstepm is the number of hstepm from age to agelim 
        nstepm is the number of stepm from age to agelin. 
        Look at function hpijx to understand why (it is linked to memory size questions) */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
        survival function given by stepm (the optimization length). Unfortunately it
        means that if the survival funtion is printed every two years of age and if
        you sum them up and add 1 year (area under the trapezoids) you won't get the same 
        results. So we changed our mind and took the option of the best precision.
     */
     hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     agelim = AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
       gp=matrix(0,nhstepm,1,nlstate);
       gm=matrix(0,nhstepm,1,nlstate);
   
   
       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   
         if (popbased==1) {
           if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=mobaverage[(int)age][i][ij];
           }
         }
     
         for(j=1; j<= nlstate; j++){
           for(h=0; h<=nhstepm; h++){
             for(i=1, gp[h][j]=0.;i<=nlstate;i++)
               gp[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
         }
         /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
         */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
           for(i=1,gpp[j]=0.; i<= nlstate; i++)
             gpp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
         /* end probability of death */
   
         for(i=1; i<=npar; i++) /* Computes gradient x - delta */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
    
         if (popbased==1) {
           if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=mobaverage[(int)age][i][ij];
           }
         }
   
         for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
           for(h=0; h<=nhstepm; h++){
             for(i=1, gm[h][j]=0.;i<=nlstate;i++)
               gm[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
         }
         /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
         */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
           for(i=1,gmp[j]=0.; i<= nlstate; i++)
            gmp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
         /* end probability of death */
   
         for(j=1; j<= nlstate; j++) /* vareij */
           for(h=0; h<=nhstepm; h++){
             gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
           }
   
         for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
           gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
         }
   
       } /* End theta */
   
       trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   
       for(h=0; h<=nhstepm; h++) /* veij */
         for(j=1; j<=nlstate;j++)
           for(theta=1; theta <=npar; theta++)
             trgradg[h][j][theta]=gradg[h][theta][j];
   
       for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
         for(theta=1; theta <=npar; theta++)
           trgradgp[j][theta]=gradgp[theta][j];
     
   
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       for(i=1;i<=nlstate;i++)
         for(j=1;j<=nlstate;j++)
           vareij[i][j][(int)age] =0.;
   
       for(h=0;h<=nhstepm;h++){
         for(k=0;k<=nhstepm;k++){
           matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
           matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
           for(i=1;i<=nlstate;i++)
             for(j=1;j<=nlstate;j++)
               vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
         }
       }
     
       /* pptj */
       matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
       matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
       for(j=nlstate+1;j<=nlstate+ndeath;j++)
         for(i=nlstate+1;i<=nlstate+ndeath;i++)
           varppt[j][i]=doldmp[j][i];
       /* end ppptj */
       /*  x centered again */
       hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
       prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
    
       if (popbased==1) {
         if(mobilav ==0){
           for(i=1; i<=nlstate;i++)
             prlim[i][i]=probs[(int)age][i][ij];
         }else{ /* mobilav */ 
           for(i=1; i<=nlstate;i++)
             prlim[i][i]=mobaverage[(int)age][i][ij];
         }
       }
                
       /* This for computing probability of death (h=1 means
          computed over hstepm (estepm) matrices product = hstepm*stepm months) 
          as a weighted average of prlim.
       */
       for(j=nlstate+1;j<=nlstate+ndeath;j++){
         for(i=1,gmp[j]=0.;i<= nlstate; i++) 
           gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
       }    
       /* end probability of death */
   
       fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
       for(j=nlstate+1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
         for(i=1; i<=nlstate;i++){
           fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
         }
       } 
       fprintf(ficresprobmorprev,"\n");
   
       fprintf(ficresvij,"%.0f ",age );
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
           fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
         }
       fprintf(ficresvij,"\n");
       free_matrix(gp,0,nhstepm,1,nlstate);
       free_matrix(gm,0,nhstepm,1,nlstate);
       free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
       free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
       free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     } /* End age */
     free_vector(gpp,nlstate+1,nlstate+ndeath);
     free_vector(gmp,nlstate+1,nlstate+ndeath);
     free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
     free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     fprintf(ficgp,"\nunset parametric;unset label; set ter png small;set size 0.65, 0.65");
     /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
     fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
   /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
   /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
   /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
     fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
     fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
     fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
     /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
   */
   /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
     fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
   
     free_vector(xp,1,npar);
     free_matrix(doldm,1,nlstate,1,nlstate);
     free_matrix(dnewm,1,nlstate,1,npar);
     free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
     free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficresprobmorprev);
     fflush(ficgp);
     fflush(fichtm); 
   }  /* end varevsij */
   
   /************ Variance of prevlim ******************/
   void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, char strstart[])
   {
     /* Variance of prevalence limit */
     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
     double **newm;
     double **dnewm,**doldm;
     int i, j, nhstepm, hstepm;
     int k, cptcode;
     double *xp;
     double *gp, *gm;
     double **gradg, **trgradg;
     double age,agelim;
     int theta;
     
     pstamp(ficresvpl);
     fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
     fprintf(ficresvpl,"# Age");
     for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %1d-%1d",i,i);
     fprintf(ficresvpl,"\n");
   
     xp=vector(1,npar);
     dnewm=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
     
     hstepm=1*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
     agelim = AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       if (stepm >= YEARM) hstepm=1;
       nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
       gradg=matrix(1,npar,1,nlstate);
       gp=vector(1,nlstate);
       gm=vector(1,nlstate);
   
       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient */
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=nlstate;i++)
           gp[i] = prlim[i][i];
       
         for(i=1; i<=npar; i++) /* Computes gradient */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=nlstate;i++)
           gm[i] = prlim[i][i];
   
         for(i=1;i<=nlstate;i++)
           gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
       } /* End theta */
   
       trgradg =matrix(1,nlstate,1,npar);
   
       for(j=1; j<=nlstate;j++)
         for(theta=1; theta <=npar; theta++)
           trgradg[j][theta]=gradg[theta][j];
   
       for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] =0.;
       matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
       matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
       for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   
       fprintf(ficresvpl,"%.0f ",age );
       for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
       fprintf(ficresvpl,"\n");
       free_vector(gp,1,nlstate);
       free_vector(gm,1,nlstate);
       free_matrix(gradg,1,npar,1,nlstate);
       free_matrix(trgradg,1,nlstate,1,npar);
     } /* End age */
   
     free_vector(xp,1,npar);
     free_matrix(doldm,1,nlstate,1,npar);
     free_matrix(dnewm,1,nlstate,1,nlstate);
   
   }
   
   /************ Variance of one-step probabilities  ******************/
   void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
   {
     int i, j=0,  i1, k1, l1, t, tj;
     int k2, l2, j1,  z1;
     int k=0,l, cptcode;
     int first=1, first1;
     double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
     double **dnewm,**doldm;
     double *xp;
     double *gp, *gm;
     double **gradg, **trgradg;
     double **mu;
     double age,agelim, cov[NCOVMAX];
     double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
     int theta;
     char fileresprob[FILENAMELENGTH];
     char fileresprobcov[FILENAMELENGTH];
     char fileresprobcor[FILENAMELENGTH];
   
     double ***varpij;
   
     strcpy(fileresprob,"prob"); 
     strcat(fileresprob,fileres);
     if((ficresprob=fopen(fileresprob,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprob);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
     }
     strcpy(fileresprobcov,"probcov"); 
     strcat(fileresprobcov,fileres);
     if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcov);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
     }
     strcpy(fileresprobcor,"probcor"); 
     strcat(fileresprobcor,fileres);
     if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcor);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
     }
     printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     pstamp(ficresprob);
     fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
     fprintf(ficresprob,"# Age");
     pstamp(ficresprobcov);
     fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
     fprintf(ficresprobcov,"# Age");
     pstamp(ficresprobcor);
     fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
     fprintf(ficresprobcor,"# Age");
   
   
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprob," p%1d-%1d (SE)",i,j);
         fprintf(ficresprobcov," p%1d-%1d ",i,j);
         fprintf(ficresprobcor," p%1d-%1d ",i,j);
       }  
    /* fprintf(ficresprob,"\n");
     fprintf(ficresprobcov,"\n");
     fprintf(ficresprobcor,"\n");
    */
     xp=vector(1,npar);
     dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
     varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
     first=1;
     fprintf(ficgp,"\n# Routine varprob");
     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
     fprintf(fichtm,"\n");
   
     fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
     fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
     file %s<br>\n",optionfilehtmcov);
     fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
   and drawn. It helps understanding how is the covariance between two incidences.\
    They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
     fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
   It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
   would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
   standard deviations wide on each axis. <br>\
    Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
    and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
   To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
   
     cov[1]=1;
     tj=cptcoveff;
     if (cptcovn<1) {tj=1;ncodemax[1]=1;}
     j1=0;
     for(t=1; t<=tj;t++){
       for(i1=1; i1<=ncodemax[t];i1++){ 
         j1++;
         if  (cptcovn>0) {
           fprintf(ficresprob, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprob, "**********\n#\n");
           fprintf(ficresprobcov, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcov, "**********\n#\n");
           
           fprintf(ficgp, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficgp, "**********\n#\n");
           
           
           fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
           
           fprintf(ficresprobcor, "\n#********** Variable ");    
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcor, "**********\n#");    
         }
         
         for (age=bage; age<=fage; age ++){ 
           cov[2]=age;
           for (k=1; k<=cptcovn;k++) {
             cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
           }
           for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
           for (k=1; k<=cptcovprod;k++)
             cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
           
           gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
           trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
           gp=vector(1,(nlstate)*(nlstate+ndeath));
           gm=vector(1,(nlstate)*(nlstate+ndeath));
       
           for(theta=1; theta <=npar; theta++){
             for(i=1; i<=npar; i++)
               xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
             
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             
             k=0;
             for(i=1; i<= (nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gp[k]=pmmij[i][j];
               }
             }
             
             for(i=1; i<=npar; i++)
               xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
       
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             k=0;
             for(i=1; i<=(nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gm[k]=pmmij[i][j];
               }
             }
        
             for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
               gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
           }
   
           for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
             for(theta=1; theta <=npar; theta++)
               trgradg[j][theta]=gradg[theta][j];
           
           matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
           matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
           free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
           free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
           free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
           free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   
           pmij(pmmij,cov,ncovmodel,x,nlstate);
           
           k=0;
           for(i=1; i<=(nlstate); i++){
             for(j=1; j<=(nlstate+ndeath);j++){
               k=k+1;
               mu[k][(int) age]=pmmij[i][j];
             }
           }
           for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
             for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
               varpij[i][j][(int)age] = doldm[i][j];
   
           /*printf("\n%d ",(int)age);
             for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             }*/
   
           fprintf(ficresprob,"\n%d ",(int)age);
           fprintf(ficresprobcov,"\n%d ",(int)age);
           fprintf(ficresprobcor,"\n%d ",(int)age);
   
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
             fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
             fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
           }
           i=0;
           for (k=1; k<=(nlstate);k++){
             for (l=1; l<=(nlstate+ndeath);l++){ 
               i=i++;
               fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
               fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
               for (j=1; j<=i;j++){
                 fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
                 fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
               }
             }
           }/* end of loop for state */
         } /* end of loop for age */
   
         /* Confidence intervalle of pij  */
         /*
           fprintf(ficgp,"\nunset parametric;unset label");
           fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
           fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
           fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
           fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
           fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
           fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
         */
   
         /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
         first1=1;
         for (k2=1; k2<=(nlstate);k2++){
           for (l2=1; l2<=(nlstate+ndeath);l2++){ 
             if(l2==k2) continue;
             j=(k2-1)*(nlstate+ndeath)+l2;
             for (k1=1; k1<=(nlstate);k1++){
               for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                 if(l1==k1) continue;
                 i=(k1-1)*(nlstate+ndeath)+l1;
                 if(i<=j) continue;
                 for (age=bage; age<=fage; age ++){ 
                   if ((int)age %5==0){
                     v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                     v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     mu1=mu[i][(int) age]/stepm*YEARM ;
                     mu2=mu[j][(int) age]/stepm*YEARM;
                     c12=cv12/sqrt(v1*v2);
                     /* Computing eigen value of matrix of covariance */
                     lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     /* Eigen vectors */
                     v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                     /*v21=sqrt(1.-v11*v11); *//* error */
                     v21=(lc1-v1)/cv12*v11;
                     v12=-v21;
                     v22=v11;
                     tnalp=v21/v11;
                     if(first1==1){
                       first1=0;
                       printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     }
                     fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     /*printf(fignu*/
                     /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                     /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                     if(first==1){
                       first=0;
                       fprintf(ficgp,"\nset parametric;unset label");
                       fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
                       fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
                       fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
    :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
   %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }else{
                       first=0;
                       fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }/* if first */
                   } /* age mod 5 */
                 } /* end loop age */
                 fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                 first=1;
               } /*l12 */
             } /* k12 */
           } /*l1 */
         }/* k1 */
       } /* loop covariates */
     }
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
     free_vector(xp,1,npar);
     fclose(ficresprob);
     fclose(ficresprobcov);
     fclose(ficresprobcor);
     fflush(ficgp);
     fflush(fichtmcov);
   }
   
   
   /******************* Printing html file ***********/
   void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                     int popforecast, int estepm ,\
                     double jprev1, double mprev1,double anprev1, \
                     double jprev2, double mprev2,double anprev2){
     int jj1, k1, i1, cpt;
   
      fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
      <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
   </ul>");
      fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
    - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
              jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
      fprintf(fichtm,"\
    - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
              stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
      fprintf(fichtm,"\
    - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
              subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
      fprintf(fichtm,"\
    - (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n",
              estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
      fprintf(fichtm,"\
    - Population projections by age and states: \
      <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
   
   fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
    m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        /* Pij */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d1.png\">%s%d1.png</a><br> \
   <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
        /* Quasi-incidences */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
    before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d2.png\">%s%d2.png</a><br> \
   <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
          /* Period (stable) prevalence in each health state */
          for(cpt=1; cpt<nlstate;cpt++){
            fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
   <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
          }
        for(cpt=1; cpt<=nlstate;cpt++) {
           fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
   <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
        }
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
   
   
    fprintf(fichtm,"\
   \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
    - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
   
    fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
    fprintf(fichtm,"\
    - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
   
    fprintf(fichtm,"\
    - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
    fprintf(fichtm,"\
    - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
            estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
    fprintf(fichtm,"\
    - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",
            estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
    fprintf(fichtm,"\
    - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
            subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   
   /*  if(popforecast==1) fprintf(fichtm,"\n */
   /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
   /*      <br>",fileres,fileres,fileres,fileres); */
   /*  else  */
   /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
    fflush(fichtm);
    fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   
    m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        for(cpt=1; cpt<=nlstate;cpt++) {
          fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
   prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
   <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
        }
        fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
   true period expectancies (those weighted with period prevalences are also\
    drawn in addition to the population based expectancies computed using\
    observed and cahotic prevalences: %s%d.png<br>\
   <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
    fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m0,cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
     int ng=0;
   /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   /*     printf("Problem with file %s",optionfilegnuplot); */
   /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   /*   } */
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
     m=pow(2,cptcoveff);
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
    /* 1eme*/
     for (cpt=1; cpt<= nlstate ; cpt ++) {
      for (k1=1; k1<= m ; k1 ++) {
        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
        fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
        fprintf(ficgp,"set xlabel \"Age\" \n\
   set ylabel \"Probability\" \n\
   set ter png small\n\
   set size 0.65,0.65\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else        fprintf(ficgp," \%%*lf (\%%*lf)");
        }
        fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        } 
        fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }  
        fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
      }
     }
     /*2 eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
       fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
       
       for (i=1; i<= nlstate+1 ; i ++) {
         k=2*i;
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         fprintf(ficgp,"\" t\"\" w l 0,");
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
         else fprintf(ficgp,"\" t\"\" w l 0,");
       }
     }
     
     /*3eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<= nlstate ; cpt ++) {
         /*       k=2+nlstate*(2*cpt-2); */
         k=2+(nlstate+1)*(cpt-1);
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
         fprintf(ficgp,"set ter png small\n\
   set size 0.65,0.65\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           
         */
         for (i=1; i< nlstate ; i ++) {
           fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1);
           /*      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
           
         } 
         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
       }
     }
     
     /* CV preval stable (period) */
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<=nlstate ; cpt ++) {
         k=3;
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   set ter png small\nset size 0.65,0.65\n\
   unset log y\n\
   plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
         
         for (i=1; i< nlstate ; i ++)
           fprintf(ficgp,"+$%d",k+i+1);
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
         
         l=3+(nlstate+ndeath)*cpt;
         fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
         for (i=1; i< nlstate ; i ++) {
           l=3+(nlstate+ndeath)*cpt;
           fprintf(ficgp,"+$%d",l+i+1);
         }
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
       } 
     }  
     
     /* proba elementaires */
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             jk++; 
             fprintf(ficgp,"\n");
           }
         }
       }
      }
   
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        for(jk=1; jk <=m; jk++) {
          fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
          if (ng==2)
            fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
          else
            fprintf(ficgp,"\nset title \"Probability\"\n");
          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
          for(k2=1; k2<=nlstate; k2++) {
            k3=i;
            for(k=1; k<=(nlstate+ndeath); k++) {
              if (k != k2){
                if(ng==2)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                else
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;
                for(j=3; j <=ncovmodel; j++) {
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                    fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                    ij++;
                  }
                  else
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
                fprintf(ficgp,")/(1");
                
                for(k1=1; k1 <=nlstate; k1++){   
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
                  for(j=3; j <=ncovmodel; j++){
                    if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                      fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                      ij++;
                    }
                    else
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                  }
                  fprintf(ficgp,")");
                }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
              }
            } /* end k */
          } /* end k2 */
        } /* end jk */
      } /* end ng */
      fflush(ficgp); 
   }  /* end gnuplot */
   
   
   /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
     int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
     double age;
   
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          we use a 5 terms etc. until the borders are no more concerned. 
       */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
           }
         }/* end age */
       }/* end mob */
     }else return -1;
     return 0;
   }/* End movingaverage */
   
   
   /************** Forecasting ******************/
   prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
     int *popage;
     double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   
   
   /**************** function prwizard **********************/
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     /* Wizard to print covariance matrix template */
   
     char ca[32], cb[32], cc[32];
     int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
   } /* end of prwizard */
   /******************* Gompertz Likelihood ******************************/
   double gompertz(double x[])
   { 
     double A,B,L=0.0,sump=0.,num=0.;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
   
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
                +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           L=L+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
    
     return -2*L*num/sump;
   }
   
   /******************* Printing html file ***********/
   void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,  double p[],double **matcov,double agemortsup){
     int i,k;
   
     fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
     fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
     for (i=1;i<=2;i++) 
       fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
     fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
     fprintf(fichtm,"</ul>");
   
   fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
   
    fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
   
    for (k=agegomp;k<(agemortsup-2);k++) 
      fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
   
    
     fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
     fprintf(ficgp,"set out \"graphmort.png\"\n "); 
     fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
     fprintf(ficgp, "set ter png small\n set log y\n"); 
     fprintf(ficgp, "set size 0.65,0.65\n");
     fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
   
   } 
   
   
   
   
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
     int linei, month, year,iout;
     int jj, ll, li, lj, lk, imk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int itimes;
     int NDIM=2;
     int vpopbased=0;
   
     char ca[32], cb[32], cc[32];
     char dummy[]="                         ";
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     struct stat info;
     double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char linetmp[MAXLINE];
       char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE], pathimach[MAXLINE]; 
     char **bp, *tok, *val; /* pathtot */
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     int agemortsup;
     float  sumlpop=0.;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double *severity;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
     double **ximort;
     char *alph[]={"a","a","b","c","d","e"}, str[4];
     int *dcwave;
   
     char z[1]="c", occ;
   
     char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
     char  *strt, strtend[80];
     char *stratrunc;
     int lstra;
   
     long total_usecs;
    
   /*   setlocale (LC_ALL, ""); */
   /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   /*   textdomain (PACKAGE); */
   /*   setlocale (LC_CTYPE, ""); */
   /*   setlocale (LC_MESSAGES, ""); */
   
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     (void) gettimeofday(&start_time,&tzp);
     curr_time=start_time;
     tm = *localtime(&start_time.tv_sec);
     tmg = *gmtime(&start_time.tv_sec);
     strcpy(strstart,asctime(&tm));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tv_sec = tp.tv_sec +86400; */
   /*  tm = *localtime(&start_time.tv_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tv_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     nberr=0; /* Number of errors and warnings */
     nbwarn=0;
     getcwd(pathcd, size);
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       fgets(pathr,FILENAMELENGTH,stdin);
       i=strlen(pathr);
       if(pathr[i-1]=='\n')
         pathr[i-1]='\0';
      for (tok = pathr; tok != NULL; ){
         printf("Pathr |%s|\n",pathr);
         while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
         printf("val= |%s| pathr=%s\n",val,pathr);
         strcpy (pathtot, val);
         if(pathr[0] == '\0') break; /* Dirty */
       }
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     /* Split argv[0], imach program to get pathimach */
     printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
     split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
     printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
    /*   strcpy(pathimach,argv[0]); */
     /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path); /* Can be a relative path */
     if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
       printf("Current directory %s!\n",pathcd);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s\n%s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: \n");
     fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     printf("Local time (at start):%s",strstart);
     fprintf(ficlog,"Local time (at start): %s",strstart);
     fflush(ficlog);
   /*   (void) gettimeofday(&curr_time,&tzp); */
   /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile %s\n",optionfile);
       fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       fflush(ficlog);
       goto end;
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n); 
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
     if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
     /* where is ncovprod ?*/
     ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7*/
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     nforces= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters like aij*/
     if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
       printf("Too complex model for current IMaCh: npar=(nlstate+ndeath-1)*nlstate*ncovmodel=%d >= %d(MAXPARM) or nlstate=%d >= %d(NLSTATEMAX) or ndeath=%d >= %d(NDEATHMAX) or ncovmodel=(k+age+#of+signs)=%d(NCOVMAX) >= %d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fprintf(ficlog,"Too complex model for current IMaCh: %d >=%d(MAXPARM) or %d >=%d(NLSTATEMAX) or %d >=%d(NDEATHMAX) or %d(NCOVMAX) >=%d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fflush(stdout);
       fclose (ficlog);
       goto end;
     }
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     delti=delti3[1][1];
     /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
     if(mle==-1){ /* Print a wizard for help writing covariance matrix */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       fclose (ficparo);
       fclose (ficlog);
       goto end;
       exit(0);
     }
     else if(mle==-3) {
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       matcov=matrix(1,npar,1,npar);
     }
     else{
       /* Read guess parameters */
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
       
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       for(i=1; i <=nlstate; i++){
         j=0;
         for(jj=1; jj <=nlstate+ndeath; jj++){
           if(jj==i) continue;
           j++;
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1 != i) && (j1 != j)){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
   It might be a problem of design; if ncovcol and the model are correct\n \
   run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           fprintf(ficparo,"%1d%1d",i1,j1);
           if(mle==1)
             printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar," %lf",&param[i][j][k]);
             if(mle==1){
               printf(" %lf",param[i][j][k]);
               fprintf(ficlog," %lf",param[i][j][k]);
             }
             else
               fprintf(ficlog," %lf",param[i][j][k]);
             fprintf(ficparo," %lf",param[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           if(mle==1)
             printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficparo,"\n");
         }
       }  
       fflush(ficlog);
   
       p=param[1][1];
       
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
   
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath-1; j++){
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1-i)*(j1-j)!=0){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           printf("%1d%1d",i,j);
           fprintf(ficparo,"%1d%1d",i1,j1);
           fprintf(ficlog,"%1d%1d",i1,j1);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar,"%le",&delti3[i][j][k]);
             printf(" %le",delti3[i][j][k]);
             fprintf(ficparo," %le",delti3[i][j][k]);
             fprintf(ficlog," %le",delti3[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           printf("\n");
           fprintf(ficparo,"\n");
           fprintf(ficlog,"\n");
         }
       }
       fflush(ficlog);
   
       delti=delti3[1][1];
   
   
       /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
     
       matcov=matrix(1,npar,1,npar);
       for(i=1; i <=npar; i++)
         for(j=1; j <=npar; j++) matcov[i][j]=0.;
         
       for(i=1; i <=npar; i++){
         fscanf(ficpar,"%s",&str);
         if(mle==1)
           printf("%s",str);
         fprintf(ficlog,"%s",str);
         fprintf(ficparo,"%s",str);
         for(j=1; j <=i; j++){
           fscanf(ficpar," %le",&matcov[i][j]);
           if(mle==1){
             printf(" %.5le",matcov[i][j]);
           }
           fprintf(ficlog," %.5le",matcov[i][j]);
           fprintf(ficparo," %.5le",matcov[i][j]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
       for(i=1; i <=npar; i++)
         for(j=i+1;j<=npar;j++)
           matcov[i][j]=matcov[j][i];
       
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       
       fflush(ficlog);
       
       /*-------- Rewriting parameter file ----------*/
       strcpy(rfileres,"r");    /* "Rparameterfile */
       strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
       strcat(rfileres,".");    /* */
       strcat(rfileres,optionfilext);    /* Other files have txt extension */
       if((ficres =fopen(rfileres,"w"))==NULL) {
         printf("Problem writing new parameter file: %s\n", fileres);goto end;
         fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
       }
       fprintf(ficres,"#%s\n",version);
     }    /* End of mle != -3 */
   
     /*-------- data file ----------*/
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem while opening datafile: %s\n", datafile);goto end;
       fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);goto end;
     }
   
     n= lastobs;
     severity = vector(1,maxwav);
     outcome=imatrix(1,maxwav+1,1,n);
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */ 
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,8);
   
     i=1;
     linei=0;
     while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
       linei=linei+1;
       for(j=strlen(line); j>=0;j--){  /* Untabifies line */
         if(line[j] == '\t')
           line[j] = ' ';
       }
       for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
         ;
       };
       line[j+1]=0;  /* Trims blanks at end of line */
       if(line[0]=='#'){
         fprintf(ficlog,"Comment line\n%s\n",line);
         printf("Comment line\n%s\n",line);
         continue;
       }
       trimbb(linetmp,line); /* Trims multiple blanks in line */
       for (j=0; line[j]!='\0';j++){
         line[j]=linetmp[j];
       }
     
   
       for (j=maxwav;j>=1;j--){
         cutv(stra, strb,line,' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
         /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
             fprintf(ficlog,"Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);
             goto end;
           }
         }
         s[j][i]=lval;
         
         strcpy(line,stra);
         cutv(stra, strb,line,' ');
         if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
         }
         else  if(iout=sscanf(strb,"%s.") != 0){
           month=99;
           year=9999;
         }else{
           printf("Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
           fprintf(ficlog,"Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);fflush(ficlog);
           goto end;
         }
         anint[j][i]= (double) year; 
         mint[j][i]= (double)month; 
         strcpy(line,stra);
       } /* ENd Waves */
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.",dummy) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
           fprintf(ficlog,"Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
           goto end;
       }
       andc[i]=(double) year; 
       moisdc[i]=(double) month; 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.") != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line,j);
         fprintf(ficlog,"Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line,j);fflush(ficlog);
           goto end;
       }
       annais[i]=(double)(year);
       moisnais[i]=(double)(month); 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       errno=0;
       dval=strtod(strb,&endptr); 
       if( strb[0]=='\0' || (*endptr != '\0')){
         printf("Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fprintf(ficlog,"Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fflush(ficlog);
         goto end;
       }
       weight[i]=dval; 
       strcpy(line,stra);
       
       for (j=ncovcol;j>=1;j--){
         cutv(stra, strb,line,' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);
             fprintf(ficlog,"Error reading data around '%d' at line number %ld for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);fflush(ficlog);
             goto end;
           }
         }
         if(lval <-1 || lval >1){
           printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);
           fprintf(ficlog,"Error reading data around '%d' at line number %ld for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
           goto end;
         }
         covar[j][i]=(double)(lval);
         strcpy(line,stra);
       }  
       lstra=strlen(stra);
        
       if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
         stratrunc = &(stra[lstra-9]);
         num[i]=atol(stratrunc);
       }
       else
         num[i]=atol(stra);
       /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
         printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
       
       i=i+1;
     } /* End loop reading  data */
     fclose(fic);
     /* printf("ii=%d", ij);
        scanf("%d",i);*/
     imx=i-1; /* Number of individuals */
   
     /* for (i=1; i<=imx; i++){
       if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
       if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
       if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
       }*/
      /*  for (i=1; i<=imx; i++){
        if (s[4][i]==9)  s[4][i]=-1; 
        printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
     
     /* for (i=1; i<=imx; i++) */
    
      /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
        else weight[i]=1;*/
   
     /* Calculation of the number of parameters from char model */
     Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. Stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
     Tprod=ivector(1,15); 
     Tvaraff=ivector(1,15); 
     Tvard=imatrix(1,15,1,2);
     Tage=ivector(1,15);      
      
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=1, k2=1;
       j=nbocc(model,'+'); /* j=Number of '+' */
       j1=nbocc(model,'*'); /* j1=Number of '*' */
       cptcovn=j+1; /* Number of covariates V1+V2+V3 =>2+1=3 */
       cptcovprod=j1; /*Number of products  V1*V2 =1 */
       
       strcpy(modelsav,model); 
       if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
         printf("Error. Non available option model=%s ",model);
         fprintf(ficlog,"Error. Non available option model=%s ",model);fflush(ficlog);
         goto end;
       }
       
       /* This loop fills the array Tvar from the string 'model'.*/
       /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
       for(i=(j+1); i>=1;i--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' 
                                        modelsav=V2+V3*age+V1+V4 strb=V3*age+V1+V4 
                                        stra=V2
                                       */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /* Model includes a product V1+V3*age+V2 strb=V3*age*/
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn: V3*age strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
           if (strcmp(strc,"age")==0) { /* Vn*age */
             cptcovprod--;
             cutv(strb,stre,strd,'V');
             Tvar[i]=atoi(stre);  /* V1+V3*age+V2 Tvar[2]=3 */
             cptcovage++; /* Sums the number of covariates including age as a product */
             Tage[cptcovage]=i;  /* Tage[1] =2 */
             /*printf("stre=%s ", stre);*/
           }
           else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutv(strb,stre,strc,'V');
             Tvar[i]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=i;
           }
           else {  /* Age is not in the model V1+V3*V2+V2  strb=V3*V2*/
             cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
             Tvar[i]=ncovcol+k1;  /* find 'n' in Vn and stores in Tvar. 
                                     If already ncovcol=2 and model=V2*V1 Tvar[1]=2+1 and Tvar[2]=2+2 etc */
             cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=i;  /* Tprod[1]  */
             Tvard[k1][1]=atoi(strc); /* m*/
             Tvard[k1][2]=atoi(stre); /* n */
             Tvar[cptcovn+k2]=Tvard[k1][1];
             Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
             for (k=1; k<=lastobs;k++) 
               covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
             k1++;
             k2=k2+2;
           }
         }
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
         cutv(strd,strc,strb,'V');
         Tvar[i]=atoi(strc);
         }
         strcpy(modelsav,stra);  /* modelsav=V2+V3*age+V1+V4 strb=V3*age+V1+V4 */ 
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);*/
   
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights*/
       for(i=1;i<=n;i++) weight[i]=1.0;
     }
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           nberr++;
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           nberr++;
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if ((int)andc[i]!=9999){
                   nbwarn++;
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] <agemin){ 
               agemin=agev[m][i];
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
             }
             else if(agev[m][i] >agemax){
               agemax=agev[m][i];
               /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           nberr++;
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           goto end;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
   
     agegomp=(int)agemin;
     free_vector(severity,1,maxwav);
     free_imatrix(outcome,1,maxwav+1,1,n);
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
   
      
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     if (cptcovn > 0) tricode(Tvar,nbcode,imx);
         
     codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
                                    the estimations*/
     h=0;
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
       for(i=1; i <=(m/pow(2,k));i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */ 
         for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate */
           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){  /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */ 
             h++;
             if (h>m) 
               h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
             printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]);
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
          printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
       
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     if(mle==-3)
       strcat(optionfilegnuplot,"-mort");
     strcat(optionfilegnuplot,".gp");
   
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       fprintf(ficgp,"set missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname); /* Main html file */
     if(mle==-3)
       strcat(optionfilehtm,"-mort");
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm);
       exit(0);
     }
   
     strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
     strcat(optionfilehtmcov,"-cov.htm");
     if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtmcov), exit(0);
     }
     else{
     fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
             optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
    - Log file of the run: <a href=\"%s\">%s</a><br>\n\
    - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
    - Date and time at start: %s</ul>\n",\
             optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
             optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
             fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
     chdir(optionfilefiname); /* Move to directory named optionfile */
     
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
   
     fprintf(fichtm,"\n");
     fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
             imx,agemin,agemax,jmin,jmax,jmean);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
   
     if (mle==-3){
       ximort=matrix(1,NDIM,1,NDIM);
       cens=ivector(1,n);
       ageexmed=vector(1,n);
       agecens=vector(1,n);
       dcwave=ivector(1,n);
    
       for (i=1; i<=imx; i++){
         dcwave[i]=-1;
         for (m=firstpass; m<=lastpass; m++)
           if (s[m][i]>nlstate) {
             dcwave[i]=m;
             /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
             break;
           }
       }
   
       for (i=1; i<=imx; i++) {
         if (wav[i]>0){
           ageexmed[i]=agev[mw[1][i]][i];
           j=wav[i];
           agecens[i]=1.; 
   
           if (ageexmed[i]> 1 && wav[i] > 0){
             agecens[i]=agev[mw[j][i]][i];
             cens[i]= 1;
           }else if (ageexmed[i]< 1) 
             cens[i]= -1;
           if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
             cens[i]=0 ;
         }
         else cens[i]=-1;
       }
       
       for (i=1;i<=NDIM;i++) {
         for (j=1;j<=NDIM;j++)
           ximort[i][j]=(i == j ? 1.0 : 0.0);
       }
       
       p[1]=0.0268; p[NDIM]=0.083;
       /*printf("%lf %lf", p[1], p[2]);*/
       
       
       printf("Powell\n");  fprintf(ficlog,"Powell\n");
       strcpy(filerespow,"pow-mort"); 
       strcat(filerespow,fileres);
       if((ficrespow=fopen(filerespow,"w"))==NULL) {
         printf("Problem with resultfile: %s\n", filerespow);
         fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
       }
       fprintf(ficrespow,"# Powell\n# iter -2*LL");
       /*  for (i=1;i<=nlstate;i++)
           for(j=1;j<=nlstate+ndeath;j++)
           if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       */
       fprintf(ficrespow,"\n");
       
       powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
       fclose(ficrespow);
       
       hesscov(matcov, p, NDIM, delti, 1e-4, gompertz); 
   
       for(i=1; i <=NDIM; i++)
         for(j=i+1;j<=NDIM;j++)
           matcov[i][j]=matcov[j][i];
       
       printf("\nCovariance matrix\n ");
       for(i=1; i <=NDIM; i++) {
         for(j=1;j<=NDIM;j++){ 
           printf("%f ",matcov[i][j]);
         }
         printf("\n ");
       }
       
       printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
       for (i=1;i<=NDIM;i++) 
         printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
   
       lsurv=vector(1,AGESUP);
       lpop=vector(1,AGESUP);
       tpop=vector(1,AGESUP);
       lsurv[agegomp]=100000;
       
       for (k=agegomp;k<=AGESUP;k++) {
         agemortsup=k;
         if (p[1]*exp(p[2]*(k-agegomp))>1) break;
       }
       
       for (k=agegomp;k<agemortsup;k++)
         lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
       
       for (k=agegomp;k<agemortsup;k++){
         lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
         sumlpop=sumlpop+lpop[k];
       }
       
       tpop[agegomp]=sumlpop;
       for (k=agegomp;k<(agemortsup-3);k++){
         /*  tpop[k+1]=2;*/
         tpop[k+1]=tpop[k]-lpop[k];
       }
       
       
       printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
       for (k=agegomp;k<(agemortsup-2);k++) 
         printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
       
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
                        stepm, weightopt,\
                        model,imx,p,matcov,agemortsup);
       
       free_vector(lsurv,1,AGESUP);
       free_vector(lpop,1,AGESUP);
       free_vector(tpop,1,AGESUP);
     } /* Endof if mle==-3 */
     
     else{ /* For mle >=1 */
       globpr=0;/* debug */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       globpr=1; /* to print the contributions */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       if(mle>=1){ /* Could be 1 or 2 */
         mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
       }
       
       /*--------- results files --------------*/
       fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
       
       
       fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(k=1; k <=(nlstate+ndeath); k++){
           if (k != i) {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%lf ",p[jk]);
               fprintf(ficlog,"%lf ",p[jk]);
               fprintf(ficres,"%lf ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       if(mle!=0){
         /* Computing hessian and covariance matrix */
         ftolhess=ftol; /* Usually correct */
         hesscov(matcov, p, npar, delti, ftolhess, func);
       }
       fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
       printf("# Scales (for hessian or gradient estimation)\n");
       fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if (j!=i) {
             fprintf(ficres,"%1d%1d",i,j);
             printf("%1d%1d",i,j);
             fprintf(ficlog,"%1d%1d",i,j);
             for(k=1; k<=ncovmodel;k++){
               printf(" %.5e",delti[jk]);
               fprintf(ficlog," %.5e",delti[jk]);
               fprintf(ficres," %.5e",delti[jk]);
               jk++;
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       
       fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       if(mle>=1)
         printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       /* # 121 Var(a12)\n\ */
       /* # 122 Cov(b12,a12) Var(b12)\n\ */
       /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
       /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
       /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
       /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
       /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
       /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
       
       
       /* Just to have a covariance matrix which will be more understandable
          even is we still don't want to manage dictionary of variables
       */
       for(itimes=1;itimes<=2;itimes++){
         jj=0;
         for(i=1; i <=nlstate; i++){
           for(j=1; j <=nlstate+ndeath; j++){
             if(j==i) continue;
             for(k=1; k<=ncovmodel;k++){
               jj++;
               ca[0]= k+'a'-1;ca[1]='\0';
               if(itimes==1){
                 if(mle>=1)
                   printf("#%1d%1d%d",i,j,k);
                 fprintf(ficlog,"#%1d%1d%d",i,j,k);
                 fprintf(ficres,"#%1d%1d%d",i,j,k);
               }else{
                 if(mle>=1)
                   printf("%1d%1d%d",i,j,k);
                 fprintf(ficlog,"%1d%1d%d",i,j,k);
                 fprintf(ficres,"%1d%1d%d",i,j,k);
               }
               ll=0;
               for(li=1;li <=nlstate; li++){
                 for(lj=1;lj <=nlstate+ndeath; lj++){
                   if(lj==li) continue;
                   for(lk=1;lk<=ncovmodel;lk++){
                     ll++;
                     if(ll<=jj){
                       cb[0]= lk +'a'-1;cb[1]='\0';
                       if(ll<jj){
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }else{
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }
                     }
                   } /* end lk */
                 } /* end lj */
               } /* end li */
               if(mle>=1)
                 printf("\n");
               fprintf(ficlog,"\n");
               fprintf(ficres,"\n");
               numlinepar++;
             } /* end k*/
           } /*end j */
         } /* end i */
       } /* end itimes */
       
       fflush(ficlog);
       fflush(ficres);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       estepm=0;
       fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
       if (estepm==0 || estepm < stepm) estepm=stepm;
       if (fage <= 2) {
         bage = ageminpar;
         fage = agemaxpar;
       }
       
       fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
       fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
       fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       
       dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
       dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
       
       fscanf(ficpar,"pop_based=%d\n",&popbased);
       fprintf(ficparo,"pop_based=%d\n",popbased);   
       fprintf(ficres,"pop_based=%d\n",popbased);   
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
       fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       /* day and month of proj2 are not used but only year anproj2.*/
       
       
       
       /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
       /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                    model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                    jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
         
      /*------------ free_vector  -------------*/
      /*  chdir(path); */
    
       free_ivector(wav,1,imx);
       free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
       free_lvector(num,1,n);
       free_vector(agedc,1,n);
       /*free_matrix(covar,0,NCOVMAX,1,n);*/
       /*free_matrix(covar,1,NCOVMAX,1,n);*/
       fclose(ficparo);
       fclose(ficres);
   
   
       /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
     
       strcpy(filerespl,"pl");
       strcat(filerespl,fileres);
       if((ficrespl=fopen(filerespl,"w"))==NULL) {
         printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
         fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
       }
       printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
       fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
       pstamp(ficrespl);
       fprintf(ficrespl,"# Period (stable) prevalence \n");
       fprintf(ficrespl,"#Age ");
       for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
       fprintf(ficrespl,"\n");
     
       prlim=matrix(1,nlstate,1,nlstate);
   
       agebase=ageminpar;
       agelim=agemaxpar;
       ftolpl=1.e-10;
       i1=cptcoveff;
       if (cptcovn < 1){i1=1;}
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           /* to clean */
           printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,codtab[cptcod][cptcov],nbcode);
           fprintf(ficrespl,"\n#******");
           printf("\n#******");
           fprintf(ficlog,"\n#******");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficrespl,"******\n");
           printf("******\n");
           fprintf(ficlog,"******\n");
           
           for (age=agebase; age<=agelim; age++){
             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
             fprintf(ficrespl,"%.0f ",age );
             for(j=1;j<=cptcoveff;j++)
               fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             for(i=1; i<=nlstate;i++)
               fprintf(ficrespl," %.5f", prlim[i][i]);
             fprintf(ficrespl,"\n");
           }
         }
       }
       fclose(ficrespl);
   
       /*------------- h Pij x at various ages ------------*/
     
       strcpy(filerespij,"pij");  strcat(filerespij,fileres);
       if((ficrespij=fopen(filerespij,"w"))==NULL) {
         printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
         fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
       }
       printf("Computing pij: result on file '%s' \n", filerespij);
       fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
       stepsize=(int) (stepm+YEARM-1)/YEARM;
       /*if (stepm<=24) stepsize=2;*/
   
       agelim=AGESUP;
       hstepm=stepsize*YEARM; /* Every year of age */
       hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
       /* hstepm=1;   aff par mois*/
       pstamp(ficrespij);
       fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           fprintf(ficrespij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrespij,"******\n");
           
           for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
             nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   
             /*      nhstepm=nhstepm*YEARM; aff par mois*/
   
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %1d-%1d",i,j);
             fprintf(ficrespij,"\n");
             for (h=0; h<=nhstepm; h++){
               fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
               for(i=1; i<=nlstate;i++)
                 for(j=1; j<=nlstate+ndeath;j++)
                   fprintf(ficrespij," %.5f", p3mat[i][j][h]);
               fprintf(ficrespij,"\n");
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             fprintf(ficrespij,"\n");
           }
         }
       }
   
       varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
   
       fclose(ficrespij);
   
       probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for(i=1;i<=AGESUP;i++)
         for(j=1;j<=NCOVMAX;j++)
           for(k=1;k<=NCOVMAX;k++)
             probs[i][j][k]=0.;
   
       /*---------- Forecasting ------------------*/
       /*if((stepm == 1) && (strcmp(model,".")==0)){*/
       if(prevfcast==1){
         /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
         /*      }  */
         /*      else{ */
         /*        erreur=108; */
         /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*      } */
       }
     
   
       /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
   
       prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
       /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
           ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
       */
   
       if (mobilav!=0) {
         mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
           fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
           printf(" Error in movingaverage mobilav=%d\n",mobilav);
         }
       }
   
   
       /*---------- Health expectancies, no variances ------------*/
   
       strcpy(filerese,"e");
       strcat(filerese,fileres);
       if((ficreseij=fopen(filerese,"w"))==NULL) {
         printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
         fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       }
       printf("Computing Health Expectancies: result on file '%s' \n", filerese);
       fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1; 
           fprintf(ficreseij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficreseij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);  
         
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         }
       }
       fclose(ficreseij);
   
   
       /*---------- Health expectancies and variances ------------*/
   
   
       strcpy(filerest,"t");
       strcat(filerest,fileres);
       if((ficrest=fopen(filerest,"w"))==NULL) {
         printf("Problem with total LE resultfile: %s\n", filerest);goto end;
         fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
       }
       printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
       fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
   
   
       strcpy(fileresstde,"stde");
       strcat(fileresstde,fileres);
       if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
         printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
         fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
       }
       printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
       fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
   
       strcpy(filerescve,"cve");
       strcat(filerescve,fileres);
       if((ficrescveij=fopen(filerescve,"w"))==NULL) {
         printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
         fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
       }
       printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
       fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
   
       strcpy(fileresv,"v");
       strcat(fileresv,fileres);
       if((ficresvij=fopen(fileresv,"w"))==NULL) {
         printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
         fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
       }
       printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
       fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1; 
           fprintf(ficrest,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrest,"******\n");
   
           fprintf(ficresstdeij,"\n#****** ");
           fprintf(ficrescveij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficresstdeij,"******\n");
           fprintf(ficrescveij,"******\n");
   
           fprintf(ficresvij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);  
    
           vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           pstamp(ficrest);
           for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
             oldm=oldms;savm=savms;
             varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart);   fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");
             if(vpopbased==1)
               fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
             else
               fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
             fprintf(ficrest,"# Age e.. (std) ");
             for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
             fprintf(ficrest,"\n");
   
             epj=vector(1,nlstate+1);
             for(age=bage; age <=fage ;age++){
               prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
               if (vpopbased==1) {
                 if(mobilav ==0){
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=probs[(int)age][i][k];
                 }else{ /* mobilav */ 
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=mobaverage[(int)age][i][k];
                 }
               }
           
               fprintf(ficrest," %4.0f",age);
               for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
                 for(i=1, epj[j]=0.;i <=nlstate;i++) {
                   epj[j] += prlim[i][i]*eij[i][j][(int)age];
                   /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
                 }
                 epj[nlstate+1] +=epj[j];
               }
   
               for(i=1, vepp=0.;i <=nlstate;i++)
                 for(j=1;j <=nlstate;j++)
                   vepp += vareij[i][j][(int)age];
               fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
               for(j=1;j <=nlstate;j++){
                 fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
               }
               fprintf(ficrest,"\n");
             }
           }
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_vector(epj,1,nlstate+1);
         }
       }
       free_vector(weight,1,n);
       free_imatrix(Tvard,1,15,1,2);
       free_imatrix(s,1,maxwav+1,1,n);
       free_matrix(anint,1,maxwav,1,n); 
       free_matrix(mint,1,maxwav,1,n);
       free_ivector(cod,1,n);
       free_ivector(tab,1,NCOVMAX);
       fclose(ficresstdeij);
       fclose(ficrescveij);
       fclose(ficresvij);
       fclose(ficrest);
       fclose(ficpar);
     
       /*------- Variance of period (stable) prevalence------*/   
   
       strcpy(fileresvpl,"vpl");
       strcat(fileresvpl,fileres);
       if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
         printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
         exit(0);
       }
       printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           fprintf(ficresvpl,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvpl,"******\n");
         
           varpl=matrix(1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
           free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
         }
       }
   
       fclose(ficresvpl);
   
       /*---------- End : free ----------------*/
       if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     }  /* mle==-3 arrives here for freeing */
    endfree:
     free_matrix(prlim,1,nlstate,1,nlstate);
       free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(covar,0,NCOVMAX,1,n);
       free_matrix(matcov,1,npar,1,npar);
       /*free_vector(delti,1,npar);*/
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       free_matrix(agev,1,maxwav,1,imx);
       free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   
       free_ivector(ncodemax,1,8);
       free_ivector(Tvar,1,15);
       free_ivector(Tprod,1,15);
       free_ivector(Tvaraff,1,15);
       free_ivector(Tage,1,15);
   
       free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
       free_imatrix(codtab,1,100,1,10);
     fflush(fichtm);
     fflush(ficgp);
     
   
     if((nberr >0) || (nbwarn>0)){
       printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
       fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
     }else{
       printf("End of Imach\n");
       fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     (void) gettimeofday(&end_time,&tzp);
     tm = *localtime(&end_time.tv_sec);
     tmg = *gmtime(&end_time.tv_sec);
     strcpy(strtend,asctime(&tm));
     printf("Local time at start %s\nLocal time at end   %s",strstart, strtend); 
     fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
     printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
   
     printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
     fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
     fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
     /*  printf("Total time was %d uSec.\n", total_usecs);*/
   /*   if(fileappend(fichtm,optionfilehtm)){ */
     fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtm);
     fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtmcov);
     fclose(ficgp);
     fclose(ficlog);
     /*------ End -----------*/
   
   
      printf("Before Current directory %s!\n",pathcd);
      if(chdir(pathcd) != 0)
       printf("Can't move to directory %s!\n",path);
     if(getcwd(pathcd,MAXLINE) > 0)
       printf("Current directory %s!\n",pathcd);
     /*strcat(plotcmd,CHARSEPARATOR);*/
     sprintf(plotcmd,"gnuplot");
   #ifndef UNIX
     sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
   #endif
     if(!stat(plotcmd,&info)){
       printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
       if(!stat(getenv("GNUPLOTBIN"),&info)){
         printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #ifdef UNIX
       strcpy(plotcmd,GNUPLOTPROGRAM);
       if(!stat(plotcmd,&info)){
         printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #endif
     }else
       strcpy(pplotcmd,plotcmd);
     
     sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
     printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
   
     if((outcmd=system(plotcmd)) != 0){
       printf("\n Problem with gnuplot\n");
     }
     printf(" Wait...");
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again and q for exiting: ");
       scanf("%s",z);
   /*     if (z[0] == 'c') system("./imach"); */
       if (z[0] == 'e') {
         printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
         system(optionfilehtm);
       }
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     end:
     while (z[0] != 'q') {
       printf("\nType  q for exiting: ");
       scanf("%s",z);
     }
   }
   
   
   
Removed from v.1.7  
changed lines
  Added in v.1.132

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