Diff for /imach/src/imach.c between versions 1.29 and 1.162

version 1.29, 2002/03/06 19:02:50 version 1.162, 2014/09/25 11:43:39
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.162  2014/09/25 11:43:39  brouard
      Summary: temporary backup 0.99!
   This program computes Healthy Life Expectancies from  
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    Revision 1.1  2014/09/16 11:06:58  brouard
   first survey ("cross") where individuals from different ages are    Summary: With some code (wrong) for nlopt
   interviewed on their health status or degree of disability (in the  
   case of a health survey which is our main interest) -2- at least a    Author:
   second wave of interviews ("longitudinal") which measure each change  
   (if any) in individual health status.  Health expectancies are    Revision 1.161  2014/09/15 20:41:41  brouard
   computed from the time spent in each health state according to a    Summary: Problem with macro SQR on Intel compiler
   model. More health states you consider, more time is necessary to reach the  
   Maximum Likelihood of the parameters involved in the model.  The    Revision 1.160  2014/09/02 09:24:05  brouard
   simplest model is the multinomial logistic model where pij is the    *** empty log message ***
   probabibility to be observed in state j at the second wave  
   conditional to be observed in state i at the first wave. Therefore    Revision 1.159  2014/09/01 10:34:10  brouard
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    Summary: WIN32
   'age' is age and 'sex' is a covariate. If you want to have a more    Author: Brouard
   complex model than "constant and age", you should modify the program  
   where the markup *Covariates have to be included here again* invites    Revision 1.158  2014/08/27 17:11:51  brouard
   you to do it.  More covariates you add, slower the    *** empty log message ***
   convergence.  
     Revision 1.157  2014/08/27 16:26:55  brouard
   The advantage of this computer programme, compared to a simple    Summary: Preparing windows Visual studio version
   multinomial logistic model, is clear when the delay between waves is not    Author: Brouard
   identical for each individual. Also, if a individual missed an  
   intermediate interview, the information is lost, but taken into    In order to compile on Visual studio, time.h is now correct and time_t
   account using an interpolation or extrapolation.      and tm struct should be used. difftime should be used but sometimes I
     just make the differences in raw time format (time(&now).
   hPijx is the probability to be observed in state i at age x+h    Trying to suppress #ifdef LINUX
   conditional to the observed state i at age x. The delay 'h' can be    Add xdg-open for __linux in order to open default browser.
   split into an exact number (nh*stepm) of unobserved intermediate  
   states. This elementary transition (by month or quarter trimester,    Revision 1.156  2014/08/25 20:10:10  brouard
   semester or year) is model as a multinomial logistic.  The hPx    *** empty log message ***
   matrix is simply the matrix product of nh*stepm elementary matrices  
   and the contribution of each individual to the likelihood is simply    Revision 1.155  2014/08/25 18:32:34  brouard
   hPijx.    Summary: New compile, minor changes
     Author: Brouard
   Also this programme outputs the covariance matrix of the parameters but also  
   of the life expectancies. It also computes the prevalence limits.    Revision 1.154  2014/06/20 17:32:08  brouard
      Summary: Outputs now all graphs of convergence to period prevalence
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).  
            Institut national d'études démographiques, Paris.    Revision 1.153  2014/06/20 16:45:46  brouard
   This software have been partly granted by Euro-REVES, a concerted action    Summary: If 3 live state, convergence to period prevalence on same graph
   from the European Union.    Author: Brouard
   It is copyrighted identically to a GNU software product, ie programme and  
   software can be distributed freely for non commercial use. Latest version    Revision 1.152  2014/06/18 17:54:09  brouard
   can be accessed at http://euroreves.ined.fr/imach .    Summary: open browser, use gnuplot on same dir than imach if not found in the path
   **********************************************************************/  
      Revision 1.151  2014/06/18 16:43:30  brouard
 #include <math.h>    *** empty log message ***
 #include <stdio.h>  
 #include <stdlib.h>    Revision 1.150  2014/06/18 16:42:35  brouard
 #include <unistd.h>    Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
     Author: brouard
 #define MAXLINE 256  
 #define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"    Revision 1.149  2014/06/18 15:51:14  brouard
 #define FILENAMELENGTH 80    Summary: Some fixes in parameter files errors
 /*#define DEBUG*/    Author: Nicolas Brouard
 #define windows  
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    Revision 1.148  2014/06/17 17:38:48  brouard
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    Summary: Nothing new
     Author: Brouard
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */  
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    Just a new packaging for OS/X version 0.98nS
   
 #define NINTERVMAX 8    Revision 1.147  2014/06/16 10:33:11  brouard
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    *** empty log message ***
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */  
 #define NCOVMAX 8 /* Maximum number of covariates */    Revision 1.146  2014/06/16 10:20:28  brouard
 #define MAXN 20000    Summary: Merge
 #define YEARM 12. /* Number of months per year */    Author: Brouard
 #define AGESUP 130  
 #define AGEBASE 40    Merge, before building revised version.
   
     Revision 1.145  2014/06/10 21:23:15  brouard
 int erreur; /* Error number */    Summary: Debugging with valgrind
 int nvar;    Author: Nicolas Brouard
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;  
 int npar=NPARMAX;    Lot of changes in order to output the results with some covariates
 int nlstate=2; /* Number of live states */    After the Edimburgh REVES conference 2014, it seems mandatory to
 int ndeath=1; /* Number of dead states */    improve the code.
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    No more memory valgrind error but a lot has to be done in order to
 int popbased=0;    continue the work of splitting the code into subroutines.
     Also, decodemodel has been improved. Tricode is still not
 int *wav; /* Number of waves for this individuual 0 is possible */    optimal. nbcode should be improved. Documentation has been added in
 int maxwav; /* Maxim number of waves */    the source code.
 int jmin, jmax; /* min, max spacing between 2 waves */  
 int mle, weightopt;    Revision 1.143  2014/01/26 09:45:38  brouard
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */  
 double jmean; /* Mean space between 2 waves */    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
 double **oldm, **newm, **savm; /* Working pointers to matrices */    (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    Revision 1.142  2014/01/26 03:57:36  brouard
 FILE *ficgp,*ficresprob,*ficpop;    Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
 FILE *ficreseij;  
   char filerese[FILENAMELENGTH];    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
  FILE  *ficresvij;  
   char fileresv[FILENAMELENGTH];    Revision 1.141  2014/01/26 02:42:01  brouard
  FILE  *ficresvpl;    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
   char fileresvpl[FILENAMELENGTH];  
     Revision 1.140  2011/09/02 10:37:54  brouard
 #define NR_END 1    Summary: times.h is ok with mingw32 now.
 #define FREE_ARG char*  
 #define FTOL 1.0e-10    Revision 1.139  2010/06/14 07:50:17  brouard
     After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
 #define NRANSI    I remember having already fixed agemin agemax which are pointers now but not cvs saved.
 #define ITMAX 200  
     Revision 1.138  2010/04/30 18:19:40  brouard
 #define TOL 2.0e-4    *** empty log message ***
   
 #define CGOLD 0.3819660    Revision 1.137  2010/04/29 18:11:38  brouard
 #define ZEPS 1.0e-10    (Module): Checking covariates for more complex models
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    than V1+V2. A lot of change to be done. Unstable.
   
 #define GOLD 1.618034    Revision 1.136  2010/04/26 20:30:53  brouard
 #define GLIMIT 100.0    (Module): merging some libgsl code. Fixing computation
 #define TINY 1.0e-20    of likelione (using inter/intrapolation if mle = 0) in order to
     get same likelihood as if mle=1.
 static double maxarg1,maxarg2;    Some cleaning of code and comments added.
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    Revision 1.135  2009/10/29 15:33:14  brouard
      (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  
 #define rint(a) floor(a+0.5)    Revision 1.134  2009/10/29 13:18:53  brouard
     (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
 static double sqrarg;  
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    Revision 1.133  2009/07/06 10:21:25  brouard
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    just nforces
   
 int imx;    Revision 1.132  2009/07/06 08:22:05  brouard
 int stepm;    Many tings
 /* Stepm, step in month: minimum step interpolation*/  
     Revision 1.131  2009/06/20 16:22:47  brouard
 int m,nb;    Some dimensions resccaled
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    Revision 1.130  2009/05/26 06:44:34  brouard
 double **pmmij, ***probs, ***mobaverage;    (Module): Max Covariate is now set to 20 instead of 8. A
 double dateintmean=0;    lot of cleaning with variables initialized to 0. Trying to make
     V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
 double *weight;  
 int **s; /* Status */    Revision 1.129  2007/08/31 13:49:27  lievre
 double *agedc, **covar, idx;    Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  
     Revision 1.128  2006/06/30 13:02:05  brouard
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    (Module): Clarifications on computing e.j
 double ftolhess; /* Tolerance for computing hessian */  
     Revision 1.127  2006/04/28 18:11:50  brouard
 /**************** split *************************/    (Module): Yes the sum of survivors was wrong since
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    imach-114 because nhstepm was no more computed in the age
 {    loop. Now we define nhstepma in the age loop.
    char *s;                             /* pointer */    (Module): In order to speed up (in case of numerous covariates) we
    int  l1, l2;                         /* length counters */    compute health expectancies (without variances) in a first step
     and then all the health expectancies with variances or standard
    l1 = strlen( path );                 /* length of path */    deviation (needs data from the Hessian matrices) which slows the
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    computation.
 #ifdef windows    In the future we should be able to stop the program is only health
    s = strrchr( path, '\\' );           /* find last / */    expectancies and graph are needed without standard deviations.
 #else  
    s = strrchr( path, '/' );            /* find last / */    Revision 1.126  2006/04/28 17:23:28  brouard
 #endif    (Module): Yes the sum of survivors was wrong since
    if ( s == NULL ) {                   /* no directory, so use current */    imach-114 because nhstepm was no more computed in the age
 #if     defined(__bsd__)                /* get current working directory */    loop. Now we define nhstepma in the age loop.
       extern char       *getwd( );    Version 0.98h
   
       if ( getwd( dirc ) == NULL ) {    Revision 1.125  2006/04/04 15:20:31  lievre
 #else    Errors in calculation of health expectancies. Age was not initialized.
       extern char       *getcwd( );    Forecasting file added.
   
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    Revision 1.124  2006/03/22 17:13:53  lievre
 #endif    Parameters are printed with %lf instead of %f (more numbers after the comma).
          return( GLOCK_ERROR_GETCWD );    The log-likelihood is printed in the log file
       }  
       strcpy( name, path );             /* we've got it */    Revision 1.123  2006/03/20 10:52:43  brouard
    } else {                             /* strip direcotry from path */    * imach.c (Module): <title> changed, corresponds to .htm file
       s++;                              /* after this, the filename */    name. <head> headers where missing.
       l2 = strlen( s );                 /* length of filename */  
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    * imach.c (Module): Weights can have a decimal point as for
       strcpy( name, s );                /* save file name */    English (a comma might work with a correct LC_NUMERIC environment,
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    otherwise the weight is truncated).
       dirc[l1-l2] = 0;                  /* add zero */    Modification of warning when the covariates values are not 0 or
    }    1.
    l1 = strlen( dirc );                 /* length of directory */    Version 0.98g
 #ifdef windows  
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    Revision 1.122  2006/03/20 09:45:41  brouard
 #else    (Module): Weights can have a decimal point as for
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }    English (a comma might work with a correct LC_NUMERIC environment,
 #endif    otherwise the weight is truncated).
    s = strrchr( name, '.' );            /* find last / */    Modification of warning when the covariates values are not 0 or
    s++;    1.
    strcpy(ext,s);                       /* save extension */    Version 0.98g
    l1= strlen( name);  
    l2= strlen( s)+1;    Revision 1.121  2006/03/16 17:45:01  lievre
    strncpy( finame, name, l1-l2);    * imach.c (Module): Comments concerning covariates added
    finame[l1-l2]= 0;  
    return( 0 );                         /* we're done */    * imach.c (Module): refinements in the computation of lli if
 }    status=-2 in order to have more reliable computation if stepm is
     not 1 month. Version 0.98f
   
 /******************************************/    Revision 1.120  2006/03/16 15:10:38  lievre
     (Module): refinements in the computation of lli if
 void replace(char *s, char*t)    status=-2 in order to have more reliable computation if stepm is
 {    not 1 month. Version 0.98f
   int i;  
   int lg=20;    Revision 1.119  2006/03/15 17:42:26  brouard
   i=0;    (Module): Bug if status = -2, the loglikelihood was
   lg=strlen(t);    computed as likelihood omitting the logarithm. Version O.98e
   for(i=0; i<= lg; i++) {  
     (s[i] = t[i]);    Revision 1.118  2006/03/14 18:20:07  brouard
     if (t[i]== '\\') s[i]='/';    (Module): varevsij Comments added explaining the second
   }    table of variances if popbased=1 .
 }    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
     (Module): Function pstamp added
 int nbocc(char *s, char occ)    (Module): Version 0.98d
 {  
   int i,j=0;    Revision 1.117  2006/03/14 17:16:22  brouard
   int lg=20;    (Module): varevsij Comments added explaining the second
   i=0;    table of variances if popbased=1 .
   lg=strlen(s);    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
   for(i=0; i<= lg; i++) {    (Module): Function pstamp added
   if  (s[i] == occ ) j++;    (Module): Version 0.98d
   }  
   return j;    Revision 1.116  2006/03/06 10:29:27  brouard
 }    (Module): Variance-covariance wrong links and
     varian-covariance of ej. is needed (Saito).
 void cutv(char *u,char *v, char*t, char occ)  
 {    Revision 1.115  2006/02/27 12:17:45  brouard
   int i,lg,j,p=0;    (Module): One freematrix added in mlikeli! 0.98c
   i=0;  
   for(j=0; j<=strlen(t)-1; j++) {    Revision 1.114  2006/02/26 12:57:58  brouard
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    (Module): Some improvements in processing parameter
   }    filename with strsep.
   
   lg=strlen(t);    Revision 1.113  2006/02/24 14:20:24  brouard
   for(j=0; j<p; j++) {    (Module): Memory leaks checks with valgrind and:
     (u[j] = t[j]);    datafile was not closed, some imatrix were not freed and on matrix
   }    allocation too.
      u[p]='\0';  
     Revision 1.112  2006/01/30 09:55:26  brouard
    for(j=0; j<= lg; j++) {    (Module): Back to gnuplot.exe instead of wgnuplot.exe
     if (j>=(p+1))(v[j-p-1] = t[j]);  
   }    Revision 1.111  2006/01/25 20:38:18  brouard
 }    (Module): Lots of cleaning and bugs added (Gompertz)
     (Module): Comments can be added in data file. Missing date values
 /********************** nrerror ********************/    can be a simple dot '.'.
   
 void nrerror(char error_text[])    Revision 1.110  2006/01/25 00:51:50  brouard
 {    (Module): Lots of cleaning and bugs added (Gompertz)
   fprintf(stderr,"ERREUR ...\n");  
   fprintf(stderr,"%s\n",error_text);    Revision 1.109  2006/01/24 19:37:15  brouard
   exit(1);    (Module): Comments (lines starting with a #) are allowed in data.
 }  
 /*********************** vector *******************/    Revision 1.108  2006/01/19 18:05:42  lievre
 double *vector(int nl, int nh)    Gnuplot problem appeared...
 {    To be fixed
   double *v;  
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    Revision 1.107  2006/01/19 16:20:37  brouard
   if (!v) nrerror("allocation failure in vector");    Test existence of gnuplot in imach path
   return v-nl+NR_END;  
 }    Revision 1.106  2006/01/19 13:24:36  brouard
     Some cleaning and links added in html output
 /************************ free vector ******************/  
 void free_vector(double*v, int nl, int nh)    Revision 1.105  2006/01/05 20:23:19  lievre
 {    *** empty log message ***
   free((FREE_ARG)(v+nl-NR_END));  
 }    Revision 1.104  2005/09/30 16:11:43  lievre
     (Module): sump fixed, loop imx fixed, and simplifications.
 /************************ivector *******************************/    (Module): If the status is missing at the last wave but we know
 int *ivector(long nl,long nh)    that the person is alive, then we can code his/her status as -2
 {    (instead of missing=-1 in earlier versions) and his/her
   int *v;    contributions to the likelihood is 1 - Prob of dying from last
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    health status (= 1-p13= p11+p12 in the easiest case of somebody in
   if (!v) nrerror("allocation failure in ivector");    the healthy state at last known wave). Version is 0.98
   return v-nl+NR_END;  
 }    Revision 1.103  2005/09/30 15:54:49  lievre
     (Module): sump fixed, loop imx fixed, and simplifications.
 /******************free ivector **************************/  
 void free_ivector(int *v, long nl, long nh)    Revision 1.102  2004/09/15 17:31:30  brouard
 {    Add the possibility to read data file including tab characters.
   free((FREE_ARG)(v+nl-NR_END));  
 }    Revision 1.101  2004/09/15 10:38:38  brouard
     Fix on curr_time
 /******************* imatrix *******************************/  
 int **imatrix(long nrl, long nrh, long ncl, long nch)    Revision 1.100  2004/07/12 18:29:06  brouard
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    Add version for Mac OS X. Just define UNIX in Makefile
 {  
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    Revision 1.99  2004/06/05 08:57:40  brouard
   int **m;    *** empty log message ***
    
   /* allocate pointers to rows */    Revision 1.98  2004/05/16 15:05:56  brouard
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    New version 0.97 . First attempt to estimate force of mortality
   if (!m) nrerror("allocation failure 1 in matrix()");    directly from the data i.e. without the need of knowing the health
   m += NR_END;    state at each age, but using a Gompertz model: log u =a + b*age .
   m -= nrl;    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
      cross-longitudinal survey is different from the mortality estimated
   /* allocate rows and set pointers to them */    from other sources like vital statistic data.
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    The same imach parameter file can be used but the option for mle should be -3.
   m[nrl] += NR_END;  
   m[nrl] -= ncl;    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.
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  
      The output is very simple: only an estimate of the intercept and of
   /* return pointer to array of pointers to rows */    the slope with 95% confident intervals.
   return m;  
 }    Current limitations:
     A) Even if you enter covariates, i.e. with the
 /****************** free_imatrix *************************/    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
 void free_imatrix(m,nrl,nrh,ncl,nch)    B) There is no computation of Life Expectancy nor Life Table.
       int **m;  
       long nch,ncl,nrh,nrl;    Revision 1.97  2004/02/20 13:25:42  lievre
      /* free an int matrix allocated by imatrix() */    Version 0.96d. Population forecasting command line is (temporarily)
 {    suppressed.
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  
   free((FREE_ARG) (m+nrl-NR_END));    Revision 1.96  2003/07/15 15:38:55  brouard
 }    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
     rewritten within the same printf. Workaround: many printfs.
 /******************* matrix *******************************/  
 double **matrix(long nrl, long nrh, long ncl, long nch)    Revision 1.95  2003/07/08 07:54:34  brouard
 {    * imach.c (Repository):
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    (Repository): Using imachwizard code to output a more meaningful covariance
   double **m;    matrix (cov(a12,c31) instead of numbers.
   
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    Revision 1.94  2003/06/27 13:00:02  brouard
   if (!m) nrerror("allocation failure 1 in matrix()");    Just cleaning
   m += NR_END;  
   m -= nrl;    Revision 1.93  2003/06/25 16:33:55  brouard
     (Module): On windows (cygwin) function asctime_r doesn't
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    exist so I changed back to asctime which exists.
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    (Module): Version 0.96b
   m[nrl] += NR_END;  
   m[nrl] -= ncl;    Revision 1.92  2003/06/25 16:30:45  brouard
     (Module): On windows (cygwin) function asctime_r doesn't
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    exist so I changed back to asctime which exists.
   return m;  
 }    Revision 1.91  2003/06/25 15:30:29  brouard
     * imach.c (Repository): Duplicated warning errors corrected.
 /*************************free matrix ************************/    (Repository): Elapsed time after each iteration is now output. It
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    helps to forecast when convergence will be reached. Elapsed time
 {    is stamped in powell.  We created a new html file for the graphs
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    concerning matrix of covariance. It has extension -cov.htm.
   free((FREE_ARG)(m+nrl-NR_END));  
 }    Revision 1.90  2003/06/24 12:34:15  brouard
     (Module): Some bugs corrected for windows. Also, when
 /******************* ma3x *******************************/    mle=-1 a template is output in file "or"mypar.txt with the design
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    of the covariance matrix to be input.
 {  
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    Revision 1.89  2003/06/24 12:30:52  brouard
   double ***m;    (Module): Some bugs corrected for windows. Also, when
     mle=-1 a template is output in file "or"mypar.txt with the design
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    of the covariance matrix to be input.
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;    Revision 1.88  2003/06/23 17:54:56  brouard
   m -= nrl;    * 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.
   
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    Revision 1.87  2003/06/18 12:26:01  brouard
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    Version 0.96
   m[nrl] += NR_END;  
   m[nrl] -= ncl;    Revision 1.86  2003/06/17 20:04:08  brouard
     (Module): Change position of html and gnuplot routines and added
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    routine fileappend.
   
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    Revision 1.85  2003/06/17 13:12:43  brouard
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    * imach.c (Repository): Check when date of death was earlier that
   m[nrl][ncl] += NR_END;    current date of interview. It may happen when the death was just
   m[nrl][ncl] -= nll;    prior to the death. In this case, dh was negative and likelihood
   for (j=ncl+1; j<=nch; j++)    was wrong (infinity). We still send an "Error" but patch by
     m[nrl][j]=m[nrl][j-1]+nlay;    assuming that the date of death was just one stepm after the
      interview.
   for (i=nrl+1; i<=nrh; i++) {    (Repository): Because some people have very long ID (first column)
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;    we changed int to long in num[] and we added a new lvector for
     for (j=ncl+1; j<=nch; j++)    memory allocation. But we also truncated to 8 characters (left
       m[i][j]=m[i][j-1]+nlay;    truncation)
   }    (Repository): No more line truncation errors.
   return m;  
 }    Revision 1.84  2003/06/13 21:44:43  brouard
     * imach.c (Repository): Replace "freqsummary" at a correct
 /*************************free ma3x ************************/    place. It differs from routine "prevalence" which may be called
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    many times. Probs is memory consuming and must be used with
 {    parcimony.
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  
   free((FREE_ARG)(m+nrl-NR_END));    Revision 1.83  2003/06/10 13:39:11  lievre
 }    *** empty log message ***
   
 /***************** f1dim *************************/    Revision 1.82  2003/06/05 15:57:20  brouard
 extern int ncom;    Add log in  imach.c and  fullversion number is now printed.
 extern double *pcom,*xicom;  
 extern double (*nrfunc)(double []);  */
    /*
 double f1dim(double x)     Interpolated Markov Chain
 {  
   int j;    Short summary of the programme:
   double f;    
   double *xt;    This program computes Healthy Life Expectancies from
      cross-longitudinal data. Cross-longitudinal data consist in: -1- a
   xt=vector(1,ncom);    first survey ("cross") where individuals from different ages are
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    interviewed on their health status or degree of disability (in the
   f=(*nrfunc)(xt);    case of a health survey which is our main interest) -2- at least a
   free_vector(xt,1,ncom);    second wave of interviews ("longitudinal") which measure each change
   return f;    (if any) in individual health status.  Health expectancies are
 }    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
 /*****************brent *************************/    Maximum Likelihood of the parameters involved in the model.  The
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    simplest model is the multinomial logistic model where pij is the
 {    probability to be observed in state j at the second wave
   int iter;    conditional to be observed in state i at the first wave. Therefore
   double a,b,d,etemp;    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
   double fu,fv,fw,fx;    'age' is age and 'sex' is a covariate. If you want to have a more
   double ftemp;    complex model than "constant and age", you should modify the program
   double p,q,r,tol1,tol2,u,v,w,x,xm;    where the markup *Covariates have to be included here again* invites
   double e=0.0;    you to do it.  More covariates you add, slower the
      convergence.
   a=(ax < cx ? ax : cx);  
   b=(ax > cx ? ax : cx);    The advantage of this computer programme, compared to a simple
   x=w=v=bx;    multinomial logistic model, is clear when the delay between waves is not
   fw=fv=fx=(*f)(x);    identical for each individual. Also, if a individual missed an
   for (iter=1;iter<=ITMAX;iter++) {    intermediate interview, the information is lost, but taken into
     xm=0.5*(a+b);    account using an interpolation or extrapolation.  
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    hPijx is the probability to be observed in state i at age x+h
     printf(".");fflush(stdout);    conditional to the observed state i at age x. The delay 'h' can be
 #ifdef DEBUG    split into an exact number (nh*stepm) of unobserved intermediate
     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);    states. This elementary transition (by month, quarter,
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    semester or year) is modelled as a multinomial logistic.  The hPx
 #endif    matrix is simply the matrix product of nh*stepm elementary matrices
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    and the contribution of each individual to the likelihood is simply
       *xmin=x;    hPijx.
       return fx;  
     }    Also this programme outputs the covariance matrix of the parameters but also
     ftemp=fu;    of the life expectancies. It also computes the period (stable) prevalence. 
     if (fabs(e) > tol1) {    
       r=(x-w)*(fx-fv);    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
       q=(x-v)*(fx-fw);             Institut national d'études démographiques, Paris.
       p=(x-v)*q-(x-w)*r;    This software have been partly granted by Euro-REVES, a concerted action
       q=2.0*(q-r);    from the European Union.
       if (q > 0.0) p = -p;    It is copyrighted identically to a GNU software product, ie programme and
       q=fabs(q);    software can be distributed freely for non commercial use. Latest version
       etemp=e;    can be accessed at http://euroreves.ined.fr/imach .
       e=d;  
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
         d=CGOLD*(e=(x >= xm ? a-x : b-x));    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
       else {    
         d=p/q;    **********************************************************************/
         u=x+d;  /*
         if (u-a < tol2 || b-u < tol2)    main
           d=SIGN(tol1,xm-x);    read parameterfile
       }    read datafile
     } else {    concatwav
       d=CGOLD*(e=(x >= xm ? a-x : b-x));    freqsummary
     }    if (mle >= 1)
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));      mlikeli
     fu=(*f)(u);    print results files
     if (fu <= fx) {    if mle==1 
       if (u >= x) a=x; else b=x;       computes hessian
       SHFT(v,w,x,u)    read end of parameter file: agemin, agemax, bage, fage, estepm
         SHFT(fv,fw,fx,fu)        begin-prev-date,...
         } else {    open gnuplot file
           if (u < x) a=u; else b=u;    open html file
           if (fu <= fw || w == x) {    period (stable) prevalence      | pl_nom    1-1 2-2 etc by covariate
             v=w;     for age prevalim()             | #****** V1=0  V2=1  V3=1  V4=0 ******
             w=u;                                    | 65 1 0 2 1 3 1 4 0  0.96326 0.03674
             fv=fw;      freexexit2 possible for memory heap.
             fw=fu;  
           } else if (fu <= fv || v == x || v == w) {    h Pij x                         | pij_nom  ficrestpij
             v=u;     # Cov Agex agex+h hpijx with i,j= 1-1 1-2     1-3     2-1     2-2     2-3
             fv=fu;         1  85   85    1.00000             0.00000 0.00000 0.00000 1.00000 0.00000
           }         1  85   86    0.68299             0.22291 0.09410 0.71093 0.00000 0.28907
         }  
   }         1  65   99    0.00364             0.00322 0.99314 0.00350 0.00310 0.99340
   nrerror("Too many iterations in brent");         1  65  100    0.00214             0.00204 0.99581 0.00206 0.00196 0.99597
   *xmin=x;    variance of p one-step probabilities varprob  | prob_nom   ficresprob #One-step probabilities and stand. devi in ()
   return fx;     Standard deviation of one-step probabilities | probcor_nom   ficresprobcor #One-step probabilities and correlation matrix
 }     Matrix of variance covariance of one-step probabilities |  probcov_nom ficresprobcov #One-step probabilities and covariance matrix
   
 /****************** mnbrak ***********************/    forecasting if prevfcast==1 prevforecast call prevalence()
     health expectancies
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,    Variance-covariance of DFLE
             double (*func)(double))    prevalence()
 {     movingaverage()
   double ulim,u,r,q, dum;    varevsij() 
   double fu;    if popbased==1 varevsij(,popbased)
      total life expectancies
   *fa=(*func)(*ax);    Variance of period (stable) prevalence
   *fb=(*func)(*bx);   end
   if (*fb > *fa) {  */
     SHFT(dum,*ax,*bx,dum)  
       SHFT(dum,*fb,*fa,dum)  
       }  
   *cx=(*bx)+GOLD*(*bx-*ax);   
   *fc=(*func)(*cx);  #include <math.h>
   while (*fb > *fc) {  #include <stdio.h>
     r=(*bx-*ax)*(*fb-*fc);  #include <stdlib.h>
     q=(*bx-*cx)*(*fb-*fa);  #include <string.h>
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  #ifdef _WIN32
     ulim=(*bx)+GLIMIT*(*cx-*bx);  #include <io.h>
     if ((*bx-u)*(u-*cx) > 0.0) {  #else
       fu=(*func)(u);  #include <unistd.h>
     } else if ((*cx-u)*(u-ulim) > 0.0) {  #endif
       fu=(*func)(u);  
       if (fu < *fc) {  #include <limits.h>
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  #include <sys/types.h>
           SHFT(*fb,*fc,fu,(*func)(u))  #include <sys/stat.h>
           }  #include <errno.h>
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  /* extern int errno; */
       u=ulim;  
       fu=(*func)(u);  /* #ifdef LINUX */
     } else {  /* #include <time.h> */
       u=(*cx)+GOLD*(*cx-*bx);  /* #include "timeval.h" */
       fu=(*func)(u);  /* #else */
     }  /* #include <sys/time.h> */
     SHFT(*ax,*bx,*cx,u)  /* #endif */
       SHFT(*fa,*fb,*fc,fu)  
       }  #include <time.h>
 }  
   #ifdef GSL
 /*************** linmin ************************/  #include <gsl/gsl_errno.h>
   #include <gsl/gsl_multimin.h>
 int ncom;  #endif
 double *pcom,*xicom;  
 double (*nrfunc)(double []);  #ifdef NLOPT
    #include <nlopt.h>
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  typedef struct {
 {    double (* function)(double [] );
   double brent(double ax, double bx, double cx,  } myfunc_data ;
                double (*f)(double), double tol, double *xmin);  #endif
   double f1dim(double x);  
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  /* #include <libintl.h> */
               double *fc, double (*func)(double));  /* #define _(String) gettext (String) */
   int j;  
   double xx,xmin,bx,ax;  #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
   double fx,fb,fa;  
    #define GNUPLOTPROGRAM "gnuplot"
   ncom=n;  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
   pcom=vector(1,n);  #define FILENAMELENGTH 132
   xicom=vector(1,n);  
   nrfunc=func;  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
   for (j=1;j<=n;j++) {  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
     pcom[j]=p[j];  
     xicom[j]=xi[j];  #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
   }  #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
   ax=0.0;  
   xx=1.0;  #define NINTERVMAX 8
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
 #ifdef DEBUG  #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  #define codtabm(h,k)  1 & (h-1) >> (k-1) ;
 #endif  #define MAXN 20000
   for (j=1;j<=n;j++) {  #define YEARM 12. /**< Number of months per year */
     xi[j] *= xmin;  #define AGESUP 130
     p[j] += xi[j];  #define AGEBASE 40
   }  #define AGEGOMP 10. /**< Minimal age for Gompertz adjustment */
   free_vector(xicom,1,n);  #ifdef _WIN32
   free_vector(pcom,1,n);  #define DIRSEPARATOR '\\'
 }  #define CHARSEPARATOR "\\"
   #define ODIRSEPARATOR '/'
 /*************** powell ************************/  #else
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  #define DIRSEPARATOR '/'
             double (*func)(double []))  #define CHARSEPARATOR "/"
 {  #define ODIRSEPARATOR '\\'
   void linmin(double p[], double xi[], int n, double *fret,  #endif
               double (*func)(double []));  
   int i,ibig,j;  /* $Id$ */
   double del,t,*pt,*ptt,*xit;  /* $State$ */
   double fp,fptt;  
   double *xits;  char version[]="Imach version 0.99, September 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121)";
   pt=vector(1,n);  char fullversion[]="$Revision$ $Date$"; 
   ptt=vector(1,n);  char strstart[80];
   xit=vector(1,n);  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
   xits=vector(1,n);  int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
   *fret=(*func)(p);  int nvar=0, nforce=0; /* Number of variables, number of forces */
   for (j=1;j<=n;j++) pt[j]=p[j];  /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
   for (*iter=1;;++(*iter)) {  int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
     fp=(*fret);  int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
     ibig=0;  int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
     del=0.0;  int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  int cptcovprodnoage=0; /**< Number of covariate products without age */   
     for (i=1;i<=n;i++)  int cptcoveff=0; /* Total number of covariates to vary for printing results */
       printf(" %d %.12f",i, p[i]);  int cptcov=0; /* Working variable */
     printf("\n");  int npar=NPARMAX;
     for (i=1;i<=n;i++) {  int nlstate=2; /* Number of live states */
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  int ndeath=1; /* Number of dead states */
       fptt=(*fret);  int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
 #ifdef DEBUG  int popbased=0;
       printf("fret=%lf \n",*fret);  
 #endif  int *wav; /* Number of waves for this individuual 0 is possible */
       printf("%d",i);fflush(stdout);  int maxwav=0; /* Maxim number of waves */
       linmin(p,xit,n,fret,func);  int jmin=0, jmax=0; /* min, max spacing between 2 waves */
       if (fabs(fptt-(*fret)) > del) {  int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
         del=fabs(fptt-(*fret));  int gipmx=0, gsw=0; /* Global variables on the number of contributions 
         ibig=i;                     to the likelihood and the sum of weights (done by funcone)*/
       }  int mle=1, weightopt=0;
 #ifdef DEBUG  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
       printf("%d %.12e",i,(*fret));  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
       for (j=1;j<=n;j++) {  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);             * wave mi and wave mi+1 is not an exact multiple of stepm. */
         printf(" x(%d)=%.12e",j,xit[j]);  int countcallfunc=0;  /* Count the number of calls to func */
       }  double jmean=1; /* Mean space between 2 waves */
       for(j=1;j<=n;j++)  double **matprod2(); /* test */
         printf(" p=%.12e",p[j]);  double **oldm, **newm, **savm; /* Working pointers to matrices */
       printf("\n");  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
 #endif  /*FILE *fic ; */ /* Used in readdata only */
     }  FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  FILE *ficlog, *ficrespow;
 #ifdef DEBUG  int globpr=0; /* Global variable for printing or not */
       int k[2],l;  double fretone; /* Only one call to likelihood */
       k[0]=1;  long ipmx=0; /* Number of contributions */
       k[1]=-1;  double sw; /* Sum of weights */
       printf("Max: %.12e",(*func)(p));  char filerespow[FILENAMELENGTH];
       for (j=1;j<=n;j++)  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
         printf(" %.12e",p[j]);  FILE *ficresilk;
       printf("\n");  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
       for(l=0;l<=1;l++) {  FILE *ficresprobmorprev;
         for (j=1;j<=n;j++) {  FILE *fichtm, *fichtmcov; /* Html File */
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  FILE *ficreseij;
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  char filerese[FILENAMELENGTH];
         }  FILE *ficresstdeij;
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  char fileresstde[FILENAMELENGTH];
       }  FILE *ficrescveij;
 #endif  char filerescve[FILENAMELENGTH];
   FILE  *ficresvij;
   char fileresv[FILENAMELENGTH];
       free_vector(xit,1,n);  FILE  *ficresvpl;
       free_vector(xits,1,n);  char fileresvpl[FILENAMELENGTH];
       free_vector(ptt,1,n);  char title[MAXLINE];
       free_vector(pt,1,n);  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
       return;  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
     }  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  char command[FILENAMELENGTH];
     for (j=1;j<=n;j++) {  int  outcmd=0;
       ptt[j]=2.0*p[j]-pt[j];  
       xit[j]=p[j]-pt[j];  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
       pt[j]=p[j];  
     }  char filelog[FILENAMELENGTH]; /* Log file */
     fptt=(*func)(ptt);  char filerest[FILENAMELENGTH];
     if (fptt < fp) {  char fileregp[FILENAMELENGTH];
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  char popfile[FILENAMELENGTH];
       if (t < 0.0) {  
         linmin(p,xit,n,fret,func);  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
         for (j=1;j<=n;j++) {  
           xi[j][ibig]=xi[j][n];  /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
           xi[j][n]=xit[j];  /* struct timezone tzp; */
         }  /* extern int gettimeofday(); */
 #ifdef DEBUG  struct tm tml, *gmtime(), *localtime();
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  
         for(j=1;j<=n;j++)  extern time_t time();
           printf(" %.12e",xit[j]);  
         printf("\n");  struct tm start_time, end_time, curr_time, last_time, forecast_time;
 #endif  time_t  rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
       }  struct tm tm;
     }  
   }  char strcurr[80], strfor[80];
 }  
   char *endptr;
 /**** Prevalence limit ****************/  long lval;
   double dval;
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  
 {  #define NR_END 1
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit  #define FREE_ARG char*
      matrix by transitions matrix until convergence is reached */  #define FTOL 1.0e-10
   
   int i, ii,j,k;  #define NRANSI 
   double min, max, maxmin, maxmax,sumnew=0.;  #define ITMAX 200 
   double **matprod2();  
   double **out, cov[NCOVMAX], **pmij();  #define TOL 2.0e-4 
   double **newm;  
   double agefin, delaymax=50 ; /* Max number of years to converge */  #define CGOLD 0.3819660 
   #define ZEPS 1.0e-10 
   for (ii=1;ii<=nlstate+ndeath;ii++)  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
     for (j=1;j<=nlstate+ndeath;j++){  
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);  #define GOLD 1.618034 
     }  #define GLIMIT 100.0 
   #define TINY 1.0e-20 
    cov[1]=1.;  
    static double maxarg1,maxarg2;
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
     newm=savm;    
     /* Covariates have to be included here again */  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
      cov[2]=agefin;  #define rint(a) floor(a+0.5)
    
       for (k=1; k<=cptcovn;k++) {  static double sqrarg;
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
       }  int agegomp= AGEGOMP;
       for (k=1; k<=cptcovage;k++)  
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  int imx; 
       for (k=1; k<=cptcovprod;k++)  int stepm=1;
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  /* Stepm, step in month: minimum step interpolation*/
   
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/  int estepm;
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
   
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  int m,nb;
   long *num;
     savm=oldm;  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
     oldm=newm;  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
     maxmax=0.;  double **pmmij, ***probs;
     for(j=1;j<=nlstate;j++){  double *ageexmed,*agecens;
       min=1.;  double dateintmean=0;
       max=0.;  
       for(i=1; i<=nlstate; i++) {  double *weight;
         sumnew=0;  int **s; /* Status */
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  double *agedc;
         prlim[i][j]= newm[i][j]/(1-sumnew);  double  **covar; /**< covar[j,i], value of jth covariate for individual i,
         max=FMAX(max,prlim[i][j]);                    * covar=matrix(0,NCOVMAX,1,n); 
         min=FMIN(min,prlim[i][j]);                    * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
       }  double  idx; 
       maxmin=max-min;  int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
       maxmax=FMAX(maxmax,maxmin);  int *Ndum; /** Freq of modality (tricode */
     }  int **codtab; /**< codtab=imatrix(1,100,1,10); */
     if(maxmax < ftolpl){  int **Tvard, *Tprod, cptcovprod, *Tvaraff;
       return prlim;  double *lsurv, *lpop, *tpop;
     }  
   }  double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
 }  double ftolhess; /**< Tolerance for computing hessian */
   
 /*************** transition probabilities ***************/  /**************** split *************************/
   static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  {
 {    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
   double s1, s2;       the name of the file (name), its extension only (ext) and its first part of the name (finame)
   /*double t34;*/    */ 
   int i,j,j1, nc, ii, jj;    char  *ss;                            /* pointer */
     int   l1, l2;                         /* length counters */
     for(i=1; i<= nlstate; i++){  
     for(j=1; j<i;j++){    l1 = strlen(path );                   /* length of path */
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
         /*s2 += param[i][j][nc]*cov[nc];*/    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    if ( ss == NULL ) {                   /* no directory, so determine current directory */
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/      strcpy( name, path );               /* we got the fullname name because no directory */
       }      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
       ps[i][j]=s2;        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/      /* get current working directory */
     }      /*    extern  char* getcwd ( char *buf , int len);*/
     for(j=i+1; j<=nlstate+ndeath;j++){      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){        return( GLOCK_ERROR_GETCWD );
         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);*/      /* got dirc from getcwd*/
       }      printf(" DIRC = %s \n",dirc);
       ps[i][j]=s2;    } else {                              /* strip direcotry from path */
     }      ss++;                               /* after this, the filename */
   }      l2 = strlen( ss );                  /* length of filename */
     /*ps[3][2]=1;*/      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
       strcpy( name, ss );         /* save file name */
   for(i=1; i<= nlstate; i++){      strncpy( dirc, path, l1 - l2 );     /* now the directory */
      s1=0;      dirc[l1-l2] = 0;                    /* add zero */
     for(j=1; j<i; j++)      printf(" DIRC2 = %s \n",dirc);
       s1+=exp(ps[i][j]);    }
     for(j=i+1; j<=nlstate+ndeath; j++)    /* We add a separator at the end of dirc if not exists */
       s1+=exp(ps[i][j]);    l1 = strlen( dirc );                  /* length of directory */
     ps[i][i]=1./(s1+1.);    if( dirc[l1-1] != DIRSEPARATOR ){
     for(j=1; j<i; j++)      dirc[l1] =  DIRSEPARATOR;
       ps[i][j]= exp(ps[i][j])*ps[i][i];      dirc[l1+1] = 0; 
     for(j=i+1; j<=nlstate+ndeath; j++)      printf(" DIRC3 = %s \n",dirc);
       ps[i][j]= exp(ps[i][j])*ps[i][i];    }
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */    ss = strrchr( name, '.' );            /* find last / */
   } /* end i */    if (ss >0){
       ss++;
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){      strcpy(ext,ss);                     /* save extension */
     for(jj=1; jj<= nlstate+ndeath; jj++){      l1= strlen( name);
       ps[ii][jj]=0;      l2= strlen(ss)+1;
       ps[ii][ii]=1;      strncpy( finame, name, l1-l2);
     }      finame[l1-l2]= 0;
   }    }
   
     return( 0 );                          /* we're done */
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){  }
     for(jj=1; jj<= nlstate+ndeath; jj++){  
      printf("%lf ",ps[ii][jj]);  
    }  /******************************************/
     printf("\n ");  
     }  void replace_back_to_slash(char *s, char*t)
     printf("\n ");printf("%lf ",cov[2]);*/  {
 /*    int i;
   for(i=1; i<= npar; i++) printf("%f ",x[i]);    int lg=0;
   goto end;*/    i=0;
     return ps;    lg=strlen(t);
 }    for(i=0; i<= lg; i++) {
       (s[i] = t[i]);
 /**************** Product of 2 matrices ******************/      if (t[i]== '\\') s[i]='/';
     }
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)  }
 {  
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times  char *trimbb(char *out, char *in)
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */  { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
   /* in, b, out are matrice of pointers which should have been initialized    char *s;
      before: only the contents of out is modified. The function returns    s=out;
      a pointer to pointers identical to out */    while (*in != '\0'){
   long i, j, k;      while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
   for(i=nrl; i<= nrh; i++)        in++;
     for(k=ncolol; k<=ncoloh; k++)      }
       for(j=ncl,out[i][k]=0.; j<=nch; j++)      *out++ = *in++;
         out[i][k] +=in[i][j]*b[j][k];    }
     *out='\0';
   return out;    return s;
 }  }
   
   char *cutl(char *blocc, char *alocc, char *in, char occ)
 /************* Higher Matrix Product ***************/  {
     /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ' 
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )       and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
 {       gives blocc="abcdef2ghi" and alocc="j".
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month       If occ is not found blocc is null and alocc is equal to in. Returns blocc
      duration (i.e. until    */
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.    char *s, *t;
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step    t=in;s=in;
      (typically every 2 years instead of every month which is too big).    while ((*in != occ) && (*in != '\0')){
      Model is determined by parameters x and covariates have to be      *alocc++ = *in++;
      included manually here.    }
     if( *in == occ){
      */      *(alocc)='\0';
       s=++in;
   int i, j, d, h, k;    }
   double **out, cov[NCOVMAX];   
   double **newm;    if (s == t) {/* occ not found */
       *(alocc-(in-s))='\0';
   /* Hstepm could be zero and should return the unit matrix */      in=s;
   for (i=1;i<=nlstate+ndeath;i++)    }
     for (j=1;j<=nlstate+ndeath;j++){    while ( *in != '\0'){
       oldm[i][j]=(i==j ? 1.0 : 0.0);      *blocc++ = *in++;
       po[i][j][0]=(i==j ? 1.0 : 0.0);    }
     }  
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    *blocc='\0';
   for(h=1; h <=nhstepm; h++){    return t;
     for(d=1; d <=hstepm; d++){  }
       newm=savm;  char *cutv(char *blocc, char *alocc, char *in, char occ)
       /* Covariates have to be included here again */  {
       cov[1]=1.;    /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ' 
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;       and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];       gives blocc="abcdef2ghi" and alocc="j".
       for (k=1; k<=cptcovage;k++)       If occ is not found blocc is null and alocc is equal to in. Returns alocc
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    */
       for (k=1; k<=cptcovprod;k++)    char *s, *t;
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    t=in;s=in;
     while (*in != '\0'){
       while( *in == occ){
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/        *blocc++ = *in++;
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/        s=in;
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,      }
                    pmij(pmmij,cov,ncovmodel,x,nlstate));      *blocc++ = *in++;
       savm=oldm;    }
       oldm=newm;    if (s == t) /* occ not found */
     }      *(blocc-(in-s))='\0';
     for(i=1; i<=nlstate+ndeath; i++)    else
       for(j=1;j<=nlstate+ndeath;j++) {      *(blocc-(in-s)-1)='\0';
         po[i][j][h]=newm[i][j];    in=s;
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);    while ( *in != '\0'){
          */      *alocc++ = *in++;
       }    }
   } /* end h */  
   return po;    *alocc='\0';
 }    return s;
   }
   
 /*************** log-likelihood *************/  int nbocc(char *s, char occ)
 double func( double *x)  {
 {    int i,j=0;
   int i, ii, j, k, mi, d, kk;    int lg=20;
   double l, ll[NLSTATEMAX], cov[NCOVMAX];    i=0;
   double **out;    lg=strlen(s);
   double sw; /* Sum of weights */    for(i=0; i<= lg; i++) {
   double lli; /* Individual log likelihood */    if  (s[i] == occ ) j++;
   long ipmx;    }
   /*extern weight */    return j;
   /* We are differentiating ll according to initial status */  }
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/  
   /*for(i=1;i<imx;i++)  /* void cutv(char *u,char *v, char*t, char occ) */
     printf(" %d\n",s[4][i]);  /* { */
   */  /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
   cov[1]=1.;  /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
   /*      gives u="abcdef2ghi" and v="j" *\/ */
   for(k=1; k<=nlstate; k++) ll[k]=0.;  /*   int i,lg,j,p=0; */
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){  /*   i=0; */
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];  /*   lg=strlen(t); */
     for(mi=1; mi<= wav[i]-1; mi++){  /*   for(j=0; j<=lg-1; j++) { */
       for (ii=1;ii<=nlstate+ndeath;ii++)  /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);  /*   } */
       for(d=0; d<dh[mi][i]; d++){  
         newm=savm;  /*   for(j=0; j<p; j++) { */
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;  /*     (u[j] = t[j]); */
         for (kk=1; kk<=cptcovage;kk++) {  /*   } */
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];  /*      u[p]='\0'; */
         }  
          /*    for(j=0; j<= lg; j++) { */
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,  /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));  /*   } */
         savm=oldm;  /* } */
         oldm=newm;  
          #ifdef _WIN32
          char * strsep(char **pp, const char *delim)
       } /* end mult */  {
          char *p, *q;
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);           
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/    if ((p = *pp) == NULL)
       ipmx +=1;      return 0;
       sw += weight[i];    if ((q = strpbrk (p, delim)) != NULL)
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;    {
     } /* end of wave */      *pp = q + 1;
   } /* end of individual */      *q = '\0';
     }
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];    else
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */      *pp = 0;
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */    return p;
   return -l;  }
 }  #endif
   
   /********************** nrerror ********************/
 /*********** Maximum Likelihood Estimation ***************/  
   void nrerror(char error_text[])
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))  {
 {    fprintf(stderr,"ERREUR ...\n");
   int i,j, iter;    fprintf(stderr,"%s\n",error_text);
   double **xi,*delti;    exit(EXIT_FAILURE);
   double fret;  }
   xi=matrix(1,npar,1,npar);  /*********************** vector *******************/
   for (i=1;i<=npar;i++)  double *vector(int nl, int nh)
     for (j=1;j<=npar;j++)  {
       xi[i][j]=(i==j ? 1.0 : 0.0);    double *v;
   printf("Powell\n");    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
   powell(p,xi,npar,ftol,&iter,&fret,func);    if (!v) nrerror("allocation failure in vector");
     return v-nl+NR_END;
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));  }
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));  
   /************************ free vector ******************/
 }  void free_vector(double*v, int nl, int nh)
   {
 /**** Computes Hessian and covariance matrix ***/    free((FREE_ARG)(v+nl-NR_END));
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))  }
 {  
   double  **a,**y,*x,pd;  /************************ivector *******************************/
   double **hess;  int *ivector(long nl,long nh)
   int i, j,jk;  {
   int *indx;    int *v;
     v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   double hessii(double p[], double delta, int theta, double delti[]);    if (!v) nrerror("allocation failure in ivector");
   double hessij(double p[], double delti[], int i, int j);    return v-nl+NR_END;
   void lubksb(double **a, int npar, int *indx, double b[]) ;  }
   void ludcmp(double **a, int npar, int *indx, double *d) ;  
   /******************free ivector **************************/
   hess=matrix(1,npar,1,npar);  void free_ivector(int *v, long nl, long nh)
   {
   printf("\nCalculation of the hessian matrix. Wait...\n");    free((FREE_ARG)(v+nl-NR_END));
   for (i=1;i<=npar;i++){  }
     printf("%d",i);fflush(stdout);  
     hess[i][i]=hessii(p,ftolhess,i,delti);  /************************lvector *******************************/
     /*printf(" %f ",p[i]);*/  long *lvector(long nl,long nh)
     /*printf(" %lf ",hess[i][i]);*/  {
   }    long *v;
      v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
   for (i=1;i<=npar;i++) {    if (!v) nrerror("allocation failure in ivector");
     for (j=1;j<=npar;j++)  {    return v-nl+NR_END;
       if (j>i) {  }
         printf(".%d%d",i,j);fflush(stdout);  
         hess[i][j]=hessij(p,delti,i,j);  /******************free lvector **************************/
         hess[j][i]=hess[i][j];      void free_lvector(long *v, long nl, long nh)
         /*printf(" %lf ",hess[i][j]);*/  {
       }    free((FREE_ARG)(v+nl-NR_END));
     }  }
   }  
   printf("\n");  /******************* imatrix *******************************/
   int **imatrix(long nrl, long nrh, long ncl, long nch) 
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
    { 
   a=matrix(1,npar,1,npar);    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
   y=matrix(1,npar,1,npar);    int **m; 
   x=vector(1,npar);    
   indx=ivector(1,npar);    /* allocate pointers to rows */ 
   for (i=1;i<=npar;i++)    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];    if (!m) nrerror("allocation failure 1 in matrix()"); 
   ludcmp(a,npar,indx,&pd);    m += NR_END; 
     m -= nrl; 
   for (j=1;j<=npar;j++) {    
     for (i=1;i<=npar;i++) x[i]=0;    
     x[j]=1;    /* allocate rows and set pointers to them */ 
     lubksb(a,npar,indx,x);    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
     for (i=1;i<=npar;i++){    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
       matcov[i][j]=x[i];    m[nrl] += NR_END; 
     }    m[nrl] -= ncl; 
   }    
     for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
   printf("\n#Hessian matrix#\n");    
   for (i=1;i<=npar;i++) {    /* return pointer to array of pointers to rows */ 
     for (j=1;j<=npar;j++) {    return m; 
       printf("%.3e ",hess[i][j]);  } 
     }  
     printf("\n");  /****************** free_imatrix *************************/
   }  void free_imatrix(m,nrl,nrh,ncl,nch)
         int **m;
   /* Recompute Inverse */        long nch,ncl,nrh,nrl; 
   for (i=1;i<=npar;i++)       /* free an int matrix allocated by imatrix() */ 
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];  { 
   ludcmp(a,npar,indx,&pd);    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
     free((FREE_ARG) (m+nrl-NR_END)); 
   /*  printf("\n#Hessian matrix recomputed#\n");  } 
   
   for (j=1;j<=npar;j++) {  /******************* matrix *******************************/
     for (i=1;i<=npar;i++) x[i]=0;  double **matrix(long nrl, long nrh, long ncl, long nch)
     x[j]=1;  {
     lubksb(a,npar,indx,x);    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
     for (i=1;i<=npar;i++){    double **m;
       y[i][j]=x[i];  
       printf("%.3e ",y[i][j]);    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     }    if (!m) nrerror("allocation failure 1 in matrix()");
     printf("\n");    m += NR_END;
   }    m -= nrl;
   */  
     m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   free_matrix(a,1,npar,1,npar);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   free_matrix(y,1,npar,1,npar);    m[nrl] += NR_END;
   free_vector(x,1,npar);    m[nrl] -= ncl;
   free_ivector(indx,1,npar);  
   free_matrix(hess,1,npar,1,npar);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     return m;
     /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
 }  m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
   that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
 /*************** hessian matrix ****************/     */
 double hessii( double x[], double delta, int theta, double delti[])  }
 {  
   int i;  /*************************free matrix ************************/
   int l=1, lmax=20;  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   double k1,k2;  {
   double p2[NPARMAX+1];    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   double res;    free((FREE_ARG)(m+nrl-NR_END));
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;  }
   double fx;  
   int k=0,kmax=10;  /******************* ma3x *******************************/
   double l1;  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
   {
   fx=func(x);    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
   for (i=1;i<=npar;i++) p2[i]=x[i];    double ***m;
   for(l=0 ; l <=lmax; l++){  
     l1=pow(10,l);    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     delts=delt;    if (!m) nrerror("allocation failure 1 in matrix()");
     for(k=1 ; k <kmax; k=k+1){    m += NR_END;
       delt = delta*(l1*k);    m -= nrl;
       p2[theta]=x[theta] +delt;  
       k1=func(p2)-fx;    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       p2[theta]=x[theta]-delt;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
       k2=func(p2)-fx;    m[nrl] += NR_END;
       /*res= (k1-2.0*fx+k2)/delt/delt; */    m[nrl] -= ncl;
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */  
          for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
 #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);    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
 #endif    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */    m[nrl][ncl] += NR_END;
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){    m[nrl][ncl] -= nll;
         k=kmax;    for (j=ncl+1; j<=nch; j++) 
       }      m[nrl][j]=m[nrl][j-1]+nlay;
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */    
         k=kmax; l=lmax*10.;    for (i=nrl+1; i<=nrh; i++) {
       }      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){      for (j=ncl+1; j<=nch; j++) 
         delts=delt;        m[i][j]=m[i][j-1]+nlay;
       }    }
     }    return m; 
   }    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
   delti[theta]=delts;             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
   return res;    */
    }
 }  
   /*************************free ma3x ************************/
 double hessij( double x[], double delti[], int thetai,int thetaj)  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
 {  {
   int i;    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
   int l=1, l1, lmax=20;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   double k1,k2,k3,k4,res,fx;    free((FREE_ARG)(m+nrl-NR_END));
   double p2[NPARMAX+1];  }
   int k;  
   /*************** function subdirf ***********/
   fx=func(x);  char *subdirf(char fileres[])
   for (k=1; k<=2; k++) {  {
     for (i=1;i<=npar;i++) p2[i]=x[i];    /* Caution optionfilefiname is hidden */
     p2[thetai]=x[thetai]+delti[thetai]/k;    strcpy(tmpout,optionfilefiname);
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    strcat(tmpout,"/"); /* Add to the right */
     k1=func(p2)-fx;    strcat(tmpout,fileres);
      return tmpout;
     p2[thetai]=x[thetai]+delti[thetai]/k;  }
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;  
     k2=func(p2)-fx;  /*************** function subdirf2 ***********/
    char *subdirf2(char fileres[], char *preop)
     p2[thetai]=x[thetai]-delti[thetai]/k;  {
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    
     k3=func(p2)-fx;    /* Caution optionfilefiname is hidden */
      strcpy(tmpout,optionfilefiname);
     p2[thetai]=x[thetai]-delti[thetai]/k;    strcat(tmpout,"/");
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    strcat(tmpout,preop);
     k4=func(p2)-fx;    strcat(tmpout,fileres);
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */    return tmpout;
 #ifdef DEBUG  }
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);  
 #endif  /*************** function subdirf3 ***********/
   }  char *subdirf3(char fileres[], char *preop, char *preop2)
   return res;  {
 }    
     /* Caution optionfilefiname is hidden */
 /************** Inverse of matrix **************/    strcpy(tmpout,optionfilefiname);
 void ludcmp(double **a, int n, int *indx, double *d)    strcat(tmpout,"/");
 {    strcat(tmpout,preop);
   int i,imax,j,k;    strcat(tmpout,preop2);
   double big,dum,sum,temp;    strcat(tmpout,fileres);
   double *vv;    return tmpout;
    }
   vv=vector(1,n);  
   *d=1.0;  char *asc_diff_time(long time_sec, char ascdiff[])
   for (i=1;i<=n;i++) {  {
     big=0.0;    long sec_left, days, hours, minutes;
     for (j=1;j<=n;j++)    days = (time_sec) / (60*60*24);
       if ((temp=fabs(a[i][j])) > big) big=temp;    sec_left = (time_sec) % (60*60*24);
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");    hours = (sec_left) / (60*60) ;
     vv[i]=1.0/big;    sec_left = (sec_left) %(60*60);
   }    minutes = (sec_left) /60;
   for (j=1;j<=n;j++) {    sec_left = (sec_left) % (60);
     for (i=1;i<j;i++) {    sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);  
       sum=a[i][j];    return ascdiff;
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];  }
       a[i][j]=sum;  
     }  /***************** f1dim *************************/
     big=0.0;  extern int ncom; 
     for (i=j;i<=n;i++) {  extern double *pcom,*xicom;
       sum=a[i][j];  extern double (*nrfunc)(double []); 
       for (k=1;k<j;k++)   
         sum -= a[i][k]*a[k][j];  double f1dim(double x) 
       a[i][j]=sum;  { 
       if ( (dum=vv[i]*fabs(sum)) >= big) {    int j; 
         big=dum;    double f;
         imax=i;    double *xt; 
       }   
     }    xt=vector(1,ncom); 
     if (j != imax) {    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
       for (k=1;k<=n;k++) {    f=(*nrfunc)(xt); 
         dum=a[imax][k];    free_vector(xt,1,ncom); 
         a[imax][k]=a[j][k];    return f; 
         a[j][k]=dum;  } 
       }  
       *d = -(*d);  /*****************brent *************************/
       vv[imax]=vv[j];  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
     }  { 
     indx[j]=imax;    int iter; 
     if (a[j][j] == 0.0) a[j][j]=TINY;    double a,b,d,etemp;
     if (j != n) {    double fu=0,fv,fw,fx;
       dum=1.0/(a[j][j]);    double ftemp;
       for (i=j+1;i<=n;i++) a[i][j] *= dum;    double p,q,r,tol1,tol2,u,v,w,x,xm; 
     }    double e=0.0; 
   }   
   free_vector(vv,1,n);  /* Doesn't work */    a=(ax < cx ? ax : cx); 
 ;    b=(ax > cx ? ax : cx); 
 }    x=w=v=bx; 
     fw=fv=fx=(*f)(x); 
 void lubksb(double **a, int n, int *indx, double b[])    for (iter=1;iter<=ITMAX;iter++) { 
 {      xm=0.5*(a+b); 
   int i,ii=0,ip,j;      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
   double sum;      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
        printf(".");fflush(stdout);
   for (i=1;i<=n;i++) {      fprintf(ficlog,".");fflush(ficlog);
     ip=indx[i];  #ifdef DEBUGBRENT
     sum=b[ip];      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);
     b[ip]=b[i];      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
     if (ii)      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];  #endif
     else if (sum) ii=i;      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
     b[i]=sum;        *xmin=x; 
   }        return fx; 
   for (i=n;i>=1;i--) {      } 
     sum=b[i];      ftemp=fu;
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];      if (fabs(e) > tol1) { 
     b[i]=sum/a[i][i];        r=(x-w)*(fx-fv); 
   }        q=(x-v)*(fx-fw); 
 }        p=(x-v)*q-(x-w)*r; 
         q=2.0*(q-r); 
 /************ Frequencies ********************/        if (q > 0.0) p = -p; 
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)        q=fabs(q); 
 {  /* Some frequencies */        etemp=e; 
          e=d; 
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
   double ***freq; /* Frequencies */          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   double *pp;        else { 
   double pos, k2, dateintsum=0,k2cpt=0;          d=p/q; 
   FILE *ficresp;          u=x+d; 
   char fileresp[FILENAMELENGTH];          if (u-a < tol2 || b-u < tol2) 
              d=SIGN(tol1,xm-x); 
   pp=vector(1,nlstate);        } 
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);      } else { 
   strcpy(fileresp,"p");        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   strcat(fileresp,fileres);      } 
   if((ficresp=fopen(fileresp,"w"))==NULL) {      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
     printf("Problem with prevalence resultfile: %s\n", fileresp);      fu=(*f)(u); 
     exit(0);      if (fu <= fx) { 
   }        if (u >= x) a=x; else b=x; 
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);        SHFT(v,w,x,u) 
   j1=0;          SHFT(fv,fw,fx,fu) 
           } else { 
   j=cptcoveff;            if (u < x) a=u; else b=u; 
   if (cptcovn<1) {j=1;ncodemax[1]=1;}            if (fu <= fw || w == x) { 
               v=w; 
   for(k1=1; k1<=j;k1++){              w=u; 
    for(i1=1; i1<=ncodemax[k1];i1++){              fv=fw; 
        j1++;              fw=fu; 
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);            } else if (fu <= fv || v == x || v == w) { 
          scanf("%d", i);*/              v=u; 
         for (i=-1; i<=nlstate+ndeath; i++)                fv=fu; 
          for (jk=-1; jk<=nlstate+ndeath; jk++)              } 
            for(m=agemin; m <= agemax+3; m++)          } 
              freq[i][jk][m]=0;    } 
     nrerror("Too many iterations in brent"); 
         dateintsum=0;    *xmin=x; 
         k2cpt=0;    return fx; 
        for (i=1; i<=imx; i++) {  } 
          bool=1;  
          if  (cptcovn>0) {  /****************** mnbrak ***********************/
            for (z1=1; z1<=cptcoveff; z1++)  
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
                bool=0;              double (*func)(double)) 
          }  { 
          if (bool==1) {    double ulim,u,r,q, dum;
            for(m=firstpass; m<=lastpass; m++){    double fu; 
              k2=anint[m][i]+(mint[m][i]/12.);   
              if ((k2>=dateprev1) && (k2<=dateprev2)) {    *fa=(*func)(*ax); 
                if(agev[m][i]==0) agev[m][i]=agemax+1;    *fb=(*func)(*bx); 
                if(agev[m][i]==1) agev[m][i]=agemax+2;    if (*fb > *fa) { 
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];      SHFT(dum,*ax,*bx,dum) 
                freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];        SHFT(dum,*fb,*fa,dum) 
                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {        } 
                  dateintsum=dateintsum+k2;    *cx=(*bx)+GOLD*(*bx-*ax); 
                  k2cpt++;    *fc=(*func)(*cx); 
                }    while (*fb > *fc) { /* Declining fa, fb, fc */
       r=(*bx-*ax)*(*fb-*fc); 
              }      q=(*bx-*cx)*(*fb-*fa); 
            }      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
          }        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscisse of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
        }      ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscisse where function can be evaluated */
              if ((*bx-u)*(u-*cx) > 0.0) { /* if u between b and c */
        fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        fu=(*func)(u); 
       } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
         if  (cptcovn>0) {        fu=(*func)(u); 
          fprintf(ficresp, "\n#********** Variable ");        if (fu < *fc) { 
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
        fprintf(ficresp, "**********\n#");            SHFT(*fb,*fc,fu,(*func)(u)) 
         }            } 
        for(i=1; i<=nlstate;i++)      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);        u=ulim; 
        fprintf(ficresp, "\n");        fu=(*func)(u); 
              } else { 
   for(i=(int)agemin; i <= (int)agemax+3; i++){        u=(*cx)+GOLD*(*cx-*bx); 
     if(i==(int)agemax+3)        fu=(*func)(u); 
       printf("Total");      } 
     else      SHFT(*ax,*bx,*cx,u) 
       printf("Age %d", i);        SHFT(*fa,*fb,*fc,fu) 
     for(jk=1; jk <=nlstate ; jk++){        } 
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)  } 
         pp[jk] += freq[jk][m][i];  
     }  /*************** linmin ************************/
     for(jk=1; jk <=nlstate ; jk++){  /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
       for(m=-1, pos=0; m <=0 ; m++)  resets p to where the function func(p) takes on a minimum along the direction xi from p ,
         pos += freq[jk][m][i];  and replaces xi by the actual vector displacement that p was moved. Also returns as fret
       if(pp[jk]>=1.e-10)  the value of func at the returned location p . This is actually all accomplished by calling the
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);  routines mnbrak and brent .*/
       else  int ncom; 
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);  double *pcom,*xicom;
     }  double (*nrfunc)(double []); 
    
      for(jk=1; jk <=nlstate ; jk++){  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
       for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)  { 
         pp[jk] += freq[jk][m][i];    double brent(double ax, double bx, double cx, 
      }                 double (*f)(double), double tol, double *xmin); 
     double f1dim(double x); 
     for(jk=1,pos=0; jk <=nlstate ; jk++)    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
       pos += pp[jk];                double *fc, double (*func)(double)); 
     for(jk=1; jk <=nlstate ; jk++){    int j; 
       if(pos>=1.e-5)    double xx,xmin,bx,ax; 
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);    double fx,fb,fa;
       else   
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);    ncom=n; 
       if( i <= (int) agemax){    pcom=vector(1,n); 
         if(pos>=1.e-5){    xicom=vector(1,n); 
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);    nrfunc=func; 
           probs[i][jk][j1]= pp[jk]/pos;    for (j=1;j<=n;j++) { 
           /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/      pcom[j]=p[j]; 
         }      xicom[j]=xi[j]; 
       else    } 
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);    ax=0.0; 
       }    xx=1.0; 
     }    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Find a bracket a,x,b in direction n=xi ie xicom */
     for(jk=-1; jk <=nlstate+ndeath; jk++)    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Find a minimum P+lambda n in that direction (lambdamin), with TOL between abscisses */
       for(m=-1; m <=nlstate+ndeath; m++)  #ifdef DEBUG
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     if(i <= (int) agemax)    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
       fprintf(ficresp,"\n");  #endif
     printf("\n");    for (j=1;j<=n;j++) { 
     }      xi[j] *= xmin; 
     }      p[j] += xi[j]; 
  }    } 
   dateintmean=dateintsum/k2cpt;    free_vector(xicom,1,n); 
      free_vector(pcom,1,n); 
   fclose(ficresp);  } 
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);  
   free_vector(pp,1,nlstate);  
   /*************** powell ************************/
   /* End of Freq */  /*
 }  Minimization of a function func of n variables. Input consists of an initial starting point
   p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
 /************ Prevalence ********************/  rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
 void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)  such that failure to decrease by more than this amount on one iteration signals doneness. On
 {  /* Some frequencies */  output, p is set to the best point found, xi is the then-current direction set, fret is the returned
    function value at p , and iter is the number of iterations taken. The routine linmin is used.
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;   */
   double ***freq; /* Frequencies */  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
   double *pp;              double (*func)(double [])) 
   double pos, k2;  { 
     void linmin(double p[], double xi[], int n, double *fret, 
   pp=vector(1,nlstate);                double (*func)(double [])); 
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    int i,ibig,j; 
      double del,t,*pt,*ptt,*xit;
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    double fp,fptt;
   j1=0;    double *xits;
      int niterf, itmp;
   j=cptcoveff;  
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    pt=vector(1,n); 
      ptt=vector(1,n); 
  for(k1=1; k1<=j;k1++){    xit=vector(1,n); 
     for(i1=1; i1<=ncodemax[k1];i1++){    xits=vector(1,n); 
       j1++;    *fret=(*func)(p); 
      for (j=1;j<=n;j++) pt[j]=p[j]; 
       for (i=-1; i<=nlstate+ndeath; i++)        rcurr_time = time(NULL);  
         for (jk=-1; jk<=nlstate+ndeath; jk++)      for (*iter=1;;++(*iter)) { 
           for(m=agemin; m <= agemax+3; m++)      fp=(*fret); 
             freq[i][jk][m]=0;      ibig=0; 
            del=0.0; 
       for (i=1; i<=imx; i++) {      rlast_time=rcurr_time;
         bool=1;      /* (void) gettimeofday(&curr_time,&tzp); */
         if  (cptcovn>0) {      rcurr_time = time(NULL);  
           for (z1=1; z1<=cptcoveff; z1++)      curr_time = *localtime(&rcurr_time);
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
               bool=0;      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
         }  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
         if (bool==1) {     for (i=1;i<=n;i++) {
           for(m=firstpass; m<=lastpass; m++){        printf(" %d %.12f",i, p[i]);
             k2=anint[m][i]+(mint[m][i]/12.);        fprintf(ficlog," %d %.12lf",i, p[i]);
             if ((k2>=dateprev1) && (k2<=dateprev2)) {        fprintf(ficrespow," %.12lf", p[i]);
               if(agev[m][i]==0) agev[m][i]=agemax+1;      }
               if(agev[m][i]==1) agev[m][i]=agemax+2;      printf("\n");
               freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];      fprintf(ficlog,"\n");
               /* freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];  */      fprintf(ficrespow,"\n");fflush(ficrespow);
             }      if(*iter <=3){
           }        tml = *localtime(&rcurr_time);
         }        strcpy(strcurr,asctime(&tml));
       }        rforecast_time=rcurr_time; 
         for(i=(int)agemin; i <= (int)agemax+3; i++){        itmp = strlen(strcurr);
           for(jk=1; jk <=nlstate ; jk++){        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)          strcurr[itmp-1]='\0';
               pp[jk] += freq[jk][m][i];        printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
           }        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
           for(jk=1; jk <=nlstate ; jk++){        for(niterf=10;niterf<=30;niterf+=10){
             for(m=-1, pos=0; m <=0 ; m++)          rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
             pos += freq[jk][m][i];          forecast_time = *localtime(&rforecast_time);
         }          strcpy(strfor,asctime(&forecast_time));
                  itmp = strlen(strfor);
          for(jk=1; jk <=nlstate ; jk++){          if(strfor[itmp-1]=='\n')
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)          strfor[itmp-1]='\0';
              pp[jk] += freq[jk][m][i];          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(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
          }          fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
                  }
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];      }
       for (i=1;i<=n;i++) { 
          for(jk=1; jk <=nlstate ; jk++){                  for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
            if( i <= (int) agemax){        fptt=(*fret); 
              if(pos>=1.e-5){  #ifdef DEBUG
                probs[i][jk][j1]= pp[jk]/pos;        printf("fret=%lf \n",*fret);
              }        fprintf(ficlog,"fret=%lf \n",*fret);
            }  #endif
          }        printf("%d",i);fflush(stdout);
                  fprintf(ficlog,"%d",i);fflush(ficlog);
         }        linmin(p,xit,n,fret,func); 
     }        if (fabs(fptt-(*fret)) > del) { 
   }          del=fabs(fptt-(*fret)); 
            ibig=i; 
          } 
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);  #ifdef DEBUG
   free_vector(pp,1,nlstate);        printf("%d %.12e",i,(*fret));
          fprintf(ficlog,"%d %.12e",i,(*fret));
 }  /* End of Freq */        for (j=1;j<=n;j++) {
           xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
 /************* Waves Concatenation ***************/          printf(" x(%d)=%.12e",j,xit[j]);
           fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)        }
 {        for(j=1;j<=n;j++) {
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.          printf(" p(%d)=%.12e",j,p[j]);
      Death is a valid wave (if date is known).          fprintf(ficlog," p(%d)=%.12e",j,p[j]);
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i        }
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]        printf("\n");
      and mw[mi+1][i]. dh depends on stepm.        fprintf(ficlog,"\n");
      */  #endif
       } /* end i */
   int i, mi, m;      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;  #ifdef DEBUG
      double sum=0., jmean=0.;*/        int k[2],l;
         k[0]=1;
   int j, k=0,jk, ju, jl;        k[1]=-1;
   double sum=0.;        printf("Max: %.12e",(*func)(p));
   jmin=1e+5;        fprintf(ficlog,"Max: %.12e",(*func)(p));
   jmax=-1;        for (j=1;j<=n;j++) {
   jmean=0.;          printf(" %.12e",p[j]);
   for(i=1; i<=imx; i++){          fprintf(ficlog," %.12e",p[j]);
     mi=0;        }
     m=firstpass;        printf("\n");
     while(s[m][i] <= nlstate){        fprintf(ficlog,"\n");
       if(s[m][i]>=1)        for(l=0;l<=1;l++) {
         mw[++mi][i]=m;          for (j=1;j<=n;j++) {
       if(m >=lastpass)            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
         break;            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
       else            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
         m++;          }
     }/* end while */          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     if (s[m][i] > nlstate){          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
       mi++;     /* Death is another wave */        }
       /* if(mi==0)  never been interviewed correctly before death */  #endif
          /* Only death is a correct wave */  
       mw[mi][i]=m;  
     }        free_vector(xit,1,n); 
         free_vector(xits,1,n); 
     wav[i]=mi;        free_vector(ptt,1,n); 
     if(mi==0)        free_vector(pt,1,n); 
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);        return; 
   }      } 
       if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
   for(i=1; i<=imx; i++){      for (j=1;j<=n;j++) { /* Computes an extrapolated point */
     for(mi=1; mi<wav[i];mi++){        ptt[j]=2.0*p[j]-pt[j]; 
       if (stepm <=0)        xit[j]=p[j]-pt[j]; 
         dh[mi][i]=1;        pt[j]=p[j]; 
       else{      } 
         if (s[mw[mi+1][i]][i] > nlstate) {      fptt=(*func)(ptt); 
           if (agedc[i] < 2*AGESUP) {      if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);        /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
           if(j==0) j=1;  /* Survives at least one month after exam */        /* From x1 (P0) distance of x2 is at h and x3 is 2h */
           k=k+1;        /* Let f"(x2) be the 2nd derivative equal everywhere.  */
           if (j >= jmax) jmax=j;        /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
           if (j <= jmin) jmin=j;        /* will reach at f3 = fm + h^2/2 f"m  ; f" = (f1 -2f2 +f3 ) / h**2 */
           sum=sum+j;        /* f1-f3 = delta(2h) = 2 h**2 f'' = 2(f1- 2f2 +f3) */
           /* if (j<10) printf("j=%d num=%d ",j,i); */        /* Thus we compare delta(2h) with observed f1-f3 */
           }        /* or best gain on one ancient line 'del' with total  */
         }        /* gain f1-f2 = f1 - f2 - 'del' with del  */
         else{        /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));  
           k=k+1;        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del);
           if (j >= jmax) jmax=j;        t= t- del*SQR(fp-fptt);
           else if (j <= jmin)jmin=j;        printf("t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t);
           /*   if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */        fprintf(ficlog,"t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t);
           sum=sum+j;  #ifdef DEBUG
         }        printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
         jk= j/stepm;               (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
         jl= j -jk*stepm;        fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
         ju= j -(jk+1)*stepm;               (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
         if(jl <= -ju)        printf("tt= %.12lf, t=%.12lf\n",2.0*(fp-2.0*(*fret)+fptt)*(fp-(*fret)-del)*(fp-(*fret)-del)-del*(fp-fptt)*(fp-fptt),t);
           dh[mi][i]=jk;        fprintf(ficlog, "tt= %.12lf, t=%.12lf\n",2.0*(fp-2.0*(*fret)+fptt)*(fp-(*fret)-del)*(fp-(*fret)-del)-del*(fp-fptt)*(fp-fptt),t);
         else  #endif
           dh[mi][i]=jk+1;        if (t < 0.0) { /* Then we use it for last direction */
         if(dh[mi][i]==0)          linmin(p,xit,n,fret,func); /* computes mean on the extrapolated direction.*/
           dh[mi][i]=1; /* At least one step */          for (j=1;j<=n;j++) { 
       }            xi[j][ibig]=xi[j][n]; /* Replace the direction with biggest decrease by n */
     }            xi[j][n]=xit[j];      /* and nth direction by the extrapolated */
   }          }
   jmean=sum/k;          printf("Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);          fprintf(ficlog,"Gaining to use average direction of P0 P%d instead of biggest increase direction :\n",n,ibig);
  }  
 /*********** Tricode ****************************/  #ifdef DEBUG
 void tricode(int *Tvar, int **nbcode, int imx)          for(j=1;j<=n;j++){
 {            printf(" %.12e",xit[j]);
   int Ndum[20],ij=1, k, j, i;            fprintf(ficlog," %.12e",xit[j]);
   int cptcode=0;          }
   cptcoveff=0;          printf("\n");
            fprintf(ficlog,"\n");
   for (k=0; k<19; k++) Ndum[k]=0;  #endif
   for (k=1; k<=7; k++) ncodemax[k]=0;        } /* end of t negative */
       } /* end if (fptt < fp)  */
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {    } 
     for (i=1; i<=imx; i++) {  } 
       ij=(int)(covar[Tvar[j]][i]);  
       Ndum[ij]++;  /**** Prevalence limit (stable or period prevalence)  ****************/
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/  
       if (ij > cptcode) cptcode=ij;  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
     }  {
     /* Computes the prevalence limit in each live state at age x by left multiplying the unit
     for (i=0; i<=cptcode; i++) {       matrix by transitions matrix until convergence is reached */
       if(Ndum[i]!=0) ncodemax[j]++;  
     }    int i, ii,j,k;
     ij=1;    double min, max, maxmin, maxmax,sumnew=0.;
     /* double **matprod2(); */ /* test */
     double **out, cov[NCOVMAX+1], **pmij();
     for (i=1; i<=ncodemax[j]; i++) {    double **newm;
       for (k=0; k<=19; k++) {    double agefin, delaymax=50 ; /* Max number of years to converge */
         if (Ndum[k] != 0) {  
           nbcode[Tvar[j]][ij]=k;    for (ii=1;ii<=nlstate+ndeath;ii++)
           ij++;      for (j=1;j<=nlstate+ndeath;j++){
         }        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         if (ij > ncodemax[j]) break;      }
       }    
     }     cov[1]=1.;
   }     
    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
  for (k=0; k<19; k++) Ndum[k]=0;    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
       newm=savm;
  for (i=1; i<=ncovmodel-2; i++) {      /* Covariates have to be included here again */
       ij=Tvar[i];      cov[2]=agefin;
       Ndum[ij]++;      
     }      for (k=1; k<=cptcovn;k++) {
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
  ij=1;        /*printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtab[%d][Tvar[%d]]=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], ij, k, codtab[ij][Tvar[k]]);*/
  for (i=1; i<=10; i++) {      }
    if((Ndum[i]!=0) && (i<=ncov)){      /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
      Tvaraff[ij]=i;      /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
      ij++;      /*   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]);*/
        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
     cptcoveff=ij-1;      /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
 }      /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
       /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
 /*********** Health Expectancies ****************/      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
       
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)      savm=oldm;
 {      oldm=newm;
   /* Health expectancies */      maxmax=0.;
   int i, j, nhstepm, hstepm, h;      for(j=1;j<=nlstate;j++){
   double age, agelim,hf;        min=1.;
   double ***p3mat;        max=0.;
          for(i=1; i<=nlstate; i++) {
   fprintf(ficreseij,"# Health expectancies\n");          sumnew=0;
   fprintf(ficreseij,"# Age");          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
   for(i=1; i<=nlstate;i++)          prlim[i][j]= newm[i][j]/(1-sumnew);
     for(j=1; j<=nlstate;j++)          /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
       fprintf(ficreseij," %1d-%1d",i,j);          max=FMAX(max,prlim[i][j]);
   fprintf(ficreseij,"\n");          min=FMIN(min,prlim[i][j]);
         }
   hstepm=1*YEARM; /*  Every j years of age (in month) */        maxmin=max-min;
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */        maxmax=FMAX(maxmax,maxmin);
       }
   agelim=AGESUP;      if(maxmax < ftolpl){
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        return prlim;
     /* nhstepm age range expressed in number of stepm */      }
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);    }
     /* Typically if 20 years = 20*12/6=40 stepm */  }
     if (stepm >= YEARM) hstepm=1;  
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */  /*************** transition probabilities ***************/ 
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
     /* Computed by stepm unit matrices, product of hstepm matrices, stored  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */  {
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);      /* According to parameters values stored in x and the covariate's values stored in cov,
        computes the probability to be observed in state j being in state i by appying the
        model to the ncovmodel covariates (including constant and age).
     for(i=1; i<=nlstate;i++)       lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
       for(j=1; j<=nlstate;j++)       and, according on how parameters are entered, the position of the coefficient xij(nc) of the
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){       ncth covariate in the global vector x is given by the formula:
           eij[i][j][(int)age] +=(p3mat[i][j][h]+p3mat[i][j][h+1])/2.0;       j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
         }       j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
           Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
     hf=1;       sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
     if (stepm >= YEARM) hf=stepm/YEARM;       Outputs ps[i][j] the probability to be observed in j being in j according to
        the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
     for(i=1; i<=nlstate;i++)    */
       for(j=1; j<=nlstate;j++){    double s1, lnpijopii;
         if (j==i) eij[i][j][(int)age]= (eij[i][j][(int)age]-0.5*stepm/12./hf);    /*double t34;*/
         }    int i,j,j1, nc, ii, jj;
   
     fprintf(ficreseij,"%3.0f",age );      for(i=1; i<= nlstate; i++){
     for(i=1; i<=nlstate;i++)        for(j=1; j<i;j++){
       for(j=1; j<=nlstate;j++){          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
         fprintf(ficreseij," %9.4f", hf*eij[i][j][(int)age]);            /*lnpijopii += param[i][j][nc]*cov[nc];*/
       }            lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
     fprintf(ficreseij,"\n");  /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          }
   }          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
 }  /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
         }
 /************ Variance ******************/        for(j=i+1; j<=nlstate+ndeath;j++){
 void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
 {            /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
   /* Variance of health expectancies */            lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/  /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
   double **newm;          }
   double **dnewm,**doldm;          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
   int i, j, nhstepm, hstepm, h;        }
   int k, cptcode;      }
   double *xp;      
   double **gp, **gm;      for(i=1; i<= nlstate; i++){
   double ***gradg, ***trgradg;        s1=0;
   double ***p3mat;        for(j=1; j<i; j++){
   double age,agelim;          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
   int theta;          /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
         }
    fprintf(ficresvij,"# Covariances of life expectancies\n");        for(j=i+1; j<=nlstate+ndeath; j++){
   fprintf(ficresvij,"# Age");          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
   for(i=1; i<=nlstate;i++)          /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
     for(j=1; j<=nlstate;j++)        }
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);        /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
   fprintf(ficresvij,"\n");        ps[i][i]=1./(s1+1.);
         /* Computing other pijs */
   xp=vector(1,npar);        for(j=1; j<i; j++)
   dnewm=matrix(1,nlstate,1,npar);          ps[i][j]= exp(ps[i][j])*ps[i][i];
   doldm=matrix(1,nlstate,1,nlstate);        for(j=i+1; j<=nlstate+ndeath; j++)
            ps[i][j]= exp(ps[i][j])*ps[i][i];
   hstepm=1*YEARM; /* Every year of age */        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */      } /* end i */
   agelim = AGESUP;      
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        for(jj=1; jj<= nlstate+ndeath; jj++){
     if (stepm >= YEARM) hstepm=1;          ps[ii][jj]=0;
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */          ps[ii][ii]=1;
     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(ii=1; ii<= nlstate+ndeath; ii++){ */
     for(theta=1; theta <=npar; theta++){      /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
       for(i=1; i<=npar; i++){ /* Computes gradient */      /*  printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);      /*   } */
       }      /*   printf("\n "); */
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        /* } */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      /* printf("\n ");printf("%lf ",cov[2]);*/
       /*
       if (popbased==1) {        for(i=1; i<= npar; i++) printf("%f ",x[i]);
         for(i=1; i<=nlstate;i++)        goto end;*/
           prlim[i][i]=probs[(int)age][i][ij];      return ps;
       }  }
    
       for(j=1; j<= nlstate; j++){  /**************** Product of 2 matrices ******************/
         for(h=0; h<=nhstepm; h++){  
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)  double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];  {
         }    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
       }       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
        /* in, b, out are matrice of pointers which should have been initialized 
       for(i=1; i<=npar; i++) /* Computes gradient */       before: only the contents of out is modified. The function returns
         xp[i] = x[i] - (i==theta ?delti[theta]:0);       a pointer to pointers identical to out */
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      int i, j, k;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    for(i=nrl; i<= nrh; i++)
        for(k=ncolol; k<=ncoloh; k++){
       if (popbased==1) {        out[i][k]=0.;
         for(i=1; i<=nlstate;i++)        for(j=ncl; j<=nch; j++)
           prlim[i][i]=probs[(int)age][i][ij];          out[i][k] +=in[i][j]*b[j][k];
       }      }
     return out;
       for(j=1; j<= nlstate; 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];  /************* Higher Matrix Product ***************/
         }  
       }  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
   {
       for(j=1; j<= nlstate; j++)    /* Computes the transition matrix starting at age 'age' over 
         for(h=0; h<=nhstepm; h++){       'nhstepm*hstepm*stepm' months (i.e. until
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
         }       nhstepm*hstepm matrices. 
     } /* End theta */       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
        (typically every 2 years instead of every month which is too big 
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);       for the memory).
        Model is determined by parameters x and covariates have to be 
     for(h=0; h<=nhstepm; h++)       included manually here. 
       for(j=1; j<=nlstate;j++)  
         for(theta=1; theta <=npar; theta++)       */
           trgradg[h][j][theta]=gradg[h][theta][j];  
     int i, j, d, h, k;
     for(i=1;i<=nlstate;i++)    double **out, cov[NCOVMAX+1];
       for(j=1;j<=nlstate;j++)    double **newm;
         vareij[i][j][(int)age] =0.;  
     for(h=0;h<=nhstepm;h++){    /* Hstepm could be zero and should return the unit matrix */
       for(k=0;k<=nhstepm;k++){    for (i=1;i<=nlstate+ndeath;i++)
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);      for (j=1;j<=nlstate+ndeath;j++){
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);        oldm[i][j]=(i==j ? 1.0 : 0.0);
         for(i=1;i<=nlstate;i++)        po[i][j][0]=(i==j ? 1.0 : 0.0);
           for(j=1;j<=nlstate;j++)      }
             vareij[i][j][(int)age] += doldm[i][j];    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
       }    for(h=1; h <=nhstepm; h++){
     }      for(d=1; d <=hstepm; d++){
     h=1;        newm=savm;
     if (stepm >= YEARM) h=stepm/YEARM;        /* Covariates have to be included here again */
     fprintf(ficresvij,"%.0f ",age );        cov[1]=1.;
     for(i=1; i<=nlstate;i++)        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
       for(j=1; j<=nlstate;j++){        for (k=1; k<=cptcovn;k++) 
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
       }        for (k=1; k<=cptcovage;k++)
     fprintf(ficresvij,"\n");          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     free_matrix(gp,0,nhstepm,1,nlstate);        for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
     free_matrix(gm,0,nhstepm,1,nlstate);          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
     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);        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
   } /* End age */        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
   free_vector(xp,1,npar);                     pmij(pmmij,cov,ncovmodel,x,nlstate));
   free_matrix(doldm,1,nlstate,1,npar);        savm=oldm;
   free_matrix(dnewm,1,nlstate,1,nlstate);        oldm=newm;
       }
 }      for(i=1; i<=nlstate+ndeath; i++)
         for(j=1;j<=nlstate+ndeath;j++) {
 /************ Variance of prevlim ******************/          po[i][j][h]=newm[i][j];
 void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)          /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
 {        }
   /* Variance of prevalence limit */      /*printf("h=%d ",h);*/
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    } /* end h */
   double **newm;  /*     printf("\n H=%d \n",h); */
   double **dnewm,**doldm;    return po;
   int i, j, nhstepm, hstepm;  }
   int k, cptcode;  
   double *xp;  #ifdef NLOPT
   double *gp, *gm;    double  myfunc(unsigned n, const double *p1, double *grad, void *pd){
   double **gradg, **trgradg;    double fret;
   double age,agelim;    double *xt;
   int theta;    int j;
        myfunc_data *d2 = (myfunc_data *) pd;
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");  /* xt = (p1-1); */
   fprintf(ficresvpl,"# Age");    xt=vector(1,n); 
   for(i=1; i<=nlstate;i++)    for (j=1;j<=n;j++)   xt[j]=p1[j-1]; /* xt[1]=p1[0] */
       fprintf(ficresvpl," %1d-%1d",i,i);  
   fprintf(ficresvpl,"\n");    fret=(d2->function)(xt); /*  p xt[1]@8 is fine */
     /* fret=(*func)(xt); /\*  p xt[1]@8 is fine *\/ */
   xp=vector(1,npar);    printf("Function = %.12lf ",fret);
   dnewm=matrix(1,nlstate,1,npar);    for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]); 
   doldm=matrix(1,nlstate,1,nlstate);    printf("\n");
     free_vector(xt,1,n);
   hstepm=1*YEARM; /* Every year of age */    return fret;
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */  }
   agelim = AGESUP;  #endif
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */  
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */  /*************** log-likelihood *************/
     if (stepm >= YEARM) hstepm=1;  double func( double *x)
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */  {
     gradg=matrix(1,npar,1,nlstate);    int i, ii, j, k, mi, d, kk;
     gp=vector(1,nlstate);    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
     gm=vector(1,nlstate);    double **out;
     double sw; /* Sum of weights */
     for(theta=1; theta <=npar; theta++){    double lli; /* Individual log likelihood */
       for(i=1; i<=npar; i++){ /* Computes gradient */    int s1, s2;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    double bbh, survp;
       }    long ipmx;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    /*extern weight */
       for(i=1;i<=nlstate;i++)    /* We are differentiating ll according to initial status */
         gp[i] = prlim[i][i];    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
        /*for(i=1;i<imx;i++) 
       for(i=1; i<=npar; i++) /* Computes gradient */      printf(" %d\n",s[4][i]);
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  
       for(i=1;i<=nlstate;i++)    ++countcallfunc;
         gm[i] = prlim[i][i];  
     cov[1]=1.;
       for(i=1;i<=nlstate;i++)  
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];    for(k=1; k<=nlstate; k++) ll[k]=0.;
     } /* End theta */  
     if(mle==1){
     trgradg =matrix(1,nlstate,1,npar);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         /* Computes the values of the ncovmodel covariates of the model
     for(j=1; j<=nlstate;j++)           depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
       for(theta=1; theta <=npar; theta++)           Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
         trgradg[j][theta]=gradg[theta][j];           to be observed in j being in i according to the model.
          */
     for(i=1;i<=nlstate;i++)        for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
       varpl[i][(int)age] =0.;          cov[2+k]=covar[Tvar[k]][i];
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);        }
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);        /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 
     for(i=1;i<=nlstate;i++)           is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] 
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */           has been calculated etc */
         for(mi=1; mi<= wav[i]-1; mi++){
     fprintf(ficresvpl,"%.0f ",age );          for (ii=1;ii<=nlstate+ndeath;ii++)
     for(i=1; i<=nlstate;i++)            for (j=1;j<=nlstate+ndeath;j++){
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     fprintf(ficresvpl,"\n");              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     free_vector(gp,1,nlstate);            }
     free_vector(gm,1,nlstate);          for(d=0; d<dh[mi][i]; d++){
     free_matrix(gradg,1,npar,1,nlstate);            newm=savm;
     free_matrix(trgradg,1,nlstate,1,npar);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   } /* End age */            for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
   free_vector(xp,1,npar);            }
   free_matrix(doldm,1,nlstate,1,npar);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   free_matrix(dnewm,1,nlstate,1,nlstate);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
 }            oldm=newm;
           } /* end mult */
 /************ Variance of one-step probabilities  ******************/        
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
 {          /* But now since version 0.9 we anticipate for bias at large stepm.
   int i, j;           * If stepm is larger than one month (smallest stepm) and if the exact delay 
   int k=0, cptcode;           * (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
   double *xp;           * we keep into memory the bias bh[mi][i] and also the previous matrix product
   double *gp, *gm;           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
   double **gradg, **trgradg;           * probability in order to take into account the bias as a fraction of the way
   double age,agelim, cov[NCOVMAX];           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
   int theta;           * -stepm/2 to stepm/2 .
   char fileresprob[FILENAMELENGTH];           * For stepm=1 the results are the same as for previous versions of Imach.
            * For stepm > 1 the results are less biased than in previous versions. 
   strcpy(fileresprob,"prob");           */
   strcat(fileresprob,fileres);          s1=s[mw[mi][i]][i];
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {          s2=s[mw[mi+1][i]][i];
     printf("Problem with resultfile: %s\n", fileresprob);          bbh=(double)bh[mi][i]/(double)stepm; 
   }          /* bias bh is positive if real duration
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);           * is higher than the multiple of stepm and negative otherwise.
             */
           /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
   xp=vector(1,npar);          if( s2 > nlstate){ 
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);            /* i.e. if s2 is a death state and if the date of death is known 
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));               then the contribution to the likelihood is the probability to 
                 die between last step unit time and current  step unit time, 
   cov[1]=1;               which is also equal to probability to die before dh 
   for (age=bage; age<=fage; age ++){               minus probability to die before dh-stepm . 
     cov[2]=age;               In version up to 0.92 likelihood was computed
     gradg=matrix(1,npar,1,9);          as if date of death was unknown. Death was treated as any other
     trgradg=matrix(1,9,1,npar);          health state: the date of the interview describes the actual state
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));          and not the date of a change in health state. The former idea was
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));          to consider that at each interview the state was recorded
              (healthy, disable or death) and IMaCh was corrected; but when we
     for(theta=1; theta <=npar; theta++){          introduced the exact date of death then we should have modified
       for(i=1; i<=npar; i++)          the contribution of an exact death to the likelihood. This new
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          contribution is smaller and very dependent of the step unit
                stepm. It is no more the probability to die between last interview
       pmij(pmmij,cov,ncovmodel,xp,nlstate);          and month of death but the probability to survive from last
              interview up to one month before death multiplied by the
       k=0;          probability to die within a month. Thanks to Chris
       for(i=1; i<= (nlstate+ndeath); i++){          Jackson for correcting this bug.  Former versions increased
         for(j=1; j<=(nlstate+ndeath);j++){          mortality artificially. The bad side is that we add another loop
            k=k+1;          which slows down the processing. The difference can be up to 10%
           gp[k]=pmmij[i][j];          lower mortality.
         }            */
       }            lli=log(out[s1][s2] - savm[s1][s2]);
   
       for(i=1; i<=npar; i++)  
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          } else if  (s2==-2) {
                for (j=1,survp=0. ; j<=nlstate; j++) 
               survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
       pmij(pmmij,cov,ncovmodel,xp,nlstate);            /*survp += out[s1][j]; */
       k=0;            lli= log(survp);
       for(i=1; i<=(nlstate+ndeath); i++){          }
         for(j=1; j<=(nlstate+ndeath);j++){          
           k=k+1;          else if  (s2==-4) { 
           gm[k]=pmmij[i][j];            for (j=3,survp=0. ; j<=nlstate; j++)  
         }              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
       }            lli= log(survp); 
                } 
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)  
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];            else if  (s2==-5) { 
     }            for (j=1,survp=0. ; j<=2; j++)  
               survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)            lli= log(survp); 
       for(theta=1; theta <=npar; theta++)          } 
       trgradg[j][theta]=gradg[theta][j];          
            else{
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);            /*  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 */
           } 
      pmij(pmmij,cov,ncovmodel,x,nlstate);          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
           /*if(lli ==000.0)*/
      k=0;          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
      for(i=1; i<=(nlstate+ndeath); i++){          ipmx +=1;
        for(j=1; j<=(nlstate+ndeath);j++){          sw += weight[i];
          k=k+1;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
          gm[k]=pmmij[i][j];        } /* end of wave */
         }      } /* end of individual */
      }    }  else if(mle==2){
            for (i=1,ipmx=0, sw=0.; i<=imx; i++){
      /*printf("\n%d ",(int)age);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){        for(mi=1; mi<= wav[i]-1; mi++){
                  for (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
      }*/              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             }
   fprintf(ficresprob,"\n%d ",(int)age);          for(d=0; d<=dh[mi][i]; d++){
             newm=savm;
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);            for (kk=1; kk<=cptcovage;kk++) {
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   }            }
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));            savm=oldm;
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);            oldm=newm;
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);          } /* end mult */
 }        
  free_vector(xp,1,npar);          s1=s[mw[mi][i]][i];
 fclose(ficresprob);          s2=s[mw[mi+1][i]][i];
           bbh=(double)bh[mi][i]/(double)stepm; 
 }          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
           ipmx +=1;
 /******************* Printing html file ***********/          sw += weight[i];
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, int lastpass, int stepm, int weightopt, char model[],int imx,int jmin, int jmax, double jmeanint,char optionfile[],char optionfilehtm[],char rfileres[] ){          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   int jj1, k1, i1, cpt;        } /* end of wave */
   FILE *fichtm;      } /* end of individual */
   /*char optionfilehtm[FILENAMELENGTH];*/    }  else if(mle==3){  /* exponential inter-extrapolation */
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   strcpy(optionfilehtm,optionfile);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   strcat(optionfilehtm,".htm");        for(mi=1; mi<= wav[i]-1; mi++){
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {          for (ii=1;ii<=nlstate+ndeath;ii++)
     printf("Problem with %s \n",optionfilehtm), exit(0);            for (j=1;j<=nlstate+ndeath;j++){
   }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               savm[ii][j]=(ii==j ? 1.0 : 0.0);
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.71 </font> <hr size=\"2\" color=\"#EC5E5E\">            }
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>          for(d=0; d<dh[mi][i]; d++){
             newm=savm;
 Total number of observations=%d <br>            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>            for (kk=1; kk<=cptcovage;kk++) {
 <hr  size=\"2\" color=\"#EC5E5E\">              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
 <li>Outputs files<br><br>\n            }
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>            savm=oldm;
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>            oldm=newm;
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>          } /* end mult */
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>        
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>          s1=s[mw[mi][i]][i];
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>          s2=s[mw[mi+1][i]][i];
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>          bbh=(double)bh[mi][i]/(double)stepm; 
         - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>          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 */
         - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>          ipmx +=1;
         <br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);          sw += weight[i];
            ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
 fprintf(fichtm," <li>Graphs</li><p>");        } /* end of wave */
       } /* end of individual */
  m=cptcoveff;    }else if (mle==4){  /* ml=4 no inter-extrapolation */
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
  jj1=0;        for(mi=1; mi<= wav[i]-1; mi++){
  for(k1=1; k1<=m;k1++){          for (ii=1;ii<=nlstate+ndeath;ii++)
    for(i1=1; i1<=ncodemax[k1];i1++){            for (j=1;j<=nlstate+ndeath;j++){
        jj1++;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
        if (cptcovn > 0) {              savm[ii][j]=(ii==j ? 1.0 : 0.0);
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");            }
          for (cpt=1; cpt<=cptcoveff;cpt++)          for(d=0; d<dh[mi][i]; d++){
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);            newm=savm;
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
        }            for (kk=1; kk<=cptcovage;kk++) {
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);                }
        for(cpt=1; cpt<nlstate;cpt++){          
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
        }            savm=oldm;
     for(cpt=1; cpt<=nlstate;cpt++) {            oldm=newm;
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident          } /* end mult */
 interval) in state (%d): v%s%d%d.gif <br>        
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);            s1=s[mw[mi][i]][i];
      }          s2=s[mw[mi+1][i]][i];
      for(cpt=1; cpt<=nlstate;cpt++) {          if( s2 > nlstate){ 
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>            lli=log(out[s1][s2] - savm[s1][s2]);
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);          }else{
      }            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
      fprintf(fichtm,"\n<br>- Total life expectancy by age and          }
 health expectancies in states (1) and (2): e%s%d.gif<br>          ipmx +=1;
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);          sw += weight[i];
 fprintf(fichtm,"\n</body>");          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]); */
    }        } /* end of wave */
 fclose(fichtm);      } /* end of individual */
 }    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
 /******************* Gnuplot file **************/        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double agemin, double agemaxpar, double fage , char pathc[], double p[]){        for(mi=1; mi<= wav[i]-1; mi++){
           for (ii=1;ii<=nlstate+ndeath;ii++)
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;            for (j=1;j<=nlstate+ndeath;j++){
               oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   strcpy(optionfilegnuplot,optionfilefiname);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   strcat(optionfilegnuplot,".plt");            }
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {          for(d=0; d<dh[mi][i]; d++){
     printf("Problem with file %s",optionfilegnuplot);            newm=savm;
   }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
 #ifdef windows              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     fprintf(ficgp,"cd \"%s\" \n",pathc);            }
 #endif          
 m=pow(2,cptcoveff);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
  /* 1eme*/            savm=oldm;
   for (cpt=1; cpt<= nlstate ; cpt ++) {            oldm=newm;
    for (k1=1; k1<= m ; k1 ++) {          } /* end mult */
         
 #ifdef windows          s1=s[mw[mi][i]][i];
     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",agemin,fage,fileres,k1-1,k1-1);          s2=s[mw[mi+1][i]][i];
 #endif          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
 #ifdef unix          ipmx +=1;
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);          sw += weight[i];
 #endif          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
 for (i=1; i<= nlstate ; i ++) {        } /* end of wave */
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      } /* end of individual */
   else fprintf(ficgp," \%%*lf (\%%*lf)");    } /* End of if */
 }    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     for (i=1; i<= nlstate ; i ++) {    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    return -l;
   else fprintf(ficgp," \%%*lf (\%%*lf)");  }
 }  
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);  /*************** log-likelihood *************/
      for (i=1; i<= nlstate ; i ++) {  double funcone( double *x)
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");  {
   else fprintf(ficgp," \%%*lf (\%%*lf)");    /* Same as likeli but slower because of a lot of printf and if */
 }      int i, ii, j, k, mi, d, kk;
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
 #ifdef unix    double **out;
 fprintf(ficgp,"\nset ter gif small size 400,300");    double lli; /* Individual log likelihood */
 #endif    double llt;
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    int s1, s2;
    }    double bbh, survp;
   }    /*extern weight */
   /*2 eme*/    /* We are differentiating ll according to initial status */
     /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   for (k1=1; k1<= m ; k1 ++) {    /*for(i=1;i<imx;i++) 
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);      printf(" %d\n",s[4][i]);
        */
     for (i=1; i<= nlstate+1 ; i ++) {    cov[1]=1.;
       k=2*i;  
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);    for(k=1; k<=nlstate; k++) ll[k]=0.;
       for (j=1; j<= nlstate+1 ; j ++) {  
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   else fprintf(ficgp," \%%*lf (\%%*lf)");      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
 }        for(mi=1; mi<= wav[i]-1; mi++){
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");        for (ii=1;ii<=nlstate+ndeath;ii++)
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);          for (j=1;j<=nlstate+ndeath;j++){
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       for (j=1; j<= nlstate+1 ; j ++) {            savm[ii][j]=(ii==j ? 1.0 : 0.0);
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          }
         else fprintf(ficgp," \%%*lf (\%%*lf)");        for(d=0; d<dh[mi][i]; d++){
 }            newm=savm;
       fprintf(ficgp,"\" t\"\" w l 0,");          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);          for (kk=1; kk<=cptcovage;kk++) {
       for (j=1; j<= nlstate+1 ; j ++) {            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          }
   else fprintf(ficgp," \%%*lf (\%%*lf)");          /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
 }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       else fprintf(ficgp,"\" t\"\" w l 0,");          /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
     }          /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);          savm=oldm;
   }          oldm=newm;
          } /* end mult */
   /*3eme*/        
         s1=s[mw[mi][i]][i];
   for (k1=1; k1<= m ; k1 ++) {        s2=s[mw[mi+1][i]][i];
     for (cpt=1; cpt<= nlstate ; cpt ++) {        bbh=(double)bh[mi][i]/(double)stepm; 
       k=2+nlstate*(cpt-1);        /* bias is positive if real duration
       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);         * is higher than the multiple of stepm and negative otherwise.
       for (i=1; i< nlstate ; i ++) {         */
         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);        if( s2 > nlstate && (mle <5) ){  /* Jackson */
       }          lli=log(out[s1][s2] - savm[s1][s2]);
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);        } else if  (s2==-2) {
     }          for (j=1,survp=0. ; j<=nlstate; j++) 
     }            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
            lli= log(survp);
   /* CV preval stat */        }else if (mle==1){
     for (k1=1; k1<= m ; k1 ++) {          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
     for (cpt=1; cpt<nlstate ; cpt ++) {        } else if(mle==2){
       k=3;          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",agemin,agemaxpar,fileres,k1,k+cpt+1,k+1);        } else if(mle==3){  /* exponential inter-extrapolation */
           lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
       for (i=1; i< nlstate ; i ++)        } else if (mle==4){  /* mle=4 no inter-extrapolation */
         fprintf(ficgp,"+$%d",k+i+1);          lli=log(out[s1][s2]); /* Original formula */
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);        } else{  /* mle=0 back to 1 */
                lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
       l=3+(nlstate+ndeath)*cpt;          /*lli=log(out[s1][s2]); */ /* Original formula */
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);        } /* End of if */
       for (i=1; i< nlstate ; i ++) {        ipmx +=1;
         l=3+(nlstate+ndeath)*cpt;        sw += weight[i];
         fprintf(ficgp,"+$%d",l+i+1);        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]); */
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);          if(globpr){
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);          fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
     }   %11.6f %11.6f %11.6f ", \
   }                    num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
                    2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
   /* proba elementaires */          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
    for(i=1,jk=1; i <=nlstate; i++){            llt +=ll[k]*gipmx/gsw;
     for(k=1; k <=(nlstate+ndeath); k++){            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
       if (k != i) {          }
         for(j=1; j <=ncovmodel; j++){          fprintf(ficresilk," %10.6f\n", -llt);
                }
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);      } /* end of wave */
           jk++;    } /* end of individual */
           fprintf(ficgp,"\n");    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
         }    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
       }    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     }    if(globpr==0){ /* First time we count the contributions and weights */
     }      gipmx=ipmx;
       gsw=sw;
     for(jk=1; jk <=m; jk++) {    }
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemaxpar);    return -l;
    i=1;  }
    for(k2=1; k2<=nlstate; k2++) {  
      k3=i;  
      for(k=1; k<=(nlstate+ndeath); k++) {  /*************** function likelione ***********/
        if (k != k2){  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);  {
 ij=1;    /* This routine should help understanding what is done with 
         for(j=3; j <=ncovmodel; j++) {       the selection of individuals/waves and
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {       to check the exact contribution to the likelihood.
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);       Plotting could be done.
             ij++;     */
           }    int k;
           else  
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    if(*globpri !=0){ /* Just counts and sums, no printings */
         }      strcpy(fileresilk,"ilk"); 
           fprintf(ficgp,")/(1");      strcat(fileresilk,fileres);
              if((ficresilk=fopen(fileresilk,"w"))==NULL) {
         for(k1=1; k1 <=nlstate; k1++){          printf("Problem with resultfile: %s\n", fileresilk);
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
 ij=1;      }
           for(j=3; j <=ncovmodel; j++){      fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
             ij++;      for(k=1; k<=nlstate; k++) 
           }        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
           else      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    }
           }  
           fprintf(ficgp,")");    *fretone=(*funcone)(p);
         }    if(*globpri !=0){
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);      fclose(ficresilk);
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
         i=i+ncovmodel;      fflush(fichtm); 
        }    } 
      }    return;
    }  }
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);  
    }  
      /*********** Maximum Likelihood Estimation ***************/
   fclose(ficgp);  
 }  /* end gnuplot */  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   {
     int i,j, iter;
 /*************** Moving average **************/    double **xi;
 void movingaverage(double agedeb, double fage,double agemin, double ***mobaverage){    double fret;
     double fretone; /* Only one call to likelihood */
   int i, cpt, cptcod;    /*  char filerespow[FILENAMELENGTH];*/
     for (agedeb=agemin; agedeb<=fage; agedeb++)  
       for (i=1; i<=nlstate;i++)  #ifdef NLOPT
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)    int creturn;
           mobaverage[(int)agedeb][i][cptcod]=0.;    nlopt_opt opt;
        /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
     for (agedeb=agemin+4; agedeb<=fage; agedeb++){    double *lb;
       for (i=1; i<=nlstate;i++){    double minf; /* the minimum objective value, upon return */
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    double * p1; /* Shifted parameters from 0 instead of 1 */
           for (cpt=0;cpt<=4;cpt++){    myfunc_data dinst, *d = &dinst;
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];  #endif
           }  
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;  
         }    xi=matrix(1,npar,1,npar);
       }    for (i=1;i<=npar;i++)
     }      for (j=1;j<=npar;j++)
            xi[i][j]=(i==j ? 1.0 : 0.0);
 }    printf("Powell\n");  fprintf(ficlog,"Powell\n");
     strcpy(filerespow,"pow"); 
     strcat(filerespow,fileres);
 /************** Forecasting ******************/    if((ficrespow=fopen(filerespow,"w"))==NULL) {
 prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double agemin, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){      printf("Problem with resultfile: %s\n", filerespow);
        fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;    }
   int *popage;    fprintf(ficrespow,"# Powell\n# iter -2*LL");
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;    for (i=1;i<=nlstate;i++)
   double *popeffectif,*popcount;      for(j=1;j<=nlstate+ndeath;j++)
   double ***p3mat;        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
   char fileresf[FILENAMELENGTH];    fprintf(ficrespow,"\n");
   #ifdef POWELL
  agelim=AGESUP;    powell(p,xi,npar,ftol,&iter,&fret,func);
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;  #endif
   
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);  #ifdef NLOPT
    #ifdef NEWUOA
      opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
   strcpy(fileresf,"f");  #else
   strcat(fileresf,fileres);    opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
   if((ficresf=fopen(fileresf,"w"))==NULL) {  #endif
     printf("Problem with forecast resultfile: %s\n", fileresf);    lb=vector(0,npar-1);
   }    for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
   printf("Computing forecasting: result on file '%s' \n", fileresf);    nlopt_set_lower_bounds(opt, lb);
     nlopt_set_initial_step1(opt, 0.1);
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    
     p1= (p+1); /*  p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
   if (mobilav==1) {    d->function = func;
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
     movingaverage(agedeb, fage, agemin, mobaverage);    nlopt_set_min_objective(opt, myfunc, d);
   }    nlopt_set_xtol_rel(opt, ftol);
     if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
   stepsize=(int) (stepm+YEARM-1)/YEARM;      printf("nlopt failed! %d\n",creturn); 
   if (stepm<=12) stepsize=1;    }
      else {
   agelim=AGESUP;      printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
        printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
   hstepm=1;      iter=1; /* not equal */
   hstepm=hstepm/stepm;    }
   yp1=modf(dateintmean,&yp);    nlopt_destroy(opt);
   anprojmean=yp;  #endif
   yp2=modf((yp1*12),&yp);    free_matrix(xi,1,npar,1,npar);
   mprojmean=yp;    fclose(ficrespow);
   yp1=modf((yp2*30.5),&yp);    printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
   jprojmean=yp;    fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
   if(jprojmean==0) jprojmean=1;    fprintf(ficres,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
   if(mprojmean==0) jprojmean=1;  
    }
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);  
    /**** Computes Hessian and covariance matrix ***/
   for(cptcov=1;cptcov<=i2;cptcov++){  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){  {
       k=k+1;    double  **a,**y,*x,pd;
       fprintf(ficresf,"\n#******");    double **hess;
       for(j=1;j<=cptcoveff;j++) {    int i, j,jk;
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    int *indx;
       }  
       fprintf(ficresf,"******\n");    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
       fprintf(ficresf,"# StartingAge FinalAge");    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);    void lubksb(double **a, int npar, int *indx, double b[]) ;
          void ludcmp(double **a, int npar, int *indx, double *d) ;
          double gompertz(double p[]);
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {    hess=matrix(1,npar,1,npar);
         fprintf(ficresf,"\n");  
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);      printf("\nCalculation of the hessian matrix. Wait...\n");
     fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){    for (i=1;i<=npar;i++){
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);      printf("%d",i);fflush(stdout);
           nhstepm = nhstepm/hstepm;      fprintf(ficlog,"%d",i);fflush(ficlog);
               
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
           oldm=oldms;savm=savms;      
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        /*  printf(" %f ",p[i]);
                  printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
           for (h=0; h<=nhstepm; h++){    }
             if (h==(int) (calagedate+YEARM*cpt)) {    
               fprintf(ficresf,"\n %.f ",agedeb+h*hstepm/YEARM*stepm);    for (i=1;i<=npar;i++) {
             }      for (j=1;j<=npar;j++)  {
             for(j=1; j<=nlstate+ndeath;j++) {        if (j>i) { 
               kk1=0.;kk2=0;          printf(".%d%d",i,j);fflush(stdout);
               for(i=1; i<=nlstate;i++) {                        fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
                 if (mobilav==1)          hess[i][j]=hessij(p,delti,i,j,func,npar);
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];          
                 else {          hess[j][i]=hess[i][j];    
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];          /*printf(" %lf ",hess[i][j]);*/
                 }        }
                      }
               }    }
               if (h==(int)(calagedate+12*cpt)){    printf("\n");
                 fprintf(ficresf," %.3f", kk1);    fprintf(ficlog,"\n");
                          
               }    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
             }    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
           }    
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    a=matrix(1,npar,1,npar);
         }    y=matrix(1,npar,1,npar);
       }    x=vector(1,npar);
     }    indx=ivector(1,npar);
   }    for (i=1;i<=npar;i++)
              for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    ludcmp(a,npar,indx,&pd);
   
   fclose(ficresf);    for (j=1;j<=npar;j++) {
 }      for (i=1;i<=npar;i++) x[i]=0;
 /************** Forecasting ******************/      x[j]=1;
 populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double agemin, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){      lubksb(a,npar,indx,x);
        for (i=1;i<=npar;i++){ 
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;        matcov[i][j]=x[i];
   int *popage;      }
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;    }
   double *popeffectif,*popcount;  
   double ***p3mat,***tabpop,***tabpopprev;    printf("\n#Hessian matrix#\n");
   char filerespop[FILENAMELENGTH];    fprintf(ficlog,"\n#Hessian matrix#\n");
     for (i=1;i<=npar;i++) { 
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      for (j=1;j<=npar;j++) { 
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        printf("%.3e ",hess[i][j]);
   agelim=AGESUP;        fprintf(ficlog,"%.3e ",hess[i][j]);
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;      }
        printf("\n");
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);      fprintf(ficlog,"\n");
      }
    
   strcpy(filerespop,"pop");    /* Recompute Inverse */
   strcat(filerespop,fileres);    for (i=1;i<=npar;i++)
   if((ficrespop=fopen(filerespop,"w"))==NULL) {      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
     printf("Problem with forecast resultfile: %s\n", filerespop);    ludcmp(a,npar,indx,&pd);
   }  
   printf("Computing forecasting: result on file '%s' \n", filerespop);    /*  printf("\n#Hessian matrix recomputed#\n");
   
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    for (j=1;j<=npar;j++) {
       for (i=1;i<=npar;i++) x[i]=0;
   if (mobilav==1) {      x[j]=1;
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      lubksb(a,npar,indx,x);
     movingaverage(agedeb, fage, agemin, mobaverage);      for (i=1;i<=npar;i++){ 
   }        y[i][j]=x[i];
         printf("%.3e ",y[i][j]);
   stepsize=(int) (stepm+YEARM-1)/YEARM;        fprintf(ficlog,"%.3e ",y[i][j]);
   if (stepm<=12) stepsize=1;      }
        printf("\n");
   agelim=AGESUP;      fprintf(ficlog,"\n");
      }
   hstepm=1;    */
   hstepm=hstepm/stepm;  
      free_matrix(a,1,npar,1,npar);
   if (popforecast==1) {    free_matrix(y,1,npar,1,npar);
     if((ficpop=fopen(popfile,"r"))==NULL) {    free_vector(x,1,npar);
       printf("Problem with population file : %s\n",popfile);exit(0);    free_ivector(indx,1,npar);
     }    free_matrix(hess,1,npar,1,npar);
     popage=ivector(0,AGESUP);  
     popeffectif=vector(0,AGESUP);  
     popcount=vector(0,AGESUP);  }
      
     i=1;    /*************** hessian matrix ****************/
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
      {
     imx=i;    int i;
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];    int l=1, lmax=20;
   }    double k1,k2;
     double p2[MAXPARM+1]; /* identical to x */
   for(cptcov=1;cptcov<=i2;cptcov++){    double res;
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
       k=k+1;    double fx;
       fprintf(ficrespop,"\n#******");    int k=0,kmax=10;
       for(j=1;j<=cptcoveff;j++) {    double l1;
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
       }    fx=func(x);
       fprintf(ficrespop,"******\n");    for (i=1;i<=npar;i++) p2[i]=x[i];
       fprintf(ficrespop,"# Age");    for(l=0 ; l <=lmax; l++){  /* Enlarging the zone around the Maximum */
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);      l1=pow(10,l);
       if (popforecast==1)  fprintf(ficrespop," [Population]");      delts=delt;
            for(k=1 ; k <kmax; k=k+1){
       for (cpt=0; cpt<=0;cpt++) {        delt = delta*(l1*k);
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);          p2[theta]=x[theta] +delt;
                k1=func(p2)-fx;   /* Might be negative if too close to the theoretical maximum */
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){        p2[theta]=x[theta]-delt;
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);        k2=func(p2)-fx;
           nhstepm = nhstepm/hstepm;        /*res= (k1-2.0*fx+k2)/delt/delt; */
                  res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        
           oldm=oldms;savm=savms;  #ifdef DEBUGHESS
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);          printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
                fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
           for (h=0; h<=nhstepm; h++){  #endif
             if (h==(int) (calagedate+YEARM*cpt)) {        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
             }          k=kmax;
             for(j=1; j<=nlstate+ndeath;j++) {        }
               kk1=0.;kk2=0;        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
               for(i=1; i<=nlstate;i++) {                        k=kmax; l=lmax*10.;
                 if (mobilav==1)        }
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
                 else {          delts=delt;
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];        }
                 }      }
               }    }
               if (h==(int)(calagedate+12*cpt)){    delti[theta]=delts;
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;    return res; 
                   /*fprintf(ficrespop," %.3f", kk1);    
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/  }
               }  
             }  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
             for(i=1; i<=nlstate;i++){  {
               kk1=0.;    int i;
                 for(j=1; j<=nlstate;j++){    int l=1, l1, lmax=20;
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];    double k1,k2,k3,k4,res,fx;
                 }    double p2[MAXPARM+1];
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];    int k;
             }  
     fx=func(x);
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)    for (k=1; k<=2; k++) {
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);      for (i=1;i<=npar;i++) p2[i]=x[i];
           }      p2[thetai]=x[thetai]+delti[thetai]/k;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
         }      k1=func(p2)-fx;
       }    
        p2[thetai]=x[thetai]+delti[thetai]/k;
   /******/      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       k2=func(p2)-fx;
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {    
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);        p2[thetai]=x[thetai]-delti[thetai]/k;
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);      k3=func(p2)-fx;
           nhstepm = nhstepm/hstepm;    
                p2[thetai]=x[thetai]-delti[thetai]/k;
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
           oldm=oldms;savm=savms;      k4=func(p2)-fx;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
           for (h=0; h<=nhstepm; h++){  #ifdef DEBUG
             if (h==(int) (calagedate+YEARM*cpt)) {      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(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);      fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
             }  #endif
             for(j=1; j<=nlstate+ndeath;j++) {    }
               kk1=0.;kk2=0;    return res;
               for(i=1; i<=nlstate;i++) {                }
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];      
               }  /************** Inverse of matrix **************/
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);  void ludcmp(double **a, int n, int *indx, double *d) 
             }  { 
           }    int i,imax,j,k; 
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    double big,dum,sum,temp; 
         }    double *vv; 
       }   
    }    vv=vector(1,n); 
   }    *d=1.0; 
      for (i=1;i<=n;i++) { 
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      big=0.0; 
       for (j=1;j<=n;j++) 
   if (popforecast==1) {        if ((temp=fabs(a[i][j])) > big) big=temp; 
     free_ivector(popage,0,AGESUP);      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
     free_vector(popeffectif,0,AGESUP);      vv[i]=1.0/big; 
     free_vector(popcount,0,AGESUP);    } 
   }    for (j=1;j<=n;j++) { 
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      for (i=1;i<j;i++) { 
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        sum=a[i][j]; 
   fclose(ficrespop);        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
 }        a[i][j]=sum; 
       } 
 /***********************************************/      big=0.0; 
 /**************** Main Program *****************/      for (i=j;i<=n;i++) { 
 /***********************************************/        sum=a[i][j]; 
         for (k=1;k<j;k++) 
 int main(int argc, char *argv[])          sum -= a[i][k]*a[k][j]; 
 {        a[i][j]=sum; 
         if ( (dum=vv[i]*fabs(sum)) >= big) { 
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;          big=dum; 
   double agedeb, agefin,hf;          imax=i; 
   double agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;        } 
       } 
   double fret;      if (j != imax) { 
   double **xi,tmp,delta;        for (k=1;k<=n;k++) { 
           dum=a[imax][k]; 
   double dum; /* Dummy variable */          a[imax][k]=a[j][k]; 
   double ***p3mat;          a[j][k]=dum; 
   int *indx;        } 
   char line[MAXLINE], linepar[MAXLINE];        *d = -(*d); 
   char title[MAXLINE];        vv[imax]=vv[j]; 
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];      } 
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];      indx[j]=imax; 
        if (a[j][j] == 0.0) a[j][j]=TINY; 
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];      if (j != n) { 
         dum=1.0/(a[j][j]); 
   char filerest[FILENAMELENGTH];        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
   char fileregp[FILENAMELENGTH];      } 
   char popfile[FILENAMELENGTH];    } 
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];    free_vector(vv,1,n);  /* Doesn't work */
   int firstobs=1, lastobs=10;  ;
   int sdeb, sfin; /* Status at beginning and end */  } 
   int c,  h , cpt,l;  
   int ju,jl, mi;  void lubksb(double **a, int n, int *indx, double b[]) 
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;  { 
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;    int i,ii=0,ip,j; 
   int mobilav=0,popforecast=0;    double sum; 
   int hstepm, nhstepm;   
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1;    for (i=1;i<=n;i++) { 
       ip=indx[i]; 
   double bage, fage, age, agelim, agebase;      sum=b[ip]; 
   double ftolpl=FTOL;      b[ip]=b[i]; 
   double **prlim;      if (ii) 
   double *severity;        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
   double ***param; /* Matrix of parameters */      else if (sum) ii=i; 
   double  *p;      b[i]=sum; 
   double **matcov; /* Matrix of covariance */    } 
   double ***delti3; /* Scale */    for (i=n;i>=1;i--) { 
   double *delti; /* Scale */      sum=b[i]; 
   double ***eij, ***vareij;      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
   double **varpl; /* Variances of prevalence limits by age */      b[i]=sum/a[i][i]; 
   double *epj, vepp;    } 
   double kk1, kk2;  } 
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;  
    void pstamp(FILE *fichier)
   {
   char version[80]="Imach version 0.71, February 2002, INED-EUROREVES ";    fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
   char *alph[]={"a","a","b","c","d","e"}, str[4];  }
   
   /************ Frequencies ********************/
   char z[1]="c", occ;  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[])
 #include <sys/time.h>  {  /* Some frequencies */
 #include <time.h>    
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];    int i, m, jk, k1,i1, j1, bool, z1,j;
      int first;
   /* long total_usecs;    double ***freq; /* Frequencies */
   struct timeval start_time, end_time;    double *pp, **prop;
      double pos,posprop, k2, dateintsum=0,k2cpt=0;
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */    char fileresp[FILENAMELENGTH];
     
     pp=vector(1,nlstate);
   printf("\n%s",version);    prop=matrix(1,nlstate,iagemin,iagemax+3);
   if(argc <=1){    strcpy(fileresp,"p");
     printf("\nEnter the parameter file name: ");    strcat(fileresp,fileres);
     scanf("%s",pathtot);    if((ficresp=fopen(fileresp,"w"))==NULL) {
   }      printf("Problem with prevalence resultfile: %s\n", fileresp);
   else{      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
     strcpy(pathtot,argv[1]);      exit(0);
   }    }
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
   /*cygwin_split_path(pathtot,path,optionfile);    j1=0;
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/    
   /* cutv(path,optionfile,pathtot,'\\');*/    j=cptcoveff;
     if (cptcovn<1) {j=1;ncodemax[1]=1;}
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);  
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);    first=1;
   chdir(path);  
   replace(pathc,path);    /* for(k1=1; k1<=j ; k1++){   /* Loop on covariates */
     /*  for(i1=1; i1<=ncodemax[k1];i1++){ /* Now it is 2 */
 /*-------- arguments in the command line --------*/    /*    j1++;
   */
   strcpy(fileres,"r");    for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
   strcat(fileres, optionfilefiname);        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
   strcat(fileres,".txt");    /* Other files have txt extension */          scanf("%d", i);*/
         for (i=-5; i<=nlstate+ndeath; i++)  
   /*---------arguments file --------*/          for (jk=-5; jk<=nlstate+ndeath; jk++)  
             for(m=iagemin; m <= iagemax+3; m++)
   if((ficpar=fopen(optionfile,"r"))==NULL)    {              freq[i][jk][m]=0;
     printf("Problem with optionfile %s\n",optionfile);        
     goto end;        for (i=1; i<=nlstate; i++)  
   }          for(m=iagemin; m <= iagemax+3; m++)
             prop[i][m]=0;
   strcpy(filereso,"o");        
   strcat(filereso,fileres);        dateintsum=0;
   if((ficparo=fopen(filereso,"w"))==NULL) {        k2cpt=0;
     printf("Problem with Output resultfile: %s\n", filereso);goto end;        for (i=1; i<=imx; i++) {
   }          bool=1;
           if  (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
   /* Reads comments: lines beginning with '#' */            for (z1=1; z1<=cptcoveff; z1++)       
   while((c=getc(ficpar))=='#' && c!= EOF){              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
     ungetc(c,ficpar);                  /* Tests if the value of each of the covariates of i is equal to filter j1 */
     fgets(line, MAXLINE, ficpar);                bool=0;
     puts(line);                /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtab[%d][%d]=%d, nbcode[Tvaraff][codtab[%d][%d]=%d, j1=%d\n", 
     fputs(line,ficparo);                  bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
   }                  j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
   ungetc(c,ficpar);                /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
               } 
   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);          }
   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);   
   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);          if (bool==1){
 while((c=getc(ficpar))=='#' && c!= EOF){            for(m=firstpass; m<=lastpass; m++){
     ungetc(c,ficpar);              k2=anint[m][i]+(mint[m][i]/12.);
     fgets(line, MAXLINE, ficpar);              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
     puts(line);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
     fputs(line,ficparo);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
   }                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
   ungetc(c,ficpar);                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];
   covar=matrix(0,NCOVMAX,1,n);                }
   cptcovn=0;                
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
                   dateintsum=dateintsum+k2;
   ncovmodel=2+cptcovn;                  k2cpt++;
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */                }
                  /*}*/
   /* Read guess parameters */            }
   /* Reads comments: lines beginning with '#' */          }
   while((c=getc(ficpar))=='#' && c!= EOF){        } /* end i */
     ungetc(c,ficpar);         
     fgets(line, MAXLINE, ficpar);        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
     puts(line);        pstamp(ficresp);
     fputs(line,ficparo);        if  (cptcovn>0) {
   }          fprintf(ficresp, "\n#********** Variable "); 
   ungetc(c,ficpar);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
            fprintf(ficresp, "**********\n#");
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);          fprintf(ficlog, "\n#********** Variable "); 
     for(i=1; i <=nlstate; i++)          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     for(j=1; j <=nlstate+ndeath-1; j++){          fprintf(ficlog, "**********\n#");
       fscanf(ficpar,"%1d%1d",&i1,&j1);        }
       fprintf(ficparo,"%1d%1d",i1,j1);        for(i=1; i<=nlstate;i++) 
       printf("%1d%1d",i,j);          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
       for(k=1; k<=ncovmodel;k++){        fprintf(ficresp, "\n");
         fscanf(ficpar," %lf",&param[i][j][k]);        
         printf(" %lf",param[i][j][k]);        for(i=iagemin; i <= iagemax+3; i++){
         fprintf(ficparo," %lf",param[i][j][k]);          if(i==iagemax+3){
       }            fprintf(ficlog,"Total");
       fscanf(ficpar,"\n");          }else{
       printf("\n");            if(first==1){
       fprintf(ficparo,"\n");              first=0;
     }              printf("See log file for details...\n");
              }
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;            fprintf(ficlog,"Age %d", i);
           }
   p=param[1][1];          for(jk=1; jk <=nlstate ; jk++){
              for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
   /* Reads comments: lines beginning with '#' */              pp[jk] += freq[jk][m][i]; 
   while((c=getc(ficpar))=='#' && c!= EOF){          }
     ungetc(c,ficpar);          for(jk=1; jk <=nlstate ; jk++){
     fgets(line, MAXLINE, ficpar);            for(m=-1, pos=0; m <=0 ; m++)
     puts(line);              pos += freq[jk][m][i];
     fputs(line,ficparo);            if(pp[jk]>=1.e-10){
   }              if(first==1){
   ungetc(c,ficpar);                printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
               }
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */            }else{
   for(i=1; i <=nlstate; i++){              if(first==1)
     for(j=1; j <=nlstate+ndeath-1; j++){                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
       fscanf(ficpar,"%1d%1d",&i1,&j1);              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
       printf("%1d%1d",i,j);            }
       fprintf(ficparo,"%1d%1d",i1,j1);          }
       for(k=1; k<=ncovmodel;k++){  
         fscanf(ficpar,"%le",&delti3[i][j][k]);          for(jk=1; jk <=nlstate ; jk++){
         printf(" %le",delti3[i][j][k]);            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
         fprintf(ficparo," %le",delti3[i][j][k]);              pp[jk] += freq[jk][m][i];
       }          }       
       fscanf(ficpar,"\n");          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
       printf("\n");            pos += pp[jk];
       fprintf(ficparo,"\n");            posprop += prop[jk][i];
     }          }
   }          for(jk=1; jk <=nlstate ; jk++){
   delti=delti3[1][1];            if(pos>=1.e-5){
                if(first==1)
   /* Reads comments: lines beginning with '#' */                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   while((c=getc(ficpar))=='#' && c!= EOF){              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
     ungetc(c,ficpar);            }else{
     fgets(line, MAXLINE, ficpar);              if(first==1)
     puts(line);                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
     fputs(line,ficparo);              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   }            }
   ungetc(c,ficpar);            if( i <= iagemax){
                if(pos>=1.e-5){
   matcov=matrix(1,npar,1,npar);                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
   for(i=1; i <=npar; i++){                /*probs[i][jk][j1]= pp[jk]/pos;*/
     fscanf(ficpar,"%s",&str);                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
     printf("%s",str);              }
     fprintf(ficparo,"%s",str);              else
     for(j=1; j <=i; j++){                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
       fscanf(ficpar," %le",&matcov[i][j]);            }
       printf(" %.5le",matcov[i][j]);          }
       fprintf(ficparo," %.5le",matcov[i][j]);          
     }          for(jk=-1; jk <=nlstate+ndeath; jk++)
     fscanf(ficpar,"\n");            for(m=-1; m <=nlstate+ndeath; m++)
     printf("\n");              if(freq[jk][m][i] !=0 ) {
     fprintf(ficparo,"\n");              if(first==1)
   }                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
   for(i=1; i <=npar; i++)                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
     for(j=i+1;j<=npar;j++)              }
       matcov[i][j]=matcov[j][i];          if(i <= iagemax)
                fprintf(ficresp,"\n");
   printf("\n");          if(first==1)
             printf("Others in log...\n");
           fprintf(ficlog,"\n");
     /*-------- Rewriting paramater file ----------*/        }
      strcpy(rfileres,"r");    /* "Rparameterfile */        /*}*/
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/    }
      strcat(rfileres,".");    /* */    dateintmean=dateintsum/k2cpt; 
      strcat(rfileres,optionfilext);    /* Other files have txt extension */   
     if((ficres =fopen(rfileres,"w"))==NULL) {    fclose(ficresp);
       printf("Problem writing new parameter file: %s\n", fileres);goto end;    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
     }    free_vector(pp,1,nlstate);
     fprintf(ficres,"#%s\n",version);    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
        /* End of Freq */
     /*-------- data file ----------*/  }
     if((fic=fopen(datafile,"r"))==NULL)    {  
       printf("Problem with datafile: %s\n", datafile);goto end;  /************ Prevalence ********************/
     }  void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
   {  
     n= lastobs;    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
     severity = vector(1,maxwav);       in each health status at the date of interview (if between dateprev1 and dateprev2).
     outcome=imatrix(1,maxwav+1,1,n);       We still use firstpass and lastpass as another selection.
     num=ivector(1,n);    */
     moisnais=vector(1,n);   
     annais=vector(1,n);    int i, m, jk, k1, i1, j1, bool, z1,j;
     moisdc=vector(1,n);    double ***freq; /* Frequencies */
     andc=vector(1,n);    double *pp, **prop;
     agedc=vector(1,n);    double pos,posprop; 
     cod=ivector(1,n);    double  y2; /* in fractional years */
     weight=vector(1,n);    int iagemin, iagemax;
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */    int first; /** to stop verbosity which is redirected to log file */
     mint=matrix(1,maxwav,1,n);  
     anint=matrix(1,maxwav,1,n);    iagemin= (int) agemin;
     s=imatrix(1,maxwav+1,1,n);    iagemax= (int) agemax;
     adl=imatrix(1,maxwav+1,1,n);        /*pp=vector(1,nlstate);*/
     tab=ivector(1,NCOVMAX);    prop=matrix(1,nlstate,iagemin,iagemax+3); 
     ncodemax=ivector(1,8);    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
     j1=0;
     i=1;    
     while (fgets(line, MAXLINE, fic) != NULL)    {    /*j=cptcoveff;*/
       if ((i >= firstobs) && (i <=lastobs)) {    if (cptcovn<1) {j=1;ncodemax[1]=1;}
            
         for (j=maxwav;j>=1;j--){    first=1;
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);    for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
           strcpy(line,stra);      /*for(i1=1; i1<=ncodemax[k1];i1++){
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);        j1++;*/
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);        
         }        for (i=1; i<=nlstate; i++)  
                  for(m=iagemin; m <= iagemax+3; m++)
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);            prop[i][m]=0.0;
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);       
         for (i=1; i<=imx; i++) { /* Each individual */
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);          bool=1;
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);          if  (cptcovn>0) {
             for (z1=1; z1<=cptcoveff; z1++) 
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
         for (j=ncov;j>=1;j--){                bool=0;
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);          } 
         }          if (bool==1) { 
         num[i]=atol(stra);            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 */
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/                if(agev[m][i]==0) agev[m][i]=iagemax+1;
                 if(agev[m][i]==1) agev[m][i]=iagemax+2;
         i=i+1;                if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
       }                if (s[m][i]>0 && s[m][i]<=nlstate) { 
     }                  /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
     /* printf("ii=%d", ij);                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
        scanf("%d",i);*/                  prop[s[m][i]][iagemax+3] += weight[i]; 
   imx=i-1; /* Number of individuals */                } 
               }
   /* for (i=1; i<=imx; i++){            } /* end selection of waves */
     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=iagemin; i <= iagemax+3; i++){  
     }          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
             posprop += prop[jk][i]; 
     for (i=1; i<=imx; i++)          } 
     if (covar[1][i]==0) printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));*/          
           for(jk=1; jk <=nlstate ; jk++){     
   /* Calculation of the number of parameter from char model*/            if( i <=  iagemax){ 
   Tvar=ivector(1,15);              if(posprop>=1.e-5){ 
   Tprod=ivector(1,15);                probs[i][jk][j1]= prop[jk][i]/posprop;
   Tvaraff=ivector(1,15);              } else{
   Tvard=imatrix(1,15,1,2);                if(first==1){
   Tage=ivector(1,15);                        first=0;
                      printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others on log file...\n",jk,i,j1,probs[i][jk][j1]);
   if (strlen(model) >1){                }
     j=0, j1=0, k1=1, k2=1;              }
     j=nbocc(model,'+');            } 
     j1=nbocc(model,'*');          }/* end jk */ 
     cptcovn=j+1;        }/* end i */ 
     cptcovprod=j1;      /*} *//* end i1 */
        } /* end j1 */
        
     strcpy(modelsav,model);    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){    /*free_vector(pp,1,nlstate);*/
       printf("Error. Non available option model=%s ",model);    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
       goto end;  }  /* End of prevalence */
     }  
      /************* Waves Concatenation ***************/
     for(i=(j+1); i>=1;i--){  
       cutv(stra,strb,modelsav,'+');  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)
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);  {
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
       /*scanf("%d",i);*/       Death is a valid wave (if date is known).
       if (strchr(strb,'*')) {       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
         cutv(strd,strc,strb,'*');       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
         if (strcmp(strc,"age")==0) {       and mw[mi+1][i]. dh depends on stepm.
           cptcovprod--;       */
           cutv(strb,stre,strd,'V');  
           Tvar[i]=atoi(stre);    int i, mi, m;
           cptcovage++;    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
             Tage[cptcovage]=i;       double sum=0., jmean=0.;*/
             /*printf("stre=%s ", stre);*/    int first;
         }    int j, k=0,jk, ju, jl;
         else if (strcmp(strd,"age")==0) {    double sum=0.;
           cptcovprod--;    first=0;
           cutv(strb,stre,strc,'V');    jmin=1e+5;
           Tvar[i]=atoi(stre);    jmax=-1;
           cptcovage++;    jmean=0.;
           Tage[cptcovage]=i;    for(i=1; i<=imx; i++){
         }      mi=0;
         else {      m=firstpass;
           cutv(strb,stre,strc,'V');      while(s[m][i] <= nlstate){
           Tvar[i]=ncov+k1;        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
           cutv(strb,strc,strd,'V');          mw[++mi][i]=m;
           Tprod[k1]=i;        if(m >=lastpass)
           Tvard[k1][1]=atoi(strc);          break;
           Tvard[k1][2]=atoi(stre);        else
           Tvar[cptcovn+k2]=Tvard[k1][1];          m++;
           Tvar[cptcovn+k2+1]=Tvard[k1][2];      }/* end while */
           for (k=1; k<=lastobs;k++)      if (s[m][i] > nlstate){
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];        mi++;     /* Death is another wave */
           k1++;        /* if(mi==0)  never been interviewed correctly before death */
           k2=k2+2;           /* Only death is a correct wave */
         }        mw[mi][i]=m;
       }      }
       else {  
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/      wav[i]=mi;
        /*  scanf("%d",i);*/      if(mi==0){
       cutv(strd,strc,strb,'V');        nbwarn++;
       Tvar[i]=atoi(strc);        if(first==0){
       }          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
       strcpy(modelsav,stra);            first=1;
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);        }
         scanf("%d",i);*/        if(first==1){
     }          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
 }        }
        } /* end mi==0 */
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);    } /* End individuals */
   printf("cptcovprod=%d ", cptcovprod);  
   scanf("%d ",i);*/    for(i=1; i<=imx; i++){
     fclose(fic);      for(mi=1; mi<wav[i];mi++){
         if (stepm <=0)
     /*  if(mle==1){*/          dh[mi][i]=1;
     if (weightopt != 1) { /* Maximisation without weights*/        else{
       for(i=1;i<=n;i++) weight[i]=1.0;          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
     }            if (agedc[i] < 2*AGESUP) {
     /*-calculation of age at interview from date of interview and age at death -*/              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
     agev=matrix(1,maxwav,1,imx);              if(j==0) j=1;  /* Survives at least one month after exam */
               else if(j<0){
    for (i=1; i<=imx; i++)                nberr++;
      for(m=2; (m<= maxwav); m++)                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]);
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){                j=1; /* Temporary Dangerous patch */
          anint[m][i]=9999;                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);
          s[m][i]=-1;                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]);
        }                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);
                  }
     for (i=1; i<=imx; i++)  {              k=k+1;
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);              if (j >= jmax){
       for(m=1; (m<= maxwav); m++){                jmax=j;
         if(s[m][i] >0){                ijmax=i;
           if (s[m][i] == nlstate+1) {              }
             if(agedc[i]>0)              if (j <= jmin){
               if(moisdc[i]!=99 && andc[i]!=9999)                jmin=j;
               agev[m][i]=agedc[i];                ijmin=i;
             else {              }
               if (andc[i]!=9999){              sum=sum+j;
               printf("Warning negative age at death: %d line:%d\n",num[i],i);              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
               agev[m][i]=-1;              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
               }            }
             }          }
           }          else{
           else if(s[m][i] !=9){ /* Should no more exist */            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);  /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
             if(mint[m][i]==99 || anint[m][i]==9999)  
               agev[m][i]=1;            k=k+1;
             else if(agev[m][i] <agemin){            if (j >= jmax) {
               agemin=agev[m][i];              jmax=j;
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/              ijmax=i;
             }            }
             else if(agev[m][i] >agemax){            else if (j <= jmin){
               agemax=agev[m][i];              jmin=j;
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/              ijmin=i;
             }            }
             /*agev[m][i]=anint[m][i]-annais[i];*/            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
             /*   agev[m][i] = age[i]+2*m;*/            /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
           }            if(j<0){
           else { /* =9 */              nberr++;
             agev[m][i]=1;              printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
             s[m][i]=-1;              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]);
           }            }
         }            sum=sum+j;
         else /*= 0 Unknown */          }
           agev[m][i]=1;          jk= j/stepm;
       }          jl= j -jk*stepm;
              ju= j -(jk+1)*stepm;
     }          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
     for (i=1; i<=imx; i++)  {            if(jl==0){
       for(m=1; (m<= maxwav); m++){              dh[mi][i]=jk;
         if (s[m][i] > (nlstate+ndeath)) {              bh[mi][i]=0;
           printf("Error: Wrong value in nlstate or ndeath\n");              }else{ /* We want a negative bias in order to only have interpolation ie
           goto end;                    * to avoid the price of an extra matrix product in likelihood */
         }              dh[mi][i]=jk+1;
       }              bh[mi][i]=ju;
     }            }
           }else{
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);            if(jl <= -ju){
               dh[mi][i]=jk;
     free_vector(severity,1,maxwav);              bh[mi][i]=jl;       /* bias is positive if real duration
     free_imatrix(outcome,1,maxwav+1,1,n);                                   * is higher than the multiple of stepm and negative otherwise.
     free_vector(moisnais,1,n);                                   */
     free_vector(annais,1,n);            }
     /* free_matrix(mint,1,maxwav,1,n);            else{
        free_matrix(anint,1,maxwav,1,n);*/              dh[mi][i]=jk+1;
     free_vector(moisdc,1,n);              bh[mi][i]=ju;
     free_vector(andc,1,n);            }
             if(dh[mi][i]==0){
                  dh[mi][i]=1; /* At least one step */
     wav=ivector(1,imx);              bh[mi][i]=ju; /* At least one step */
     dh=imatrix(1,lastpass-firstpass+1,1,imx);              /*  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);*/
     mw=imatrix(1,lastpass-firstpass+1,1,imx);            }
              } /* end if mle */
     /* Concatenates waves */        }
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);      } /* end wave */
     }
     jmean=sum/k;
       Tcode=ivector(1,100);    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);
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);    fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %d) Max=%d (%d) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
       ncodemax[1]=1;   }
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);  
        /*********** Tricode ****************************/
    codtab=imatrix(1,100,1,10);  void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
    h=0;  {
    m=pow(2,cptcoveff);    /**< Uses cptcovn+2*cptcovprod as the number of covariates */
      /*      Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 
    for(k=1;k<=cptcoveff; k++){    /* Boring subroutine which should only output nbcode[Tvar[j]][k]
      for(i=1; i <=(m/pow(2,k));i++){     * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
        for(j=1; j <= ncodemax[k]; j++){    /* nbcode[Tvar[j]][1]= 
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){    */
            h++;  
            if (h>m) h=1;codtab[h][k]=j;    int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
          }    int modmaxcovj=0; /* Modality max of covariates j */
        }    int cptcode=0; /* Modality max of covariates j */
      }    int modmincovj=0; /* Modality min of covariates j */
    }  
   
     cptcoveff=0; 
    /*for(i=1; i <=m ;i++){   
      for(k=1; k <=cptcovn; k++){    for (k=-1; k < maxncov; k++) Ndum[k]=0;
        printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);    for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
      }  
      printf("\n");    /* Loop on covariates without age and products */
    }    for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */
    scanf("%d",i);*/      for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the 
                                     modality of this covariate Vj*/ 
    /* Calculates basic frequencies. Computes observed prevalence at single age        ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
        and prints on file fileres'p'. */                                      * If product of Vn*Vm, still boolean *:
                                       * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
                                          * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
            /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                                        modality of the nth covariate of individual i. */
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        if (ij > modmaxcovj)
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          modmaxcovj=ij; 
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        else if (ij < modmincovj) 
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */          modmincovj=ij; 
              if ((ij < -1) && (ij > NCOVMAX)){
     /* For Powell, parameters are in a vector p[] starting at p[1]          printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */          exit(1);
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */        }else
         Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
     if(mle==1){        /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
     }        /* getting the maximum value of the modality of the covariate
               (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
     /*--------- results files --------------*/           female is 1, then modmaxcovj=1.*/
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, weightopt,model);      }
        printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
       cptcode=modmaxcovj;
    jk=1;      /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
    fprintf(ficres,"# Parameters\n");     /*for (i=0; i<=cptcode; i++) {*/
    printf("# Parameters\n");      for (i=modmincovj;  i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
    for(i=1,jk=1; i <=nlstate; i++){        printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
      for(k=1; k <=(nlstate+ndeath); k++){        if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
        if (k != i)          ncodemax[j]++;  /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
          {        }
            printf("%d%d ",i,k);        /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for
            fprintf(ficres,"%1d%1d ",i,k);           historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
            for(j=1; j <=ncovmodel; j++){      } /* Ndum[-1] number of undefined modalities */
              printf("%f ",p[jk]);  
              fprintf(ficres,"%f ",p[jk]);      /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
              jk++;      /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
            }      /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
            printf("\n");         modmincovj=3; modmaxcovj = 7;
            fprintf(ficres,"\n");         There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
          }         which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy 
      }         variables V1_1 and V1_2.
    }         nbcode[Tvar[j]][ij]=k;
  if(mle==1){         nbcode[Tvar[j]][1]=0;
     /* Computing hessian and covariance matrix */         nbcode[Tvar[j]][2]=1;
     ftolhess=ftol; /* Usually correct */         nbcode[Tvar[j]][3]=2;
     hesscov(matcov, p, npar, delti, ftolhess, func);      */
  }      ij=1; /* ij is similar to i but can jumps over null modalities */
     fprintf(ficres,"# Scales\n");      for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
     printf("# Scales\n");        for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
      for(i=1,jk=1; i <=nlstate; i++){          /*recode from 0 */
       for(j=1; j <=nlstate+ndeath; j++){          if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
         if (j!=i) {            nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode. 
           fprintf(ficres,"%1d%1d",i,j);                                       k is a modality. If we have model=V1+V1*sex 
           printf("%1d%1d",i,j);                                       then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
           for(k=1; k<=ncovmodel;k++){            ij++;
             printf(" %.5e",delti[jk]);          }
             fprintf(ficres," %.5e",delti[jk]);          if (ij > ncodemax[j]) break; 
             jk++;        }  /* end of loop on */
           }      } /* end of loop on modality */ 
           printf("\n");    } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/  
           fprintf(ficres,"\n");    
         }   for (k=-1; k< maxncov; k++) Ndum[k]=0; 
       }    
      }    for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */ 
         /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/ 
     k=1;     ij=Tvar[i]; /* Tvar might be -1 if status was unknown */ 
     fprintf(ficres,"# Covariance\n");     Ndum[ij]++; 
     printf("# Covariance\n");   } 
     for(i=1;i<=npar;i++){  
       /*  if (k>nlstate) k=1;   ij=1;
       i1=(i-1)/(ncovmodel*nlstate)+1;   for (i=0; i<=  maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);     /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
       printf("%s%d%d",alph[k],i1,tab[i]);*/     if((Ndum[i]!=0) && (i<=ncovcol)){
       fprintf(ficres,"%3d",i);       /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
       printf("%3d",i);       Tvaraff[ij]=i; /*For printing (unclear) */
       for(j=1; j<=i;j++){       ij++;
         fprintf(ficres," %.5e",matcov[i][j]);     }else
         printf(" %.5e",matcov[i][j]);         Tvaraff[ij]=0;
       }   }
       fprintf(ficres,"\n");   ij--;
       printf("\n");   cptcoveff=ij; /*Number of total covariates*/
       k++;  
     }  }
      
     while((c=getc(ficpar))=='#' && c!= EOF){  
       ungetc(c,ficpar);  /*********** Health Expectancies ****************/
       fgets(line, MAXLINE, ficpar);  
       puts(line);  void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
       fputs(line,ficparo);  
     }  {
     ungetc(c,ficpar);    /* Health expectancies, no variances */
      int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemaxpar, &bage, &fage);    int nhstepma, nstepma; /* Decreasing with age */
        double age, agelim, hf;
     if (fage <= 2) {    double ***p3mat;
       bage = agemin;    double eip;
       fage = agemaxpar;  
     }    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(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");    fprintf(ficreseij,"# Age");
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemaxpar,bage,fage);    for(i=1; i<=nlstate;i++){
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemaxpar,bage,fage);      for(j=1; j<=nlstate;j++){
          fprintf(ficreseij," e%1d%1d ",i,j);
     while((c=getc(ficpar))=='#' && c!= EOF){      }
     ungetc(c,ficpar);      fprintf(ficreseij," e%1d. ",i);
     fgets(line, MAXLINE, ficpar);    }
     puts(line);    fprintf(ficreseij,"\n");
     fputs(line,ficparo);  
   }    
   ungetc(c,ficpar);    if(estepm < stepm){
        printf ("Problem %d lower than %d\n",estepm, stepm);
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);    }
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    else  hstepm=estepm;   
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    /* We compute the life expectancy from trapezoids spaced every estepm months
           * This is mainly to measure the difference between two models: for example
   while((c=getc(ficpar))=='#' && c!= EOF){     * if stepm=24 months pijx are given only every 2 years and by summing them
     ungetc(c,ficpar);     * we are calculating an estimate of the Life Expectancy assuming a linear 
     fgets(line, MAXLINE, ficpar);     * progression in between and thus overestimating or underestimating according
     puts(line);     * to the curvature of the survival function. If, for the same date, we 
     fputs(line,ficparo);     * 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 
   ungetc(c,ficpar);     * hypothesis. A more precise result, taking into account a more precise
       * curvature will be obtained if estepm is as small as stepm. */
   
    dateprev1=anprev1+mprev1/12.+jprev1/365.;    /* For example we decided to compute the life expectancy with the smallest unit */
    dateprev2=anprev2+mprev2/12.+jprev2/365.;    /* 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 
   fscanf(ficpar,"pop_based=%d\n",&popbased);       nstepm is the number of stepm from age to agelin. 
   fprintf(ficparo,"pop_based=%d\n",popbased);         Look at hpijx to understand the reason of that which relies in memory size
   fprintf(ficres,"pop_based=%d\n",popbased);         and note for a fixed period like estepm months */
      /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   while((c=getc(ficpar))=='#' && c!= EOF){       survival function given by stepm (the optimization length). Unfortunately it
     ungetc(c,ficpar);       means that if the survival funtion is printed only each two years of age and if
     fgets(line, MAXLINE, ficpar);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
     puts(line);       results. So we changed our mind and took the option of the best precision.
     fputs(line,ficparo);    */
   }    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   ungetc(c,ficpar);  
     agelim=AGESUP;
   fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mov_average=%d\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);    /* If stepm=6 months */
 fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);      /* Computed by stepm unit matrices, product of hstepm matrices, stored
 fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
       
   /* nhstepm age range expressed in number of stepm */
 while((c=getc(ficpar))=='#' && c!= EOF){    nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
     ungetc(c,ficpar);    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     fgets(line, MAXLINE, ficpar);    /* if (stepm >= YEARM) hstepm=1;*/
     puts(line);    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     fputs(line,ficparo);    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   }  
   ungetc(c,ficpar);    for (age=bage; age<=fage; age ++){ 
       nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);      /* if (stepm >= YEARM) hstepm=1;*/
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
   
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);      /* If stepm=6 months */
       /* Computed by stepm unit matrices, product of hstepma matrices, stored
 /*------------ gnuplot -------------*/         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, agemin,agemaxpar,fage, pathc,p);      
        hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
 /*------------ free_vector  -------------*/      
  chdir(path);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
        
  free_ivector(wav,1,imx);      printf("%d|",(int)age);fflush(stdout);
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);        
  free_ivector(num,1,n);      /* Computing expectancies */
  free_vector(agedc,1,n);      for(i=1; i<=nlstate;i++)
  /*free_matrix(covar,1,NCOVMAX,1,n);*/        for(j=1; j<=nlstate;j++)
  fclose(ficparo);          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
  fclose(ficres);            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
             
 /*--------- index.htm --------*/            /* 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]);*/
   
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres);          }
   
        fprintf(ficreseij,"%3.0f",age );
   /*--------------- Prevalence limit --------------*/      for(i=1; i<=nlstate;i++){
          eip=0;
   strcpy(filerespl,"pl");        for(j=1; j<=nlstate;j++){
   strcat(filerespl,fileres);          eip +=eij[i][j][(int)age];
   if((ficrespl=fopen(filerespl,"w"))==NULL) {          fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;        }
   }        fprintf(ficreseij,"%9.4f", eip );
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);      }
   fprintf(ficrespl,"#Prevalence limit\n");      fprintf(ficreseij,"\n");
   fprintf(ficrespl,"#Age ");      
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);    }
   fprintf(ficrespl,"\n");    free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
      printf("\n");
   prlim=matrix(1,nlstate,1,nlstate);    fprintf(ficlog,"\n");
   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 */  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[] )
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */  
   k=0;  {
   agebase=agemin;    /* Covariances of health expectancies eij and of total life expectancies according
   agelim=agemaxpar;     to initial status i, ei. .
   ftolpl=1.e-10;    */
   i1=cptcoveff;    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
   if (cptcovn < 1){i1=1;}    int nhstepma, nstepma; /* Decreasing with age */
     double age, agelim, hf;
   for(cptcov=1;cptcov<=i1;cptcov++){    double ***p3matp, ***p3matm, ***varhe;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    double **dnewm,**doldm;
         k=k+1;    double *xp, *xm;
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/    double **gp, **gm;
         fprintf(ficrespl,"\n#******");    double ***gradg, ***trgradg;
         for(j=1;j<=cptcoveff;j++)    int theta;
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
         fprintf(ficrespl,"******\n");    double eip, vip;
          
         for (age=agebase; age<=agelim; age++){    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    xp=vector(1,npar);
           fprintf(ficrespl,"%.0f",age );    xm=vector(1,npar);
           for(i=1; i<=nlstate;i++)    dnewm=matrix(1,nlstate*nlstate,1,npar);
           fprintf(ficrespl," %.5f", prlim[i][i]);    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
           fprintf(ficrespl,"\n");    
         }    pstamp(ficresstdeij);
       }    fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
     }    fprintf(ficresstdeij,"# Age");
   fclose(ficrespl);    for(i=1; i<=nlstate;i++){
       for(j=1; j<=nlstate;j++)
   /*------------- h Pij x at various ages ------------*/        fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
        fprintf(ficresstdeij," e%1d. ",i);
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);    }
   if((ficrespij=fopen(filerespij,"w"))==NULL) {    fprintf(ficresstdeij,"\n");
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;  
   }    pstamp(ficrescveij);
   printf("Computing pij: result on file '%s' \n", filerespij);    fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
      fprintf(ficrescveij,"# Age");
   stepsize=(int) (stepm+YEARM-1)/YEARM;    for(i=1; i<=nlstate;i++)
   /*if (stepm<=24) stepsize=2;*/      for(j=1; j<=nlstate;j++){
         cptj= (j-1)*nlstate+i;
   agelim=AGESUP;        for(i2=1; i2<=nlstate;i2++)
   hstepm=stepsize*YEARM; /* Every year of age */          for(j2=1; j2<=nlstate;j2++){
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */            cptj2= (j2-1)*nlstate+i2;
              if(cptj2 <= cptj)
   k=0;              fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
   for(cptcov=1;cptcov<=i1;cptcov++){          }
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      }
       k=k+1;    fprintf(ficrescveij,"\n");
         fprintf(ficrespij,"\n#****** ");    
         for(j=1;j<=cptcoveff;j++)    if(estepm < stepm){
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      printf ("Problem %d lower than %d\n",estepm, stepm);
         fprintf(ficrespij,"******\n");    }
            else  hstepm=estepm;   
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */    /* We compute the life expectancy from trapezoids spaced every estepm months
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */     * This is mainly to measure the difference between two models: for example
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */     * if stepm=24 months pijx are given only every 2 years and by summing them
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);     * we are calculating an estimate of the Life Expectancy assuming a linear 
           oldm=oldms;savm=savms;     * progression in between and thus overestimating or underestimating according
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);       * to the curvature of the survival function. If, for the same date, we 
           fprintf(ficrespij,"# Age");     * estimate the model with stepm=1 month, we can keep estepm to 24 months
           for(i=1; i<=nlstate;i++)     * to compare the new estimate of Life expectancy with the same linear 
             for(j=1; j<=nlstate+ndeath;j++)     * hypothesis. A more precise result, taking into account a more precise
               fprintf(ficrespij," %1d-%1d",i,j);     * curvature will be obtained if estepm is as small as stepm. */
           fprintf(ficrespij,"\n");  
           for (h=0; h<=nhstepm; h++){    /* For example we decided to compute the life expectancy with the smallest unit */
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
             for(i=1; i<=nlstate;i++)       nhstepm is the number of hstepm from age to agelim 
               for(j=1; j<=nlstate+ndeath;j++)       nstepm is the number of stepm from age to agelin. 
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);       Look at hpijx to understand the reason of that which relies in memory size
             fprintf(ficrespij,"\n");       and note for a fixed period like estepm months */
           }    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);       survival function given by stepm (the optimization length). Unfortunately it
           fprintf(ficrespij,"\n");       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 */ 
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/  
     /* If stepm=6 months */
   fclose(ficrespij);    /* nhstepm age range expressed in number of stepm */
     agelim=AGESUP;
     nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
   /*---------- Forecasting ------------------*/    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   if(stepm == 1) {    /* if (stepm >= YEARM) hstepm=1;*/
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
 if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);    
     free_matrix(mint,1,maxwav,1,n);    p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);    p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     free_vector(weight,1,n);}    gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
   else{    trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
     erreur=108;    gp=matrix(0,nhstepm,1,nlstate*nlstate);
     printf("Error %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d\n", erreur, stepm);    gm=matrix(0,nhstepm,1,nlstate*nlstate);
   }  
      for (age=bage; age<=fage; age ++){ 
       nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
   /*---------- Health expectancies and variances ------------*/      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       /* if (stepm >= YEARM) hstepm=1;*/
   strcpy(filerest,"t");      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
   strcat(filerest,fileres);  
   if((ficrest=fopen(filerest,"w"))==NULL) {      /* If stepm=6 months */
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;      /* Computed by stepm unit matrices, product of hstepma matrices, stored
   }         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
   printf("Computing Total LEs with variances: file '%s' \n", filerest);      
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   
   strcpy(filerese,"e");      /* Computing  Variances of health expectancies */
   strcat(filerese,fileres);      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
   if((ficreseij=fopen(filerese,"w"))==NULL) {         decrease memory allocation */
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);      for(theta=1; theta <=npar; theta++){
   }        for(i=1; i<=npar; i++){ 
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
           xm[i] = x[i] - (i==theta ?delti[theta]:0);
  strcpy(fileresv,"v");        }
   strcat(fileresv,fileres);        hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
   if((ficresvij=fopen(fileresv,"w"))==NULL) {        hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);    
   }        for(j=1; j<= nlstate; j++){
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);          for(i=1; i<=nlstate; i++){
             for(h=0; h<=nhstepm-1; h++){
   k=0;              gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
   for(cptcov=1;cptcov<=i1;cptcov++){              gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
     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]]);        for(ij=1; ij<= nlstate*nlstate; ij++)
       fprintf(ficrest,"******\n");          for(h=0; h<=nhstepm-1; h++){
             gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
       fprintf(ficreseij,"\n#****** ");          }
       for(j=1;j<=cptcoveff;j++)      }/* End theta */
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);      
       fprintf(ficreseij,"******\n");      
       for(h=0; h<=nhstepm-1; h++)
       fprintf(ficresvij,"\n#****** ");        for(j=1; j<=nlstate*nlstate;j++)
       for(j=1;j<=cptcoveff;j++)          for(theta=1; theta <=npar; theta++)
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);            trgradg[h][j][theta]=gradg[h][theta][j];
       fprintf(ficresvij,"******\n");      
   
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);       for(ij=1;ij<=nlstate*nlstate;ij++)
       oldm=oldms;savm=savms;        for(ji=1;ji<=nlstate*nlstate;ji++)
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);            varhe[ij][ji][(int)age] =0.;
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);  
       oldm=oldms;savm=savms;       printf("%d|",(int)age);fflush(stdout);
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);       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);
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);          for(ij=1;ij<=nlstate*nlstate;ij++)
       fprintf(ficrest,"\n");            for(ji=1;ji<=nlstate*nlstate;ji++)
               varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
       hf=1;        }
       if (stepm >= YEARM) hf=stepm/YEARM;      }
       epj=vector(1,nlstate+1);  
       for(age=bage; age <=fage ;age++){      /* Computing expectancies */
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);      hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
         if (popbased==1) {      for(i=1; i<=nlstate;i++)
           for(i=1; i<=nlstate;i++)        for(j=1; j<=nlstate;j++)
             prlim[i][i]=probs[(int)age][i][k];          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
         }            eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
                    
         fprintf(ficrest," %.0f",age);            /* 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, epj[nlstate+1]=0.;j <=nlstate;j++){  
           for(i=1, epj[j]=0.;i <=nlstate;i++) {          }
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];  
           }      fprintf(ficresstdeij,"%3.0f",age );
           epj[nlstate+1] +=epj[j];      for(i=1; i<=nlstate;i++){
         }        eip=0.;
         for(i=1, vepp=0.;i <=nlstate;i++)        vip=0.;
           for(j=1;j <=nlstate;j++)        for(j=1; j<=nlstate;j++){
             vepp += vareij[i][j][(int)age];          eip += eij[i][j][(int)age];
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));          for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
         for(j=1;j <=nlstate;j++){            vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(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(ficrest,"\n");        fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
       }      }
     }      fprintf(ficresstdeij,"\n");
   }  
       fprintf(ficrescveij,"%3.0f",age );
   fclose(ficreseij);      for(i=1; i<=nlstate;i++)
   fclose(ficresvij);        for(j=1; j<=nlstate;j++){
   fclose(ficrest);          cptj= (j-1)*nlstate+i;
   fclose(ficpar);          for(i2=1; i2<=nlstate;i2++)
   free_vector(epj,1,nlstate+1);            for(j2=1; j2<=nlstate;j2++){
                cptj2= (j2-1)*nlstate+i2;
   /*------- Variance limit prevalence------*/                if(cptj2 <= cptj)
                 fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
   strcpy(fileresvpl,"vpl");            }
   strcat(fileresvpl,fileres);        }
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {      fprintf(ficrescveij,"\n");
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);     
     exit(0);    }
   }    free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);    free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
   k=0;    free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
   for(cptcov=1;cptcov<=i1;cptcov++){    free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       k=k+1;    printf("\n");
       fprintf(ficresvpl,"\n#****** ");    fprintf(ficlog,"\n");
       for(j=1;j<=cptcoveff;j++)  
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    free_vector(xm,1,npar);
       fprintf(ficresvpl,"******\n");    free_vector(xp,1,npar);
          free_matrix(dnewm,1,nlstate*nlstate,1,npar);
       varpl=matrix(1,nlstate,(int) bage, (int) fage);    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
       oldm=oldms;savm=savms;    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);  }
     }  
  }  /************ 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[])
   fclose(ficresvpl);  {
     /* Variance of health expectancies */
   /*---------- End : free ----------------*/    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);    /* double **newm;*/
      double **dnewm,**doldm;
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);    double **dnewmp,**doldmp;
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);    int i, j, nhstepm, hstepm, h, nstepm ;
      int k, cptcode;
      double *xp;
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);    double **gp, **gm;  /* for var eij */
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);    double ***gradg, ***trgradg; /*for var eij */
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);    double **gradgp, **trgradgp; /* for var p point j */
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);    double *gpp, *gmp; /* for var p point j */
      double **varppt; /* for var p point j nlstate to nlstate+ndeath */
   free_matrix(matcov,1,npar,1,npar);    double ***p3mat;
   free_vector(delti,1,npar);    double age,agelim, hf;
   free_matrix(agev,1,maxwav,1,imx);    double ***mobaverage;
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    int theta;
     char digit[4];
   if(erreur >0)    char digitp[25];
     printf("End of Imach with error %d\n",erreur);  
   else   printf("End of Imach\n");    char fileresprobmorprev[FILENAMELENGTH];
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */  
      if(popbased==1){
   /* 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);*/      if(mobilav!=0)
   /*printf("Total time was %d uSec.\n", total_usecs);*/        strcpy(digitp,"-populbased-mobilav-");
   /*------ End -----------*/      else strcpy(digitp,"-populbased-nomobil-");
     }
     else 
  end:      strcpy(digitp,"-stablbased-");
 #ifdef windows  
   /* chdir(pathcd);*/    if (mobilav!=0) {
 #endif      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
  /*system("wgnuplot graph.plt");*/      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
  /*system("../gp37mgw/wgnuplot graph.plt");*/        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
  /*system("cd ../gp37mgw");*/        printf(" Error in movingaverage mobilav=%d\n",mobilav);
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/      }
  strcpy(plotcmd,GNUPLOTPROGRAM);    }
  strcat(plotcmd," ");  
  strcat(plotcmd,optionfilegnuplot);    strcpy(fileresprobmorprev,"prmorprev"); 
  system(plotcmd);    sprintf(digit,"%-d",ij);
     /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
 #ifdef windows    strcat(fileresprobmorprev,digit); /* Tvar to be done */
   while (z[0] != 'q') {    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
     chdir(path);    strcat(fileresprobmorprev,fileres);
     printf("\nType e to edit output files, c to start again, and q for exiting: ");    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
     scanf("%s",z);      printf("Problem with resultfile: %s\n", fileresprobmorprev);
     if (z[0] == 'c') system("./imach");      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
     else if (z[0] == 'e') {    }
       chdir(path);    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
       system(optionfilehtm);   
     }    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     else if (z[0] == 'q') exit(0);    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);
 #endif    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 size 320, 240");
     /* 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 lt 1 ",subdirf(fileresprobmorprev));
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l lt 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, first2;
     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+1];
     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; */
     tj = (int) pow(2,cptcoveff);
     if (cptcovn<1) {tj=1;ncodemax[1]=1;}
     j1=0;
     for(j1=1; j1<=tj;j1++){
       /*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#");    
         }
         
         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 (age=bage; age<=fage; age ++){ 
           cov[2]=age;
           for (k=1; k<=cptcovn;k++) {
             cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
                                                            * 1  1 1 1 1
                                                            * 2  2 1 1 1
                                                            * 3  1 2 1 1
                                                            */
             /* nbcode[1][1]=0 nbcode[1][2]=1;*/
           }
           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]]];
           
       
           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);
   
           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++;
               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++){
                 /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
                 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 */
         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);
         
         /* 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;first2=2;
         for (k2=1; k2<=(nlstate);k2++){
           for (l2=1; l2<=(nlstate+ndeath);l2++){ 
             if(l2==k2) continue;
             j=(k2-1)*(nlstate+ndeath)+l2;
             for (k1=1; k1<=(nlstate);k1++){
               for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                 if(l1==k1) continue;
                 i=(k1-1)*(nlstate+ndeath)+l1;
                 if(i<=j) continue;
                 for (age=bage; age<=fage; age ++){ 
                   if ((int)age %5==0){
                     v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                     v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     mu1=mu[i][(int) age]/stepm*YEARM ;
                     mu2=mu[j][(int) age]/stepm*YEARM;
                     c12=cv12/sqrt(v1*v2);
                     /* Computing eigen value of matrix of covariance */
                     lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     if ((lc2 <0) || (lc1 <0) ){
                       if(first2==1){
                         first1=0;
                       printf("Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS. See log file for details...\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);
                       }
                       fprintf(ficlog,"Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS.\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);fflush(ficlog);
                       /* lc1=fabs(lc1); */ /* If we want to have them positive */
                       /* lc2=fabs(lc2); */
                     }
   
                     /* Eigen vectors */
                     v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                     /*v21=sqrt(1.-v11*v11); *//* error */
                     v21=(lc1-v1)/cv12*v11;
                     v12=-v21;
                     v22=v11;
                     tnalp=v21/v11;
                     if(first1==1){
                       first1=0;
                       printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     }
                     fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     /*printf(fignu*/
                     /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                     /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                     if(first==1){
                       first=0;
                       fprintf(ficgp,"\nset parametric;unset label");
                       fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
                       fprintf(ficgp,"\nset ter png small size 320, 240");
                       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=pow(2,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%d_1.png\">%s%d_1.png</a><br> \
   <img src=\"%s%d_1.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%d_2.png\">%s%d_2.png</a><br> \
   <img src=\"%s%d_2.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>- Convergence from each state (1 to %d) to period (stable) prevalence in state %d <a href=\"%s%d_%d.png\">%s%d_%d.png</a><br> \
   <img src=\"%s%d_%d.png\">",nlstate, cpt, 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 in each alive state (1 to %d) : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
   <img src=\"%s%d%d.png\">",cpt,nlstate,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=pow(2,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*/
     fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
     for (cpt=1; cpt<= nlstate ; cpt ++) {
       for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
        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 size 320, 240\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else        fprintf(ficgp," \%%*lf (\%%*lf)");
        }
        fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 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 lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }  
        fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
      }
     }
     /*2 eme*/
     fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
     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 size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
       
       for (i=1; i<= nlstate+1 ; i ++) {
         k=2*i;
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         fprintf(ficgp,"\" t\"\" w l lt 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 lt 0");
         else fprintf(ficgp,"\" t\"\" w l lt 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 size 320, 240\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 each multivariate if any */
       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
         k=3;
         fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
         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 size 320, 240\n\
   unset log y\n\
   plot [%.f:%.f]  ", ageminpar, agemaxpar);
         for (i=1; i<= nlstate ; i ++){
           if(i==1)
             fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
           else
             fprintf(ficgp,", '' ");
           l=(nlstate+ndeath)*(i-1)+1;
           fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
           for (j=1; j<= (nlstate-1) ; j ++)
             fprintf(ficgp,"+$%d",k+l+j);
           fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
         } /* nlstate */
         fprintf(ficgp,"\n");
       } /* end cpt state*/ 
     } /* end covariate */  
     
     /* 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");
           }
         }
       }
      }
     /*goto avoid;*/
      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 size 320, 240\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
          for(k2=1; k2<=nlstate; k2++) {
            k3=i;
            for(k=1; k<=(nlstate+ndeath); k++) {
              if (k != k2){
                if(ng==2)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                else
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;/* To be checked else nbcode[0][0] wrong */
                for(j=3; j <=ncovmodel; j++) {
                  /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /\* Bug valgrind *\/ */
                  /*        /\*fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);*\/ */
                  /*        ij++; */
                  /* } */
                  /* else */
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
                fprintf(ficgp,")/(1");
                
                for(k1=1; k1 <=nlstate; k1++){   
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
                  for(j=3; j <=ncovmodel; j++){
                    /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { */
                    /*   fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); */
                    /*   ij++; */
                    /* } */
                    /* else */
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                  }
                  fprintf(ficgp,")");
                }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
              }
            } /* end k */
          } /* end k2 */
        } /* end jk */
      } /* end ng */
    avoid:
      fflush(ficgp); 
   }  /* end gnuplot */
   
   
   /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
     int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
     double age;
   
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          we use a 5 terms etc. until the borders are no more concerned. 
       */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
           }
         }/* end age */
       }/* end mob */
     }else return -1;
     return 0;
   }/* End movingaverage */
   
   
   /************** Forecasting ******************/
   prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
     int *popage;
     double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   
   
   /**************** function prwizard **********************/
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     /* Wizard to print covariance matrix template */
   
     char ca[32], cb[32], cc[32];
     int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
   } /* end of prwizard */
   /******************* Gompertz Likelihood ******************************/
   double gompertz(double x[])
   { 
     double A,B,L=0.0,sump=0.,num=0.;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
   
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
                +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           L=L+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
    
     return -2*L*num/sump;
   }
   
   #ifdef GSL
   /******************* Gompertz_f Likelihood ******************************/
   double gompertz_f(const gsl_vector *v, void *params)
   { 
     double A,B,LL=0.0,sump=0.,num=0.;
     double *x= (double *) v->data;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
     printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
                +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           LL=LL+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
     printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
    
     return -2*LL*num/sump;
   }
   #endif
   
   /******************* Printing html file ***********/
   void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,  double p[],double **matcov,double agemortsup){
     int i,k;
   
     fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
     fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
     for (i=1;i<=2;i++) 
       fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
     fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
     fprintf(fichtm,"</ul>");
   
   fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
   
    fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
   
    for (k=agegomp;k<(agemortsup-2);k++) 
      fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
   
    
     fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
     fprintf(ficgp,"set out \"graphmort.png\"\n "); 
     fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
     fprintf(ficgp, "set ter png small size 320, 240\n set log y\n"); 
     /* fprintf(ficgp, "set size 0.65,0.65\n"); */
     fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
   
   } 
   
   int readdata(char datafile[], int firstobs, int lastobs, int *imax)
   {
   
     /*-------- data file ----------*/
     FILE *fic;
     char dummy[]="                         ";
     int i, j, n;
     int linei, month, year,iout;
     char line[MAXLINE], linetmp[MAXLINE];
     char stra[80], strb[80];
     char *stratrunc;
     int lstra;
   
   
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem while opening datafile: %s\n", datafile);return 1;
       fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
     }
   
     i=1;
     linei=0;
     while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
       linei=linei+1;
       for(j=strlen(line); j>=0;j--){  /* Untabifies line */
         if(line[j] == '\t')
           line[j] = ' ';
       }
       for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
         ;
       };
       line[j+1]=0;  /* Trims blanks at end of line */
       if(line[0]=='#'){
         fprintf(ficlog,"Comment line\n%s\n",line);
         printf("Comment line\n%s\n",line);
         continue;
       }
       trimbb(linetmp,line); /* Trims multiple blanks in line */
       for (j=0; line[j]!='\0';j++){
         line[j]=linetmp[j];
       }
     
   
       for (j=maxwav;j>=1;j--){
         cutv(stra, strb, line, ' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
         /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
             fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);
             return 1;
           }
         }
         s[j][i]=lval;
         
         strcpy(line,stra);
         cutv(stra, strb,line,' ');
         if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
         }
         else  if(iout=sscanf(strb,"%s.",dummy) != 0){
           month=99;
           year=9999;
         }else{
           printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);fflush(ficlog);
           return 1;
         }
         anint[j][i]= (double) year; 
         mint[j][i]= (double)month; 
         strcpy(line,stra);
       } /* ENd Waves */
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.",dummy) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
       }
       andc[i]=(double) year; 
       moisdc[i]=(double) month; 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.", dummy) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
       }
       if (year==9999) {
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given.  Exiting.\n",strb, linei,i,line);
         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
   
       }
       annais[i]=(double)(year);
       moisnais[i]=(double)(month); 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       errno=0;
       dval=strtod(strb,&endptr); 
       if( strb[0]=='\0' || (*endptr != '\0')){
         printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fprintf(ficlog,"Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fflush(ficlog);
         return 1;
       }
       weight[i]=dval; 
       strcpy(line,stra);
       
       for (j=ncovcol;j>=1;j--){
         cutv(stra, strb,line,' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);
             fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);fflush(ficlog);
             return 1;
           }
         }
         if(lval <-1 || lval >1){
           printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);
           fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
           return 1;
         }
         covar[j][i]=(double)(lval);
         strcpy(line,stra);
       }  
       lstra=strlen(stra);
        
       if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
         stratrunc = &(stra[lstra-9]);
         num[i]=atol(stratrunc);
       }
       else
         num[i]=atol(stra);
       /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
         printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
       
       i=i+1;
     } /* End loop reading  data */
   
     *imax=i-1; /* Number of individuals */
     fclose(fic);
    
     return (0);
     endread:
       printf("Exiting readdata: ");
       fclose(fic);
       return (1);
   
   
   
   }
   void removespace(char *str) {
     char *p1 = str, *p2 = str;
     do
       while (*p2 == ' ')
         p2++;
     while (*p1++ = *p2++);
   }
   
   int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
      * Model  V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age
      * - cptcovt total number of covariates of the model nbocc(+)+1 = 8
      * - cptcovn or number of covariates k of the models excluding age*products =6
      * - cptcovage number of covariates with age*products =2
      * - cptcovs number of simple covariates
      * - Tvar[k] is the id of the kth covariate Tvar[1]@12 {1, 2, 3, 8, 10, 11, 8, 3, 7, 8, 5, 6}, thus Tvar[5=V7*V8]=10
      *     which is a new column after the 9 (ncovcol) variables. 
      * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
      * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
      *    Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
      * - Tvard[k]  p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
    */
   {
     int i, j, k, ks;
     int i1, j1, k1, k2;
     char modelsav[80];
     char stra[80], strb[80], strc[80], strd[80],stre[80];
   
     /*removespace(model);*/
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
       j=nbocc(model,'+'); /**< j=Number of '+' */
       j1=nbocc(model,'*'); /**< j1=Number of '*' */
       cptcovs=j+1-j1; /**<  Number of simple covariates V1+V2*age+V3 +V3*V4=> V1 + V3 =2  */
       cptcovt= j+1; /* Number of total covariates in the model V1 + V2*age+ V3 + V3*V4=> 4*/
                     /* including age products which are counted in cptcovage.
                     /* but the covariates which are products must be treated separately: ncovn=4- 2=2 (V1+V3). */
       cptcovprod=j1; /**< Number of products  V1*V2 +v3*age = 2 */
       cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1  */
       strcpy(modelsav,model); 
       if (strstr(model,"AGE") !=0){
         printf("Error. AGE must be in lower case 'age' model=%s ",model);
         fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
         return 1;
       }
       if (strstr(model,"v") !=0){
         printf("Error. 'v' must be in upper case 'V' model=%s ",model);
         fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
         return 1;
       }
       
       /*   Design
        *  V1   V2   V3   V4  V5  V6  V7  V8  V9 Weight
        *  <          ncovcol=8                >
        * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
        *   k=  1    2      3       4     5       6      7        8
        *  cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
        *  covar[k,i], value of kth covariate if not including age for individual i:
        *       covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
        *  Tvar[k] # of the kth covariate:  Tvar[1]=2  Tvar[4]=3 Tvar[8]=8
        *       if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and 
        *  Tage[++cptcovage]=k
        *       if products, new covar are created after ncovcol with k1
        *  Tvar[k]=ncovcol+k1; # of the kth covariate product:  Tvar[5]=ncovcol+1=10  Tvar[6]=ncovcol+1=11
        *  Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
        *  Tvard[k1][1]=m Tvard[k1][2]=m; Tvard[1][1]=5 (V5) Tvard[1][2]=6 Tvard[2][1]=7 (V7) Tvard[2][2]=8
        *  Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
        *  Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
        *  V1   V2   V3   V4  V5  V6  V7  V8  V9  V10  V11
        *  <          ncovcol=8                >
        *       Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8    d1   d1   d2  d2
        *          k=  1    2      3       4     5       6      7        8    9   10   11  12
        *     Tvar[k]= 2    1      3       3    10      11      8        8    5    6    7   8
        * p Tvar[1]@12={2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
        * p Tprod[1]@2={                         6, 5}
        *p Tvard[1][1]@4= {7, 8, 5, 6}
        * covar[k][i]= V2   V1      ?      V3    V5*V6?   V7*V8?  ?       V8   
        *  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
        *How to reorganize?
        * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
        * Tvars {2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
        *       {2,   1,     4,      8,    5,      6,     3,       7}
        * Struct []
        */
   
       /* This loop fills the array Tvar from the string 'model'.*/
       /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
       /*   modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4  */
       /*  k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
       /*  k=3 V4 Tvar[k=3]= 4 (from V4) */
       /*  k=2 V1 Tvar[k=2]= 1 (from V1) */
       /*  k=1 Tvar[1]=2 (from V2) */
       /*  k=5 Tvar[5] */
       /* for (k=1; k<=cptcovn;k++) { */
       /*  cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
       /*  } */
       /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
       /*
        * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
       for(k=cptcovt; k>=1;k--) /**< Number of covariates */
           Tvar[k]=0;
       cptcovage=0;
       for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
         cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' 
                                        modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
           cutl(strc,strd,strb,'*'); /**< strd*strc  Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
           if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
             /* covar is not filled and then is empty */
             cptcovprod--;
             cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
             Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2 */
             cptcovage++; /* Sums the number of covariates which include age as a product */
             Tage[cptcovage]=k;  /* Tage[1] = 4 */
             /*printf("stre=%s ", stre);*/
           } else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutl(stre,strb,strc,'V');
             Tvar[k]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=k;
           } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/
             /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
             cptcovn++;
             cptcovprodnoage++;k1++;
             cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
             Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
                                     because this model-covariate is a construction we invent a new column
                                     ncovcol + k1
                                     If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
                                     Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
             cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */
             Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
             Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
             k2=k2+2;
             Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
             Tvar[cptcovt+k2+1]=Tvard[k1][2];  /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
             for (i=1; i<=lastobs;i++){
               /* Computes the new covariate which is a product of
                  covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
               covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
             }
           } /* End age is not in the model */
         } /* End if model includes a product */
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
           cutl(strd,strc,strb,'V');
           ks++; /**< Number of simple covariates */
           cptcovn++;
           Tvar[k]=atoi(strd);
         }
         strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+V1+V4 */ 
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);*/
   
   
     return (0); /* with covar[new additional covariate if product] and Tage if age */ 
     endread:
       printf("Exiting decodemodel: ");
       return (1);
   }
   
   calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
   {
     int i, m;
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           *nberr++;
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           *nberr++;
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if ((int)andc[i]!=9999){
                   nbwarn++;
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] < *agemin){ 
               *agemin=agev[m][i];
               printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
             }
             else if(agev[m][i] >*agemax){
               *agemax=agev[m][i];
               /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           *nberr++;
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           return 1;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax); 
   
     return (0);
     endread:
       printf("Exiting calandcheckages: ");
       return (1);
   }
   
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
   #ifdef GSL
     const gsl_multimin_fminimizer_type *T;
     size_t iteri = 0, it;
     int rval = GSL_CONTINUE;
     int status = GSL_SUCCESS;
     double ssval;
   #endif
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
     int linei, month, year,iout;
     int jj, ll, li, lj, lk, imk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int itimes;
     int NDIM=2;
     int vpopbased=0;
   
     char ca[32], cb[32], cc[32];
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     struct stat info;
     double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE], pathimach[MAXLINE]; 
     char **bp, *tok, *val; /* pathtot */
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,*tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     int agemortsup;
     float  sumlpop=0.;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
     double **ximort;
     char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
     int *dcwave;
   
     char z[1]="c", occ;
   
     /*char  *strt;*/
     char strtend[80];
   
     long total_usecs;
    
   /*   setlocale (LC_ALL, ""); */
   /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   /*   textdomain (PACKAGE); */
   /*   setlocale (LC_CTYPE, ""); */
   /*   setlocale (LC_MESSAGES, ""); */
   
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     rstart_time = time(NULL);  
     /*  (void) gettimeofday(&start_time,&tzp);*/
     start_time = *localtime(&rstart_time);
     curr_time=start_time;
     /*tml = *localtime(&start_time.tm_sec);*/
     /* strcpy(strstart,asctime(&tml)); */
     strcpy(strstart,asctime(&start_time));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tm_sec = tp.tm_sec +86400; */
   /*  tm = *localtime(&start_time.tm_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.tm_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';
       i=strlen(pathr);
       if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
         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.tm_sec-start_time.tm_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' with errno='%s'\n",optionfile,strerror(errno));
       fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
       fflush(ficlog);
       /* goto end; */
       exit(70); 
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       fputs(line,stdout);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       fputs(line, stdout);
       //puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n);  /**< used in readdata */
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
     /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
        v1+v2*age+v2*v3 makes cptcovn = 3
     */
     if (strlen(model)>1) 
       ncovmodel=2+nbocc(model,'+')+1; /*Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7*/
     else
       ncovmodel=2;
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
     npar= nforce*ncovmodel; /* Number of parameters like aij*/
     if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
       printf("Too complex model for current IMaCh: npar=(nlstate+ndeath-1)*nlstate*ncovmodel=%d >= %d(MAXPARM) or nlstate=%d >= %d(NLSTATEMAX) or ndeath=%d >= %d(NDEATHMAX) or ncovmodel=(k+age+#of+signs)=%d(NCOVMAX) >= %d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fprintf(ficlog,"Too complex model for current IMaCh: %d >=%d(MAXPARM) or %d >=%d(NLSTATEMAX) or %d >=%d(NDEATHMAX) or %d(NCOVMAX) >=%d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fflush(stdout);
       fclose (ficlog);
       goto end;
     }
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     delti=delti3[1][1];
     /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
     if(mle==-1){ /* Print a wizard for help writing covariance matrix */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       fclose (ficparo);
       fclose (ficlog);
       goto end;
       exit(0);
     }
     else if(mle==-3) {
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       matcov=matrix(1,npar,1,npar);
     }
     else{
       /* Read guessed parameters */
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
       
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       for(i=1; i <=nlstate; i++){
         j=0;
         for(jj=1; jj <=nlstate+ndeath; jj++){
           if(jj==i) continue;
           j++;
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1 != i) && (j1 != j)){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
   It might be a problem of design; if ncovcol and the model are correct\n \
   run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           fprintf(ficparo,"%1d%1d",i1,j1);
           if(mle==1)
             printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar," %lf",&param[i][j][k]);
             if(mle==1){
               printf(" %lf",param[i][j][k]);
               fprintf(ficlog," %lf",param[i][j][k]);
             }
             else
               fprintf(ficlog," %lf",param[i][j][k]);
             fprintf(ficparo," %lf",param[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           if(mle==1)
             printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficparo,"\n");
         }
       }  
       fflush(ficlog);
   
       /* Reads scales values */
       p=param[1][1];
       
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
   
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath-1; j++){
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1-i)*(j1-j)!=0){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           printf("%1d%1d",i,j);
           fprintf(ficparo,"%1d%1d",i1,j1);
           fprintf(ficlog,"%1d%1d",i1,j1);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar,"%le",&delti3[i][j][k]);
             printf(" %le",delti3[i][j][k]);
             fprintf(ficparo," %le",delti3[i][j][k]);
             fprintf(ficlog," %le",delti3[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           printf("\n");
           fprintf(ficparo,"\n");
           fprintf(ficlog,"\n");
         }
       }
       fflush(ficlog);
   
       /* Reads covariance matrix */
       delti=delti3[1][1];
   
   
       /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
     
       matcov=matrix(1,npar,1,npar);
       for(i=1; i <=npar; i++)
         for(j=1; j <=npar; j++) matcov[i][j]=0.;
         
       for(i=1; i <=npar; i++){
         fscanf(ficpar,"%s",str);
         if(mle==1)
           printf("%s",str);
         fprintf(ficlog,"%s",str);
         fprintf(ficparo,"%s",str);
         for(j=1; j <=i; j++){
           fscanf(ficpar," %le",&matcov[i][j]);
           if(mle==1){
             printf(" %.5le",matcov[i][j]);
           }
           fprintf(ficlog," %.5le",matcov[i][j]);
           fprintf(ficparo," %.5le",matcov[i][j]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
       for(i=1; i <=npar; i++)
         for(j=i+1;j<=npar;j++)
           matcov[i][j]=matcov[j][i];
       
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       
       fflush(ficlog);
       
       /*-------- Rewriting parameter file ----------*/
       strcpy(rfileres,"r");    /* "Rparameterfile */
       strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
       strcat(rfileres,".");    /* */
       strcat(rfileres,optionfilext);    /* Other files have txt extension */
       if((ficres =fopen(rfileres,"w"))==NULL) {
         printf("Problem writing new parameter file: %s\n", fileres);goto end;
         fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
       }
       fprintf(ficres,"#%s\n",version);
     }    /* End of mle != -3 */
   
   
     n= lastobs;
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */ 
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
   
     /* Reads data from file datafile */
     if (readdata(datafile, firstobs, lastobs, &imx)==1)
       goto end;
   
     /* Calculation of the number of parameters from char model */
       /*    modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 
           k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
           k=3 V4 Tvar[k=3]= 4 (from V4)
           k=2 V1 Tvar[k=2]= 1 (from V1)
           k=1 Tvar[1]=2 (from V2)
       */
     Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
     /*  V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs). 
         For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4, 
         Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
     */
     /* For model-covariate k tells which data-covariate to use but
       because this model-covariate is a construction we invent a new column
       ncovcol + k1
       If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
       Tvar[3=V1*V4]=4+1 etc */
     Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
     /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
        if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2)
     */
     Tvaraff=ivector(1,NCOVMAX); /* Unclear */
     Tvard=imatrix(1,NCOVMAX,1,2); /* n=Tvard[k1][1]  and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm
                               * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd. 
                               * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
     Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
                            4 covariates (3 plus signs)
                            Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
                         */  
   
     if(decodemodel(model, lastobs) == 1)
       goto end;
   
     if((double)(lastobs-imx)/(double)imx > 1.10){
       nbwarn++;
       printf("Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
       fprintf(ficlog,"Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
     }
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
       for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
     }
   
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
       goto end;
   
   
     agegomp=(int)agemin;
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
     /* */
     
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
     /* */
    
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     Ndum =ivector(-1,NCOVMAX);  
     if (ncovmodel > 2)
       tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
   
     codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
     /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
     h=0;
   
   
     /*if (cptcovn > 0) */
         
    
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
       for(i=1; i <=pow(2,cptcoveff-k);i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */ 
         for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
           for(cpt=1; cpt <=pow(2,k-1); cpt++){  /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */ 
             h++;
             if (h>m) 
               h=1;
             /**< codtab(h,k)  k   = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
              *     h     1     2     3     4
              *______________________________  
              *     1 i=1 1 i=1 1 i=1 1 i=1 1
              *     2     2     1     1     1
              *     3 i=2 1     2     1     1
              *     4     2     2     1     1
              *     5 i=3 1 i=2 1     2     1
              *     6     2     1     2     1
              *     7 i=4 1     2     2     1
              *     8     2     2     2     1
              *     9 i=5 1 i=3 1 i=2 1     1
              *    10     2     1     1     1
              *    11 i=6 1     2     1     1
              *    12     2     2     1     1
              *    13 i=7 1 i=4 1     2     1    
              *    14     2     1     2     1
              *    15 i=8 1     2     2     1
              *    16     2     2     2     1
              */
             codtab[h][k]=j;
             /*codtab[h][Tvar[k]]=j;*/
             printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]);
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
          printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
   
    free_ivector(Ndum,-1,NCOVMAX);
   
   
       
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     if(mle==-3)
       strcat(optionfilegnuplot,"-mort");
     strcat(optionfilegnuplot,".gp");
   
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       //fprintf(ficgp,"set missing 'NaNq'\n");
       fprintf(ficgp,"set datafile missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname); /* Main html file */
     if(mle==-3)
       strcat(optionfilehtm,"-mort");
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm);
       exit(0);
     }
   
     strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
     strcat(optionfilehtmcov,"-cov.htm");
     if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtmcov), exit(0);
     }
     else{
     fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
             optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
    - Log file of the run: <a href=\"%s\">%s</a><br>\n\
    - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
    - Date and time at start: %s</ul>\n",\
             optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
             optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
             fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
     chdir(optionfilefiname); /* Move to directory named optionfile */
     
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
   
     fprintf(fichtm,"\n");
     fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
             imx,agemin,agemax,jmin,jmax,jmean);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
   
     if (mle==-3){
       ximort=matrix(1,NDIM,1,NDIM); 
   /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
       cens=ivector(1,n);
       ageexmed=vector(1,n);
       agecens=vector(1,n);
       dcwave=ivector(1,n);
    
       for (i=1; i<=imx; i++){
         dcwave[i]=-1;
         for (m=firstpass; m<=lastpass; m++)
           if (s[m][i]>nlstate) {
             dcwave[i]=m;
             /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
             break;
           }
       }
   
       for (i=1; i<=imx; i++) {
         if (wav[i]>0){
           ageexmed[i]=agev[mw[1][i]][i];
           j=wav[i];
           agecens[i]=1.; 
   
           if (ageexmed[i]> 1 && wav[i] > 0){
             agecens[i]=agev[mw[j][i]][i];
             cens[i]= 1;
           }else if (ageexmed[i]< 1) 
             cens[i]= -1;
           if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
             cens[i]=0 ;
         }
         else cens[i]=-1;
       }
       
       for (i=1;i<=NDIM;i++) {
         for (j=1;j<=NDIM;j++)
           ximort[i][j]=(i == j ? 1.0 : 0.0);
       }
       
       /*p[1]=0.0268; p[NDIM]=0.083;*/
       /*printf("%lf %lf", p[1], p[2]);*/
       
       
   #ifdef GSL
       printf("GSL optimization\n");  fprintf(ficlog,"Powell\n");
   #else
       printf("Powell\n");  fprintf(ficlog,"Powell\n");
   #endif
       strcpy(filerespow,"pow-mort"); 
       strcat(filerespow,fileres);
       if((ficrespow=fopen(filerespow,"w"))==NULL) {
         printf("Problem with resultfile: %s\n", filerespow);
         fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
       }
   #ifdef GSL
       fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
   #else
       fprintf(ficrespow,"# Powell\n# iter -2*LL");
   #endif
       /*  for (i=1;i<=nlstate;i++)
           for(j=1;j<=nlstate+ndeath;j++)
           if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       */
       fprintf(ficrespow,"\n");
   #ifdef GSL
       /* gsl starts here */ 
       T = gsl_multimin_fminimizer_nmsimplex;
       gsl_multimin_fminimizer *sfm = NULL;
       gsl_vector *ss, *x;
       gsl_multimin_function minex_func;
   
       /* Initial vertex size vector */
       ss = gsl_vector_alloc (NDIM);
       
       if (ss == NULL){
         GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
       }
       /* Set all step sizes to 1 */
       gsl_vector_set_all (ss, 0.001);
   
       /* Starting point */
       
       x = gsl_vector_alloc (NDIM);
       
       if (x == NULL){
         gsl_vector_free(ss);
         GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
       }
     
       /* Initialize method and iterate */
       /*     p[1]=0.0268; p[NDIM]=0.083; */
   /*     gsl_vector_set(x, 0, 0.0268); */
   /*     gsl_vector_set(x, 1, 0.083); */
       gsl_vector_set(x, 0, p[1]);
       gsl_vector_set(x, 1, p[2]);
   
       minex_func.f = &gompertz_f;
       minex_func.n = NDIM;
       minex_func.params = (void *)&p; /* ??? */
       
       sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
       gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
       
       printf("Iterations beginning .....\n\n");
       printf("Iter. #    Intercept       Slope     -Log Likelihood     Simplex size\n");
   
       iteri=0;
       while (rval == GSL_CONTINUE){
         iteri++;
         status = gsl_multimin_fminimizer_iterate(sfm);
         
         if (status) printf("error: %s\n", gsl_strerror (status));
         fflush(0);
         
         if (status) 
           break;
         
         rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
         ssval = gsl_multimin_fminimizer_size (sfm);
         
         if (rval == GSL_SUCCESS)
           printf ("converged to a local maximum at\n");
         
         printf("%5d ", iteri);
         for (it = 0; it < NDIM; it++){
           printf ("%10.5f ", gsl_vector_get (sfm->x, it));
         }
         printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
       }
       
       printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
       
       gsl_vector_free(x); /* initial values */
       gsl_vector_free(ss); /* inital step size */
       for (it=0; it<NDIM; it++){
         p[it+1]=gsl_vector_get(sfm->x,it);
         fprintf(ficrespow," %.12lf", p[it]);
       }
       gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1)  */
   #endif
   #ifdef POWELL
        powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
   #endif  
       fclose(ficrespow);
       
       hesscov(matcov, p, NDIM, delti, 1e-4, gompertz); 
   
       for(i=1; i <=NDIM; i++)
         for(j=i+1;j<=NDIM;j++)
           matcov[i][j]=matcov[j][i];
       
       printf("\nCovariance matrix\n ");
       for(i=1; i <=NDIM; i++) {
         for(j=1;j<=NDIM;j++){ 
           printf("%f ",matcov[i][j]);
         }
         printf("\n ");
       }
       
       printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
       for (i=1;i<=NDIM;i++) 
         printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
   
       lsurv=vector(1,AGESUP);
       lpop=vector(1,AGESUP);
       tpop=vector(1,AGESUP);
       lsurv[agegomp]=100000;
       
       for (k=agegomp;k<=AGESUP;k++) {
         agemortsup=k;
         if (p[1]*exp(p[2]*(k-agegomp))>1) break;
       }
       
       for (k=agegomp;k<agemortsup;k++)
         lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
       
       for (k=agegomp;k<agemortsup;k++){
         lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
         sumlpop=sumlpop+lpop[k];
       }
       
       tpop[agegomp]=sumlpop;
       for (k=agegomp;k<(agemortsup-3);k++){
         /*  tpop[k+1]=2;*/
         tpop[k+1]=tpop[k]-lpop[k];
       }
       
       
       printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
       for (k=agegomp;k<(agemortsup-2);k++) 
         printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
       
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
                        stepm, weightopt,\
                        model,imx,p,matcov,agemortsup);
       
       free_vector(lsurv,1,AGESUP);
       free_vector(lpop,1,AGESUP);
       free_vector(tpop,1,AGESUP);
   #ifdef GSL
       free_ivector(cens,1,n);
       free_vector(agecens,1,n);
       free_ivector(dcwave,1,n);
       free_matrix(ximort,1,NDIM,1,NDIM);
   #endif
     } /* Endof if mle==-3 */
     
     else{ /* For mle >=1 */
       globpr=0;/* debug */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       globpr=1; /* to print the contributions */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       if(mle>=1){ /* Could be 1 or 2 */
         mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
       }
       
       /*--------- results files --------------*/
       fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
       
       
       fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(k=1; k <=(nlstate+ndeath); k++){
           if (k != i) {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%lf ",p[jk]);
               fprintf(ficlog,"%lf ",p[jk]);
               fprintf(ficres,"%lf ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       if(mle!=0){
         /* Computing hessian and covariance matrix */
         ftolhess=ftol; /* Usually correct */
         hesscov(matcov, p, npar, delti, ftolhess, func);
       }
       fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
       printf("# Scales (for hessian or gradient estimation)\n");
       fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if (j!=i) {
             fprintf(ficres,"%1d%1d",i,j);
             printf("%1d%1d",i,j);
             fprintf(ficlog,"%1d%1d",i,j);
             for(k=1; k<=ncovmodel;k++){
               printf(" %.5e",delti[jk]);
               fprintf(ficlog," %.5e",delti[jk]);
               fprintf(ficres," %.5e",delti[jk]);
               jk++;
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       
       fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       if(mle>=1)
         printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       /* # 121 Var(a12)\n\ */
       /* # 122 Cov(b12,a12) Var(b12)\n\ */
       /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
       /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
       /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
       /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
       /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
       /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
       
       
       /* Just to have a covariance matrix which will be more understandable
          even is we still don't want to manage dictionary of variables
       */
       for(itimes=1;itimes<=2;itimes++){
         jj=0;
         for(i=1; i <=nlstate; i++){
           for(j=1; j <=nlstate+ndeath; j++){
             if(j==i) continue;
             for(k=1; k<=ncovmodel;k++){
               jj++;
               ca[0]= k+'a'-1;ca[1]='\0';
               if(itimes==1){
                 if(mle>=1)
                   printf("#%1d%1d%d",i,j,k);
                 fprintf(ficlog,"#%1d%1d%d",i,j,k);
                 fprintf(ficres,"#%1d%1d%d",i,j,k);
               }else{
                 if(mle>=1)
                   printf("%1d%1d%d",i,j,k);
                 fprintf(ficlog,"%1d%1d%d",i,j,k);
                 fprintf(ficres,"%1d%1d%d",i,j,k);
               }
               ll=0;
               for(li=1;li <=nlstate; li++){
                 for(lj=1;lj <=nlstate+ndeath; lj++){
                   if(lj==li) continue;
                   for(lk=1;lk<=ncovmodel;lk++){
                     ll++;
                     if(ll<=jj){
                       cb[0]= lk +'a'-1;cb[1]='\0';
                       if(ll<jj){
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }else{
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }
                     }
                   } /* end lk */
                 } /* end lj */
               } /* end li */
               if(mle>=1)
                 printf("\n");
               fprintf(ficlog,"\n");
               fprintf(ficres,"\n");
               numlinepar++;
             } /* end k*/
           } /*end j */
         } /* end i */
       } /* end itimes */
       
       fflush(ficlog);
       fflush(ficres);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       estepm=0;
       fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
       if (estepm==0 || estepm < stepm) estepm=stepm;
       if (fage <= 2) {
         bage = ageminpar;
         fage = agemaxpar;
       }
       
       fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
       fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
       fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       
       dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
       dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
       
       fscanf(ficpar,"pop_based=%d\n",&popbased);
       fprintf(ficparo,"pop_based=%d\n",popbased);   
       fprintf(ficres,"pop_based=%d\n",popbased);   
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
       fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       /* day and month of proj2 are not used but only year anproj2.*/
       
       
       
        /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
       /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                    model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                    jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
         
      /*------------ free_vector  -------------*/
      /*  chdir(path); */
    
       free_ivector(wav,1,imx);
       free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
       free_lvector(num,1,n);
       free_vector(agedc,1,n);
       /*free_matrix(covar,0,NCOVMAX,1,n);*/
       /*free_matrix(covar,1,NCOVMAX,1,n);*/
       fclose(ficparo);
       fclose(ficres);
   
   
       /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
   #include "prevlim.h"  /* Use ficrespl, ficlog */
       fclose(ficrespl);
   
   #ifdef FREEEXIT2
   #include "freeexit2.h"
   #endif
   
       /*------------- h Pij x at various ages ------------*/
   #include "hpijx.h"
       fclose(ficrespij);
   
     /*-------------- Variance of one-step probabilities---*/
       k=1;
       varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
   
   
       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++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           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++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           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);  
           /*
            */
           /* goto endfree; */
    
           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; /* Segmentation fault */
             cptcod= 0; /* To be deleted */
             varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */
             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,NCOVMAX,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++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficresvpl,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvpl,"******\n");
         
           varpl=matrix(1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
           free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
         /*}*/
       }
   
       fclose(ficresvpl);
   
       /*---------- End : free ----------------*/
       if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
     }  /* mle==-3 arrives here for freeing */
    endfree:
       free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
       free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(covar,0,NCOVMAX,1,n);
       free_matrix(matcov,1,npar,1,npar);
       /*free_vector(delti,1,npar);*/
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       free_matrix(agev,1,maxwav,1,imx);
       free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   
       free_ivector(ncodemax,1,NCOVMAX);
       free_ivector(Tvar,1,NCOVMAX);
       free_ivector(Tprod,1,NCOVMAX);
       free_ivector(Tvaraff,1,NCOVMAX);
       free_ivector(Tage,1,NCOVMAX);
   
       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);*/
     rend_time = time(NULL);  
     end_time = *localtime(&rend_time);
     /* tml = *localtime(&end_time.tm_sec); */
     strcpy(strtend,asctime(&end_time));
     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(rend_time -rstart_time,tmpout));
   
     printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
     fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
     fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
     /*  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");
   #ifdef _WIN32
     sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
   #endif
     if(!stat(plotcmd,&info)){
       printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
       if(!stat(getenv("GNUPLOTBIN"),&info)){
         printf("Error or 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("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
       printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
       sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
       if((outcmd=system(plotcmd)) != 0)
         printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
     }
     printf(" Successful, please wait...");
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
       scanf("%s",z);
   /*     if (z[0] == 'c') system("./imach"); */
       if (z[0] == 'e') {
   #ifdef __APPLE__
         sprintf(pplotcmd, "open %s", optionfilehtm);
   #elif __linux
         sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
   #else
         sprintf(pplotcmd, "%s", optionfilehtm);
   #endif
         printf("Starting browser with: %s",pplotcmd);fflush(stdout);
         system(pplotcmd);
       }
       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.1.29  
changed lines
  Added in v.1.162


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