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version 1.52, 2002/07/19 18:49:30 version 1.141, 2014/01/26 02:42:01
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 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.141  2014/01/26 02:42:01  brouard
      * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
   This program computes Healthy Life Expectancies from  
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    Revision 1.140  2011/09/02 10:37:54  brouard
   first survey ("cross") where individuals from different ages are    Summary: times.h is ok with mingw32 now.
   interviewed on their health status or degree of disability (in the  
   case of a health survey which is our main interest) -2- at least a    Revision 1.139  2010/06/14 07:50:17  brouard
   second wave of interviews ("longitudinal") which measure each change    After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
   (if any) in individual health status.  Health expectancies are    I remember having already fixed agemin agemax which are pointers now but not cvs saved.
   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    Revision 1.138  2010/04/30 18:19:40  brouard
   Maximum Likelihood of the parameters involved in the model.  The    *** empty log message ***
   simplest model is the multinomial logistic model where pij is the  
   probability to be observed in state j at the second wave    Revision 1.137  2010/04/29 18:11:38  brouard
   conditional to be observed in state i at the first wave. Therefore    (Module): Checking covariates for more complex models
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    than V1+V2. A lot of change to be done. Unstable.
   'age' is age and 'sex' is a covariate. If you want to have a more  
   complex model than "constant and age", you should modify the program    Revision 1.136  2010/04/26 20:30:53  brouard
   where the markup *Covariates have to be included here again* invites    (Module): merging some libgsl code. Fixing computation
   you to do it.  More covariates you add, slower the    of likelione (using inter/intrapolation if mle = 0) in order to
   convergence.    get same likelihood as if mle=1.
     Some cleaning of code and comments added.
   The advantage of this computer programme, compared to a simple  
   multinomial logistic model, is clear when the delay between waves is not    Revision 1.135  2009/10/29 15:33:14  brouard
   identical for each individual. Also, if a individual missed an    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
   intermediate interview, the information is lost, but taken into  
   account using an interpolation or extrapolation.      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.
   hPijx is the probability to be observed in state i at age x+h  
   conditional to the observed state i at age x. The delay 'h' can be    Revision 1.133  2009/07/06 10:21:25  brouard
   split into an exact number (nh*stepm) of unobserved intermediate    just nforces
   states. This elementary transition (by month or quarter trimester,  
   semester or year) is model as a multinomial logistic.  The hPx    Revision 1.132  2009/07/06 08:22:05  brouard
   matrix is simply the matrix product of nh*stepm elementary matrices    Many tings
   and the contribution of each individual to the likelihood is simply  
   hPijx.    Revision 1.131  2009/06/20 16:22:47  brouard
     Some dimensions resccaled
   Also this programme outputs the covariance matrix of the parameters but also  
   of the life expectancies. It also computes the prevalence limits.    Revision 1.130  2009/05/26 06:44:34  brouard
      (Module): Max Covariate is now set to 20 instead of 8. A
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    lot of cleaning with variables initialized to 0. Trying to make
            Institut national d'études démographiques, Paris.    V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
   This software have been partly granted by Euro-REVES, a concerted action  
   from the European Union.    Revision 1.129  2007/08/31 13:49:27  lievre
   It is copyrighted identically to a GNU software product, ie programme and    Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
   software can be distributed freely for non commercial use. Latest version  
   can be accessed at http://euroreves.ined.fr/imach .    Revision 1.128  2006/06/30 13:02:05  brouard
   **********************************************************************/    (Module): Clarifications on computing e.j
    
 #include <math.h>    Revision 1.127  2006/04/28 18:11:50  brouard
 #include <stdio.h>    (Module): Yes the sum of survivors was wrong since
 #include <stdlib.h>    imach-114 because nhstepm was no more computed in the age
 #include <unistd.h>    loop. Now we define nhstepma in the age loop.
     (Module): In order to speed up (in case of numerous covariates) we
 #define MAXLINE 256    compute health expectancies (without variances) in a first step
 #define GNUPLOTPROGRAM "gnuplot"    and then all the health expectancies with variances or standard
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/    deviation (needs data from the Hessian matrices) which slows the
 #define FILENAMELENGTH 80    computation.
 /*#define DEBUG*/    In the future we should be able to stop the program is only health
 #define windows    expectancies and graph are needed without standard deviations.
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */  
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    Revision 1.126  2006/04/28 17:23:28  brouard
     (Module): Yes the sum of survivors was wrong since
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    imach-114 because nhstepm was no more computed in the age
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    loop. Now we define nhstepma in the age loop.
     Version 0.98h
 #define NINTERVMAX 8  
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    Revision 1.125  2006/04/04 15:20:31  lievre
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    Errors in calculation of health expectancies. Age was not initialized.
 #define NCOVMAX 8 /* Maximum number of covariates */    Forecasting file added.
 #define MAXN 20000  
 #define YEARM 12. /* Number of months per year */    Revision 1.124  2006/03/22 17:13:53  lievre
 #define AGESUP 130    Parameters are printed with %lf instead of %f (more numbers after the comma).
 #define AGEBASE 40    The log-likelihood is printed in the log file
 #ifdef windows  
 #define DIRSEPARATOR '\\'    Revision 1.123  2006/03/20 10:52:43  brouard
 #define ODIRSEPARATOR '/'    * imach.c (Module): <title> changed, corresponds to .htm file
 #else    name. <head> headers where missing.
 #define DIRSEPARATOR '/'  
 #define ODIRSEPARATOR '\\'    * imach.c (Module): Weights can have a decimal point as for
 #endif    English (a comma might work with a correct LC_NUMERIC environment,
     otherwise the weight is truncated).
 char version[80]="Imach version 0.8i, June 2002, INED-EUROREVES ";    Modification of warning when the covariates values are not 0 or
 int erreur; /* Error number */    1.
 int nvar;    Version 0.98g
 int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;  
 int npar=NPARMAX;    Revision 1.122  2006/03/20 09:45:41  brouard
 int nlstate=2; /* Number of live states */    (Module): Weights can have a decimal point as for
 int ndeath=1; /* Number of dead states */    English (a comma might work with a correct LC_NUMERIC environment,
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    otherwise the weight is truncated).
 int popbased=0;    Modification of warning when the covariates values are not 0 or
     1.
 int *wav; /* Number of waves for this individuual 0 is possible */    Version 0.98g
 int maxwav; /* Maxim number of waves */  
 int jmin, jmax; /* min, max spacing between 2 waves */    Revision 1.121  2006/03/16 17:45:01  lievre
 int mle, weightopt;    * imach.c (Module): Comments concerning covariates added
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */  
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    * imach.c (Module): refinements in the computation of lli if
 double jmean; /* Mean space between 2 waves */    status=-2 in order to have more reliable computation if stepm is
 double **oldm, **newm, **savm; /* Working pointers to matrices */    not 1 month. Version 0.98f
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    Revision 1.120  2006/03/16 15:10:38  lievre
 FILE *ficlog;    (Module): refinements in the computation of lli if
 FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;    status=-2 in order to have more reliable computation if stepm is
 FILE *ficresprobmorprev;    not 1 month. Version 0.98f
 FILE *fichtm; /* Html File */  
 FILE *ficreseij;    Revision 1.119  2006/03/15 17:42:26  brouard
 char filerese[FILENAMELENGTH];    (Module): Bug if status = -2, the loglikelihood was
 FILE  *ficresvij;    computed as likelihood omitting the logarithm. Version O.98e
 char fileresv[FILENAMELENGTH];  
 FILE  *ficresvpl;    Revision 1.118  2006/03/14 18:20:07  brouard
 char fileresvpl[FILENAMELENGTH];    (Module): varevsij Comments added explaining the second
 char title[MAXLINE];    table of variances if popbased=1 .
 char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];    (Module): Function pstamp added
     (Module): Version 0.98d
 char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];  
 char filelog[FILENAMELENGTH]; /* Log file */    Revision 1.117  2006/03/14 17:16:22  brouard
 char filerest[FILENAMELENGTH];    (Module): varevsij Comments added explaining the second
 char fileregp[FILENAMELENGTH];    table of variances if popbased=1 .
 char popfile[FILENAMELENGTH];    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
     (Module): Function pstamp added
 char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];    (Module): Version 0.98d
   
 #define NR_END 1    Revision 1.116  2006/03/06 10:29:27  brouard
 #define FREE_ARG char*    (Module): Variance-covariance wrong links and
 #define FTOL 1.0e-10    varian-covariance of ej. is needed (Saito).
   
 #define NRANSI    Revision 1.115  2006/02/27 12:17:45  brouard
 #define ITMAX 200    (Module): One freematrix added in mlikeli! 0.98c
   
 #define TOL 2.0e-4    Revision 1.114  2006/02/26 12:57:58  brouard
     (Module): Some improvements in processing parameter
 #define CGOLD 0.3819660    filename with strsep.
 #define ZEPS 1.0e-10  
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    Revision 1.113  2006/02/24 14:20:24  brouard
     (Module): Memory leaks checks with valgrind and:
 #define GOLD 1.618034    datafile was not closed, some imatrix were not freed and on matrix
 #define GLIMIT 100.0    allocation too.
 #define TINY 1.0e-20  
     Revision 1.112  2006/01/30 09:55:26  brouard
 static double maxarg1,maxarg2;    (Module): Back to gnuplot.exe instead of wgnuplot.exe
 #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 1.111  2006/01/25 20:38:18  brouard
      (Module): Lots of cleaning and bugs added (Gompertz)
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    (Module): Comments can be added in data file. Missing date values
 #define rint(a) floor(a+0.5)    can be a simple dot '.'.
   
 static double sqrarg;    Revision 1.110  2006/01/25 00:51:50  brouard
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    (Module): Lots of cleaning and bugs added (Gompertz)
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  
     Revision 1.109  2006/01/24 19:37:15  brouard
 int imx;    (Module): Comments (lines starting with a #) are allowed in data.
 int stepm;  
 /* Stepm, step in month: minimum step interpolation*/    Revision 1.108  2006/01/19 18:05:42  lievre
     Gnuplot problem appeared...
 int estepm;    To be fixed
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/  
     Revision 1.107  2006/01/19 16:20:37  brouard
 int m,nb;    Test existence of gnuplot in imach path
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    Revision 1.106  2006/01/19 13:24:36  brouard
 double **pmmij, ***probs, ***mobaverage;    Some cleaning and links added in html output
 double dateintmean=0;  
     Revision 1.105  2006/01/05 20:23:19  lievre
 double *weight;    *** empty log message ***
 int **s; /* Status */  
 double *agedc, **covar, idx;    Revision 1.104  2005/09/30 16:11:43  lievre
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    (Module): sump fixed, loop imx fixed, and simplifications.
     (Module): If the status is missing at the last wave but we know
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    that the person is alive, then we can code his/her status as -2
 double ftolhess; /* Tolerance for computing hessian */    (instead of missing=-1 in earlier versions) and his/her
     contributions to the likelihood is 1 - Prob of dying from last
 /**************** split *************************/    health status (= 1-p13= p11+p12 in the easiest case of somebody in
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    the healthy state at last known wave). Version is 0.98
 {  
    char *s;                             /* pointer */    Revision 1.103  2005/09/30 15:54:49  lievre
    int  l1, l2;                         /* length counters */    (Module): sump fixed, loop imx fixed, and simplifications.
   
    l1 = strlen( path );                 /* length of path */    Revision 1.102  2004/09/15 17:31:30  brouard
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    Add the possibility to read data file including tab characters.
    s= strrchr( path, DIRSEPARATOR );            /* find last / */  
    if ( s == NULL ) {                   /* no directory, so use current */    Revision 1.101  2004/09/15 10:38:38  brouard
      /*if(strrchr(path, ODIRSEPARATOR )==NULL)    Fix on curr_time
        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/  
 #if     defined(__bsd__)                /* get current working directory */    Revision 1.100  2004/07/12 18:29:06  brouard
       extern char       *getwd( );    Add version for Mac OS X. Just define UNIX in Makefile
   
       if ( getwd( dirc ) == NULL ) {    Revision 1.99  2004/06/05 08:57:40  brouard
 #else    *** empty log message ***
       extern char       *getcwd( );  
     Revision 1.98  2004/05/16 15:05:56  brouard
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    New version 0.97 . First attempt to estimate force of mortality
 #endif    directly from the data i.e. without the need of knowing the health
          return( GLOCK_ERROR_GETCWD );    state at each age, but using a Gompertz model: log u =a + b*age .
       }    This is the basic analysis of mortality and should be done before any
       strcpy( name, path );             /* we've got it */    other analysis, in order to test if the mortality estimated from the
    } else {                             /* strip direcotry from path */    cross-longitudinal survey is different from the mortality estimated
       s++;                              /* after this, the filename */    from other sources like vital statistic data.
       l2 = strlen( s );                 /* length of filename */  
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    The same imach parameter file can be used but the option for mle should be -3.
       strcpy( name, s );                /* save file name */  
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    Agnès, who wrote this part of the code, tried to keep most of the
       dirc[l1-l2] = 0;                  /* add zero */    former routines in order to include the new code within the former code.
    }  
    l1 = strlen( dirc );                 /* length of directory */    The output is very simple: only an estimate of the intercept and of
 #ifdef windows    the slope with 95% confident intervals.
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  
 #else    Current limitations:
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }    A) Even if you enter covariates, i.e. with the
 #endif    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
    s = strrchr( name, '.' );            /* find last / */    B) There is no computation of Life Expectancy nor Life Table.
    s++;  
    strcpy(ext,s);                       /* save extension */    Revision 1.97  2004/02/20 13:25:42  lievre
    l1= strlen( name);    Version 0.96d. Population forecasting command line is (temporarily)
    l2= strlen( s)+1;    suppressed.
    strncpy( finame, name, l1-l2);  
    finame[l1-l2]= 0;    Revision 1.96  2003/07/15 15:38:55  brouard
    return( 0 );                         /* we're done */    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
 }    rewritten within the same printf. Workaround: many printfs.
   
     Revision 1.95  2003/07/08 07:54:34  brouard
 /******************************************/    * imach.c (Repository):
     (Repository): Using imachwizard code to output a more meaningful covariance
 void replace(char *s, char*t)    matrix (cov(a12,c31) instead of numbers.
 {  
   int i;    Revision 1.94  2003/06/27 13:00:02  brouard
   int lg=20;    Just cleaning
   i=0;  
   lg=strlen(t);    Revision 1.93  2003/06/25 16:33:55  brouard
   for(i=0; i<= lg; i++) {    (Module): On windows (cygwin) function asctime_r doesn't
     (s[i] = t[i]);    exist so I changed back to asctime which exists.
     if (t[i]== '\\') s[i]='/';    (Module): Version 0.96b
   }  
 }    Revision 1.92  2003/06/25 16:30:45  brouard
     (Module): On windows (cygwin) function asctime_r doesn't
 int nbocc(char *s, char occ)    exist so I changed back to asctime which exists.
 {  
   int i,j=0;    Revision 1.91  2003/06/25 15:30:29  brouard
   int lg=20;    * imach.c (Repository): Duplicated warning errors corrected.
   i=0;    (Repository): Elapsed time after each iteration is now output. It
   lg=strlen(s);    helps to forecast when convergence will be reached. Elapsed time
   for(i=0; i<= lg; i++) {    is stamped in powell.  We created a new html file for the graphs
   if  (s[i] == occ ) j++;    concerning matrix of covariance. It has extension -cov.htm.
   }  
   return j;    Revision 1.90  2003/06/24 12:34:15  brouard
 }    (Module): Some bugs corrected for windows. Also, when
     mle=-1 a template is output in file "or"mypar.txt with the design
 void cutv(char *u,char *v, char*t, char occ)    of the covariance matrix to be input.
 {  
   /* cuts string t into u and v where u is ended by char occ excluding it    Revision 1.89  2003/06/24 12:30:52  brouard
      and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)    (Module): Some bugs corrected for windows. Also, when
      gives u="abcedf" and v="ghi2j" */    mle=-1 a template is output in file "or"mypar.txt with the design
   int i,lg,j,p=0;    of the covariance matrix to be input.
   i=0;  
   for(j=0; j<=strlen(t)-1; j++) {    Revision 1.88  2003/06/23 17:54:56  brouard
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    * 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.
   }  
     Revision 1.87  2003/06/18 12:26:01  brouard
   lg=strlen(t);    Version 0.96
   for(j=0; j<p; j++) {  
     (u[j] = t[j]);    Revision 1.86  2003/06/17 20:04:08  brouard
   }    (Module): Change position of html and gnuplot routines and added
      u[p]='\0';    routine fileappend.
   
    for(j=0; j<= lg; j++) {    Revision 1.85  2003/06/17 13:12:43  brouard
     if (j>=(p+1))(v[j-p-1] = t[j]);    * imach.c (Repository): Check when date of death was earlier that
   }    current date of interview. It may happen when the death was just
 }    prior to the death. In this case, dh was negative and likelihood
     was wrong (infinity). We still send an "Error" but patch by
 /********************** nrerror ********************/    assuming that the date of death was just one stepm after the
     interview.
 void nrerror(char error_text[])    (Repository): Because some people have very long ID (first column)
 {    we changed int to long in num[] and we added a new lvector for
   fprintf(stderr,"ERREUR ...\n");    memory allocation. But we also truncated to 8 characters (left
   fprintf(stderr,"%s\n",error_text);    truncation)
   exit(1);    (Repository): No more line truncation errors.
 }  
 /*********************** vector *******************/    Revision 1.84  2003/06/13 21:44:43  brouard
 double *vector(int nl, int nh)    * imach.c (Repository): Replace "freqsummary" at a correct
 {    place. It differs from routine "prevalence" which may be called
   double *v;    many times. Probs is memory consuming and must be used with
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    parcimony.
   if (!v) nrerror("allocation failure in vector");    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
   return v-nl+NR_END;  
 }    Revision 1.83  2003/06/10 13:39:11  lievre
     *** empty log message ***
 /************************ free vector ******************/  
 void free_vector(double*v, int nl, int nh)    Revision 1.82  2003/06/05 15:57:20  brouard
 {    Add log in  imach.c and  fullversion number is now printed.
   free((FREE_ARG)(v+nl-NR_END));  
 }  */
   /*
 /************************ivector *******************************/     Interpolated Markov Chain
 int *ivector(long nl,long nh)  
 {    Short summary of the programme:
   int *v;    
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    This program computes Healthy Life Expectancies from
   if (!v) nrerror("allocation failure in ivector");    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
   return v-nl+NR_END;    first survey ("cross") where individuals from different ages are
 }    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
 /******************free ivector **************************/    second wave of interviews ("longitudinal") which measure each change
 void free_ivector(int *v, long nl, long nh)    (if any) in individual health status.  Health expectancies are
 {    computed from the time spent in each health state according to a
   free((FREE_ARG)(v+nl-NR_END));    model. More health states you consider, more time is necessary to reach the
 }    Maximum Likelihood of the parameters involved in the model.  The
     simplest model is the multinomial logistic model where pij is the
 /******************* imatrix *******************************/    probability to be observed in state j at the second wave
 int **imatrix(long nrl, long nrh, long ncl, long nch)    conditional to be observed in state i at the first wave. Therefore
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
 {    'age' is age and 'sex' is a covariate. If you want to have a more
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    complex model than "constant and age", you should modify the program
   int **m;    where the markup *Covariates have to be included here again* invites
      you to do it.  More covariates you add, slower the
   /* allocate pointers to rows */    convergence.
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");    The advantage of this computer programme, compared to a simple
   m += NR_END;    multinomial logistic model, is clear when the delay between waves is not
   m -= nrl;    identical for each individual. Also, if a individual missed an
      intermediate interview, the information is lost, but taken into
      account using an interpolation or extrapolation.  
   /* allocate rows and set pointers to them */  
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    hPijx is the probability to be observed in state i at age x+h
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    conditional to the observed state i at age x. The delay 'h' can be
   m[nrl] += NR_END;    split into an exact number (nh*stepm) of unobserved intermediate
   m[nrl] -= ncl;    states. This elementary transition (by month, quarter,
      semester or year) is modelled as a multinomial logistic.  The hPx
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    matrix is simply the matrix product of nh*stepm elementary matrices
      and the contribution of each individual to the likelihood is simply
   /* return pointer to array of pointers to rows */    hPijx.
   return m;  
 }    Also this programme outputs the covariance matrix of the parameters but also
     of the life expectancies. It also computes the period (stable) prevalence. 
 /****************** free_imatrix *************************/    
 void free_imatrix(m,nrl,nrh,ncl,nch)    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
       int **m;             Institut national d'études démographiques, Paris.
       long nch,ncl,nrh,nrl;    This software have been partly granted by Euro-REVES, a concerted action
      /* free an int matrix allocated by imatrix() */    from the European Union.
 {    It is copyrighted identically to a GNU software product, ie programme and
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    software can be distributed freely for non commercial use. Latest version
   free((FREE_ARG) (m+nrl-NR_END));    can be accessed at http://euroreves.ined.fr/imach .
 }  
     Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
 /******************* matrix *******************************/    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
 double **matrix(long nrl, long nrh, long ncl, long nch)    
 {    **********************************************************************/
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  /*
   double **m;    main
     read parameterfile
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    read datafile
   if (!m) nrerror("allocation failure 1 in matrix()");    concatwav
   m += NR_END;    freqsummary
   m -= nrl;    if (mle >= 1)
       mlikeli
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    print results files
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    if mle==1 
   m[nrl] += NR_END;       computes hessian
   m[nrl] -= ncl;    read end of parameter file: agemin, agemax, bage, fage, estepm
         begin-prev-date,...
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    open gnuplot file
   return m;    open html file
 }    period (stable) prevalence
      for age prevalim()
 /*************************free matrix ************************/    h Pij x
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    variance of p varprob
 {    forecasting if prevfcast==1 prevforecast call prevalence()
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    health expectancies
   free((FREE_ARG)(m+nrl-NR_END));    Variance-covariance of DFLE
 }    prevalence()
      movingaverage()
 /******************* ma3x *******************************/    varevsij() 
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    if popbased==1 varevsij(,popbased)
 {    total life expectancies
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    Variance of period (stable) prevalence
   double ***m;   end
   */
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;  
   m -= nrl;   
   #include <math.h>
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  #include <stdio.h>
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  #include <stdlib.h>
   m[nrl] += NR_END;  #include <string.h>
   m[nrl] -= ncl;  #include <unistd.h>
   
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  #include <limits.h>
   #include <sys/types.h>
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  #include <sys/stat.h>
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  #include <errno.h>
   m[nrl][ncl] += NR_END;  extern int errno;
   m[nrl][ncl] -= nll;  
   for (j=ncl+1; j<=nch; j++)  #ifdef LINUX
     m[nrl][j]=m[nrl][j-1]+nlay;  #include <time.h>
    #include "timeval.h"
   for (i=nrl+1; i<=nrh; i++) {  #else
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  #include <sys/time.h>
     for (j=ncl+1; j<=nch; j++)  #endif
       m[i][j]=m[i][j-1]+nlay;  
   }  #ifdef GSL
   return m;  #include <gsl/gsl_errno.h>
 }  #include <gsl/gsl_multimin.h>
   #endif
 /*************************free ma3x ************************/  
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  /* #include <libintl.h> */
 {  /* #define _(String) gettext (String) */
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
   free((FREE_ARG)(m+nrl-NR_END));  
 }  #define GNUPLOTPROGRAM "gnuplot"
   /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 /***************** f1dim *************************/  #define FILENAMELENGTH 132
 extern int ncom;  
 extern double *pcom,*xicom;  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 extern double (*nrfunc)(double []);  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
    
 double f1dim(double x)  #define MAXPARM 128 /* Maximum number of parameters for the optimization */
 {  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
   int j;  
   double f;  #define NINTERVMAX 8
   double *xt;  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
    #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
   xt=vector(1,ncom);  #define NCOVMAX 20 /* Maximum number of covariates */
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  #define MAXN 20000
   f=(*nrfunc)(xt);  #define YEARM 12. /* Number of months per year */
   free_vector(xt,1,ncom);  #define AGESUP 130
   return f;  #define AGEBASE 40
 }  #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
   #ifdef UNIX
 /*****************brent *************************/  #define DIRSEPARATOR '/'
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  #define CHARSEPARATOR "/"
 {  #define ODIRSEPARATOR '\\'
   int iter;  #else
   double a,b,d,etemp;  #define DIRSEPARATOR '\\'
   double fu,fv,fw,fx;  #define CHARSEPARATOR "\\"
   double ftemp;  #define ODIRSEPARATOR '/'
   double p,q,r,tol1,tol2,u,v,w,x,xm;  #endif
   double e=0.0;  
    /* $Id$ */
   a=(ax < cx ? ax : cx);  /* $State$ */
   b=(ax > cx ? ax : cx);  
   x=w=v=bx;  char version[]="Imach version 0.98n, January 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Sicentific Research 25293121)";
   fw=fv=fx=(*f)(x);  char fullversion[]="$Revision$ $Date$"; 
   for (iter=1;iter<=ITMAX;iter++) {  char strstart[80];
     xm=0.5*(a+b);  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  int nvar=0, nforce=0; /* Number of variables, number of forces */
     printf(".");fflush(stdout);  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov=0; /* Number of covariates, of covariates with '*age' */
     fprintf(ficlog,".");fflush(ficlog);  int npar=NPARMAX;
 #ifdef DEBUG  int nlstate=2; /* Number of live states */
     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);  int ndeath=1; /* Number of dead states */
     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);  int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  int popbased=0;
 #endif  
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  int *wav; /* Number of waves for this individuual 0 is possible */
       *xmin=x;  int maxwav=0; /* Maxim number of waves */
       return fx;  int jmin=0, jmax=0; /* min, max spacing between 2 waves */
     }  int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
     ftemp=fu;  int gipmx=0, gsw=0; /* Global variables on the number of contributions 
     if (fabs(e) > tol1) {                     to the likelihood and the sum of weights (done by funcone)*/
       r=(x-w)*(fx-fv);  int mle=1, weightopt=0;
       q=(x-v)*(fx-fw);  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
       p=(x-v)*q-(x-w)*r;  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
       q=2.0*(q-r);  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
       if (q > 0.0) p = -p;             * wave mi and wave mi+1 is not an exact multiple of stepm. */
       q=fabs(q);  double jmean=1; /* Mean space between 2 waves */
       etemp=e;  double **oldm, **newm, **savm; /* Working pointers to matrices */
       e=d;  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  /*FILE *fic ; */ /* Used in readdata only */
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
       else {  FILE *ficlog, *ficrespow;
         d=p/q;  int globpr=0; /* Global variable for printing or not */
         u=x+d;  double fretone; /* Only one call to likelihood */
         if (u-a < tol2 || b-u < tol2)  long ipmx=0; /* Number of contributions */
           d=SIGN(tol1,xm-x);  double sw; /* Sum of weights */
       }  char filerespow[FILENAMELENGTH];
     } else {  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  FILE *ficresilk;
     }  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  FILE *ficresprobmorprev;
     fu=(*f)(u);  FILE *fichtm, *fichtmcov; /* Html File */
     if (fu <= fx) {  FILE *ficreseij;
       if (u >= x) a=x; else b=x;  char filerese[FILENAMELENGTH];
       SHFT(v,w,x,u)  FILE *ficresstdeij;
         SHFT(fv,fw,fx,fu)  char fileresstde[FILENAMELENGTH];
         } else {  FILE *ficrescveij;
           if (u < x) a=u; else b=u;  char filerescve[FILENAMELENGTH];
           if (fu <= fw || w == x) {  FILE  *ficresvij;
             v=w;  char fileresv[FILENAMELENGTH];
             w=u;  FILE  *ficresvpl;
             fv=fw;  char fileresvpl[FILENAMELENGTH];
             fw=fu;  char title[MAXLINE];
           } else if (fu <= fv || v == x || v == w) {  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
             v=u;  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
             fv=fu;  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
           }  char command[FILENAMELENGTH];
         }  int  outcmd=0;
   }  
   nrerror("Too many iterations in brent");  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   *xmin=x;  
   return fx;  char filelog[FILENAMELENGTH]; /* Log file */
 }  char filerest[FILENAMELENGTH];
   char fileregp[FILENAMELENGTH];
 /****************** mnbrak ***********************/  char popfile[FILENAMELENGTH];
   
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
             double (*func)(double))  
 {  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
   double ulim,u,r,q, dum;  struct timezone tzp;
   double fu;  extern int gettimeofday();
    struct tm tmg, tm, tmf, *gmtime(), *localtime();
   *fa=(*func)(*ax);  long time_value;
   *fb=(*func)(*bx);  extern long time();
   if (*fb > *fa) {  char strcurr[80], strfor[80];
     SHFT(dum,*ax,*bx,dum)  
       SHFT(dum,*fb,*fa,dum)  char *endptr;
       }  long lval;
   *cx=(*bx)+GOLD*(*bx-*ax);  double dval;
   *fc=(*func)(*cx);  
   while (*fb > *fc) {  #define NR_END 1
     r=(*bx-*ax)*(*fb-*fc);  #define FREE_ARG char*
     q=(*bx-*cx)*(*fb-*fa);  #define FTOL 1.0e-10
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  #define NRANSI 
     ulim=(*bx)+GLIMIT*(*cx-*bx);  #define ITMAX 200 
     if ((*bx-u)*(u-*cx) > 0.0) {  
       fu=(*func)(u);  #define TOL 2.0e-4 
     } else if ((*cx-u)*(u-ulim) > 0.0) {  
       fu=(*func)(u);  #define CGOLD 0.3819660 
       if (fu < *fc) {  #define ZEPS 1.0e-10 
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
           SHFT(*fb,*fc,fu,(*func)(u))  
           }  #define GOLD 1.618034 
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  #define GLIMIT 100.0 
       u=ulim;  #define TINY 1.0e-20 
       fu=(*func)(u);  
     } else {  static double maxarg1,maxarg2;
       u=(*cx)+GOLD*(*cx-*bx);  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
       fu=(*func)(u);  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
     }    
     SHFT(*ax,*bx,*cx,u)  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
       SHFT(*fa,*fb,*fc,fu)  #define rint(a) floor(a+0.5)
       }  
 }  static double sqrarg;
   #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
 /*************** linmin ************************/  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
   int agegomp= AGEGOMP;
 int ncom;  
 double *pcom,*xicom;  int imx; 
 double (*nrfunc)(double []);  int stepm=1;
    /* Stepm, step in month: minimum step interpolation*/
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  
 {  int estepm;
   double brent(double ax, double bx, double cx,  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
                double (*f)(double), double tol, double *xmin);  
   double f1dim(double x);  int m,nb;
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  long *num;
               double *fc, double (*func)(double));  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
   int j;  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
   double xx,xmin,bx,ax;  double **pmmij, ***probs;
   double fx,fb,fa;  double *ageexmed,*agecens;
    double dateintmean=0;
   ncom=n;  
   pcom=vector(1,n);  double *weight;
   xicom=vector(1,n);  int **s; /* Status */
   nrfunc=func;  double *agedc;
   for (j=1;j<=n;j++) {  double  **covar; /**< covar[i,j], value of jth covariate for individual i,
     pcom[j]=p[j];                    * covar=matrix(0,NCOVMAX,1,n); 
     xicom[j]=xi[j];                    * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
   }  double  idx; 
   ax=0.0;  int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
   xx=1.0;  int **codtab; /**< codtab=imatrix(1,100,1,10); */
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  int **Tvard, *Tprod, cptcovprod, *Tvaraff;
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  double *lsurv, *lpop, *tpop;
 #ifdef DEBUG  
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  double ftolhess; /* Tolerance for computing hessian */
 #endif  
   for (j=1;j<=n;j++) {  /**************** split *************************/
     xi[j] *= xmin;  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
     p[j] += xi[j];  {
   }    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
   free_vector(xicom,1,n);       the name of the file (name), its extension only (ext) and its first part of the name (finame)
   free_vector(pcom,1,n);    */ 
 }    char  *ss;                            /* pointer */
     int   l1, l2;                         /* length counters */
 /*************** powell ************************/  
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,    l1 = strlen(path );                   /* length of path */
             double (*func)(double []))    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
 {    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
   void linmin(double p[], double xi[], int n, double *fret,    if ( ss == NULL ) {                   /* no directory, so determine current directory */
               double (*func)(double []));      strcpy( name, path );               /* we got the fullname name because no directory */
   int i,ibig,j;      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
   double del,t,*pt,*ptt,*xit;        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
   double fp,fptt;      /* get current working directory */
   double *xits;      /*    extern  char* getcwd ( char *buf , int len);*/
   pt=vector(1,n);      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
   ptt=vector(1,n);        return( GLOCK_ERROR_GETCWD );
   xit=vector(1,n);      }
   xits=vector(1,n);      /* got dirc from getcwd*/
   *fret=(*func)(p);      printf(" DIRC = %s \n",dirc);
   for (j=1;j<=n;j++) pt[j]=p[j];    } else {                              /* strip direcotry from path */
   for (*iter=1;;++(*iter)) {      ss++;                               /* after this, the filename */
     fp=(*fret);      l2 = strlen( ss );                  /* length of filename */
     ibig=0;      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
     del=0.0;      strcpy( name, ss );         /* save file name */
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);      strncpy( dirc, path, l1 - l2 );     /* now the directory */
     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);      dirc[l1-l2] = 0;                    /* add zero */
     for (i=1;i<=n;i++)      printf(" DIRC2 = %s \n",dirc);
       printf(" %d %.12f",i, p[i]);    }
     fprintf(ficlog," %d %.12f",i, p[i]);    /* We add a separator at the end of dirc if not exists */
     printf("\n");    l1 = strlen( dirc );                  /* length of directory */
     fprintf(ficlog,"\n");    if( dirc[l1-1] != DIRSEPARATOR ){
     for (i=1;i<=n;i++) {      dirc[l1] =  DIRSEPARATOR;
       for (j=1;j<=n;j++) xit[j]=xi[j][i];      dirc[l1+1] = 0; 
       fptt=(*fret);      printf(" DIRC3 = %s \n",dirc);
 #ifdef DEBUG    }
       printf("fret=%lf \n",*fret);    ss = strrchr( name, '.' );            /* find last / */
       fprintf(ficlog,"fret=%lf \n",*fret);    if (ss >0){
 #endif      ss++;
       printf("%d",i);fflush(stdout);      strcpy(ext,ss);                     /* save extension */
       fprintf(ficlog,"%d",i);fflush(ficlog);      l1= strlen( name);
       linmin(p,xit,n,fret,func);      l2= strlen(ss)+1;
       if (fabs(fptt-(*fret)) > del) {      strncpy( finame, name, l1-l2);
         del=fabs(fptt-(*fret));      finame[l1-l2]= 0;
         ibig=i;    }
       }  
 #ifdef DEBUG    return( 0 );                          /* we're done */
       printf("%d %.12e",i,(*fret));  }
       fprintf(ficlog,"%d %.12e",i,(*fret));  
       for (j=1;j<=n;j++) {  
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  /******************************************/
         printf(" x(%d)=%.12e",j,xit[j]);  
         fprintf(ficlog," x(%d)=%.12e",j,xit[j]);  void replace_back_to_slash(char *s, char*t)
       }  {
       for(j=1;j<=n;j++) {    int i;
         printf(" p=%.12e",p[j]);    int lg=0;
         fprintf(ficlog," p=%.12e",p[j]);    i=0;
       }    lg=strlen(t);
       printf("\n");    for(i=0; i<= lg; i++) {
       fprintf(ficlog,"\n");      (s[i] = t[i]);
 #endif      if (t[i]== '\\') s[i]='/';
     }    }
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  }
 #ifdef DEBUG  
       int k[2],l;  char *trimbb(char *out, char *in)
       k[0]=1;  { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
       k[1]=-1;    char *s;
       printf("Max: %.12e",(*func)(p));    s=out;
       fprintf(ficlog,"Max: %.12e",(*func)(p));    while (*in != '\0'){
       for (j=1;j<=n;j++) {      while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
         printf(" %.12e",p[j]);        in++;
         fprintf(ficlog," %.12e",p[j]);      }
       }      *out++ = *in++;
       printf("\n");    }
       fprintf(ficlog,"\n");    *out='\0';
       for(l=0;l<=1;l++) {    return s;
         for (j=1;j<=n;j++) {  }
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  char *cutv(char *blocc, char *alocc, char *in, char occ)
           fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  {
         }    /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ' 
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));       and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
         fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));       gives blocc="abcdef2ghi" and alocc="j".
       }       If occ is not found blocc is null and alocc is equal to in. Returns alocc
 #endif    */
     char *s, *t;
     t=in;s=in;
       free_vector(xit,1,n);    while (*in != '\0'){
       free_vector(xits,1,n);      while( *in == occ){
       free_vector(ptt,1,n);        *blocc++ = *in++;
       free_vector(pt,1,n);        s=in;
       return;      }
     }      *blocc++ = *in++;
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    }
     for (j=1;j<=n;j++) {    if (s == t) /* occ not found */
       ptt[j]=2.0*p[j]-pt[j];      *(blocc-(in-s))='\0';
       xit[j]=p[j]-pt[j];    else
       pt[j]=p[j];      *(blocc-(in-s)-1)='\0';
     }    in=s;
     fptt=(*func)(ptt);    while ( *in != '\0'){
     if (fptt < fp) {      *alocc++ = *in++;
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);    }
       if (t < 0.0) {  
         linmin(p,xit,n,fret,func);    *alocc='\0';
         for (j=1;j<=n;j++) {    return s;
           xi[j][ibig]=xi[j][n];  }
           xi[j][n]=xit[j];  
         }  int nbocc(char *s, char occ)
 #ifdef DEBUG  {
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);    int i,j=0;
         fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);    int lg=20;
         for(j=1;j<=n;j++){    i=0;
           printf(" %.12e",xit[j]);    lg=strlen(s);
           fprintf(ficlog," %.12e",xit[j]);    for(i=0; i<= lg; i++) {
         }    if  (s[i] == occ ) j++;
         printf("\n");    }
         fprintf(ficlog,"\n");    return j;
 #endif  }
       }  
     }  /* void cutv(char *u,char *v, char*t, char occ) */
   }  /* { */
 }  /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
   /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
 /**** Prevalence limit ****************/  /*      gives u="abcdef2ghi" and v="j" *\/ */
   /*   int i,lg,j,p=0; */
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  /*   i=0; */
 {  /*   lg=strlen(t); */
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit  /*   for(j=0; j<=lg-1; j++) { */
      matrix by transitions matrix until convergence is reached */  /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
   /*   } */
   int i, ii,j,k;  
   double min, max, maxmin, maxmax,sumnew=0.;  /*   for(j=0; j<p; j++) { */
   double **matprod2();  /*     (u[j] = t[j]); */
   double **out, cov[NCOVMAX], **pmij();  /*   } */
   double **newm;  /*      u[p]='\0'; */
   double agefin, delaymax=50 ; /* Max number of years to converge */  
   /*    for(j=0; j<= lg; j++) { */
   for (ii=1;ii<=nlstate+ndeath;ii++)  /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
     for (j=1;j<=nlstate+ndeath;j++){  /*   } */
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);  /* } */
     }  
   /********************** nrerror ********************/
    cov[1]=1.;  
    void nrerror(char error_text[])
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */  {
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){    fprintf(stderr,"ERREUR ...\n");
     newm=savm;    fprintf(stderr,"%s\n",error_text);
     /* Covariates have to be included here again */    exit(EXIT_FAILURE);
      cov[2]=agefin;  }
    /*********************** vector *******************/
       for (k=1; k<=cptcovn;k++) {  double *vector(int nl, int nh)
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  {
         /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/    double *v;
       }    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    if (!v) nrerror("allocation failure in vector");
       for (k=1; k<=cptcovprod;k++)    return v-nl+NR_END;
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  }
   
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/  /************************ free vector ******************/
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/  void free_vector(double*v, int nl, int nh)
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/  {
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);    free((FREE_ARG)(v+nl-NR_END));
   }
     savm=oldm;  
     oldm=newm;  /************************ivector *******************************/
     maxmax=0.;  int *ivector(long nl,long nh)
     for(j=1;j<=nlstate;j++){  {
       min=1.;    int *v;
       max=0.;    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
       for(i=1; i<=nlstate; i++) {    if (!v) nrerror("allocation failure in ivector");
         sumnew=0;    return v-nl+NR_END;
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  }
         prlim[i][j]= newm[i][j]/(1-sumnew);  
         max=FMAX(max,prlim[i][j]);  /******************free ivector **************************/
         min=FMIN(min,prlim[i][j]);  void free_ivector(int *v, long nl, long nh)
       }  {
       maxmin=max-min;    free((FREE_ARG)(v+nl-NR_END));
       maxmax=FMAX(maxmax,maxmin);  }
     }  
     if(maxmax < ftolpl){  /************************lvector *******************************/
       return prlim;  long *lvector(long nl,long nh)
     }  {
   }    long *v;
 }    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
     if (!v) nrerror("allocation failure in ivector");
 /*************** transition probabilities ***************/    return v-nl+NR_END;
   }
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  
 {  /******************free lvector **************************/
   double s1, s2;  void free_lvector(long *v, long nl, long nh)
   /*double t34;*/  {
   int i,j,j1, nc, ii, jj;    free((FREE_ARG)(v+nl-NR_END));
   }
     for(i=1; i<= nlstate; i++){  
     for(j=1; j<i;j++){  /******************* imatrix *******************************/
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  int **imatrix(long nrl, long nrh, long ncl, long nch) 
         /*s2 += param[i][j][nc]*cov[nc];*/       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  { 
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
       }    int **m; 
       ps[i][j]=s2;    
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/    /* allocate pointers to rows */ 
     }    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
     for(j=i+1; j<=nlstate+ndeath;j++){    if (!m) nrerror("allocation failure 1 in matrix()"); 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    m += NR_END; 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    m -= nrl; 
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/    
       }    
       ps[i][j]=s2;    /* allocate rows and set pointers to them */ 
     }    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
   }    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
     /*ps[3][2]=1;*/    m[nrl] += NR_END; 
     m[nrl] -= ncl; 
   for(i=1; i<= nlstate; i++){    
      s1=0;    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
     for(j=1; j<i; j++)    
       s1+=exp(ps[i][j]);    /* return pointer to array of pointers to rows */ 
     for(j=i+1; j<=nlstate+ndeath; j++)    return m; 
       s1+=exp(ps[i][j]);  } 
     ps[i][i]=1./(s1+1.);  
     for(j=1; j<i; j++)  /****************** free_imatrix *************************/
       ps[i][j]= exp(ps[i][j])*ps[i][i];  void free_imatrix(m,nrl,nrh,ncl,nch)
     for(j=i+1; j<=nlstate+ndeath; j++)        int **m;
       ps[i][j]= exp(ps[i][j])*ps[i][i];        long nch,ncl,nrh,nrl; 
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */       /* free an int matrix allocated by imatrix() */ 
   } /* end i */  { 
     free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){    free((FREE_ARG) (m+nrl-NR_END)); 
     for(jj=1; jj<= nlstate+ndeath; jj++){  } 
       ps[ii][jj]=0;  
       ps[ii][ii]=1;  /******************* matrix *******************************/
     }  double **matrix(long nrl, long nrh, long ncl, long nch)
   }  {
     long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
     double **m;
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){  
     for(jj=1; jj<= nlstate+ndeath; jj++){    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
      printf("%lf ",ps[ii][jj]);    if (!m) nrerror("allocation failure 1 in matrix()");
    }    m += NR_END;
     printf("\n ");    m -= nrl;
     }  
     printf("\n ");printf("%lf ",cov[2]);*/    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
 /*    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   for(i=1; i<= npar; i++) printf("%f ",x[i]);    m[nrl] += NR_END;
   goto end;*/    m[nrl] -= ncl;
     return ps;  
 }    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     return m;
 /**************** Product of 2 matrices ******************/    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
      */
 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  /*************************free matrix ************************/
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   /* in, b, out are matrice of pointers which should have been initialized  {
      before: only the contents of out is modified. The function returns    free((FREE_ARG)(m[nrl]+ncl-NR_END));
      a pointer to pointers identical to out */    free((FREE_ARG)(m+nrl-NR_END));
   long i, j, k;  }
   for(i=nrl; i<= nrh; i++)  
     for(k=ncolol; k<=ncoloh; k++)  /******************* ma3x *******************************/
       for(j=ncl,out[i][k]=0.; j<=nch; j++)  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
         out[i][k] +=in[i][j]*b[j][k];  {
     long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
   return out;    double ***m;
 }  
     m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     if (!m) nrerror("allocation failure 1 in matrix()");
 /************* Higher Matrix Product ***************/    m += NR_END;
     m -= nrl;
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )  
 {    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
      duration (i.e. until    m[nrl] += NR_END;
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.    m[nrl] -= ncl;
      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).    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
      Model is determined by parameters x and covariates have to be  
      included manually here.    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
     if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
      */    m[nrl][ncl] += NR_END;
     m[nrl][ncl] -= nll;
   int i, j, d, h, k;    for (j=ncl+1; j<=nch; j++) 
   double **out, cov[NCOVMAX];      m[nrl][j]=m[nrl][j-1]+nlay;
   double **newm;    
     for (i=nrl+1; i<=nrh; i++) {
   /* Hstepm could be zero and should return the unit matrix */      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
   for (i=1;i<=nlstate+ndeath;i++)      for (j=ncl+1; j<=nch; j++) 
     for (j=1;j<=nlstate+ndeath;j++){        m[i][j]=m[i][j-1]+nlay;
       oldm[i][j]=(i==j ? 1.0 : 0.0);    }
       po[i][j][0]=(i==j ? 1.0 : 0.0);    return m; 
     }    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
   for(h=1; h <=nhstepm; h++){    */
     for(d=1; d <=hstepm; d++){  }
       newm=savm;  
       /* Covariates have to be included here again */  /*************************free ma3x ************************/
       cov[1]=1.;  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;  {
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
       for (k=1; k<=cptcovage;k++)    free((FREE_ARG)(m[nrl]+ncl-NR_END));
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    free((FREE_ARG)(m+nrl-NR_END));
       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]]];  
   /*************** function subdirf ***********/
   char *subdirf(char fileres[])
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/  {
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/    /* Caution optionfilefiname is hidden */
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,    strcpy(tmpout,optionfilefiname);
                    pmij(pmmij,cov,ncovmodel,x,nlstate));    strcat(tmpout,"/"); /* Add to the right */
       savm=oldm;    strcat(tmpout,fileres);
       oldm=newm;    return tmpout;
     }  }
     for(i=1; i<=nlstate+ndeath; i++)  
       for(j=1;j<=nlstate+ndeath;j++) {  /*************** function subdirf2 ***********/
         po[i][j][h]=newm[i][j];  char *subdirf2(char fileres[], char *preop)
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);  {
          */    
       }    /* Caution optionfilefiname is hidden */
   } /* end h */    strcpy(tmpout,optionfilefiname);
   return po;    strcat(tmpout,"/");
 }    strcat(tmpout,preop);
     strcat(tmpout,fileres);
     return tmpout;
 /*************** log-likelihood *************/  }
 double func( double *x)  
 {  /*************** function subdirf3 ***********/
   int i, ii, j, k, mi, d, kk;  char *subdirf3(char fileres[], char *preop, char *preop2)
   double l, ll[NLSTATEMAX], cov[NCOVMAX];  {
   double **out;    
   double sw; /* Sum of weights */    /* Caution optionfilefiname is hidden */
   double lli; /* Individual log likelihood */    strcpy(tmpout,optionfilefiname);
   long ipmx;    strcat(tmpout,"/");
   /*extern weight */    strcat(tmpout,preop);
   /* We are differentiating ll according to initial status */    strcat(tmpout,preop2);
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    strcat(tmpout,fileres);
   /*for(i=1;i<imx;i++)    return tmpout;
     printf(" %d\n",s[4][i]);  }
   */  
   cov[1]=1.;  /***************** f1dim *************************/
   extern int ncom; 
   for(k=1; k<=nlstate; k++) ll[k]=0.;  extern double *pcom,*xicom;
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){  extern double (*nrfunc)(double []); 
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];   
     for(mi=1; mi<= wav[i]-1; mi++){  double f1dim(double x) 
       for (ii=1;ii<=nlstate+ndeath;ii++)  { 
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);    int j; 
       for(d=0; d<dh[mi][i]; d++){    double f;
         newm=savm;    double *xt; 
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;   
         for (kk=1; kk<=cptcovage;kk++) {    xt=vector(1,ncom); 
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
         }    f=(*nrfunc)(xt); 
            free_vector(xt,1,ncom); 
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,    return f; 
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));  } 
         savm=oldm;  
         oldm=newm;  /*****************brent *************************/
          double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
          { 
       } /* end mult */    int iter; 
          double a,b,d,etemp;
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);    double fu,fv,fw,fx;
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/    double ftemp;
       ipmx +=1;    double p,q,r,tol1,tol2,u,v,w,x,xm; 
       sw += weight[i];    double e=0.0; 
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;   
     } /* end of wave */    a=(ax < cx ? ax : cx); 
   } /* end of individual */    b=(ax > cx ? ax : cx); 
     x=w=v=bx; 
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];    fw=fv=fx=(*f)(x); 
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */    for (iter=1;iter<=ITMAX;iter++) { 
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */      xm=0.5*(a+b); 
   return -l;      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
 }      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
       printf(".");fflush(stdout);
       fprintf(ficlog,".");fflush(ficlog);
 /*********** Maximum Likelihood Estimation ***************/  #ifdef DEBUG
       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);
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
 {      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
   int i,j, iter;  #endif
   double **xi,*delti;      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
   double fret;        *xmin=x; 
   xi=matrix(1,npar,1,npar);        return fx; 
   for (i=1;i<=npar;i++)      } 
     for (j=1;j<=npar;j++)      ftemp=fu;
       xi[i][j]=(i==j ? 1.0 : 0.0);      if (fabs(e) > tol1) { 
   printf("Powell\n");  fprintf(ficlog,"Powell\n");        r=(x-w)*(fx-fv); 
   powell(p,xi,npar,ftol,&iter,&fret,func);        q=(x-v)*(fx-fw); 
         p=(x-v)*q-(x-w)*r; 
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));        q=2.0*(q-r); 
   fprintf(ficlog,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));        if (q > 0.0) p = -p; 
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));        q=fabs(q); 
         etemp=e; 
 }        e=d; 
         if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
 /**** Computes Hessian and covariance matrix ***/          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))        else { 
 {          d=p/q; 
   double  **a,**y,*x,pd;          u=x+d; 
   double **hess;          if (u-a < tol2 || b-u < tol2) 
   int i, j,jk;            d=SIGN(tol1,xm-x); 
   int *indx;        } 
       } else { 
   double hessii(double p[], double delta, int theta, double delti[]);        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   double hessij(double p[], double delti[], int i, int j);      } 
   void lubksb(double **a, int npar, int *indx, double b[]) ;      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
   void ludcmp(double **a, int npar, int *indx, double *d) ;      fu=(*f)(u); 
       if (fu <= fx) { 
   hess=matrix(1,npar,1,npar);        if (u >= x) a=x; else b=x; 
         SHFT(v,w,x,u) 
   printf("\nCalculation of the hessian matrix. Wait...\n");          SHFT(fv,fw,fx,fu) 
   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");          } else { 
   for (i=1;i<=npar;i++){            if (u < x) a=u; else b=u; 
     printf("%d",i);fflush(stdout);            if (fu <= fw || w == x) { 
     fprintf(ficlog,"%d",i);fflush(ficlog);              v=w; 
     hess[i][i]=hessii(p,ftolhess,i,delti);              w=u; 
     /*printf(" %f ",p[i]);*/              fv=fw; 
     /*printf(" %lf ",hess[i][i]);*/              fw=fu; 
   }            } else if (fu <= fv || v == x || v == w) { 
                v=u; 
   for (i=1;i<=npar;i++) {              fv=fu; 
     for (j=1;j<=npar;j++)  {            } 
       if (j>i) {          } 
         printf(".%d%d",i,j);fflush(stdout);    } 
         fprintf(ficlog,".%d%d",i,j);fflush(ficlog);    nrerror("Too many iterations in brent"); 
         hess[i][j]=hessij(p,delti,i,j);    *xmin=x; 
         hess[j][i]=hess[i][j];        return fx; 
         /*printf(" %lf ",hess[i][j]);*/  } 
       }  
     }  /****************** mnbrak ***********************/
   }  
   printf("\n");  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
   fprintf(ficlog,"\n");              double (*func)(double)) 
   { 
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");    double ulim,u,r,q, dum;
   fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");    double fu; 
     
   a=matrix(1,npar,1,npar);    *fa=(*func)(*ax); 
   y=matrix(1,npar,1,npar);    *fb=(*func)(*bx); 
   x=vector(1,npar);    if (*fb > *fa) { 
   indx=ivector(1,npar);      SHFT(dum,*ax,*bx,dum) 
   for (i=1;i<=npar;i++)        SHFT(dum,*fb,*fa,dum) 
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];        } 
   ludcmp(a,npar,indx,&pd);    *cx=(*bx)+GOLD*(*bx-*ax); 
     *fc=(*func)(*cx); 
   for (j=1;j<=npar;j++) {    while (*fb > *fc) { 
     for (i=1;i<=npar;i++) x[i]=0;      r=(*bx-*ax)*(*fb-*fc); 
     x[j]=1;      q=(*bx-*cx)*(*fb-*fa); 
     lubksb(a,npar,indx,x);      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
     for (i=1;i<=npar;i++){        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
       matcov[i][j]=x[i];      ulim=(*bx)+GLIMIT*(*cx-*bx); 
     }      if ((*bx-u)*(u-*cx) > 0.0) { 
   }        fu=(*func)(u); 
       } else if ((*cx-u)*(u-ulim) > 0.0) { 
   printf("\n#Hessian matrix#\n");        fu=(*func)(u); 
   fprintf(ficlog,"\n#Hessian matrix#\n");        if (fu < *fc) { 
   for (i=1;i<=npar;i++) {          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
     for (j=1;j<=npar;j++) {            SHFT(*fb,*fc,fu,(*func)(u)) 
       printf("%.3e ",hess[i][j]);            } 
       fprintf(ficlog,"%.3e ",hess[i][j]);      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
     }        u=ulim; 
     printf("\n");        fu=(*func)(u); 
     fprintf(ficlog,"\n");      } else { 
   }        u=(*cx)+GOLD*(*cx-*bx); 
         fu=(*func)(u); 
   /* Recompute Inverse */      } 
   for (i=1;i<=npar;i++)      SHFT(*ax,*bx,*cx,u) 
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];        SHFT(*fa,*fb,*fc,fu) 
   ludcmp(a,npar,indx,&pd);        } 
   } 
   /*  printf("\n#Hessian matrix recomputed#\n");  
   /*************** linmin ************************/
   for (j=1;j<=npar;j++) {  
     for (i=1;i<=npar;i++) x[i]=0;  int ncom; 
     x[j]=1;  double *pcom,*xicom;
     lubksb(a,npar,indx,x);  double (*nrfunc)(double []); 
     for (i=1;i<=npar;i++){   
       y[i][j]=x[i];  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
       printf("%.3e ",y[i][j]);  { 
       fprintf(ficlog,"%.3e ",y[i][j]);    double brent(double ax, double bx, double cx, 
     }                 double (*f)(double), double tol, double *xmin); 
     printf("\n");    double f1dim(double x); 
     fprintf(ficlog,"\n");    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
   }                double *fc, double (*func)(double)); 
   */    int j; 
     double xx,xmin,bx,ax; 
   free_matrix(a,1,npar,1,npar);    double fx,fb,fa;
   free_matrix(y,1,npar,1,npar);   
   free_vector(x,1,npar);    ncom=n; 
   free_ivector(indx,1,npar);    pcom=vector(1,n); 
   free_matrix(hess,1,npar,1,npar);    xicom=vector(1,n); 
     nrfunc=func; 
     for (j=1;j<=n;j++) { 
 }      pcom[j]=p[j]; 
       xicom[j]=xi[j]; 
 /*************** hessian matrix ****************/    } 
 double hessii( double x[], double delta, int theta, double delti[])    ax=0.0; 
 {    xx=1.0; 
   int i;    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
   int l=1, lmax=20;    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
   double k1,k2;  #ifdef DEBUG
   double p2[NPARMAX+1];    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   double res;    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;  #endif
   double fx;    for (j=1;j<=n;j++) { 
   int k=0,kmax=10;      xi[j] *= xmin; 
   double l1;      p[j] += xi[j]; 
     } 
   fx=func(x);    free_vector(xicom,1,n); 
   for (i=1;i<=npar;i++) p2[i]=x[i];    free_vector(pcom,1,n); 
   for(l=0 ; l <=lmax; l++){  } 
     l1=pow(10,l);  
     delts=delt;  char *asc_diff_time(long time_sec, char ascdiff[])
     for(k=1 ; k <kmax; k=k+1){  {
       delt = delta*(l1*k);    long sec_left, days, hours, minutes;
       p2[theta]=x[theta] +delt;    days = (time_sec) / (60*60*24);
       k1=func(p2)-fx;    sec_left = (time_sec) % (60*60*24);
       p2[theta]=x[theta]-delt;    hours = (sec_left) / (60*60) ;
       k2=func(p2)-fx;    sec_left = (sec_left) %(60*60);
       /*res= (k1-2.0*fx+k2)/delt/delt; */    minutes = (sec_left) /60;
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */    sec_left = (sec_left) % (60);
          sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);  
 #ifdef DEBUG    return ascdiff;
       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);  
 #endif  /*************** powell ************************/
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){              double (*func)(double [])) 
         k=kmax;  { 
       }    void linmin(double p[], double xi[], int n, double *fret, 
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */                double (*func)(double [])); 
         k=kmax; l=lmax*10.;    int i,ibig,j; 
       }    double del,t,*pt,*ptt,*xit;
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){    double fp,fptt;
         delts=delt;    double *xits;
       }    int niterf, itmp;
     }  
   }    pt=vector(1,n); 
   delti[theta]=delts;    ptt=vector(1,n); 
   return res;    xit=vector(1,n); 
      xits=vector(1,n); 
 }    *fret=(*func)(p); 
     for (j=1;j<=n;j++) pt[j]=p[j]; 
 double hessij( double x[], double delti[], int thetai,int thetaj)    for (*iter=1;;++(*iter)) { 
 {      fp=(*fret); 
   int i;      ibig=0; 
   int l=1, l1, lmax=20;      del=0.0; 
   double k1,k2,k3,k4,res,fx;      last_time=curr_time;
   double p2[NPARMAX+1];      (void) gettimeofday(&curr_time,&tzp);
   int k;      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);
       fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec); fflush(ficlog);
   fx=func(x);  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
   for (k=1; k<=2; k++) {     for (i=1;i<=n;i++) {
     for (i=1;i<=npar;i++) p2[i]=x[i];        printf(" %d %.12f",i, p[i]);
     p2[thetai]=x[thetai]+delti[thetai]/k;        fprintf(ficlog," %d %.12lf",i, p[i]);
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;        fprintf(ficrespow," %.12lf", p[i]);
     k1=func(p2)-fx;      }
        printf("\n");
     p2[thetai]=x[thetai]+delti[thetai]/k;      fprintf(ficlog,"\n");
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;      fprintf(ficrespow,"\n");fflush(ficrespow);
     k2=func(p2)-fx;      if(*iter <=3){
          tm = *localtime(&curr_time.tv_sec);
     p2[thetai]=x[thetai]-delti[thetai]/k;        strcpy(strcurr,asctime(&tm));
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  /*       asctime_r(&tm,strcurr); */
     k3=func(p2)-fx;        forecast_time=curr_time; 
          itmp = strlen(strcurr);
     p2[thetai]=x[thetai]-delti[thetai]/k;        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          strcurr[itmp-1]='\0';
     k4=func(p2)-fx;        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
 #ifdef DEBUG        for(niterf=10;niterf<=30;niterf+=10){
     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);          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
     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);          tmf = *localtime(&forecast_time.tv_sec);
 #endif  /*      asctime_r(&tmf,strfor); */
   }          strcpy(strfor,asctime(&tmf));
   return res;          itmp = strlen(strfor);
 }          if(strfor[itmp-1]=='\n')
           strfor[itmp-1]='\0';
 /************** Inverse of matrix **************/          printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
 void ludcmp(double **a, int n, int *indx, double *d)          fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
 {        }
   int i,imax,j,k;      }
   double big,dum,sum,temp;      for (i=1;i<=n;i++) { 
   double *vv;        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
          fptt=(*fret); 
   vv=vector(1,n);  #ifdef DEBUG
   *d=1.0;        printf("fret=%lf \n",*fret);
   for (i=1;i<=n;i++) {        fprintf(ficlog,"fret=%lf \n",*fret);
     big=0.0;  #endif
     for (j=1;j<=n;j++)        printf("%d",i);fflush(stdout);
       if ((temp=fabs(a[i][j])) > big) big=temp;        fprintf(ficlog,"%d",i);fflush(ficlog);
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");        linmin(p,xit,n,fret,func); 
     vv[i]=1.0/big;        if (fabs(fptt-(*fret)) > del) { 
   }          del=fabs(fptt-(*fret)); 
   for (j=1;j<=n;j++) {          ibig=i; 
     for (i=1;i<j;i++) {        } 
       sum=a[i][j];  #ifdef DEBUG
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];        printf("%d %.12e",i,(*fret));
       a[i][j]=sum;        fprintf(ficlog,"%d %.12e",i,(*fret));
     }        for (j=1;j<=n;j++) {
     big=0.0;          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
     for (i=j;i<=n;i++) {          printf(" x(%d)=%.12e",j,xit[j]);
       sum=a[i][j];          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
       for (k=1;k<j;k++)        }
         sum -= a[i][k]*a[k][j];        for(j=1;j<=n;j++) {
       a[i][j]=sum;          printf(" p=%.12e",p[j]);
       if ( (dum=vv[i]*fabs(sum)) >= big) {          fprintf(ficlog," p=%.12e",p[j]);
         big=dum;        }
         imax=i;        printf("\n");
       }        fprintf(ficlog,"\n");
     }  #endif
     if (j != imax) {      } 
       for (k=1;k<=n;k++) {      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
         dum=a[imax][k];  #ifdef DEBUG
         a[imax][k]=a[j][k];        int k[2],l;
         a[j][k]=dum;        k[0]=1;
       }        k[1]=-1;
       *d = -(*d);        printf("Max: %.12e",(*func)(p));
       vv[imax]=vv[j];        fprintf(ficlog,"Max: %.12e",(*func)(p));
     }        for (j=1;j<=n;j++) {
     indx[j]=imax;          printf(" %.12e",p[j]);
     if (a[j][j] == 0.0) a[j][j]=TINY;          fprintf(ficlog," %.12e",p[j]);
     if (j != n) {        }
       dum=1.0/(a[j][j]);        printf("\n");
       for (i=j+1;i<=n;i++) a[i][j] *= dum;        fprintf(ficlog,"\n");
     }        for(l=0;l<=1;l++) {
   }          for (j=1;j<=n;j++) {
   free_vector(vv,1,n);  /* Doesn't work */            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
 ;            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
 }            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
           }
 void lubksb(double **a, int n, int *indx, double b[])          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
 {          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   int i,ii=0,ip,j;        }
   double sum;  #endif
    
   for (i=1;i<=n;i++) {  
     ip=indx[i];        free_vector(xit,1,n); 
     sum=b[ip];        free_vector(xits,1,n); 
     b[ip]=b[i];        free_vector(ptt,1,n); 
     if (ii)        free_vector(pt,1,n); 
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];        return; 
     else if (sum) ii=i;      } 
     b[i]=sum;      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
   }      for (j=1;j<=n;j++) { 
   for (i=n;i>=1;i--) {        ptt[j]=2.0*p[j]-pt[j]; 
     sum=b[i];        xit[j]=p[j]-pt[j]; 
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];        pt[j]=p[j]; 
     b[i]=sum/a[i][i];      } 
   }      fptt=(*func)(ptt); 
 }      if (fptt < fp) { 
         t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
 /************ Frequencies ********************/        if (t < 0.0) { 
 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)          linmin(p,xit,n,fret,func); 
 {  /* Some frequencies */          for (j=1;j<=n;j++) { 
              xi[j][ibig]=xi[j][n]; 
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;            xi[j][n]=xit[j]; 
   int first;          }
   double ***freq; /* Frequencies */  #ifdef DEBUG
   double *pp;          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   double pos, k2, dateintsum=0,k2cpt=0;          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   FILE *ficresp;          for(j=1;j<=n;j++){
   char fileresp[FILENAMELENGTH];            printf(" %.12e",xit[j]);
              fprintf(ficlog," %.12e",xit[j]);
   pp=vector(1,nlstate);          }
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);          printf("\n");
   strcpy(fileresp,"p");          fprintf(ficlog,"\n");
   strcat(fileresp,fileres);  #endif
   if((ficresp=fopen(fileresp,"w"))==NULL) {        }
     printf("Problem with prevalence resultfile: %s\n", fileresp);      } 
     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);    } 
     exit(0);  } 
   }  
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);  /**** Prevalence limit (stable or period prevalence)  ****************/
   j1=0;  
    double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
   j=cptcoveff;  {
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
        matrix by transitions matrix until convergence is reached */
   first=1;  
     int i, ii,j,k;
   for(k1=1; k1<=j;k1++){    double min, max, maxmin, maxmax,sumnew=0.;
     for(i1=1; i1<=ncodemax[k1];i1++){    double **matprod2();
       j1++;    double **out, cov[NCOVMAX+1], **pmij();
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);    double **newm;
         scanf("%d", i);*/    double agefin, delaymax=50 ; /* Max number of years to converge */
       for (i=-1; i<=nlstate+ndeath; i++)    
         for (jk=-1; jk<=nlstate+ndeath; jk++)      for (ii=1;ii<=nlstate+ndeath;ii++)
           for(m=agemin; m <= agemax+3; m++)      for (j=1;j<=nlstate+ndeath;j++){
             freq[i][jk][m]=0;        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
            }
       dateintsum=0;  
       k2cpt=0;     cov[1]=1.;
       for (i=1; i<=imx; i++) {   
         bool=1;   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
         if  (cptcovn>0) {    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
           for (z1=1; z1<=cptcoveff; z1++)      newm=savm;
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])      /* Covariates have to be included here again */
               bool=0;      cov[2]=agefin;
         }      
         if (bool==1) {      for (k=1; k<=cptcovn;k++) {
           for(m=firstpass; m<=lastpass; m++){        cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
             k2=anint[m][i]+(mint[m][i]/12.);        /*        printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
             if ((k2>=dateprev1) && (k2<=dateprev2)) {      }
               if(agev[m][i]==0) agev[m][i]=agemax+1;      for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
               if(agev[m][i]==1) agev[m][i]=agemax+2;      for (k=1; k<=cptcovprod;k++)
               if (m<lastpass) {        cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];      
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];      /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
               }      /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
                    /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
                 dateintsum=dateintsum+k2;      
                 k2cpt++;      savm=oldm;
               }      oldm=newm;
             }      maxmax=0.;
           }      for(j=1;j<=nlstate;j++){
         }        min=1.;
       }        max=0.;
                for(i=1; i<=nlstate; i++) {
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);          sumnew=0;
           for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
       if  (cptcovn>0) {          prlim[i][j]= newm[i][j]/(1-sumnew);
         fprintf(ficresp, "\n#********** Variable ");          max=FMAX(max,prlim[i][j]);
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          min=FMIN(min,prlim[i][j]);
         fprintf(ficresp, "**********\n#");        }
       }        maxmin=max-min;
       for(i=1; i<=nlstate;i++)        maxmax=FMAX(maxmax,maxmin);
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);      }
       fprintf(ficresp, "\n");      if(maxmax < ftolpl){
              return prlim;
       for(i=(int)agemin; i <= (int)agemax+3; i++){      }
         if(i==(int)agemax+3){    }
           fprintf(ficlog,"Total");  }
         }else{  
           if(first==1){  /*************** transition probabilities ***************/ 
             first=0;  
             printf("See log file for details...\n");  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
           }  {
           fprintf(ficlog,"Age %d", i);    /* 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
         for(jk=1; jk <=nlstate ; jk++){       model to the ncovmodel covariates (including constant and age).
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)       lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
             pp[jk] += freq[jk][m][i];       and, according on how parameters are entered, the position of the coefficient xij(nc) of the
         }       ncth covariate in the global vector x is given by the formula:
         for(jk=1; jk <=nlstate ; jk++){       j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
           for(m=-1, pos=0; m <=0 ; m++)       j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
             pos += freq[jk][m][i];       Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
           if(pp[jk]>=1.e-10){       sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
             if(first==1){       Outputs ps[i][j] the probability to be observed in j being in j according to
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);       the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
             }    */
             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);    double s1, lnpijopii;
           }else{    /*double t34;*/
             if(first==1)    int i,j,j1, nc, ii, jj;
               printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);  
             fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);      for(i=1; i<= nlstate; i++){
           }        for(j=1; j<i;j++){
         }          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
             /*lnpijopii += param[i][j][nc]*cov[nc];*/
         for(jk=1; jk <=nlstate ; jk++){            lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)  /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
             pp[jk] += freq[jk][m][i];          }
         }          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
   /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
         for(jk=1,pos=0; jk <=nlstate ; jk++)        }
           pos += pp[jk];        for(j=i+1; j<=nlstate+ndeath;j++){
         for(jk=1; jk <=nlstate ; jk++){          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
           if(pos>=1.e-5){            /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
             if(first==1)            lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
               printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);  /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
             fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);          }
           }else{          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
             if(first==1)        }
               printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);      }
             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);      
           }      for(i=1; i<= nlstate; i++){
           if( i <= (int) agemax){        s1=0;
             if(pos>=1.e-5){        for(j=1; j<i; j++){
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
               probs[i][jk][j1]= pp[jk]/pos;          /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/        }
             }        for(j=i+1; j<=nlstate+ndeath; j++){
             else          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);          /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
           }        }
         }        /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
                ps[i][i]=1./(s1+1.);
         for(jk=-1; jk <=nlstate+ndeath; jk++)        /* Computing other pijs */
           for(m=-1; m <=nlstate+ndeath; m++)        for(j=1; j<i; j++)
             if(freq[jk][m][i] !=0 ) {          ps[i][j]= exp(ps[i][j])*ps[i][i];
             if(first==1)        for(j=i+1; j<=nlstate+ndeath; j++)
               printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);          ps[i][j]= exp(ps[i][j])*ps[i][i];
               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
             }      } /* end i */
         if(i <= (int) agemax)      
           fprintf(ficresp,"\n");      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
         if(first==1)        for(jj=1; jj<= nlstate+ndeath; jj++){
           printf("Others in log...\n");          ps[ii][jj]=0;
         fprintf(ficlog,"\n");          ps[ii][ii]=1;
       }        }
     }      }
   }      
   dateintmean=dateintsum/k2cpt;  
    /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
   fclose(ficresp);  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);  /*         printf("ddd %lf ",ps[ii][jj]); */
   free_vector(pp,1,nlstate);  /*       } */
    /*       printf("\n "); */
   /* End of Freq */  /*        } */
 }  /*        printf("\n ");printf("%lf ",cov[2]); */
          /*
 /************ Prevalence ********************/        for(i=1; i<= npar; i++) printf("%f ",x[i]);
 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)        goto end;*/
 {  /* Some frequencies */      return ps;
    }
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;  
   double ***freq; /* Frequencies */  /**************** Product of 2 matrices ******************/
   double *pp;  
   double pos, k2;  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
   {
   pp=vector(1,nlstate);    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
      /* in, b, out are matrice of pointers which should have been initialized 
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);       before: only the contents of out is modified. The function returns
   j1=0;       a pointer to pointers identical to out */
      long i, j, k;
   j=cptcoveff;    for(i=nrl; i<= nrh; i++)
   if (cptcovn<1) {j=1;ncodemax[1]=1;}      for(k=ncolol; k<=ncoloh; k++)
          for(j=ncl,out[i][k]=0.; j<=nch; j++)
   for(k1=1; k1<=j;k1++){          out[i][k] +=in[i][j]*b[j][k];
     for(i1=1; i1<=ncodemax[k1];i1++){  
       j1++;    return out;
        }
       for (i=-1; i<=nlstate+ndeath; i++)    
         for (jk=-1; jk<=nlstate+ndeath; jk++)    
           for(m=agemin; m <= agemax+3; m++)  /************* Higher Matrix Product ***************/
             freq[i][jk][m]=0;  
        double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
       for (i=1; i<=imx; i++) {  {
         bool=1;    /* Computes the transition matrix starting at age 'age' over 
         if  (cptcovn>0) {       'nhstepm*hstepm*stepm' months (i.e. until
           for (z1=1; z1<=cptcoveff; z1++)       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])       nhstepm*hstepm matrices. 
               bool=0;       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 
         if (bool==1) {       for the memory).
           for(m=firstpass; m<=lastpass; m++){       Model is determined by parameters x and covariates have to be 
             k2=anint[m][i]+(mint[m][i]/12.);       included manually here. 
             if ((k2>=dateprev1) && (k2<=dateprev2)) {  
               if(agev[m][i]==0) agev[m][i]=agemax+1;       */
               if(agev[m][i]==1) agev[m][i]=agemax+2;  
               if (m<lastpass) {    int i, j, d, h, k;
                 if (calagedate>0)    double **out, cov[NCOVMAX+1];
                   freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];    double **newm;
                 else  
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    /* Hstepm could be zero and should return the unit matrix */
                 freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];    for (i=1;i<=nlstate+ndeath;i++)
               }      for (j=1;j<=nlstate+ndeath;j++){
             }        oldm[i][j]=(i==j ? 1.0 : 0.0);
           }        po[i][j][0]=(i==j ? 1.0 : 0.0);
         }      }
       }    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
       for(i=(int)agemin; i <= (int)agemax+3; i++){    for(h=1; h <=nhstepm; h++){
         for(jk=1; jk <=nlstate ; jk++){      for(d=1; d <=hstepm; d++){
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        newm=savm;
             pp[jk] += freq[jk][m][i];        /* Covariates have to be included here again */
         }        cov[1]=1.;
         for(jk=1; jk <=nlstate ; jk++){        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
           for(m=-1, pos=0; m <=0 ; m++)        for (k=1; k<=cptcovn;k++) 
             pos += freq[jk][m][i];          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
         }        for (k=1; k<=cptcovage;k++)
                  cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
         for(jk=1; jk <=nlstate ; jk++){        for (k=1; k<=cptcovprod;k++)
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
             pp[jk] += freq[jk][m][i];  
         }  
                /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
         for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];        /*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, 
         for(jk=1; jk <=nlstate ; jk++){                         pmij(pmmij,cov,ncovmodel,x,nlstate));
           if( i <= (int) agemax){        savm=oldm;
             if(pos>=1.e-5){        oldm=newm;
               probs[i][jk][j1]= pp[jk]/pos;      }
             }      for(i=1; i<=nlstate+ndeath; i++)
           }        for(j=1;j<=nlstate+ndeath;j++) {
         }/* end jk */          po[i][j][h]=newm[i][j];
       }/* end i */          /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
     } /* end i1 */        }
   } /* end k1 */      /*printf("h=%d ",h);*/
     } /* end h */
    /*     printf("\n H=%d \n",h); */
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    return po;
   free_vector(pp,1,nlstate);  }
    
 }  /* End of Freq */  
   /*************** log-likelihood *************/
 /************* Waves Concatenation ***************/  double func( double *x)
   {
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)    int i, ii, j, k, mi, d, kk;
 {    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.    double **out;
      Death is a valid wave (if date is known).    double sw; /* Sum of weights */
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i    double lli; /* Individual log likelihood */
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]    int s1, s2;
      and mw[mi+1][i]. dh depends on stepm.    double bbh, survp;
      */    long ipmx;
     /*extern weight */
   int i, mi, m;    /* We are differentiating ll according to initial status */
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
      double sum=0., jmean=0.;*/    /*for(i=1;i<imx;i++) 
   int first;      printf(" %d\n",s[4][i]);
   int j, k=0,jk, ju, jl;    */
   double sum=0.;    cov[1]=1.;
   first=0;  
   jmin=1e+5;    for(k=1; k<=nlstate; k++) ll[k]=0.;
   jmax=-1;  
   jmean=0.;    if(mle==1){
   for(i=1; i<=imx; i++){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     mi=0;        /* Computes the values of the ncovmodel covariates of the model
     m=firstpass;           depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
     while(s[m][i] <= nlstate){           Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
       if(s[m][i]>=1)           to be observed in j being in i according to the model.
         mw[++mi][i]=m;         */
       if(m >=lastpass)        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         break;        /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 
       else           is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] 
         m++;           has been calculated etc */
     }/* end while */        for(mi=1; mi<= wav[i]-1; mi++){
     if (s[m][i] > nlstate){          for (ii=1;ii<=nlstate+ndeath;ii++)
       mi++;     /* Death is another wave */            for (j=1;j<=nlstate+ndeath;j++){
       /* if(mi==0)  never been interviewed correctly before death */              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
          /* Only death is a correct wave */              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       mw[mi][i]=m;            }
     }          for(d=0; d<dh[mi][i]; d++){
             newm=savm;
     wav[i]=mi;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     if(mi==0){            for (kk=1; kk<=cptcovage;kk++) {
       if(first==0){              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
         printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);            }
         first=1;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       if(first==1){            savm=oldm;
         fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i);            oldm=newm;
       }          } /* end mult */
     } /* end mi==0 */        
   }          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
           /* But now since version 0.9 we anticipate for bias at large stepm.
   for(i=1; i<=imx; i++){           * If stepm is larger than one month (smallest stepm) and if the exact delay 
     for(mi=1; mi<wav[i];mi++){           * (in months) between two waves is not a multiple of stepm, we rounded to 
       if (stepm <=0)           * the nearest (and in case of equal distance, to the lowest) interval but now
         dh[mi][i]=1;           * we keep into memory the bias bh[mi][i] and also the previous matrix product
       else{           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
         if (s[mw[mi+1][i]][i] > nlstate) {           * probability in order to take into account the bias as a fraction of the way
           if (agedc[i] < 2*AGESUP) {           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);           * -stepm/2 to stepm/2 .
           if(j==0) j=1;  /* Survives at least one month after exam */           * For stepm=1 the results are the same as for previous versions of Imach.
           k=k+1;           * For stepm > 1 the results are less biased than in previous versions. 
           if (j >= jmax) jmax=j;           */
           if (j <= jmin) jmin=j;          s1=s[mw[mi][i]][i];
           sum=sum+j;          s2=s[mw[mi+1][i]][i];
           /*if (j<0) printf("j=%d num=%d \n",j,i); */          bbh=(double)bh[mi][i]/(double)stepm; 
           }          /* bias bh is positive if real duration
         }           * is higher than the multiple of stepm and negative otherwise.
         else{           */
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
           k=k+1;          if( s2 > nlstate){ 
           if (j >= jmax) jmax=j;            /* i.e. if s2 is a death state and if the date of death is known 
           else if (j <= jmin)jmin=j;               then the contribution to the likelihood is the probability to 
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */               die between last step unit time and current  step unit time, 
           sum=sum+j;               which is also equal to probability to die before dh 
         }               minus probability to die before dh-stepm . 
         jk= j/stepm;               In version up to 0.92 likelihood was computed
         jl= j -jk*stepm;          as if date of death was unknown. Death was treated as any other
         ju= j -(jk+1)*stepm;          health state: the date of the interview describes the actual state
         if(jl <= -ju)          and not the date of a change in health state. The former idea was
           dh[mi][i]=jk;          to consider that at each interview the state was recorded
         else          (healthy, disable or death) and IMaCh was corrected; but when we
           dh[mi][i]=jk+1;          introduced the exact date of death then we should have modified
         if(dh[mi][i]==0)          the contribution of an exact death to the likelihood. This new
           dh[mi][i]=1; /* At least one step */          contribution is smaller and very dependent of the step unit
       }          stepm. It is no more the probability to die between last interview
     }          and month of death but the probability to survive from last
   }          interview up to one month before death multiplied by the
   jmean=sum/k;          probability to die within a month. Thanks to Chris
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);          Jackson for correcting this bug.  Former versions increased
   fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);          mortality artificially. The bad side is that we add another loop
  }          which slows down the processing. The difference can be up to 10%
           lower mortality.
 /*********** Tricode ****************************/            */
 void tricode(int *Tvar, int **nbcode, int imx)            lli=log(out[s1][s2] - savm[s1][s2]);
 {  
   int Ndum[20],ij=1, k, j, i;  
   int cptcode=0;          } else if  (s2==-2) {
   cptcoveff=0;            for (j=1,survp=0. ; j<=nlstate; j++) 
                survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   for (k=0; k<19; k++) Ndum[k]=0;            /*survp += out[s1][j]; */
   for (k=1; k<=7; k++) ncodemax[k]=0;            lli= log(survp);
           }
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {          
     for (i=1; i<=imx; i++) {          else if  (s2==-4) { 
       ij=(int)(covar[Tvar[j]][i]);            for (j=3,survp=0. ; j<=nlstate; j++)  
       Ndum[ij]++;              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/            lli= log(survp); 
       if (ij > cptcode) cptcode=ij;          } 
     }  
           else if  (s2==-5) { 
     for (i=0; i<=cptcode; i++) {            for (j=1,survp=0. ; j<=2; j++)  
       if(Ndum[i]!=0) ncodemax[j]++;              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
     }            lli= log(survp); 
     ij=1;          } 
           
           else{
     for (i=1; i<=ncodemax[j]; i++) {            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
       for (k=0; k<=19; k++) {            /*  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 */
         if (Ndum[k] != 0) {          } 
           nbcode[Tvar[j]][ij]=k;          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
                    /*if(lli ==000.0)*/
           ij++;          /*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); */
         }          ipmx +=1;
         if (ij > ncodemax[j]) break;          sw += weight[i];
       }            ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     }        } /* end of wave */
   }        } /* end of individual */
     }  else if(mle==2){
  for (k=0; k<19; k++) Ndum[k]=0;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
  for (i=1; i<=ncovmodel-2; i++) {        for(mi=1; mi<= wav[i]-1; mi++){
    ij=Tvar[i];          for (ii=1;ii<=nlstate+ndeath;ii++)
    Ndum[ij]++;            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);
  ij=1;            }
  for (i=1; i<=10; i++) {          for(d=0; d<=dh[mi][i]; d++){
    if((Ndum[i]!=0) && (i<=ncovcol)){            newm=savm;
      Tvaraff[ij]=i;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
      ij++;            for (kk=1; kk<=cptcovage;kk++) {
    }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
  }            }
              out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
  cptcoveff=ij-1;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 }            savm=oldm;
             oldm=newm;
 /*********** Health Expectancies ****************/          } /* end mult */
         
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )          s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
 {          bbh=(double)bh[mi][i]/(double)stepm; 
   /* Health expectancies */          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 */
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;          ipmx +=1;
   double age, agelim, hf;          sw += weight[i];
   double ***p3mat,***varhe;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   double **dnewm,**doldm;        } /* end of wave */
   double *xp;      } /* end of individual */
   double **gp, **gm;    }  else if(mle==3){  /* exponential inter-extrapolation */
   double ***gradg, ***trgradg;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   int theta;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for(mi=1; mi<= wav[i]-1; mi++){
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);          for (ii=1;ii<=nlstate+ndeath;ii++)
   xp=vector(1,npar);            for (j=1;j<=nlstate+ndeath;j++){
   dnewm=matrix(1,nlstate*2,1,npar);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   doldm=matrix(1,nlstate*2,1,nlstate*2);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
              }
   fprintf(ficreseij,"# Health expectancies\n");          for(d=0; d<dh[mi][i]; d++){
   fprintf(ficreseij,"# Age");            newm=savm;
   for(i=1; i<=nlstate;i++)            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     for(j=1; j<=nlstate;j++)            for (kk=1; kk<=cptcovage;kk++) {
       fprintf(ficreseij," %1d-%1d (SE)",i,j);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   fprintf(ficreseij,"\n");            }
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   if(estepm < stepm){                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     printf ("Problem %d lower than %d\n",estepm, stepm);            savm=oldm;
   }            oldm=newm;
   else  hstepm=estepm;            } /* end mult */
   /* We compute the life expectancy from trapezoids spaced every estepm months        
    * This is mainly to measure the difference between two models: for example          s1=s[mw[mi][i]][i];
    * if stepm=24 months pijx are given only every 2 years and by summing them          s2=s[mw[mi+1][i]][i];
    * we are calculating an estimate of the Life Expectancy assuming a linear          bbh=(double)bh[mi][i]/(double)stepm; 
    * progression inbetween and thus overestimating or underestimating according          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 */
    * to the curvature of the survival function. If, for the same date, we          ipmx +=1;
    * estimate the model with stepm=1 month, we can keep estepm to 24 months          sw += weight[i];
    * to compare the new estimate of Life expectancy with the same linear          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
    * hypothesis. A more precise result, taking into account a more precise        } /* end of wave */
    * curvature will be obtained if estepm is as small as stepm. */      } /* end of individual */
     }else if (mle==4){  /* ml=4 no inter-extrapolation */
   /* For example we decided to compute the life expectancy with the smallest unit */      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
      nhstepm is the number of hstepm from age to agelim        for(mi=1; mi<= wav[i]-1; mi++){
      nstepm is the number of stepm from age to agelin.          for (ii=1;ii<=nlstate+ndeath;ii++)
      Look at hpijx to understand the reason of that which relies in memory size            for (j=1;j<=nlstate+ndeath;j++){
      and note for a fixed period like estepm months */              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the              savm[ii][j]=(ii==j ? 1.0 : 0.0);
      survival function given by stepm (the optimization length). Unfortunately it            }
      means that if the survival funtion is printed only each two years of age and if          for(d=0; d<dh[mi][i]; d++){
      you sum them up and add 1 year (area under the trapezoids) you won't get the same            newm=savm;
      results. So we changed our mind and took the option of the best precision.            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   */            for (kk=1; kk<=cptcovage;kk++) {
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             }
   agelim=AGESUP;          
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     /* nhstepm age range expressed in number of stepm */                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     nstepm=(int) rint((agelim-age)*YEARM/stepm);            savm=oldm;
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */            oldm=newm;
     /* if (stepm >= YEARM) hstepm=1;*/          } /* end mult */
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */        
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          s1=s[mw[mi][i]][i];
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);          s2=s[mw[mi+1][i]][i];
     gp=matrix(0,nhstepm,1,nlstate*2);          if( s2 > nlstate){ 
     gm=matrix(0,nhstepm,1,nlstate*2);            lli=log(out[s1][s2] - savm[s1][s2]);
           }else{
     /* Computed by stepm unit matrices, product of hstepm matrices, stored            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */          }
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);            ipmx +=1;
            sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */  /*      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 */
     /* Computing Variances of health expectancies */      } /* end of individual */
     }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
      for(theta=1; theta <=npar; theta++){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       for(i=1; i<=npar; i++){        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        for(mi=1; mi<= wav[i]-1; mi++){
       }          for (ii=1;ii<=nlstate+ndeath;ii++)
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);              for (j=1;j<=nlstate+ndeath;j++){
                oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       cptj=0;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       for(j=1; j<= nlstate; j++){            }
         for(i=1; i<=nlstate; i++){          for(d=0; d<dh[mi][i]; d++){
           cptj=cptj+1;            newm=savm;
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;            for (kk=1; kk<=cptcovage;kk++) {
           }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         }            }
       }          
                  out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                               1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       for(i=1; i<=npar; i++)            savm=oldm;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);            oldm=newm;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            } /* end mult */
              
       cptj=0;          s1=s[mw[mi][i]][i];
       for(j=1; j<= nlstate; j++){          s2=s[mw[mi+1][i]][i];
         for(i=1;i<=nlstate;i++){          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
           cptj=cptj+1;          ipmx +=1;
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){          sw += weight[i];
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;          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 */
       }      } /* end of individual */
       for(j=1; j<= nlstate*2; j++)    } /* End of if */
         for(h=0; h<=nhstepm-1; h++){    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
         }    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
      }    return -l;
      }
 /* End theta */  
   /*************** log-likelihood *************/
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);  double funcone( double *x)
   {
      for(h=0; h<=nhstepm-1; h++)    /* Same as likeli but slower because of a lot of printf and if */
       for(j=1; j<=nlstate*2;j++)    int i, ii, j, k, mi, d, kk;
         for(theta=1; theta <=npar; theta++)    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
           trgradg[h][j][theta]=gradg[h][theta][j];    double **out;
          double lli; /* Individual log likelihood */
     double llt;
      for(i=1;i<=nlstate*2;i++)    int s1, s2;
       for(j=1;j<=nlstate*2;j++)    double bbh, survp;
         varhe[i][j][(int)age] =0.;    /*extern weight */
     /* We are differentiating ll according to initial status */
      printf("%d|",(int)age);fflush(stdout);    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);    /*for(i=1;i<imx;i++) 
      for(h=0;h<=nhstepm-1;h++){      printf(" %d\n",s[4][i]);
       for(k=0;k<=nhstepm-1;k++){    */
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);    cov[1]=1.;
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);  
         for(i=1;i<=nlstate*2;i++)    for(k=1; k<=nlstate; k++) ll[k]=0.;
           for(j=1;j<=nlstate*2;j++)  
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       }      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     }      for(mi=1; mi<= wav[i]-1; mi++){
     /* Computing expectancies */        for (ii=1;ii<=nlstate+ndeath;ii++)
     for(i=1; i<=nlstate;i++)          for (j=1;j<=nlstate+ndeath;j++){
       for(j=1; j<=nlstate;j++)            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){            savm[ii][j]=(ii==j ? 1.0 : 0.0);
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;          }
                  for(d=0; d<dh[mi][i]; d++){
 /* 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]);*/          newm=savm;
           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         }          for (kk=1; kk<=cptcovage;kk++) {
             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     fprintf(ficreseij,"%3.0f",age );          }
     cptj=0;          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     for(i=1; i<=nlstate;i++)                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       for(j=1; j<=nlstate;j++){          savm=oldm;
         cptj++;          oldm=newm;
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );        } /* end mult */
       }        
     fprintf(ficreseij,"\n");        s1=s[mw[mi][i]][i];
            s2=s[mw[mi+1][i]][i];
     free_matrix(gm,0,nhstepm,1,nlstate*2);        bbh=(double)bh[mi][i]/(double)stepm; 
     free_matrix(gp,0,nhstepm,1,nlstate*2);        /* bias is positive if real duration
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);         * is higher than the multiple of stepm and negative otherwise.
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);         */
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        if( s2 > nlstate && (mle <5) ){  /* Jackson */
   }          lli=log(out[s1][s2] - savm[s1][s2]);
   printf("\n");        } else if  (s2==-2) {
   fprintf(ficlog,"\n");          for (j=1,survp=0. ; j<=nlstate; j++) 
             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   free_vector(xp,1,npar);          lli= log(survp);
   free_matrix(dnewm,1,nlstate*2,1,npar);        }else if (mle==1){
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);        } else if(mle==2){
 }          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
         } else if(mle==3){  /* exponential inter-extrapolation */
 /************ Variance ******************/          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 */
 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)        } else if (mle==4){  /* mle=4 no inter-extrapolation */
 {          lli=log(out[s1][s2]); /* Original formula */
   /* Variance of health expectancies */        } else{  /* mle=0 back to 1 */
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   /* double **newm;*/          /*lli=log(out[s1][s2]); */ /* Original formula */
   double **dnewm,**doldm;        } /* End of if */
   double **dnewmp,**doldmp;        ipmx +=1;
   int i, j, nhstepm, hstepm, h, nstepm ;        sw += weight[i];
   int k, cptcode;        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   double *xp;        /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
   double **gp, **gm;  /* for var eij */        if(globpr){
   double ***gradg, ***trgradg; /*for var eij */          fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
   double **gradgp, **trgradgp; /* for var p point j */   %11.6f %11.6f %11.6f ", \
   double *gpp, *gmp; /* for var p point j */                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
   double **varppt; /* for var p point j nlstate to nlstate+ndeath */                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
   double ***p3mat;          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
   double age,agelim, hf;            llt +=ll[k]*gipmx/gsw;
   int theta;            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
   char digit[4];          }
   char digitp[16];          fprintf(ficresilk," %10.6f\n", -llt);
         }
   char fileresprobmorprev[FILENAMELENGTH];      } /* end of wave */
     } /* end of individual */
   if(popbased==1)    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     strcpy(digitp,"-populbased-");    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   else    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     strcpy(digitp,"-stablbased-");    if(globpr==0){ /* First time we count the contributions and weights */
       gipmx=ipmx;
   strcpy(fileresprobmorprev,"prmorprev");      gsw=sw;
   sprintf(digit,"%-d",ij);    }
   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/    return -l;
   strcat(fileresprobmorprev,digit); /* Tvar to be done */  }
   strcat(fileresprobmorprev,digitp); /* Popbased or not */  
   strcat(fileresprobmorprev,fileres);  
   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {  /*************** function likelione ***********/
     printf("Problem with resultfile: %s\n", fileresprobmorprev);  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);  {
   }    /* This routine should help understanding what is done with 
   printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);       the selection of individuals/waves and
   fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);       to check the exact contribution to the likelihood.
   fprintf(ficresprobmorprev,"# probabilities of dying during a year and weighted mean w1*p1j+w2*p2j+... stand dev in()\n");       Plotting could be done.
   fprintf(ficresprobmorprev,"# Age cov=%-d",ij);     */
   for(j=nlstate+1; j<=(nlstate+ndeath);j++){    int k;
     fprintf(ficresprobmorprev," p.%-d SE",j);  
     for(i=1; i<=nlstate;i++)    if(*globpri !=0){ /* Just counts and sums, no printings */
       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);      strcpy(fileresilk,"ilk"); 
   }        strcat(fileresilk,fileres);
   fprintf(ficresprobmorprev,"\n");      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {        printf("Problem with resultfile: %s\n", fileresilk);
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
     fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);      }
     exit(0);      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");
   }      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
   else{      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
     fprintf(ficgp,"\n# Routine varevsij");      for(k=1; k<=nlstate; k++) 
   }        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
     printf("Problem with html file: %s\n", optionfilehtm);    }
     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);  
     exit(0);    *fretone=(*funcone)(p);
   }    if(*globpri !=0){
   else{      fclose(ficresilk);
     fprintf(fichtm,"\n<li><h4> Computing probabilities of dying as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
   }      fflush(fichtm); 
   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);    } 
     return;
   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");  }
   fprintf(ficresvij,"# Age");  
   for(i=1; i<=nlstate;i++)  
     for(j=1; j<=nlstate;j++)  /*********** Maximum Likelihood Estimation ***************/
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);  
   fprintf(ficresvij,"\n");  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   {
   xp=vector(1,npar);    int i,j, iter;
   dnewm=matrix(1,nlstate,1,npar);    double **xi;
   doldm=matrix(1,nlstate,1,nlstate);    double fret;
   dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);    double fretone; /* Only one call to likelihood */
   doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);    /*  char filerespow[FILENAMELENGTH];*/
     xi=matrix(1,npar,1,npar);
   gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);    for (i=1;i<=npar;i++)
   gpp=vector(nlstate+1,nlstate+ndeath);      for (j=1;j<=npar;j++)
   gmp=vector(nlstate+1,nlstate+ndeath);        xi[i][j]=(i==j ? 1.0 : 0.0);
   trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/    printf("Powell\n");  fprintf(ficlog,"Powell\n");
      strcpy(filerespow,"pow"); 
   if(estepm < stepm){    strcat(filerespow,fileres);
     printf ("Problem %d lower than %d\n",estepm, stepm);    if((ficrespow=fopen(filerespow,"w"))==NULL) {
   }      printf("Problem with resultfile: %s\n", filerespow);
   else  hstepm=estepm;        fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
   /* 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.    fprintf(ficrespow,"# Powell\n# iter -2*LL");
      nhstepm is the number of hstepm from age to agelim    for (i=1;i<=nlstate;i++)
      nstepm is the number of stepm from age to agelin.      for(j=1;j<=nlstate+ndeath;j++)
      Look at hpijx to understand the reason of that which relies in memory size        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
      and note for a fixed period like k years */    fprintf(ficrespow,"\n");
   /* 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    powell(p,xi,npar,ftol,&iter,&fret,func);
      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    free_matrix(xi,1,npar,1,npar);
      results. So we changed our mind and took the option of the best precision.    fclose(ficrespow);
   */    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   agelim = AGESUP;    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   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);  /**** Computes Hessian and covariance matrix ***/
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
     gp=matrix(0,nhstepm,1,nlstate);  {
     gm=matrix(0,nhstepm,1,nlstate);    double  **a,**y,*x,pd;
     double **hess;
     int i, j,jk;
     for(theta=1; theta <=npar; theta++){    int *indx;
       for(i=1; i<=npar; i++){ /* Computes gradient */  
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
       }    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      void lubksb(double **a, int npar, int *indx, double b[]) ;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    void ludcmp(double **a, int npar, int *indx, double *d) ;
     double gompertz(double p[]);
       if (popbased==1) {    hess=matrix(1,npar,1,npar);
         for(i=1; i<=nlstate;i++)  
           prlim[i][i]=probs[(int)age][i][ij];    printf("\nCalculation of the hessian matrix. Wait...\n");
       }    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
      for (i=1;i<=npar;i++){
       for(j=1; j<= nlstate; j++){      printf("%d",i);fflush(stdout);
         for(h=0; h<=nhstepm; h++){      fprintf(ficlog,"%d",i);fflush(ficlog);
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)     
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
         }      
       }      /*  printf(" %f ",p[i]);
       /* This for computing forces of mortality (h=1)as a weighted average */          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
       for(j=nlstate+1,gpp[j]=0.;j<=nlstate+ndeath;j++){    }
         for(i=1; i<= nlstate; i++)    
           gpp[j] += prlim[i][i]*p3mat[i][j][1];    for (i=1;i<=npar;i++) {
       }          for (j=1;j<=npar;j++)  {
       /* end force of mortality */        if (j>i) { 
           printf(".%d%d",i,j);fflush(stdout);
       for(i=1; i<=npar; i++) /* Computes gradient */          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          hess[i][j]=hessij(p,delti,i,j,func,npar);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          hess[j][i]=hess[i][j];    
            /*printf(" %lf ",hess[i][j]);*/
       if (popbased==1) {        }
         for(i=1; i<=nlstate;i++)      }
           prlim[i][i]=probs[(int)age][i][ij];    }
       }    printf("\n");
     fprintf(ficlog,"\n");
       for(j=1; j<= nlstate; j++){  
         for(h=0; h<=nhstepm; h++){    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];    
         }    a=matrix(1,npar,1,npar);
       }    y=matrix(1,npar,1,npar);
       /* This for computing force of mortality (h=1)as a weighted average */    x=vector(1,npar);
       for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){    indx=ivector(1,npar);
         for(i=1; i<= nlstate; i++)    for (i=1;i<=npar;i++)
           gmp[j] += prlim[i][i]*p3mat[i][j][1];      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
       }        ludcmp(a,npar,indx,&pd);
       /* end force of mortality */  
     for (j=1;j<=npar;j++) {
       for(j=1; j<= nlstate; j++) /* vareij */      for (i=1;i<=npar;i++) x[i]=0;
         for(h=0; h<=nhstepm; h++){      x[j]=1;
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];      lubksb(a,npar,indx,x);
         }      for (i=1;i<=npar;i++){ 
       for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */        matcov[i][j]=x[i];
         gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];      }
       }    }
   
     } /* End theta */    printf("\n#Hessian matrix#\n");
     fprintf(ficlog,"\n#Hessian matrix#\n");
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */    for (i=1;i<=npar;i++) { 
       for (j=1;j<=npar;j++) { 
     for(h=0; h<=nhstepm; h++) /* veij */        printf("%.3e ",hess[i][j]);
       for(j=1; j<=nlstate;j++)        fprintf(ficlog,"%.3e ",hess[i][j]);
         for(theta=1; theta <=npar; theta++)      }
           trgradg[h][j][theta]=gradg[h][theta][j];      printf("\n");
       fprintf(ficlog,"\n");
     for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */    }
       for(theta=1; theta <=npar; theta++)  
         trgradgp[j][theta]=gradgp[theta][j];    /* Recompute Inverse */
     for (i=1;i<=npar;i++)
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
     for(i=1;i<=nlstate;i++)    ludcmp(a,npar,indx,&pd);
       for(j=1;j<=nlstate;j++)  
         vareij[i][j][(int)age] =0.;    /*  printf("\n#Hessian matrix recomputed#\n");
   
     for(h=0;h<=nhstepm;h++){    for (j=1;j<=npar;j++) {
       for(k=0;k<=nhstepm;k++){      for (i=1;i<=npar;i++) x[i]=0;
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);      x[j]=1;
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);      lubksb(a,npar,indx,x);
         for(i=1;i<=nlstate;i++)      for (i=1;i<=npar;i++){ 
           for(j=1;j<=nlstate;j++)        y[i][j]=x[i];
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;        printf("%.3e ",y[i][j]);
       }        fprintf(ficlog,"%.3e ",y[i][j]);
     }      }
       printf("\n");
     /* pptj */      fprintf(ficlog,"\n");
     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++)    free_matrix(a,1,npar,1,npar);
         varppt[j][i]=doldmp[j][i];    free_matrix(y,1,npar,1,npar);
     /* end ppptj */    free_vector(x,1,npar);
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);      free_ivector(indx,1,npar);
     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);    free_matrix(hess,1,npar,1,npar);
    
     if (popbased==1) {  
       for(i=1; i<=nlstate;i++)  }
         prlim[i][i]=probs[(int)age][i][ij];  
     }  /*************** hessian matrix ****************/
      double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
     /* This for computing force of mortality (h=1)as a weighted average */  {
     for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){    int i;
       for(i=1; i<= nlstate; i++)    int l=1, lmax=20;
         gmp[j] += prlim[i][i]*p3mat[i][j][1];    double k1,k2;
     }        double p2[MAXPARM+1]; /* identical to x */
     /* end force of mortality */    double res;
     double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);    double fx;
     for(j=nlstate+1; j<=(nlstate+ndeath);j++){    int k=0,kmax=10;
       fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));    double l1;
       for(i=1; i<=nlstate;i++){  
         fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);    fx=func(x);
       }    for (i=1;i<=npar;i++) p2[i]=x[i];
     }    for(l=0 ; l <=lmax; l++){
     fprintf(ficresprobmorprev,"\n");      l1=pow(10,l);
       delts=delt;
     fprintf(ficresvij,"%.0f ",age );      for(k=1 ; k <kmax; k=k+1){
     for(i=1; i<=nlstate;i++)        delt = delta*(l1*k);
       for(j=1; j<=nlstate;j++){        p2[theta]=x[theta] +delt;
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);        k1=func(p2)-fx;
       }        p2[theta]=x[theta]-delt;
     fprintf(ficresvij,"\n");        k2=func(p2)-fx;
     free_matrix(gp,0,nhstepm,1,nlstate);        /*res= (k1-2.0*fx+k2)/delt/delt; */
     free_matrix(gm,0,nhstepm,1,nlstate);        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);        
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);  #ifdef DEBUGHESS
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        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);
   } /* End age */        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);
   free_vector(gpp,nlstate+1,nlstate+ndeath);  #endif
   free_vector(gmp,nlstate+1,nlstate+ndeath);        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
   free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
   free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/          k=kmax;
   fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");        }
   /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
   fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");          k=kmax; l=lmax*10.;
   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);        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm);          delts=delt;
   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);        }
   fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,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);    }
 */    delti[theta]=delts;
   fprintf(ficgp,"\nset out \"varmuptjgr%s%s.png\";replot;",digitp,digit);    return res; 
     
   free_vector(xp,1,npar);  }
   free_matrix(doldm,1,nlstate,1,nlstate);  
   free_matrix(dnewm,1,nlstate,1,npar);  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
   free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);  {
   free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);    int i;
   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);    int l=1, l1, lmax=20;
   fclose(ficresprobmorprev);    double k1,k2,k3,k4,res,fx;
   fclose(ficgp);    double p2[MAXPARM+1];
   fclose(fichtm);    int k;
   
 }    fx=func(x);
     for (k=1; k<=2; k++) {
 /************ Variance of prevlim ******************/      for (i=1;i<=npar;i++) p2[i]=x[i];
 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)      p2[thetai]=x[thetai]+delti[thetai]/k;
 {      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   /* Variance of prevalence limit */      k1=func(p2)-fx;
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    
   double **newm;      p2[thetai]=x[thetai]+delti[thetai]/k;
   double **dnewm,**doldm;      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   int i, j, nhstepm, hstepm;      k2=func(p2)-fx;
   int k, cptcode;    
   double *xp;      p2[thetai]=x[thetai]-delti[thetai]/k;
   double *gp, *gm;      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   double **gradg, **trgradg;      k3=func(p2)-fx;
   double age,agelim;    
   int theta;      p2[thetai]=x[thetai]-delti[thetai]/k;
          p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n");      k4=func(p2)-fx;
   fprintf(ficresvpl,"# Age");      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
   for(i=1; i<=nlstate;i++)  #ifdef DEBUG
       fprintf(ficresvpl," %1d-%1d",i,i);      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(ficresvpl,"\n");      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
   xp=vector(1,npar);    }
   dnewm=matrix(1,nlstate,1,npar);    return res;
   doldm=matrix(1,nlstate,1,nlstate);  }
    
   hstepm=1*YEARM; /* Every year of age */  /************** Inverse of matrix **************/
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */  void ludcmp(double **a, int n, int *indx, double *d) 
   agelim = AGESUP;  { 
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    int i,imax,j,k; 
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    double big,dum,sum,temp; 
     if (stepm >= YEARM) hstepm=1;    double *vv; 
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */   
     gradg=matrix(1,npar,1,nlstate);    vv=vector(1,n); 
     gp=vector(1,nlstate);    *d=1.0; 
     gm=vector(1,nlstate);    for (i=1;i<=n;i++) { 
       big=0.0; 
     for(theta=1; theta <=npar; theta++){      for (j=1;j<=n;j++) 
       for(i=1; i<=npar; i++){ /* Computes gradient */        if ((temp=fabs(a[i][j])) > big) big=temp; 
         xp[i] = x[i] + (i==theta ?delti[theta]:0);      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
       }      vv[i]=1.0/big; 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    } 
       for(i=1;i<=nlstate;i++)    for (j=1;j<=n;j++) { 
         gp[i] = prlim[i][i];      for (i=1;i<j;i++) { 
            sum=a[i][j]; 
       for(i=1; i<=npar; i++) /* Computes gradient */        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        a[i][j]=sum; 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      } 
       for(i=1;i<=nlstate;i++)      big=0.0; 
         gm[i] = prlim[i][i];      for (i=j;i<=n;i++) { 
         sum=a[i][j]; 
       for(i=1;i<=nlstate;i++)        for (k=1;k<j;k++) 
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];          sum -= a[i][k]*a[k][j]; 
     } /* End theta */        a[i][j]=sum; 
         if ( (dum=vv[i]*fabs(sum)) >= big) { 
     trgradg =matrix(1,nlstate,1,npar);          big=dum; 
           imax=i; 
     for(j=1; j<=nlstate;j++)        } 
       for(theta=1; theta <=npar; theta++)      } 
         trgradg[j][theta]=gradg[theta][j];      if (j != imax) { 
         for (k=1;k<=n;k++) { 
     for(i=1;i<=nlstate;i++)          dum=a[imax][k]; 
       varpl[i][(int)age] =0.;          a[imax][k]=a[j][k]; 
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);          a[j][k]=dum; 
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);        } 
     for(i=1;i<=nlstate;i++)        *d = -(*d); 
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */        vv[imax]=vv[j]; 
       } 
     fprintf(ficresvpl,"%.0f ",age );      indx[j]=imax; 
     for(i=1; i<=nlstate;i++)      if (a[j][j] == 0.0) a[j][j]=TINY; 
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));      if (j != n) { 
     fprintf(ficresvpl,"\n");        dum=1.0/(a[j][j]); 
     free_vector(gp,1,nlstate);        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
     free_vector(gm,1,nlstate);      } 
     free_matrix(gradg,1,npar,1,nlstate);    } 
     free_matrix(trgradg,1,nlstate,1,npar);    free_vector(vv,1,n);  /* Doesn't work */
   } /* End age */  ;
   } 
   free_vector(xp,1,npar);  
   free_matrix(doldm,1,nlstate,1,npar);  void lubksb(double **a, int n, int *indx, double b[]) 
   free_matrix(dnewm,1,nlstate,1,nlstate);  { 
     int i,ii=0,ip,j; 
 }    double sum; 
    
 /************ Variance of one-step probabilities  ******************/    for (i=1;i<=n;i++) { 
 void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)      ip=indx[i]; 
 {      sum=b[ip]; 
   int i, j=0,  i1, k1, l1, t, tj;      b[ip]=b[i]; 
   int k2, l2, j1,  z1;      if (ii) 
   int k=0,l, cptcode;        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
   int first=1, first1;      else if (sum) ii=i; 
   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;      b[i]=sum; 
   double **dnewm,**doldm;    } 
   double *xp;    for (i=n;i>=1;i--) { 
   double *gp, *gm;      sum=b[i]; 
   double **gradg, **trgradg;      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
   double **mu;      b[i]=sum/a[i][i]; 
   double age,agelim, cov[NCOVMAX];    } 
   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */  } 
   int theta;  
   char fileresprob[FILENAMELENGTH];  void pstamp(FILE *fichier)
   char fileresprobcov[FILENAMELENGTH];  {
   char fileresprobcor[FILENAMELENGTH];    fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
   }
   double ***varpij;  
   /************ Frequencies ********************/
   strcpy(fileresprob,"prob");  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[])
   strcat(fileresprob,fileres);  {  /* Some frequencies */
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {    
     printf("Problem with resultfile: %s\n", fileresprob);    int i, m, jk, k1,i1, j1, bool, z1,j;
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);    int first;
   }    double ***freq; /* Frequencies */
   strcpy(fileresprobcov,"probcov");    double *pp, **prop;
   strcat(fileresprobcov,fileres);    double pos,posprop, k2, dateintsum=0,k2cpt=0;
   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {    char fileresp[FILENAMELENGTH];
     printf("Problem with resultfile: %s\n", fileresprobcov);    
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);    pp=vector(1,nlstate);
   }    prop=matrix(1,nlstate,iagemin,iagemax+3);
   strcpy(fileresprobcor,"probcor");    strcpy(fileresp,"p");
   strcat(fileresprobcor,fileres);    strcat(fileresp,fileres);
   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {    if((ficresp=fopen(fileresp,"w"))==NULL) {
     printf("Problem with resultfile: %s\n", fileresprobcor);      printf("Problem with prevalence resultfile: %s\n", fileresp);
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
   }      exit(0);
   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);    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);    j1=0;
   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);    j=cptcoveff;
   fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
    
   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");    first=1;
   fprintf(ficresprob,"# Age");  
   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");    for(k1=1; k1<=j;k1++){
   fprintf(ficresprobcov,"# Age");      for(i1=1; i1<=ncodemax[k1];i1++){
   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");        j1++;
   fprintf(ficresprobcov,"# Age");        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
           scanf("%d", i);*/
         for (i=-5; i<=nlstate+ndeath; i++)  
   for(i=1; i<=nlstate;i++)          for (jk=-5; jk<=nlstate+ndeath; jk++)  
     for(j=1; j<=(nlstate+ndeath);j++){            for(m=iagemin; m <= iagemax+3; m++)
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);              freq[i][jk][m]=0;
       fprintf(ficresprobcov," p%1d-%1d ",i,j);  
       fprintf(ficresprobcor," p%1d-%1d ",i,j);      for (i=1; i<=nlstate; i++)  
     }          for(m=iagemin; m <= iagemax+3; m++)
   fprintf(ficresprob,"\n");          prop[i][m]=0;
   fprintf(ficresprobcov,"\n");        
   fprintf(ficresprobcor,"\n");        dateintsum=0;
   xp=vector(1,npar);        k2cpt=0;
   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);        for (i=1; i<=imx; i++) {
   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));          bool=1;
   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);          if  (cptcovn>0) {
   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);            for (z1=1; z1<=cptcoveff; z1++) 
   first=1;              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {                bool=0;
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);          }
     fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);          if (bool==1){
     exit(0);            for(m=firstpass; m<=lastpass; m++){
   }              k2=anint[m][i]+(mint[m][i]/12.);
   else{              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
     fprintf(ficgp,"\n# Routine varprob");                if(agev[m][i]==0) agev[m][i]=iagemax+1;
   }                if(agev[m][i]==1) agev[m][i]=iagemax+2;
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
     printf("Problem with html file: %s\n", optionfilehtm);                if (m<lastpass) {
     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
     exit(0);                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
   }                }
   else{                
     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
     fprintf(fichtm,"\n");                  dateintsum=dateintsum+k2;
                   k2cpt++;
     fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");                }
     fprintf(fichtm,"\nWe have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");                /*}*/
     fprintf(fichtm,"\n<br> We have drawn x'cov<sup>-1</sup>x = 4 where x is the column vector (pij,pkl). It means that if pij and pkl where uncorrelated the (2X2) matrix 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> When both incidences are correlated we diagonalised the inverse of the covariance matrix and made the appropriate rotation.<br> \n");            }
           }
   }        }
          
          /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
   cov[1]=1;        pstamp(ficresp);
   tj=cptcoveff;        if  (cptcovn>0) {
   if (cptcovn<1) {tj=1;ncodemax[1]=1;}          fprintf(ficresp, "\n#********** Variable "); 
   j1=0;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   for(t=1; t<=tj;t++){          fprintf(ficresp, "**********\n#");
     for(i1=1; i1<=ncodemax[t];i1++){        }
       j1++;        for(i=1; i<=nlstate;i++) 
                fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
       if  (cptcovn>0) {        fprintf(ficresp, "\n");
         fprintf(ficresprob, "\n#********** Variable ");        
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);        for(i=iagemin; i <= iagemax+3; i++){
         fprintf(ficresprob, "**********\n#");          if(i==iagemax+3){
         fprintf(ficresprobcov, "\n#********** Variable ");            fprintf(ficlog,"Total");
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          }else{
         fprintf(ficresprobcov, "**********\n#");            if(first==1){
                      first=0;
         fprintf(ficgp, "\n#********** Variable ");              printf("See log file for details...\n");
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);            }
         fprintf(ficgp, "**********\n#");            fprintf(ficlog,"Age %d", i);
                  }
                  for(jk=1; jk <=nlstate ; jk++){
         fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);              pp[jk] += freq[jk][m][i]; 
         fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");          }
                  for(jk=1; jk <=nlstate ; jk++){
         fprintf(ficresprobcor, "\n#********** Variable ");                for(m=-1, pos=0; m <=0 ; m++)
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);              pos += freq[jk][m][i];
         fprintf(ficgp, "**********\n#");                if(pp[jk]>=1.e-10){
       }              if(first==1){
                      printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
       for (age=bage; age<=fage; age ++){              }
         cov[2]=age;              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
         for (k=1; k<=cptcovn;k++) {            }else{
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];              if(first==1)
         }                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
         for (k=1; k<=cptcovprod;k++)            }
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];          }
          
         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));          for(jk=1; jk <=nlstate ; jk++){
         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
         gp=vector(1,(nlstate)*(nlstate+ndeath));              pp[jk] += freq[jk][m][i];
         gm=vector(1,(nlstate)*(nlstate+ndeath));          }       
              for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
         for(theta=1; theta <=npar; theta++){            pos += pp[jk];
           for(i=1; i<=npar; i++)            posprop += prop[jk][i];
             xp[i] = x[i] + (i==theta ?delti[theta]:0);          }
                    for(jk=1; jk <=nlstate ; jk++){
           pmij(pmmij,cov,ncovmodel,xp,nlstate);            if(pos>=1.e-5){
                        if(first==1)
           k=0;                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
           for(i=1; i<= (nlstate); i++){              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
             for(j=1; j<=(nlstate+ndeath);j++){            }else{
               k=k+1;              if(first==1)
               gp[k]=pmmij[i][j];                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
             }              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
           }            }
                      if( i <= iagemax){
           for(i=1; i<=npar; i++)              if(pos>=1.e-5){
             xp[i] = x[i] - (i==theta ?delti[theta]:0);                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
                    /*probs[i][jk][j1]= pp[jk]/pos;*/
           pmij(pmmij,cov,ncovmodel,xp,nlstate);                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
           k=0;              }
           for(i=1; i<=(nlstate); i++){              else
             for(j=1; j<=(nlstate+ndeath);j++){                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
               k=k+1;            }
               gm[k]=pmmij[i][j];          }
             }          
           }          for(jk=-1; jk <=nlstate+ndeath; jk++)
                  for(m=-1; m <=nlstate+ndeath; m++)
           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)              if(freq[jk][m][i] !=0 ) {
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];                if(first==1)
         }                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
                 fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)              }
           for(theta=1; theta <=npar; theta++)          if(i <= iagemax)
             trgradg[j][theta]=gradg[theta][j];            fprintf(ficresp,"\n");
                  if(first==1)
         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);            printf("Others in log...\n");
         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);          fprintf(ficlog,"\n");
                }
         pmij(pmmij,cov,ncovmodel,x,nlstate);      }
            }
         k=0;    dateintmean=dateintsum/k2cpt; 
         for(i=1; i<=(nlstate); i++){   
           for(j=1; j<=(nlstate+ndeath);j++){    fclose(ficresp);
             k=k+1;    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
             mu[k][(int) age]=pmmij[i][j];    free_vector(pp,1,nlstate);
           }    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
         }    /* End of Freq */
         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)  }
           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)  
             varpij[i][j][(int)age] = doldm[i][j];  /************ 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)
         /*printf("\n%d ",(int)age);  {  
      for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));       in each health status at the date of interview (if between dateprev1 and dateprev2).
        fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));       We still use firstpass and lastpass as another selection.
      }*/    */
    
         fprintf(ficresprob,"\n%d ",(int)age);    int i, m, jk, k1, i1, j1, bool, z1,j;
         fprintf(ficresprobcov,"\n%d ",(int)age);    double ***freq; /* Frequencies */
         fprintf(ficresprobcor,"\n%d ",(int)age);    double *pp, **prop;
     double pos,posprop; 
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)    double  y2; /* in fractional years */
           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));    int iagemin, iagemax;
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){  
           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);    iagemin= (int) agemin;
           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);    iagemax= (int) agemax;
         }    /*pp=vector(1,nlstate);*/
         i=0;    prop=matrix(1,nlstate,iagemin,iagemax+3); 
         for (k=1; k<=(nlstate);k++){    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
           for (l=1; l<=(nlstate+ndeath);l++){    j1=0;
             i=i++;    
             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);    j=cptcoveff;
             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
             for (j=1; j<=i;j++){    
               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);    for(k1=1; k1<=j;k1++){
               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));      for(i1=1; i1<=ncodemax[k1];i1++){
             }        j1++;
           }        
         }/* end of loop for state */        for (i=1; i<=nlstate; i++)  
       } /* end of loop for age */          for(m=iagemin; m <= iagemax+3; m++)
             prop[i][m]=0.0;
       /* Confidence intervalle of pij  */       
       /*        for (i=1; i<=imx; i++) { /* Each individual */
       fprintf(ficgp,"\nset noparametric;unset label");          bool=1;
       fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");          if  (cptcovn>0) {
       fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");            for (z1=1; z1<=cptcoveff; z1++) 
       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);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
       fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);                bool=0;
       fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);          } 
       fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);          if (bool==1) { 
       */            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
               y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
       first1=1;                if(agev[m][i]==0) agev[m][i]=iagemax+1;
       for (k2=1; k2<=(nlstate);k2++){                if(agev[m][i]==1) agev[m][i]=iagemax+2;
         for (l2=1; l2<=(nlstate+ndeath);l2++){                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(l2==k2) continue;                if (s[m][i]>0 && s[m][i]<=nlstate) { 
           j=(k2-1)*(nlstate+ndeath)+l2;                  /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
           for (k1=1; k1<=(nlstate);k1++){                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
             for (l1=1; l1<=(nlstate+ndeath);l1++){                  prop[s[m][i]][iagemax+3] += weight[i]; 
               if(l1==k1) continue;                } 
               i=(k1-1)*(nlstate+ndeath)+l1;              }
               if(i<=j) continue;            } /* end selection of waves */
               for (age=bage; age<=fage; age ++){          }
                 if ((int)age %5==0){        }
                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;        for(i=iagemin; i <= iagemax+3; i++){  
                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;          
                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
                   mu1=mu[i][(int) age]/stepm*YEARM ;            posprop += prop[jk][i]; 
                   mu2=mu[j][(int) age]/stepm*YEARM;          } 
                   c12=cv12/sqrt(v1*v2);  
                   /* Computing eigen value of matrix of covariance */          for(jk=1; jk <=nlstate ; jk++){     
                   lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;            if( i <=  iagemax){ 
                   lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;              if(posprop>=1.e-5){ 
                   /* Eigen vectors */                probs[i][jk][j1]= prop[jk][i]/posprop;
                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));              } else
                   /*v21=sqrt(1.-v11*v11); *//* error */                printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\n",jk,i,j1,probs[i][jk][j1]);
                   v21=(lc1-v1)/cv12*v11;            } 
                   v12=-v21;          }/* end jk */ 
                   v22=v11;        }/* end i */ 
                   tnalp=v21/v11;      } /* end i1 */
                   if(first1==1){    } /* end k1 */
                     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);    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
                   }    /*free_vector(pp,1,nlstate);*/
                   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);    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
                   /*printf(fignu*/  }  /* End of prevalence */
                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */  
                   /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */  /************* Waves Concatenation ***************/
                   if(first==1){  
                     first=0;  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)
                     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);    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
                     fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");       Death is a valid wave (if date is known).
                     fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%d%1d%1d-%1d%1d.png\">varpijgr%s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2);       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
                     fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
                     fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);       and mw[mi+1][i]. dh depends on stepm.
                     fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, 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);    int i, mi, m;
                     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",\    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\       double sum=0., jmean=0.;*/
                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));    int first;
                   }else{    int j, k=0,jk, ju, jl;
                     first=0;    double sum=0.;
                     fprintf(fichtm," %d (%.3f),",(int) age, c12);    first=0;
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);    jmin=1e+5;
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);    jmax=-1;
                     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",\    jmean=0.;
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\    for(i=1; i<=imx; i++){
                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));      mi=0;
                   }/* if first */      m=firstpass;
                 } /* age mod 5 */      while(s[m][i] <= nlstate){
               } /* end loop age */        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
               fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);          mw[++mi][i]=m;
               first=1;        if(m >=lastpass)
             } /*l12 */          break;
           } /* k12 */        else
         } /*l1 */          m++;
       }/* k1 */      }/* end while */
     } /* loop covariates */      if (s[m][i] > nlstate){
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);        mi++;     /* Death is another wave */
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));        /* if(mi==0)  never been interviewed correctly before death */
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));           /* Only death is a correct wave */
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);        mw[mi][i]=m;
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);      }
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);  
   }      wav[i]=mi;
   free_vector(xp,1,npar);      if(mi==0){
   fclose(ficresprob);        nbwarn++;
   fclose(ficresprobcov);        if(first==0){
   fclose(ficresprobcor);          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
   fclose(ficgp);          first=1;
   fclose(fichtm);        }
 }        if(first==1){
           fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
         }
 /******************* Printing html file ***********/      } /* end mi==0 */
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \    } /* End individuals */
                   int lastpass, int stepm, int weightopt, char model[],\  
                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\    for(i=1; i<=imx; i++){
                   int popforecast, int estepm ,\      for(mi=1; mi<wav[i];mi++){
                   double jprev1, double mprev1,double anprev1, \        if (stepm <=0)
                   double jprev2, double mprev2,double anprev2){          dh[mi][i]=1;
   int jj1, k1, i1, cpt;        else{
   /*char optionfilehtm[FILENAMELENGTH];*/          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {            if (agedc[i] < 2*AGESUP) {
     printf("Problem with %s \n",optionfilehtm), exit(0);              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
     fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);              if(j==0) j=1;  /* Survives at least one month after exam */
   }              else if(j<0){
                 nberr++;
    fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n                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]);
  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"p%s\">p%s</a> <br>\n                j=1; /* Temporary Dangerous patch */
  - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n                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);
  - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n                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]);
  - Life expectancies by age and initial health status (estepm=%2d months):                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);
    <a href=\"e%s\">e%s</a> <br>\n</li>", \              }
   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);              k=k+1;
               if (j >= jmax){
 fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");                jmax=j;
                 ijmax=i;
  m=cptcoveff;              }
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}              if (j <= jmin){
                 jmin=j;
  jj1=0;                ijmin=i;
  for(k1=1; k1<=m;k1++){              }
    for(i1=1; i1<=ncodemax[k1];i1++){              sum=sum+j;
      jj1++;              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
      if (cptcovn > 0) {              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
        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]]);          else{
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
      }  /*        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]); */
      /* Pij */  
      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before: pe%s%d1.png<br>            k=k+1;
 <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);                if (j >= jmax) {
      /* Quasi-incidences */              jmax=j;
      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: pe%s%d2.png<br>              ijmax=i;
 <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);            }
        /* Stable prevalence in each health state */            else if (j <= jmin){
        for(cpt=1; cpt<nlstate;cpt++){              jmin=j;
          fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>              ijmin=i;
 <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);            }
        }            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
      for(cpt=1; cpt<=nlstate;cpt++) {            /*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]);*/
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>            if(j<0){
 <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);              nberr++;
      }              printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
      fprintf(fichtm,"\n<br>- Total life expectancy by age and              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]);
 health expectancies in states (1) and (2): e%s%d.png<br>            }
 <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);            sum=sum+j;
    } /* end i1 */          }
  }/* End k1 */          jk= j/stepm;
  fprintf(fichtm,"</ul>");          jl= j -jk*stepm;
           ju= j -(jk+1)*stepm;
           if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
  fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n            if(jl==0){
  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n              dh[mi][i]=jk;
  - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n              bh[mi][i]=0;
  - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n            }else{ /* We want a negative bias in order to only have interpolation ie
  - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n                    * to avoid the price of an extra matrix product in likelihood */
  - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n              dh[mi][i]=jk+1;
  - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n              bh[mi][i]=ju;
  - Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);            }
           }else{
  if(popforecast==1) fprintf(fichtm,"\n            if(jl <= -ju){
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n              dh[mi][i]=jk;
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n              bh[mi][i]=jl;       /* bias is positive if real duration
         <br>",fileres,fileres,fileres,fileres);                                   * is higher than the multiple of stepm and negative otherwise.
  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);            }
 fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");            else{
               dh[mi][i]=jk+1;
  m=cptcoveff;              bh[mi][i]=ju;
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}            }
             if(dh[mi][i]==0){
  jj1=0;              dh[mi][i]=1; /* At least one step */
  for(k1=1; k1<=m;k1++){              bh[mi][i]=ju; /* At least one step */
    for(i1=1; i1<=ncodemax[k1];i1++){              /*  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);*/
      jj1++;            }
      if (cptcovn > 0) {          } /* end if mle */
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");        }
        for (cpt=1; cpt<=cptcoveff;cpt++)      } /* end wave */
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);    }
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");    jmean=sum/k;
      }    printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
      for(cpt=1; cpt<=nlstate;cpt++) {    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);
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident   }
 interval) in state (%d): v%s%d%d.png <br>  
 <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    /*********** Tricode ****************************/
      }  void tricode(int *Tvar, int **nbcode, int imx)
    } /* end i1 */  {
  }/* End k1 */    /* Uses cptcovn+2*cptcovprod as the number of covariates */
  fprintf(fichtm,"</ul>");    /*      Tvar[i]=atoi(stre); /* find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 */
 fclose(fichtm);  
 }    int Ndum[20],ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
     int modmaxcovj=0; /* Modality max of covariates j */
 /******************* Gnuplot file **************/    cptcoveff=0; 
 void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){   
     for (k=0; k<maxncov; k++) Ndum[k]=0;
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;    for (k=1; k<=7; k++) ncodemax[k]=0; /* Horrible constant again */
   int ng;  
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {    for (j=1; j<=(cptcovn+2*cptcovprod); j++) { /* For each covariate j */
     printf("Problem with file %s",optionfilegnuplot);      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum value of the 
     fprintf(ficlog,"Problem with file %s",optionfilegnuplot);                                 modality of this covariate Vj*/ 
   }        ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Finds for covariate j, n=Tvar[j] of Vn . ij is the
                                         modality of the nth covariate of individual i. */
 #ifdef windows        Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
     fprintf(ficgp,"cd \"%s\" \n",pathc);        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
 #endif        if (ij > modmaxcovj) modmaxcovj=ij; 
 m=pow(2,cptcoveff);        /* 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
  /* 1eme*/           female is 1, then modmaxcovj=1.*/
   for (cpt=1; cpt<= nlstate ; cpt ++) {      }
    for (k1=1; k1<= m ; k1 ++) {      /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
       for (i=0; i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each modality of model-cov j */
 #ifdef windows        if( Ndum[i] != 0 )
      fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);          ncodemax[j]++; 
      fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);        /* Number of modalities of the j th covariate. In fact
 #endif           ncodemax[j]=2 (dichotom. variables only) but it could be more for
 #ifdef unix           historical reasons */
 fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);      } /* Ndum[-1] number of undefined modalities */
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);  
 #endif      /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
       ij=1; 
 for (i=1; i<= nlstate ; i ++) {      for (i=1; i<=ncodemax[j]; i++) { /* i= 1 to 2 for dichotomous */
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        for (k=0; k<= modmaxcovj; k++) { /* k=-1 ? NCOVMAX*//* maxncov or modmaxcovj */
   else fprintf(ficgp," \%%*lf (\%%*lf)");          if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
 }            nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode. 
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);                                       k is a modality. If we have model=V1+V1*sex 
     for (i=1; i<= nlstate ; i ++) {                                       then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");            ij++;
   else fprintf(ficgp," \%%*lf (\%%*lf)");          }
 }          if (ij > ncodemax[j]) break; 
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);        }  /* end of loop on */
      for (i=1; i<= nlstate ; i ++) {      } /* end of loop on modality */ 
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/  
   else fprintf(ficgp," \%%*lf (\%%*lf)");    
 }      for (k=0; k< maxncov; k++) Ndum[k]=0;
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));    
 #ifdef unix    for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */
 fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
 #endif     ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
    }     Ndum[ij]++;
   }   }
   /*2 eme*/  
    ij=1;
   for (k1=1; k1<= m ; k1 ++) {   for (i=1; i<= maxncov; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
     fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);     if((Ndum[i]!=0) && (i<=ncovcol)){
     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);       Tvaraff[ij]=i; /*For printing */
           ij++;
     for (i=1; i<= nlstate+1 ; i ++) {     }
       k=2*i;   }
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);   ij--;
       for (j=1; j<= nlstate+1 ; j ++) {   cptcoveff=ij; /*Number of simple covariates*/
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");  }
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }    /*********** Health Expectancies ****************/
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");  
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);  void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);  
       for (j=1; j<= nlstate+1 ; j ++) {  {
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    /* Health expectancies, no variances */
         else fprintf(ficgp," \%%*lf (\%%*lf)");    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
 }      int nhstepma, nstepma; /* Decreasing with age */
       fprintf(ficgp,"\" t\"\" w l 0,");    double age, agelim, hf;
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);    double ***p3mat;
       for (j=1; j<= nlstate+1 ; j ++) {    double eip;
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");    pstamp(ficreseij);
 }      fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");    fprintf(ficreseij,"# Age");
       else fprintf(ficgp,"\" t\"\" w l 0,");    for(i=1; i<=nlstate;i++){
     }      for(j=1; j<=nlstate;j++){
   }        fprintf(ficreseij," e%1d%1d ",i,j);
        }
   /*3eme*/      fprintf(ficreseij," e%1d. ",i);
     }
   for (k1=1; k1<= m ; k1 ++) {    fprintf(ficreseij,"\n");
     for (cpt=1; cpt<= nlstate ; cpt ++) {  
       k=2+nlstate*(2*cpt-2);    
       fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);    if(estepm < stepm){
       fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);      printf ("Problem %d lower than %d\n",estepm, stepm);
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);    }
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");    else  hstepm=estepm;   
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);    /* We compute the life expectancy from trapezoids spaced every estepm months
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);     * This is mainly to measure the difference between two models: for example
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");     * if stepm=24 months pijx are given only every 2 years and by summing them
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);     * we are calculating an estimate of the Life Expectancy assuming a linear 
      * progression in between and thus overestimating or underestimating according
 */     * to the curvature of the survival function. If, for the same date, we 
       for (i=1; i< nlstate ; i ++) {     * estimate the model with stepm=1 month, we can keep estepm to 24 months
         fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);     * to compare the new estimate of Life expectancy with the same linear 
      * hypothesis. A more precise result, taking into account a more precise
       }     * curvature will be obtained if estepm is as small as stepm. */
     }  
   }    /* For 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. 
   /* CV preval stat */       nhstepm is the number of hstepm from age to agelim 
     for (k1=1; k1<= m ; k1 ++) {       nstepm is the number of stepm from age to agelin. 
     for (cpt=1; cpt<nlstate ; cpt ++) {       Look at hpijx to understand the reason of that which relies in memory size
       k=3;       and note for a fixed period like estepm months */
       fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);       survival function given by stepm (the optimization length). Unfortunately it
        means that if the survival funtion is printed only each two years of age and if
       for (i=1; i< nlstate ; i ++)       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
         fprintf(ficgp,"+$%d",k+i+1);       results. So we changed our mind and took the option of the best precision.
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);    */
          hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
       l=3+(nlstate+ndeath)*cpt;  
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);    agelim=AGESUP;
       for (i=1; i< nlstate ; i ++) {    /* If stepm=6 months */
         l=3+(nlstate+ndeath)*cpt;      /* Computed by stepm unit matrices, product of hstepm matrices, stored
         fprintf(ficgp,"+$%d",l+i+1);         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
       }      
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);    /* nhstepm age range expressed in number of stepm */
     }    nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
   }      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
      /* if (stepm >= YEARM) hstepm=1;*/
   /* proba elementaires */    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
    for(i=1,jk=1; i <=nlstate; i++){    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     for(k=1; k <=(nlstate+ndeath); k++){  
       if (k != i) {    for (age=bage; age<=fage; age ++){ 
         for(j=1; j <=ncovmodel; j++){      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
           jk++;      /* if (stepm >= YEARM) hstepm=1;*/
           fprintf(ficgp,"\n");      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
         }  
       }      /* If stepm=6 months */
     }      /* Computed by stepm unit matrices, product of hstepma matrices, stored
    }         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
       
    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/      hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
      for(jk=1; jk <=m; jk++) {      
        fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
        if (ng==2)      
          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");      printf("%d|",(int)age);fflush(stdout);
        else      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
          fprintf(ficgp,"\nset title \"Probability\"\n");      
        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);      /* Computing expectancies */
        i=1;      for(i=1; i<=nlstate;i++)
        for(k2=1; k2<=nlstate; k2++) {        for(j=1; j<=nlstate;j++)
          k3=i;          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
          for(k=1; k<=(nlstate+ndeath); k++) {            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
            if (k != k2){            
              if(ng==2)            /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
                fprintf(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;      fprintf(ficreseij,"%3.0f",age );
              for(j=3; j <=ncovmodel; j++) {      for(i=1; i<=nlstate;i++){
                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {        eip=0;
                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);        for(j=1; j<=nlstate;j++){
                  ij++;          eip +=eij[i][j][(int)age];
                }          fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
                else        }
                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);        fprintf(ficreseij,"%9.4f", eip );
              }      }
              fprintf(ficgp,")/(1");      fprintf(ficreseij,"\n");
                    
              for(k1=1; k1 <=nlstate; k1++){      }
                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);    free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                ij=1;    printf("\n");
                for(j=3; j <=ncovmodel; j++){    fprintf(ficlog,"\n");
                  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++;  
                  }  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[] )
                  else  
                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);  {
                }    /* Covariances of health expectancies eij and of total life expectancies according
                fprintf(ficgp,")");     to initial status i, ei. .
              }    */
              fprintf(ficgp,") t \"p%d%d\" ", k2,k);    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");    int nhstepma, nstepma; /* Decreasing with age */
              i=i+ncovmodel;    double age, agelim, hf;
            }    double ***p3matp, ***p3matm, ***varhe;
          } /* end k */    double **dnewm,**doldm;
        } /* end k2 */    double *xp, *xm;
      } /* end jk */    double **gp, **gm;
    } /* end ng */    double ***gradg, ***trgradg;
    fclose(ficgp);    int theta;
 }  /* end gnuplot */  
     double eip, vip;
   
 /*************** Moving average **************/    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){    xp=vector(1,npar);
     xm=vector(1,npar);
   int i, cpt, cptcod;    dnewm=matrix(1,nlstate*nlstate,1,npar);
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
       for (i=1; i<=nlstate;i++)    
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)    pstamp(ficresstdeij);
           mobaverage[(int)agedeb][i][cptcod]=0.;    fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
        fprintf(ficresstdeij,"# Age");
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){    for(i=1; i<=nlstate;i++){
       for (i=1; i<=nlstate;i++){      for(j=1; j<=nlstate;j++)
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){        fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
           for (cpt=0;cpt<=4;cpt++){      fprintf(ficresstdeij," e%1d. ",i);
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];    }
           }    fprintf(ficresstdeij,"\n");
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;  
         }    pstamp(ficrescveij);
       }    fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
     }    fprintf(ficrescveij,"# Age");
        for(i=1; i<=nlstate;i++)
 }      for(j=1; j<=nlstate;j++){
         cptj= (j-1)*nlstate+i;
         for(i2=1; i2<=nlstate;i2++)
 /************** Forecasting ******************/          for(j2=1; j2<=nlstate;j2++){
 prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){            cptj2= (j2-1)*nlstate+i2;
              if(cptj2 <= cptj)
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;              fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
   int *popage;          }
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;      }
   double *popeffectif,*popcount;    fprintf(ficrescveij,"\n");
   double ***p3mat;    
   char fileresf[FILENAMELENGTH];    if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
  agelim=AGESUP;    }
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;    else  hstepm=estepm;   
     /* We compute the life expectancy from trapezoids spaced every estepm months
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);     * This is mainly to measure the difference between two models: for example
       * if stepm=24 months pijx are given only every 2 years and by summing them
       * we are calculating an estimate of the Life Expectancy assuming a linear 
   strcpy(fileresf,"f");     * progression in between and thus overestimating or underestimating according
   strcat(fileresf,fileres);     * to the curvature of the survival function. If, for the same date, we 
   if((ficresf=fopen(fileresf,"w"))==NULL) {     * estimate the model with stepm=1 month, we can keep estepm to 24 months
     printf("Problem with forecast resultfile: %s\n", fileresf);     * to compare the new estimate of Life expectancy with the same linear 
     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);     * hypothesis. A more precise result, taking into account a more precise
   }     * curvature will be obtained if estepm is as small as stepm. */
   printf("Computing forecasting: result on file '%s' \n", fileresf);  
   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);    /* 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. 
   if (cptcoveff==0) ncodemax[cptcoveff]=1;       nhstepm is the number of hstepm from age to agelim 
        nstepm is the number of stepm from age to agelin. 
   if (mobilav==1) {       Look at hpijx to understand the reason of that which relies in memory size
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);       and note for a fixed period like estepm months */
     movingaverage(agedeb, fage, ageminpar, mobaverage);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   }       survival function given by stepm (the optimization length). Unfortunately it
        means that if the survival funtion is printed only each two years of age and if
   stepsize=(int) (stepm+YEARM-1)/YEARM;       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   if (stepm<=12) stepsize=1;       results. So we changed our mind and took the option of the best precision.
      */
   agelim=AGESUP;    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
    
   hstepm=1;    /* If stepm=6 months */
   hstepm=hstepm/stepm;    /* nhstepm age range expressed in number of stepm */
   yp1=modf(dateintmean,&yp);    agelim=AGESUP;
   anprojmean=yp;    nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
   yp2=modf((yp1*12),&yp);    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   mprojmean=yp;    /* if (stepm >= YEARM) hstepm=1;*/
   yp1=modf((yp2*30.5),&yp);    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   jprojmean=yp;    
   if(jprojmean==0) jprojmean=1;    p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   if(mprojmean==0) jprojmean=1;    p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);    trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
      gp=matrix(0,nhstepm,1,nlstate*nlstate);
   for(cptcov=1;cptcov<=i2;cptcov++){    gm=matrix(0,nhstepm,1,nlstate*nlstate);
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){  
       k=k+1;    for (age=bage; age<=fage; age ++){ 
       fprintf(ficresf,"\n#******");      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
       for(j=1;j<=cptcoveff;j++) {      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      /* if (stepm >= YEARM) hstepm=1;*/
       }      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
       fprintf(ficresf,"******\n");  
       fprintf(ficresf,"# StartingAge FinalAge");      /* If stepm=6 months */
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);      /* Computed by stepm unit matrices, product of hstepma matrices, stored
               in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
            
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
         fprintf(ficresf,"\n");  
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);        /* Computing  Variances of health expectancies */
       /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){         decrease memory allocation */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);      for(theta=1; theta <=npar; theta++){
           nhstepm = nhstepm/hstepm;        for(i=1; i<=npar; i++){ 
                    xp[i] = x[i] + (i==theta ?delti[theta]:0);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          xm[i] = x[i] - (i==theta ?delti[theta]:0);
           oldm=oldms;savm=savms;        }
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);          hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
                hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
           for (h=0; h<=nhstepm; h++){    
             if (h==(int) (calagedate+YEARM*cpt)) {        for(j=1; j<= nlstate; j++){
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);          for(i=1; i<=nlstate; i++){
             }            for(h=0; h<=nhstepm-1; h++){
             for(j=1; j<=nlstate+ndeath;j++) {              gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
               kk1=0.;kk2=0;              gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
               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];        for(ij=1; ij<= nlstate*nlstate; ij++)
                 }          for(h=0; h<=nhstepm-1; h++){
                            gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
               }          }
               if (h==(int)(calagedate+12*cpt)){      }/* End theta */
                 fprintf(ficresf," %.3f", kk1);      
                              
               }      for(h=0; h<=nhstepm-1; h++)
             }        for(j=1; j<=nlstate*nlstate;j++)
           }          for(theta=1; theta <=npar; theta++)
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            trgradg[h][j][theta]=gradg[h][theta][j];
         }      
       }  
     }       for(ij=1;ij<=nlstate*nlstate;ij++)
   }        for(ji=1;ji<=nlstate*nlstate;ji++)
                  varhe[ij][ji][(int)age] =0.;
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  
        printf("%d|",(int)age);fflush(stdout);
   fclose(ficresf);       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
 }       for(h=0;h<=nhstepm-1;h++){
 /************** Forecasting ******************/        for(k=0;k<=nhstepm-1;k++){
 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){          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
            matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;          for(ij=1;ij<=nlstate*nlstate;ij++)
   int *popage;            for(ji=1;ji<=nlstate*nlstate;ji++)
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
   double *popeffectif,*popcount;        }
   double ***p3mat,***tabpop,***tabpopprev;      }
   char filerespop[FILENAMELENGTH];  
       /* Computing expectancies */
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      for(i=1; i<=nlstate;i++)
   agelim=AGESUP;        for(j=1; j<=nlstate;j++)
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;          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;
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);            
              /* 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]);*/
    
   strcpy(filerespop,"pop");          }
   strcat(filerespop,fileres);  
   if((ficrespop=fopen(filerespop,"w"))==NULL) {      fprintf(ficresstdeij,"%3.0f",age );
     printf("Problem with forecast resultfile: %s\n", filerespop);      for(i=1; i<=nlstate;i++){
     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);        eip=0.;
   }        vip=0.;
   printf("Computing forecasting: result on file '%s' \n", filerespop);        for(j=1; j<=nlstate;j++){
   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);          eip += eij[i][j][(int)age];
           for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
   if (cptcoveff==0) ncodemax[cptcoveff]=1;            vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
           fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
   if (mobilav==1) {        }
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
     movingaverage(agedeb, fage, ageminpar, mobaverage);      }
   }      fprintf(ficresstdeij,"\n");
   
   stepsize=(int) (stepm+YEARM-1)/YEARM;      fprintf(ficrescveij,"%3.0f",age );
   if (stepm<=12) stepsize=1;      for(i=1; i<=nlstate;i++)
          for(j=1; j<=nlstate;j++){
   agelim=AGESUP;          cptj= (j-1)*nlstate+i;
            for(i2=1; i2<=nlstate;i2++)
   hstepm=1;            for(j2=1; j2<=nlstate;j2++){
   hstepm=hstepm/stepm;              cptj2= (j2-1)*nlstate+i2;
                if(cptj2 <= cptj)
   if (popforecast==1) {                fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
     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);      fprintf(ficrescveij,"\n");
     }     
     popage=ivector(0,AGESUP);    }
     popeffectif=vector(0,AGESUP);    free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
     popcount=vector(0,AGESUP);    free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
        free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
     i=1;      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;    free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
        free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     imx=i;    printf("\n");
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];    fprintf(ficlog,"\n");
   }  
     free_vector(xm,1,npar);
   for(cptcov=1;cptcov<=i2;cptcov++){    free_vector(xp,1,npar);
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
       k=k+1;    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
       fprintf(ficrespop,"\n#******");    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
       for(j=1;j<=cptcoveff;j++) {  }
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
       }  /************ Variance ******************/
       fprintf(ficrespop,"******\n");  void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
       fprintf(ficrespop,"# Age");  {
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);    /* Variance of health expectancies */
       if (popforecast==1)  fprintf(ficrespop," [Population]");    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
          /* double **newm;*/
       for (cpt=0; cpt<=0;cpt++) {    double **dnewm,**doldm;
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);      double **dnewmp,**doldmp;
            int i, j, nhstepm, hstepm, h, nstepm ;
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    int k, cptcode;
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    double *xp;
           nhstepm = nhstepm/hstepm;    double **gp, **gm;  /* for var eij */
              double ***gradg, ***trgradg; /*for var eij */
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    double **gradgp, **trgradgp; /* for var p point j */
           oldm=oldms;savm=savms;    double *gpp, *gmp; /* for var p point j */
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      double **varppt; /* for var p point j nlstate to nlstate+ndeath */
            double ***p3mat;
           for (h=0; h<=nhstepm; h++){    double age,agelim, hf;
             if (h==(int) (calagedate+YEARM*cpt)) {    double ***mobaverage;
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);    int theta;
             }    char digit[4];
             for(j=1; j<=nlstate+ndeath;j++) {    char digitp[25];
               kk1=0.;kk2=0;  
               for(i=1; i<=nlstate;i++) {                  char fileresprobmorprev[FILENAMELENGTH];
                 if (mobilav==1)  
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];    if(popbased==1){
                 else {      if(mobilav!=0)
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];        strcpy(digitp,"-populbased-mobilav-");
                 }      else strcpy(digitp,"-populbased-nomobil-");
               }    }
               if (h==(int)(calagedate+12*cpt)){    else 
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;      strcpy(digitp,"-stablbased-");
                   /*fprintf(ficrespop," %.3f", kk1);  
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/    if (mobilav!=0) {
               }      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
             }      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
             for(i=1; i<=nlstate;i++){        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
               kk1=0.;        printf(" Error in movingaverage mobilav=%d\n",mobilav);
                 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+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];    strcpy(fileresprobmorprev,"prmorprev"); 
             }    sprintf(digit,"%-d",ij);
     /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)    strcat(fileresprobmorprev,digit); /* Tvar to be done */
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
           }    strcat(fileresprobmorprev,fileres);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
         }      printf("Problem with resultfile: %s\n", fileresprobmorprev);
       }      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
      }
   /******/    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
    
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);      pstamp(ficresprobmorprev);
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    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);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
           nhstepm = nhstepm/hstepm;    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
                fprintf(ficresprobmorprev," p.%-d SE",j);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      for(i=1; i<=nlstate;i++)
           oldm=oldms;savm=savms;        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      }  
           for (h=0; h<=nhstepm; h++){    fprintf(ficresprobmorprev,"\n");
             if (h==(int) (calagedate+YEARM*cpt)) {    fprintf(ficgp,"\n# Routine varevsij");
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);    /* 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");
             for(j=1; j<=nlstate+ndeath;j++) {    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
               kk1=0.;kk2=0;  /*   } */
               for(i=1; i<=nlstate;i++) {                  varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];        pstamp(ficresvij);
               }    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);    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
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      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");
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  
     xp=vector(1,npar);
   if (popforecast==1) {    dnewm=matrix(1,nlstate,1,npar);
     free_ivector(popage,0,AGESUP);    doldm=matrix(1,nlstate,1,nlstate);
     free_vector(popeffectif,0,AGESUP);    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
     free_vector(popcount,0,AGESUP);    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   }  
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    gpp=vector(nlstate+1,nlstate+ndeath);
   fclose(ficrespop);    gmp=vector(nlstate+1,nlstate+ndeath);
 }    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     
 /***********************************************/    if(estepm < stepm){
 /**************** Main Program *****************/      printf ("Problem %d lower than %d\n",estepm, stepm);
 /***********************************************/    }
     else  hstepm=estepm;   
 int main(int argc, char *argv[])    /* 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 
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;       nstepm is the number of stepm from age to agelin. 
   double agedeb, agefin,hf;       Look at function hpijx to understand why (it is linked to memory size questions) */
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;    /* 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
   double fret;       means that if the survival funtion is printed every two years of age and if
   double **xi,tmp,delta;       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.
   double dum; /* Dummy variable */    */
   double ***p3mat;    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   int *indx;    agelim = AGESUP;
   char line[MAXLINE], linepar[MAXLINE];    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   char path[80],pathc[80],pathcd[80],pathtot[80],model[80];      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
   int firstobs=1, lastobs=10;      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   int sdeb, sfin; /* Status at beginning and end */      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   int c,  h , cpt,l;      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
   int ju,jl, mi;      gp=matrix(0,nhstepm,1,nlstate);
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;      gm=matrix(0,nhstepm,1,nlstate);
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;  
   int mobilav=0,popforecast=0;  
   int hstepm, nhstepm;      for(theta=1; theta <=npar; theta++){
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
   double bage, fage, age, agelim, agebase;        }
   double ftolpl=FTOL;        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   double **prlim;        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   double *severity;  
   double ***param; /* Matrix of parameters */        if (popbased==1) {
   double  *p;          if(mobilav ==0){
   double **matcov; /* Matrix of covariance */            for(i=1; i<=nlstate;i++)
   double ***delti3; /* Scale */              prlim[i][i]=probs[(int)age][i][ij];
   double *delti; /* Scale */          }else{ /* mobilav */ 
   double ***eij, ***vareij;            for(i=1; i<=nlstate;i++)
   double **varpl; /* Variances of prevalence limits by age */              prlim[i][i]=mobaverage[(int)age][i][ij];
   double *epj, vepp;          }
   double kk1, kk2;        }
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;    
          for(j=1; j<= nlstate; j++){
           for(h=0; h<=nhstepm; h++){
   char *alph[]={"a","a","b","c","d","e"}, str[4];            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
               gp[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
   char z[1]="c", occ;        }
 #include <sys/time.h>        /* This for computing probability of death (h=1 means
 #include <time.h>           computed over hstepm matrices product = hstepm*stepm months) 
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];           as a weighted average of prlim.
          */
   /* long total_usecs;        for(j=nlstate+1;j<=nlstate+ndeath;j++){
   struct timeval start_time, end_time;          for(i=1,gpp[j]=0.; i<= nlstate; i++)
              gpp[j] += prlim[i][i]*p3mat[i][j][1];
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */        }    
   getcwd(pathcd, size);        /* end probability of death */
   
   printf("\n%s",version);        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
   if(argc <=1){          xp[i] = x[i] - (i==theta ?delti[theta]:0);
     printf("\nEnter the parameter file name: ");        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     scanf("%s",pathtot);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   }   
   else{        if (popbased==1) {
     strcpy(pathtot,argv[1]);          if(mobilav ==0){
   }            for(i=1; i<=nlstate;i++)
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/              prlim[i][i]=probs[(int)age][i][ij];
   /*cygwin_split_path(pathtot,path,optionfile);          }else{ /* mobilav */ 
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/            for(i=1; i<=nlstate;i++)
   /* cutv(path,optionfile,pathtot,'\\');*/              prlim[i][i]=mobaverage[(int)age][i][ij];
           }
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);        }
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);  
   chdir(path);        for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
   replace(pathc,path);          for(h=0; h<=nhstepm; h++){
             for(i=1, gm[h][j]=0.;i<=nlstate;i++)
 /*-------- arguments in the command line --------*/              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
   /* Log file */        }
   strcat(filelog, optionfilefiname);        /* This for computing probability of death (h=1 means
   strcat(filelog,".log");    /* */           computed over hstepm matrices product = hstepm*stepm months) 
   if((ficlog=fopen(filelog,"w"))==NULL)    {           as a weighted average of prlim.
     printf("Problem with logfile %s\n",filelog);        */
     goto end;        for(j=nlstate+1;j<=nlstate+ndeath;j++){
   }          for(i=1,gmp[j]=0.; i<= nlstate; i++)
   fprintf(ficlog,"Log filename:%s\n",filelog);           gmp[j] += prlim[i][i]*p3mat[i][j][1];
   fprintf(ficlog,"\n%s",version);        }    
   fprintf(ficlog,"\nEnter the parameter file name: ");        /* end probability of death */
   fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);  
   fflush(ficlog);        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];
   strcpy(fileres,"r");          }
   strcat(fileres, optionfilefiname);  
   strcat(fileres,".txt");    /* Other files have txt extension */        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
           gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
   /*---------arguments file --------*/        }
   
   if((ficpar=fopen(optionfile,"r"))==NULL)    {      } /* End theta */
     printf("Problem with optionfile %s\n",optionfile);  
     fprintf(ficlog,"Problem with optionfile %s\n",optionfile);      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
     goto end;  
   }      for(h=0; h<=nhstepm; h++) /* veij */
         for(j=1; j<=nlstate;j++)
   strcpy(filereso,"o");          for(theta=1; theta <=npar; theta++)
   strcat(filereso,fileres);            trgradg[h][j][theta]=gradg[h][theta][j];
   if((ficparo=fopen(filereso,"w"))==NULL) {  
     printf("Problem with Output resultfile: %s\n", filereso);      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);        for(theta=1; theta <=npar; theta++)
     goto end;          trgradgp[j][theta]=gradgp[theta][j];
   }    
   
   /* Reads comments: lines beginning with '#' */      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   while((c=getc(ficpar))=='#' && c!= EOF){      for(i=1;i<=nlstate;i++)
     ungetc(c,ficpar);        for(j=1;j<=nlstate;j++)
     fgets(line, MAXLINE, ficpar);          vareij[i][j][(int)age] =0.;
     puts(line);  
     fputs(line,ficparo);      for(h=0;h<=nhstepm;h++){
   }        for(k=0;k<=nhstepm;k++){
   ungetc(c,ficpar);          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
           matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
   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);          for(i=1;i<=nlstate;i++)
   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);            for(j=1;j<=nlstate;j++)
   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);              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
 while((c=getc(ficpar))=='#' && c!= EOF){        }
     ungetc(c,ficpar);      }
     fgets(line, MAXLINE, ficpar);    
     puts(line);      /* pptj */
     fputs(line,ficparo);      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);
   ungetc(c,ficpar);      for(j=nlstate+1;j<=nlstate+ndeath;j++)
          for(i=nlstate+1;i<=nlstate+ndeath;i++)
              varppt[j][i]=doldmp[j][i];
   covar=matrix(0,NCOVMAX,1,n);      /* end ppptj */
   cptcovn=0;      /*  x centered again */
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
       prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
   ncovmodel=2+cptcovn;   
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */      if (popbased==1) {
          if(mobilav ==0){
   /* Read guess parameters */          for(i=1; i<=nlstate;i++)
   /* Reads comments: lines beginning with '#' */            prlim[i][i]=probs[(int)age][i][ij];
   while((c=getc(ficpar))=='#' && c!= EOF){        }else{ /* mobilav */ 
     ungetc(c,ficpar);          for(i=1; i<=nlstate;i++)
     fgets(line, MAXLINE, ficpar);            prlim[i][i]=mobaverage[(int)age][i][ij];
     puts(line);        }
     fputs(line,ficparo);      }
   }               
   ungetc(c,ficpar);      /* This for computing probability of death (h=1 means
           computed over hstepm (estepm) matrices product = hstepm*stepm months) 
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);         as a weighted average of prlim.
     for(i=1; i <=nlstate; i++)      */
     for(j=1; j <=nlstate+ndeath-1; j++){      for(j=nlstate+1;j<=nlstate+ndeath;j++){
       fscanf(ficpar,"%1d%1d",&i1,&j1);        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
       fprintf(ficparo,"%1d%1d",i1,j1);          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
       if(mle==1)      }    
         printf("%1d%1d",i,j);      /* end probability of death */
       fprintf(ficlog,"%1d%1d",i,j);  
       for(k=1; k<=ncovmodel;k++){      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
         fscanf(ficpar," %lf",&param[i][j][k]);      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
         if(mle==1){        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
           printf(" %lf",param[i][j][k]);        for(i=1; i<=nlstate;i++){
           fprintf(ficlog," %lf",param[i][j][k]);          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
         }        }
         else      } 
           fprintf(ficlog," %lf",param[i][j][k]);      fprintf(ficresprobmorprev,"\n");
         fprintf(ficparo," %lf",param[i][j][k]);  
       }      fprintf(ficresvij,"%.0f ",age );
       fscanf(ficpar,"\n");      for(i=1; i<=nlstate;i++)
       if(mle==1)        for(j=1; j<=nlstate;j++){
         printf("\n");          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
       fprintf(ficlog,"\n");        }
       fprintf(ficparo,"\n");      fprintf(ficresvij,"\n");
     }      free_matrix(gp,0,nhstepm,1,nlstate);
        free_matrix(gm,0,nhstepm,1,nlstate);
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
       free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
   p=param[1][1];      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
      } /* End age */
   /* Reads comments: lines beginning with '#' */    free_vector(gpp,nlstate+1,nlstate+ndeath);
   while((c=getc(ficpar))=='#' && c!= EOF){    free_vector(gmp,nlstate+1,nlstate+ndeath);
     ungetc(c,ficpar);    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
     fgets(line, MAXLINE, ficpar);    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     puts(line);    fprintf(ficgp,"\nunset parametric;unset label; set ter png small;set size 0.65, 0.65");
     fputs(line,ficparo);    /* 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)\";");
   ungetc(c,ficpar);  /*   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); */
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
   for(i=1; i <=nlstate; i++){    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
     for(j=1; j <=nlstate+ndeath-1; j++){    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
       fscanf(ficpar,"%1d%1d",&i1,&j1);    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
       printf("%1d%1d",i,j);    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(ficparo,"%1d%1d",i1,j1);    /*  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);
       for(k=1; k<=ncovmodel;k++){  */
         fscanf(ficpar,"%le",&delti3[i][j][k]);  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
         printf(" %le",delti3[i][j][k]);    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
         fprintf(ficparo," %le",delti3[i][j][k]);  
       }    free_vector(xp,1,npar);
       fscanf(ficpar,"\n");    free_matrix(doldm,1,nlstate,1,nlstate);
       printf("\n");    free_matrix(dnewm,1,nlstate,1,npar);
       fprintf(ficparo,"\n");    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);
   delti=delti3[1][1];    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
      fclose(ficresprobmorprev);
   /* Reads comments: lines beginning with '#' */    fflush(ficgp);
   while((c=getc(ficpar))=='#' && c!= EOF){    fflush(fichtm); 
     ungetc(c,ficpar);  }  /* end varevsij */
     fgets(line, MAXLINE, ficpar);  
     puts(line);  /************ Variance of prevlim ******************/
     fputs(line,ficparo);  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[])
   }  {
   ungetc(c,ficpar);    /* Variance of prevalence limit */
      /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
   matcov=matrix(1,npar,1,npar);    double **newm;
   for(i=1; i <=npar; i++){    double **dnewm,**doldm;
     fscanf(ficpar,"%s",&str);    int i, j, nhstepm, hstepm;
     if(mle==1)    int k, cptcode;
       printf("%s",str);    double *xp;
     fprintf(ficlog,"%s",str);    double *gp, *gm;
     fprintf(ficparo,"%s",str);    double **gradg, **trgradg;
     for(j=1; j <=i; j++){    double age,agelim;
       fscanf(ficpar," %le",&matcov[i][j]);    int theta;
       if(mle==1){    
         printf(" %.5le",matcov[i][j]);    pstamp(ficresvpl);
         fprintf(ficlog," %.5le",matcov[i][j]);    fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
       }    fprintf(ficresvpl,"# Age");
       else    for(i=1; i<=nlstate;i++)
         fprintf(ficlog," %.5le",matcov[i][j]);        fprintf(ficresvpl," %1d-%1d",i,i);
       fprintf(ficparo," %.5le",matcov[i][j]);    fprintf(ficresvpl,"\n");
     }  
     fscanf(ficpar,"\n");    xp=vector(1,npar);
     if(mle==1)    dnewm=matrix(1,nlstate,1,npar);
       printf("\n");    doldm=matrix(1,nlstate,1,nlstate);
     fprintf(ficlog,"\n");    
     fprintf(ficparo,"\n");    hstepm=1*YEARM; /* Every year of age */
   }    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
   for(i=1; i <=npar; i++)    agelim = AGESUP;
     for(j=i+1;j<=npar;j++)    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       matcov[i][j]=matcov[j][i];      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
          if (stepm >= YEARM) hstepm=1;
   if(mle==1)      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
     printf("\n");      gradg=matrix(1,npar,1,nlstate);
   fprintf(ficlog,"\n");      gp=vector(1,nlstate);
       gm=vector(1,nlstate);
   
     /*-------- Rewriting paramater file ----------*/      for(theta=1; theta <=npar; theta++){
      strcpy(rfileres,"r");    /* "Rparameterfile */        for(i=1; i<=npar; i++){ /* Computes gradient */
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/          xp[i] = x[i] + (i==theta ?delti[theta]:0);
      strcat(rfileres,".");    /* */        }
      strcat(rfileres,optionfilext);    /* Other files have txt extension */        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     if((ficres =fopen(rfileres,"w"))==NULL) {        for(i=1;i<=nlstate;i++)
       printf("Problem writing new parameter file: %s\n", fileres);goto end;          gp[i] = prlim[i][i];
       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;      
     }        for(i=1; i<=npar; i++) /* Computes gradient */
     fprintf(ficres,"#%s\n",version);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
            prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     /*-------- data file ----------*/        for(i=1;i<=nlstate;i++)
     if((fic=fopen(datafile,"r"))==NULL)    {          gm[i] = prlim[i][i];
       printf("Problem with datafile: %s\n", datafile);goto end;  
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;        for(i=1;i<=nlstate;i++)
     }          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
       } /* End theta */
     n= lastobs;  
     severity = vector(1,maxwav);      trgradg =matrix(1,nlstate,1,npar);
     outcome=imatrix(1,maxwav+1,1,n);  
     num=ivector(1,n);      for(j=1; j<=nlstate;j++)
     moisnais=vector(1,n);        for(theta=1; theta <=npar; theta++)
     annais=vector(1,n);          trgradg[j][theta]=gradg[theta][j];
     moisdc=vector(1,n);  
     andc=vector(1,n);      for(i=1;i<=nlstate;i++)
     agedc=vector(1,n);        varpl[i][(int)age] =0.;
     cod=ivector(1,n);      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
     weight=vector(1,n);      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */      for(i=1;i<=nlstate;i++)
     mint=matrix(1,maxwav,1,n);        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
     anint=matrix(1,maxwav,1,n);  
     s=imatrix(1,maxwav+1,1,n);      fprintf(ficresvpl,"%.0f ",age );
     adl=imatrix(1,maxwav+1,1,n);          for(i=1; i<=nlstate;i++)
     tab=ivector(1,NCOVMAX);        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
     ncodemax=ivector(1,8);      fprintf(ficresvpl,"\n");
       free_vector(gp,1,nlstate);
     i=1;      free_vector(gm,1,nlstate);
     while (fgets(line, MAXLINE, fic) != NULL)    {      free_matrix(gradg,1,npar,1,nlstate);
       if ((i >= firstobs) && (i <=lastobs)) {      free_matrix(trgradg,1,nlstate,1,npar);
            } /* End age */
         for (j=maxwav;j>=1;j--){  
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);    free_vector(xp,1,npar);
           strcpy(line,stra);    free_matrix(doldm,1,nlstate,1,npar);
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    free_matrix(dnewm,1,nlstate,1,nlstate);
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);  
         }  }
          
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);  /************ Variance of one-step probabilities  ******************/
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);  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[])
   {
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);    int i, j=0,  i1, k1, l1, t, tj;
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);    int k2, l2, j1,  z1;
     int k=0,l, cptcode;
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);    int first=1, first1;
         for (j=ncovcol;j>=1;j--){    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);    double **dnewm,**doldm;
         }    double *xp;
         num[i]=atol(stra);    double *gp, *gm;
            double **gradg, **trgradg;
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){    double **mu;
           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;}*/    double age,agelim, cov[NCOVMAX];
     double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
         i=i+1;    int theta;
       }    char fileresprob[FILENAMELENGTH];
     }    char fileresprobcov[FILENAMELENGTH];
     /* printf("ii=%d", ij);    char fileresprobcor[FILENAMELENGTH];
        scanf("%d",i);*/  
   imx=i-1; /* Number of individuals */    double ***varpij;
   
   /* for (i=1; i<=imx; i++){    strcpy(fileresprob,"prob"); 
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;    strcat(fileresprob,fileres);
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;      printf("Problem with resultfile: %s\n", fileresprob);
     }*/      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
    /*  for (i=1; i<=imx; i++){    }
      if (s[4][i]==9)  s[4][i]=-1;    strcpy(fileresprobcov,"probcov"); 
      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]));}*/    strcat(fileresprobcov,fileres);
      if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
        printf("Problem with resultfile: %s\n", fileresprobcov);
   /* Calculation of the number of parameter from char model*/      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
   Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */    }
   Tprod=ivector(1,15);    strcpy(fileresprobcor,"probcor"); 
   Tvaraff=ivector(1,15);    strcat(fileresprobcor,fileres);
   Tvard=imatrix(1,15,1,2);    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
   Tage=ivector(1,15);            printf("Problem with resultfile: %s\n", fileresprobcor);
          fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
   if (strlen(model) >1){    }
     j=0, j1=0, k1=1, k2=1;    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     j=nbocc(model,'+');    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     j1=nbocc(model,'*');    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     cptcovn=j+1;    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     cptcovprod=j1;    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);
     strcpy(modelsav,model);    pstamp(ficresprob);
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
       printf("Error. Non available option model=%s ",model);    fprintf(ficresprob,"# Age");
       fprintf(ficlog,"Error. Non available option model=%s ",model);    pstamp(ficresprobcov);
       goto end;    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
     }    fprintf(ficresprobcov,"# Age");
        pstamp(ficresprobcor);
     for(i=(j+1); i>=1;i--){    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
       cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */    fprintf(ficresprobcor,"# Age");
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyze it */  
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/  
       /*scanf("%d",i);*/    for(i=1; i<=nlstate;i++)
       if (strchr(strb,'*')) {  /* Model includes a product */      for(j=1; j<=(nlstate+ndeath);j++){
         cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
         if (strcmp(strc,"age")==0) { /* Vn*age */        fprintf(ficresprobcov," p%1d-%1d ",i,j);
           cptcovprod--;        fprintf(ficresprobcor," p%1d-%1d ",i,j);
           cutv(strb,stre,strd,'V');      }  
           Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/   /* fprintf(ficresprob,"\n");
           cptcovage++;    fprintf(ficresprobcov,"\n");
             Tage[cptcovage]=i;    fprintf(ficresprobcor,"\n");
             /*printf("stre=%s ", stre);*/   */
         }    xp=vector(1,npar);
         else if (strcmp(strd,"age")==0) { /* or age*Vn */    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
           cptcovprod--;    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
           cutv(strb,stre,strc,'V');    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
           Tvar[i]=atoi(stre);    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
           cptcovage++;    first=1;
           Tage[cptcovage]=i;    fprintf(ficgp,"\n# Routine varprob");
         }    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
         else {  /* Age is not in the model */    fprintf(fichtm,"\n");
           cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/  
           Tvar[i]=ncovcol+k1;    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
           cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */    fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
           Tprod[k1]=i;    file %s<br>\n",optionfilehtmcov);
           Tvard[k1][1]=atoi(strc); /* m*/    fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
           Tvard[k1][2]=atoi(stre); /* n */  and drawn. It helps understanding how is the covariance between two incidences.\
           Tvar[cptcovn+k2]=Tvard[k1][1];   They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
           Tvar[cptcovn+k2+1]=Tvard[k1][2];    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. \
           for (k=1; k<=lastobs;k++)  It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];  would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
           k1++;  standard deviations wide on each axis. <br>\
           k2=k2+2;   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");
       else { /* no more sum */  
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/    cov[1]=1;
        /*  scanf("%d",i);*/    tj=cptcoveff;
       cutv(strd,strc,strb,'V');    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
       Tvar[i]=atoi(strc);    j1=0;
       }    for(t=1; t<=tj;t++){
       strcpy(modelsav,stra);        for(i1=1; i1<=ncodemax[t];i1++){ 
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);        j1++;
         scanf("%d",i);*/        if  (cptcovn>0) {
     } /* end of loop + */          fprintf(ficresprob, "\n#********** Variable "); 
   } /* end model */          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
            fprintf(ficresprob, "**********\n#\n");
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);          fprintf(ficresprobcov, "\n#********** Variable "); 
   printf("cptcovprod=%d ", cptcovprod);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);          fprintf(ficresprobcov, "**********\n#\n");
   scanf("%d ",i);*/          
     fclose(fic);          fprintf(ficgp, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     /*  if(mle==1){*/          fprintf(ficgp, "**********\n#\n");
     if (weightopt != 1) { /* Maximisation without weights*/          
       for(i=1;i<=n;i++) weight[i]=1.0;          
     }          fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
     /*-calculation of age at interview from date of interview and age at death -*/          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     agev=matrix(1,maxwav,1,imx);          fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
           
     for (i=1; i<=imx; i++) {          fprintf(ficresprobcor, "\n#********** Variable ");    
       for(m=2; (m<= maxwav); m++) {          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){          fprintf(ficresprobcor, "**********\n#");    
          anint[m][i]=9999;        }
          s[m][i]=-1;        
        }        for (age=bage; age<=fage; age ++){ 
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;          cov[2]=age;
       }          for (k=1; k<=cptcovn;k++) {
     }            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
           }
     for (i=1; i<=imx; i++)  {          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);          for (k=1; k<=cptcovprod;k++)
       for(m=1; (m<= maxwav); m++){            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
         if(s[m][i] >0){          
           if (s[m][i] >= nlstate+1) {          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
             if(agedc[i]>0)          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
               if(moisdc[i]!=99 && andc[i]!=9999)          gp=vector(1,(nlstate)*(nlstate+ndeath));
                 agev[m][i]=agedc[i];          gm=vector(1,(nlstate)*(nlstate+ndeath));
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/      
            else {          for(theta=1; theta <=npar; theta++){
               if (andc[i]!=9999){            for(i=1; i<=npar; i++)
               printf("Warning negative age at death: %d line:%d\n",num[i],i);              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
               fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);            
               agev[m][i]=-1;            pmij(pmmij,cov,ncovmodel,xp,nlstate);
               }            
             }            k=0;
           }            for(i=1; i<= (nlstate); i++){
           else if(s[m][i] !=9){ /* Should no more exist */              for(j=1; j<=(nlstate+ndeath);j++){
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);                k=k+1;
             if(mint[m][i]==99 || anint[m][i]==9999)                gp[k]=pmmij[i][j];
               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);*/            for(i=1; i<=npar; i++)
             }              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
             else if(agev[m][i] >agemax){      
               agemax=agev[m][i];            pmij(pmmij,cov,ncovmodel,xp,nlstate);
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/            k=0;
             }            for(i=1; i<=(nlstate); i++){
             /*agev[m][i]=anint[m][i]-annais[i];*/              for(j=1; j<=(nlstate+ndeath);j++){
             /*   agev[m][i] = age[i]+2*m;*/                k=k+1;
           }                gm[k]=pmmij[i][j];
           else { /* =9 */              }
             agev[m][i]=1;            }
             s[m][i]=-1;       
           }            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
         }              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
         else /*= 0 Unknown */          }
           agev[m][i]=1;  
       }          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
                for(theta=1; theta <=npar; theta++)
     }              trgradg[j][theta]=gradg[theta][j];
     for (i=1; i<=imx; i++)  {          
       for(m=1; (m<= maxwav); m++){          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
         if (s[m][i] > (nlstate+ndeath)) {          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
           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);            free_vector(gp,1,(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);            free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
           goto end;          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
         }          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
       }  
     }          pmij(pmmij,cov,ncovmodel,x,nlstate);
           
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);          k=0;
  fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);          for(i=1; i<=(nlstate); i++){
             for(j=1; j<=(nlstate+ndeath);j++){
     free_vector(severity,1,maxwav);              k=k+1;
     free_imatrix(outcome,1,maxwav+1,1,n);              mu[k][(int) age]=pmmij[i][j];
     free_vector(moisnais,1,n);            }
     free_vector(annais,1,n);          }
     /* free_matrix(mint,1,maxwav,1,n);          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
        free_matrix(anint,1,maxwav,1,n);*/            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
     free_vector(moisdc,1,n);              varpij[i][j][(int)age] = doldm[i][j];
     free_vector(andc,1,n);  
           /*printf("\n%d ",(int)age);
                for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
     wav=ivector(1,imx);            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
     dh=imatrix(1,lastpass-firstpass+1,1,imx);            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
     mw=imatrix(1,lastpass-firstpass+1,1,imx);            }*/
      
     /* Concatenates waves */          fprintf(ficresprob,"\n%d ",(int)age);
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);          fprintf(ficresprobcov,"\n%d ",(int)age);
           fprintf(ficresprobcor,"\n%d ",(int)age);
   
       Tcode=ivector(1,100);          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
       ncodemax[1]=1;          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
                  fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
    codtab=imatrix(1,100,1,10);          }
    h=0;          i=0;
    m=pow(2,cptcoveff);          for (k=1; k<=(nlstate);k++){
              for (l=1; l<=(nlstate+ndeath);l++){ 
    for(k=1;k<=cptcoveff; k++){              i=i++;
      for(i=1; i <=(m/pow(2,k));i++){              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
        for(j=1; j <= ncodemax[k]; j++){              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){              for (j=1; j<=i;j++){
            h++;                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/              }
          }            }
        }          }/* end of loop for state */
      }        } /* end of loop for age */
    }  
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);        /* Confidence intervalle of pij  */
       codtab[1][2]=1;codtab[2][2]=2; */        /*
    /* for(i=1; i <=m ;i++){          fprintf(ficgp,"\nunset parametric;unset label");
       for(k=1; k <=cptcovn; k++){          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);          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);
       printf("\n");          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
       }          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
       scanf("%d",i);*/          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
            */
    /* Calculates basic frequencies. Computes observed prevalence at single age  
        and prints on file fileres'p'. */        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
         first1=1;
            for (k2=1; k2<=(nlstate);k2++){
              for (l2=1; l2<=(nlstate+ndeath);l2++){ 
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            if(l2==k2) continue;
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            j=(k2-1)*(nlstate+ndeath)+l2;
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            for (k1=1; k1<=(nlstate);k1++){
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */                if(l1==k1) continue;
                      i=(k1-1)*(nlstate+ndeath)+l1;
     /* For Powell, parameters are in a vector p[] starting at p[1]                if(i<=j) continue;
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */                for (age=bage; age<=fage; age ++){ 
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */                  if ((int)age %5==0){
                     v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
     if(mle==1){                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
     }                    mu1=mu[i][(int) age]/stepm*YEARM ;
                        mu2=mu[j][(int) age]/stepm*YEARM;
     /*--------- results files --------------*/                    c12=cv12/sqrt(v1*v2);
     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);                    /* 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.;
    jk=1;                    if ((lc2 <0) || (lc1 <0) ){
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");                      printf("Error: One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Continuing by making them positive: WRONG RESULTS.\n", lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");                      fprintf(ficlog,"Error: One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e\n", lc1, lc2, v1, v2, cv12);fflush(ficlog);
    fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");                      lc1=fabs(lc1);
    for(i=1,jk=1; i <=nlstate; i++){                      lc2=fabs(lc2);
      for(k=1; k <=(nlstate+ndeath); k++){                    }
        if (k != i)  
          {                    /* Eigen vectors */
            printf("%d%d ",i,k);                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
            fprintf(ficlog,"%d%d ",i,k);                    /*v21=sqrt(1.-v11*v11); *//* error */
            fprintf(ficres,"%1d%1d ",i,k);                    v21=(lc1-v1)/cv12*v11;
            for(j=1; j <=ncovmodel; j++){                    v12=-v21;
              printf("%f ",p[jk]);                    v22=v11;
              fprintf(ficlog,"%f ",p[jk]);                    tnalp=v21/v11;
              fprintf(ficres,"%f ",p[jk]);                    if(first1==1){
              jk++;                      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);
            printf("\n");                    }
            fprintf(ficlog,"\n");                    fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
            fprintf(ficres,"\n");                    /*printf(fignu*/
          }                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
      }                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
    }                    if(first==1){
    if(mle==1){                      first=0;
      /* Computing hessian and covariance matrix */                      fprintf(ficgp,"\nset parametric;unset label");
      ftolhess=ftol; /* Usually correct */                      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);
      hesscov(matcov, p, npar, delti, ftolhess, func);                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
    }                      fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
    fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");   :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
    printf("# Scales (for hessian or gradient estimation)\n");  %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
    fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
    for(i=1,jk=1; i <=nlstate; i++){                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
      for(j=1; j <=nlstate+ndeath; j++){                      fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
        if (j!=i) {                      fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
          fprintf(ficres,"%1d%1d",i,j);                      fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
          printf("%1d%1d",i,j);                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
          fprintf(ficlog,"%1d%1d",i,j);                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
          for(k=1; k<=ncovmodel;k++){                      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",\
            printf(" %.5e",delti[jk]);                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
            fprintf(ficlog," %.5e",delti[jk]);                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
            fprintf(ficres," %.5e",delti[jk]);                    }else{
            jk++;                      first=0;
          }                      fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
          printf("\n");                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
          fprintf(ficlog,"\n");                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
          fprintf(ficres,"\n");                      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 */
    k=1;                } /* end loop age */
    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");                fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
    if(mle==1)                first=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");              } /*l12 */
    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");            } /* k12 */
    for(i=1;i<=npar;i++){          } /*l1 */
      /*  if (k>nlstate) k=1;        }/* k1 */
          i1=(i-1)/(ncovmodel*nlstate)+1;      } /* loop covariates */
          fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);    }
          printf("%s%d%d",alph[k],i1,tab[i]);*/    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
      fprintf(ficres,"%3d",i);    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
      if(mle==1)    free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
        printf("%3d",i);    free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
      fprintf(ficlog,"%3d",i);    free_vector(xp,1,npar);
      for(j=1; j<=i;j++){    fclose(ficresprob);
        fprintf(ficres," %.5e",matcov[i][j]);    fclose(ficresprobcov);
        if(mle==1)    fclose(ficresprobcor);
          printf(" %.5e",matcov[i][j]);    fflush(ficgp);
        fprintf(ficlog," %.5e",matcov[i][j]);    fflush(fichtmcov);
      }  }
      fprintf(ficres,"\n");  
      if(mle==1)  
        printf("\n");  /******************* Printing html file ***********/
      fprintf(ficlog,"\n");  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
      k++;                    int lastpass, int stepm, int weightopt, char model[],\
    }                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                        int popforecast, int estepm ,\
    while((c=getc(ficpar))=='#' && c!= EOF){                    double jprev1, double mprev1,double anprev1, \
      ungetc(c,ficpar);                    double jprev2, double mprev2,double anprev2){
      fgets(line, MAXLINE, ficpar);    int jj1, k1, i1, cpt;
      puts(line);  
      fputs(line,ficparo);     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 \
    ungetc(c,ficpar);  </ul>");
    estepm=0;     fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
    fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);   - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
    if (estepm==0 || estepm < stepm) estepm=stepm;             jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
    if (fage <= 2) {     fprintf(fichtm,"\
      bage = ageminpar;   - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
      fage = agemaxpar;             stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
    }     fprintf(fichtm,"\
       - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
    fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");             subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
    fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);     fprintf(fichtm,"\
    fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);   - (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",
    while((c=getc(ficpar))=='#' && c!= EOF){             estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
      ungetc(c,ficpar);     fprintf(fichtm,"\
      fgets(line, MAXLINE, ficpar);   - Population projections by age and states: \
      puts(line);     <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
      fputs(line,ficparo);  
    }  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
    ungetc(c,ficpar);  
     m=cptcoveff;
    fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
    fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);  
    fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);   jj1=0;
       for(k1=1; k1<=m;k1++){
    while((c=getc(ficpar))=='#' && c!= EOF){     for(i1=1; i1<=ncodemax[k1];i1++){
      ungetc(c,ficpar);       jj1++;
      fgets(line, MAXLINE, ficpar);       if (cptcovn > 0) {
      puts(line);         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
      fputs(line,ficparo);         for (cpt=1; cpt<=cptcoveff;cpt++) 
    }           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
    ungetc(c,ficpar);         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
         }
        /* Pij */
    dateprev1=anprev1+mprev1/12.+jprev1/365.;       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d1.png\">%s%d1.png</a><br> \
    dateprev2=anprev2+mprev2/12.+jprev2/365.;  <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
        /* Quasi-incidences */
   fscanf(ficpar,"pop_based=%d\n",&popbased);       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
   fprintf(ficparo,"pop_based=%d\n",popbased);     before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d2.png\">%s%d2.png</a><br> \
   fprintf(ficres,"pop_based=%d\n",popbased);    <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
           /* Period (stable) prevalence in each health state */
   while((c=getc(ficpar))=='#' && c!= EOF){         for(cpt=1; cpt<nlstate;cpt++){
     ungetc(c,ficpar);           fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
     fgets(line, MAXLINE, ficpar);  <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
     puts(line);         }
     fputs(line,ficparo);       for(cpt=1; cpt<=nlstate;cpt++) {
   }          fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
   ungetc(c,ficpar);  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
        }
   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);     } /* end i1 */
 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);   }/* End k1 */
 fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);   fprintf(fichtm,"</ul>");
   
   
 while((c=getc(ficpar))=='#' && c!= EOF){   fprintf(fichtm,"\
     ungetc(c,ficpar);  \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
     fgets(line, MAXLINE, ficpar);   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
     puts(line);  
     fputs(line,ficparo);   fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
   }           subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
   ungetc(c,ficpar);   fprintf(fichtm,"\
    - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);           subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);  
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);   fprintf(fichtm,"\
    - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);           subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
    fprintf(fichtm,"\
 /*------------ gnuplot -------------*/   - 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): \
   strcpy(optionfilegnuplot,optionfilefiname);     <a href=\"%s\">%s</a> <br>\n</li>",
   strcat(optionfilegnuplot,".gp");             estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {   fprintf(fichtm,"\
     printf("Problem with file %s",optionfilegnuplot);   - (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>",
   fclose(ficgp);             estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
  printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);   fprintf(fichtm,"\
 /*--------- index.htm --------*/   - 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"));
   strcpy(optionfilehtm,optionfile);   fprintf(fichtm,"\
   strcat(optionfilehtm,".htm");   - 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",
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {           estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
     printf("Problem with %s \n",optionfilehtm), exit(0);   fprintf(fichtm,"\
   }   - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
            subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   fprintf(fichtm,"<body> <font size=\"2\">%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  /*  if(popforecast==1) fprintf(fichtm,"\n */
 \n  /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
 Total number of observations=%d <br>\n  /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n  /*      <br>",fileres,fileres,fileres,fileres); */
 <hr  size=\"2\" color=\"#EC5E5E\">  /*  else  */
  <ul><li><h4>Parameter files</h4>\n  /*    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); */
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n   fflush(fichtm);
  - Log file of the run: <a href=\"%s\">%s</a><br>\n   fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
  - Gnuplot file name: <a href=\"%s\">%s</a></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,filelog,filelog,optionfilegnuplot,optionfilegnuplot);  
   fclose(fichtm);   m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
  printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);  
     jj1=0;
 /*------------ free_vector  -------------*/   for(k1=1; k1<=m;k1++){
  chdir(path);     for(i1=1; i1<=ncodemax[k1];i1++){
         jj1++;
  free_ivector(wav,1,imx);       if (cptcovn > 0) {
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);           for (cpt=1; cpt<=cptcoveff;cpt++) 
  free_ivector(num,1,n);           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
  free_vector(agedc,1,n);         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
  /*free_matrix(covar,1,NCOVMAX,1,n);*/       }
  fclose(ficparo);       for(cpt=1; cpt<=nlstate;cpt++) {
  fclose(ficres);         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);  
   /*--------------- Prevalence limit --------------*/       }
         fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   strcpy(filerespl,"pl");  health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
   strcat(filerespl,fileres);  true period expectancies (those weighted with period prevalences are also\
   if((ficrespl=fopen(filerespl,"w"))==NULL) {   drawn in addition to the population based expectancies computed using\
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;   observed and cahotic prevalences: %s%d.png<br>\
     fprintf(ficlog,"Problem with Prev limit resultfile: %s\n", filerespl);goto end;  <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
   }     } /* end i1 */
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);   }/* End k1 */
   fprintf(ficlog,"Computing prevalence limit: result on file '%s' \n", filerespl);   fprintf(fichtm,"</ul>");
   fprintf(ficrespl,"#Prevalence limit\n");   fflush(fichtm);
   fprintf(ficrespl,"#Age ");  }
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);  
   fprintf(ficrespl,"\n");  /******************* Gnuplot file **************/
    void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   prlim=matrix(1,nlstate,1,nlstate);  
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    char dirfileres[132],optfileres[132];
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    int m0,cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    int ng=0;
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */  /*     printf("Problem with file %s",optionfilegnuplot); */
   k=0;  /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   agebase=ageminpar;  /*   } */
   agelim=agemaxpar;  
   ftolpl=1.e-10;    /*#ifdef windows */
   i1=cptcoveff;    fprintf(ficgp,"cd \"%s\" \n",pathc);
   if (cptcovn < 1){i1=1;}      /*#endif */
     m=pow(2,cptcoveff);
   for(cptcov=1;cptcov<=i1;cptcov++){  
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    strcpy(dirfileres,optionfilefiname);
         k=k+1;    strcpy(optfileres,"vpl");
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/   /* 1eme*/
         fprintf(ficrespl,"\n#******");    for (cpt=1; cpt<= nlstate ; cpt ++) {
         printf("\n#******");     for (k1=1; k1<= m ; k1 ++) {
         fprintf(ficlog,"\n#******");       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
         for(j=1;j<=cptcoveff;j++) {       fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);       fprintf(ficgp,"set xlabel \"Age\" \n\
           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  set ylabel \"Probability\" \n\
           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  set ter png small\n\
         }  set size 0.65,0.65\n\
         fprintf(ficrespl,"******\n");  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
         printf("******\n");  
         fprintf(ficlog,"******\n");       for (i=1; i<= nlstate ; i ++) {
                 if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
         for (age=agebase; age<=agelim; age++){         else        fprintf(ficgp," \%%*lf (\%%*lf)");
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);       }
           fprintf(ficrespl,"%.0f",age );       fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
           for(i=1; i<=nlstate;i++)       for (i=1; i<= nlstate ; i ++) {
           fprintf(ficrespl," %.5f", prlim[i][i]);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
           fprintf(ficrespl,"\n");         else fprintf(ficgp," \%%*lf (\%%*lf)");
         }       } 
       }       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
     }       for (i=1; i<= nlstate ; i ++) {
   fclose(ficrespl);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
   /*------------- h Pij x at various ages ------------*/       }  
         fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);     }
   if((ficrespij=fopen(filerespij,"w"))==NULL) {    }
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;    /*2 eme*/
     fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;    
   }    for (k1=1; k1<= m ; k1 ++) { 
   printf("Computing pij: result on file '%s' \n", filerespij);      fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
   fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
        
   stepsize=(int) (stepm+YEARM-1)/YEARM;      for (i=1; i<= nlstate+1 ; i ++) {
   /*if (stepm<=24) stepsize=2;*/        k=2*i;
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
   agelim=AGESUP;        for (j=1; j<= nlstate+1 ; j ++) {
   hstepm=stepsize*YEARM; /* Every year of age */          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */          else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
   /* hstepm=1;   aff par mois*/        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
   k=0;        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
   for(cptcov=1;cptcov<=i1;cptcov++){        for (j=1; j<= nlstate+1 ; j ++) {
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
       k=k+1;          else fprintf(ficgp," \%%*lf (\%%*lf)");
         fprintf(ficrespij,"\n#****** ");        }   
         for(j=1;j<=cptcoveff;j++)        fprintf(ficgp,"\" t\"\" w l 0,");
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         fprintf(ficrespij,"******\n");        for (j=1; j<= nlstate+1 ; j ++) {
                  if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */          else fprintf(ficgp," \%%*lf (\%%*lf)");
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        }   
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
         else fprintf(ficgp,"\" t\"\" w l 0,");
           /*      nhstepm=nhstepm*YEARM; aff par mois*/      }
     }
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    
           oldm=oldms;savm=savms;    /*3eme*/
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      
           fprintf(ficrespij,"# Age");    for (k1=1; k1<= m ; k1 ++) { 
           for(i=1; i<=nlstate;i++)      for (cpt=1; cpt<= nlstate ; cpt ++) {
             for(j=1; j<=nlstate+ndeath;j++)        /*       k=2+nlstate*(2*cpt-2); */
               fprintf(ficrespij," %1d-%1d",i,j);        k=2+(nlstate+1)*(cpt-1);
           fprintf(ficrespij,"\n");        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
            for (h=0; h<=nhstepm; h++){        fprintf(ficgp,"set ter png small\n\
             fprintf(ficrespij,"%d %f %f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );  set size 0.65,0.65\n\
             for(i=1; i<=nlstate;i++)  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
               for(j=1; j<=nlstate+ndeath;j++)        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
             fprintf(ficrespij,"\n");          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
              }          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficrespij,"\n");          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);
   varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);          /*      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);*/
           
   fclose(ficrespij);        } 
         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
       }
   /*---------- Forecasting ------------------*/    }
   if((stepm == 1) && (strcmp(model,".")==0)){    
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);    /* CV preval stable (period) */
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);    for (k1=1; k1<= m ; k1 ++) { 
   }      for (cpt=1; cpt<=nlstate ; cpt ++) {
   else{        k=3;
     erreur=108;        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
     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(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
     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);  set ter png small\nset size 0.65,0.65\n\
   }  unset log y\n\
    plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
         
   /*---------- Health expectancies and variances ------------*/        for (i=1; i< nlstate ; i ++)
           fprintf(ficgp,"+$%d",k+i+1);
   strcpy(filerest,"t");        fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
   strcat(filerest,fileres);        
   if((ficrest=fopen(filerest,"w"))==NULL) {        l=3+(nlstate+ndeath)*cpt;
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;        fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
     fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;        for (i=1; i< nlstate ; i ++) {
   }          l=3+(nlstate+ndeath)*cpt;
   printf("Computing Total LEs with variances: file '%s' \n", filerest);          fprintf(ficgp,"+$%d",l+i+1);
   fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);        }
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
       } 
   strcpy(filerese,"e");    }  
   strcat(filerese,fileres);    
   if((ficreseij=fopen(filerese,"w"))==NULL) {    /* proba elementaires */
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);    for(i=1,jk=1; i <=nlstate; i++){
     fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);      for(k=1; k <=(nlstate+ndeath); k++){
   }        if (k != i) {
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);          for(j=1; j <=ncovmodel; j++){
   fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);            fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             jk++; 
   strcpy(fileresv,"v");            fprintf(ficgp,"\n");
   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);     for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
   fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);       for(jk=1; jk <=m; jk++) {
   calagedate=-1;         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);         if (ng==2)
            fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
   k=0;         else
   for(cptcov=1;cptcov<=i1;cptcov++){           fprintf(ficgp,"\nset title \"Probability\"\n");
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
       k=k+1;         i=1;
       fprintf(ficrest,"\n#****** ");         for(k2=1; k2<=nlstate; k2++) {
       for(j=1;j<=cptcoveff;j++)           k3=i;
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);           for(k=1; k<=(nlstate+ndeath); k++) {
       fprintf(ficrest,"******\n");             if (k != k2){
                if(ng==2)
       fprintf(ficreseij,"\n#****** ");                 fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
       for(j=1;j<=cptcoveff;j++)               else
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                 fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
       fprintf(ficreseij,"******\n");               ij=1;/* To be checked else nbcode[0][0] wrong */
                for(j=3; j <=ncovmodel; j++) {
       fprintf(ficresvij,"\n#****** ");                 if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
       for(j=1;j<=cptcoveff;j++)                   fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                   ij++;
       fprintf(ficresvij,"******\n");                 }
                  else
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);                   fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
       oldm=oldms;savm=savms;               }
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);                 fprintf(ficgp,")/(1");
                 
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);               for(k1=1; k1 <=nlstate; k1++){   
       oldm=oldms;savm=savms;                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
       varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0);                 ij=1;
       if(popbased==1){                 for(j=3; j <=ncovmodel; j++){
         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased);                   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++;
                     }
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");                   else
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
       fprintf(ficrest,"\n");                 }
                  fprintf(ficgp,")");
       epj=vector(1,nlstate+1);               }
       for(age=bage; age <=fage ;age++){               fprintf(ficgp,") t \"p%d%d\" ", k2,k);
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);               if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
         if (popbased==1) {               i=i+ncovmodel;
           for(i=1; i<=nlstate;i++)             }
             prlim[i][i]=probs[(int)age][i][k];           } /* end k */
         }         } /* end k2 */
               } /* end jk */
         fprintf(ficrest," %4.0f",age);     } /* end ng */
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){     fflush(ficgp); 
           for(i=1, epj[j]=0.;i <=nlstate;i++) {  }  /* end gnuplot */
             epj[j] += prlim[i][i]*eij[i][j][(int)age];  
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/  
           }  /*************** Moving average **************/
           epj[nlstate+1] +=epj[j];  int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
         }  
     int i, cpt, cptcod;
         for(i=1, vepp=0.;i <=nlstate;i++)    int modcovmax =1;
           for(j=1;j <=nlstate;j++)    int mobilavrange, mob;
             vepp += vareij[i][j][(int)age];    double age;
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));  
         for(j=1;j <=nlstate;j++){    modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));                             a covariate has 2 modalities */
         }    if (cptcovn<1) modcovmax=1; /* At least 1 pass */
         fprintf(ficrest,"\n");  
       }    if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
     }      if(mobilav==1) mobilavrange=5; /* default */
   }      else mobilavrange=mobilav;
 free_matrix(mint,1,maxwav,1,n);      for (age=bage; age<=fage; age++)
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);        for (i=1; i<=nlstate;i++)
     free_vector(weight,1,n);          for (cptcod=1;cptcod<=modcovmax;cptcod++)
   fclose(ficreseij);            mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
   fclose(ficresvij);      /* We keep the original values on the extreme ages bage, fage and for 
   fclose(ficrest);         fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
   fclose(ficpar);         we use a 5 terms etc. until the borders are no more concerned. 
   free_vector(epj,1,nlstate+1);      */ 
        for (mob=3;mob <=mobilavrange;mob=mob+2){
   /*------- Variance limit prevalence------*/          for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
   strcpy(fileresvpl,"vpl");            for (cptcod=1;cptcod<=modcovmax;cptcod++){
   strcat(fileresvpl,fileres);              mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {                for (cpt=1;cpt<=(mob-1)/2;cpt++){
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);                  mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
     exit(0);                  mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
   }                }
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);              mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
   k=0;          }
   for(cptcov=1;cptcov<=i1;cptcov++){        }/* end age */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      }/* end mob */
       k=k+1;    }else return -1;
       fprintf(ficresvpl,"\n#****** ");    return 0;
       for(j=1;j<=cptcoveff;j++)  }/* End movingaverage */
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
       fprintf(ficresvpl,"******\n");  
        /************** Forecasting ******************/
       varpl=matrix(1,nlstate,(int) bage, (int) fage);  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){
       oldm=oldms;savm=savms;    /* proj1, year, month, day of starting projection 
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);       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).
     */
   fclose(ficresvpl);    int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
     int *popage;
   /*---------- End : free ----------------*/    double agec; /* generic age */
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);    double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
      double *popeffectif,*popcount;
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);    double ***p3mat;
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);    double ***mobaverage;
      char fileresf[FILENAMELENGTH];
    
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);    agelim=AGESUP;
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);    prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);   
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);    strcpy(fileresf,"f"); 
      strcat(fileresf,fileres);
   free_matrix(matcov,1,npar,1,npar);    if((ficresf=fopen(fileresf,"w"))==NULL) {
   free_vector(delti,1,npar);      printf("Problem with forecast resultfile: %s\n", fileresf);
   free_matrix(agev,1,maxwav,1,imx);      fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
   fprintf(fichtm,"\n</body>");    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   fclose(fichtm);  
   fclose(ficgp);    if (cptcoveff==0) ncodemax[cptcoveff]=1;
    
     if (mobilav!=0) {
   if(erreur >0){      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     printf("End of Imach with error or warning %d\n",erreur);      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
     fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
   }else{        printf(" Error in movingaverage mobilav=%d\n",mobilav);
    printf("End of Imach\n");      }
    fprintf(ficlog,"End of Imach\n");    }
   }  
   printf("See log file on %s\n",filelog);    stepsize=(int) (stepm+YEARM-1)/YEARM;
   fclose(ficlog);    if (stepm<=12) stepsize=1;
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */    if(estepm < stepm){
        printf ("Problem %d lower than %d\n",estepm, stepm);
   /* 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);*/    }
   /*printf("Total time was %d uSec.\n", total_usecs);*/    else  hstepm=estepm;   
   /*------ End -----------*/  
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
  end:                                 fractional in yp1 */
 #ifdef windows    anprojmean=yp;
   /* chdir(pathcd);*/    yp2=modf((yp1*12),&yp);
 #endif    mprojmean=yp;
  /*system("wgnuplot graph.plt");*/    yp1=modf((yp2*30.5),&yp);
  /*system("../gp37mgw/wgnuplot graph.plt");*/    jprojmean=yp;
  /*system("cd ../gp37mgw");*/    if(jprojmean==0) jprojmean=1;
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/    if(mprojmean==0) jprojmean=1;
  strcpy(plotcmd,GNUPLOTPROGRAM);  
  strcat(plotcmd," ");    i1=cptcoveff;
  strcat(plotcmd,optionfilegnuplot);    if (cptcovn < 1){i1=1;}
  system(plotcmd);    
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
 #ifdef windows    
   while (z[0] != 'q') {    fprintf(ficresf,"#****** Routine prevforecast **\n");
     /* chdir(path); */  
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");  /*            if (h==(int)(YEARM*yearp)){ */
     scanf("%s",z);    for(cptcov=1, k=0;cptcov<=i1;cptcov++){
     if (z[0] == 'c') system("./imach");      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
     else if (z[0] == 'e') system(optionfilehtm);        k=k+1;
     else if (z[0] == 'g') system(plotcmd);        fprintf(ficresf,"\n#******");
     else if (z[0] == 'q') exit(0);        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]]);
 #endif        }
 }        fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   
   
   /**************** function prwizard **********************/
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     /* Wizard to print covariance matrix template */
   
     char ca[32], cb[32], cc[32];
     int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
   } /* end of prwizard */
   /******************* Gompertz Likelihood ******************************/
   double gompertz(double x[])
   { 
     double A,B,L=0.0,sump=0.,num=0.;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
   
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
                +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           L=L+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
    
     return -2*L*num/sump;
   }
   
   #ifdef GSL
   /******************* Gompertz_f Likelihood ******************************/
   double gompertz_f(const gsl_vector *v, void *params)
   { 
     double A,B,LL=0.0,sump=0.,num=0.;
     double *x= (double *) v->data;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
     printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
                +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           LL=LL+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
     printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
    
     return -2*LL*num/sump;
   }
   #endif
   
   /******************* Printing html file ***********/
   void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,  double p[],double **matcov,double agemortsup){
     int i,k;
   
     fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
     fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
     for (i=1;i<=2;i++) 
       fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
     fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
     fprintf(fichtm,"</ul>");
   
   fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
   
    fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
   
    for (k=agegomp;k<(agemortsup-2);k++) 
      fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
   
    
     fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
     fprintf(ficgp,"set out \"graphmort.png\"\n "); 
     fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
     fprintf(ficgp, "set ter png small\n set log y\n"); 
     fprintf(ficgp, "set size 0.65,0.65\n");
     fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
   
   } 
   
   int readdata(char datafile[], int firstobs, int lastobs, int *imax)
   {
   
     /*-------- data file ----------*/
     FILE *fic;
     char dummy[]="                         ";
     int i, j, n;
     int linei, month, year,iout;
     char line[MAXLINE], linetmp[MAXLINE];
     char stra[80], strb[80];
     char *stratrunc;
     int lstra;
   
   
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem while opening datafile: %s\n", datafile);return 1;
       fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
     }
   
     i=1;
     linei=0;
     while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
       linei=linei+1;
       for(j=strlen(line); j>=0;j--){  /* Untabifies line */
         if(line[j] == '\t')
           line[j] = ' ';
       }
       for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
         ;
       };
       line[j+1]=0;  /* Trims blanks at end of line */
       if(line[0]=='#'){
         fprintf(ficlog,"Comment line\n%s\n",line);
         printf("Comment line\n%s\n",line);
         continue;
       }
       trimbb(linetmp,line); /* Trims multiple blanks in line */
       for (j=0; line[j]!='\0';j++){
         line[j]=linetmp[j];
       }
     
   
       for (j=maxwav;j>=1;j--){
         cutv(stra, strb, line, ' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
         /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
             fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);
             return 1;
           }
         }
         s[j][i]=lval;
         
         strcpy(line,stra);
         cutv(stra, strb,line,' ');
         if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
         }
         else  if(iout=sscanf(strb,"%s.") != 0){
           month=99;
           year=9999;
         }else{
           printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);fflush(ficlog);
           return 1;
         }
         anint[j][i]= (double) year; 
         mint[j][i]= (double)month; 
         strcpy(line,stra);
       } /* ENd Waves */
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.",dummy) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
       }
       andc[i]=(double) year; 
       moisdc[i]=(double) month; 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.") != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
       }
       if (year==9999) {
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given.  Exiting.\n",strb, linei,i,line);
         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
   
       }
       annais[i]=(double)(year);
       moisnais[i]=(double)(month); 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       errno=0;
       dval=strtod(strb,&endptr); 
       if( strb[0]=='\0' || (*endptr != '\0')){
         printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fprintf(ficlog,"Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fflush(ficlog);
         return 1;
       }
       weight[i]=dval; 
       strcpy(line,stra);
       
       for (j=ncovcol;j>=1;j--){
         cutv(stra, strb,line,' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);
             fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);fflush(ficlog);
             return 1;
           }
         }
         if(lval <-1 || lval >1){
           printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);
           fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
           return 1;
         }
         covar[j][i]=(double)(lval);
         strcpy(line,stra);
       }  
       lstra=strlen(stra);
        
       if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
         stratrunc = &(stra[lstra-9]);
         num[i]=atol(stratrunc);
       }
       else
         num[i]=atol(stra);
       /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
         printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
       
       i=i+1;
     } /* End loop reading  data */
   
     *imax=i-1; /* Number of individuals */
     fclose(fic);
    
     return (0);
     endread:
       printf("Exiting readdata: ");
       fclose(fic);
       return (1);
   
   
   
   }
   
   int decodemodel ( char model[], int lastobs)
   {
     int i, j, k;
     int i1, j1, k1, k2;
     char modelsav[80];
      char stra[80], strb[80], strc[80], strd[80],stre[80];
   
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=1, k2=1;
       j=nbocc(model,'+'); /* j=Number of '+' */
       j1=nbocc(model,'*'); /* j1=Number of '*' */
       cptcovn=j+1; /* Number of covariates V1+V2*age+V3 =>(2 plus signs) + 1=3 
                     but the covariates which are product must be computed and stored. */
       cptcovprod=j1; /*Number of products  V1*V2 +v3*age = 2 */
       
       strcpy(modelsav,model); 
       if (strstr(model,"AGE") !=0){
         printf("Error. AGE must be in lower case 'age' model=%s ",model);
         fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
         return 1;
       }
       if (strstr(model,"v") !=0){
         printf("Error. 'v' must be in upper case 'V' model=%s ",model);
         fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
         return 1;
       }
       
       /* This loop fills the array Tvar from the string 'model'.*/
       /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
       /*   modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4  */
       /*  k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
       /*  k=3 V4 Tvar[k=3]= 4 (from V4) */
       /*  k=2 V1 Tvar[k=2]= 1 (from V1) */
       /*  k=1 Tvar[1]=2 (from V2) */
       /*  k=5 Tvar[5] */
       /* for (k=1; k<=cptcovn;k++) { */
       /*  cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
       /*  } */
       /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
       for(k=cptcovn; k>=1;k--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' 
                                        modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 
                                       */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /* Model includes a product V2+V1+V4+V3*age strb=V3*age */
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn: strb=V3*age strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
           if (strcmp(strc,"age")==0) { /* Vn*age */
             cptcovprod--;
             cutv(strb,stre,strd,'V'); /* stre="V3" */
             Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=2 ; V1+V2*age Tvar[2]=2 */
             cptcovage++; /* Sums the number of covariates which include age as a product */
             Tage[cptcovage]=k;  /* Tage[1] = 4 */
             /*printf("stre=%s ", stre);*/
           } else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutv(strb,stre,strc,'V');
             Tvar[k]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=k;
           } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/
             /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
             cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
             Tvar[k]=ncovcol+k1;  /* For model-covariate k tells which data-covariate to use but
                                     because this model-covariate is a construction we invent a new column
                                     ncovcol + k1
                                     If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
                                     Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
             cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */
             Tvard[k1][1]=atoi(strc); /* m 1 for V1*/
             Tvard[k1][2]=atoi(stre); /* n 4 for V4*/
             Tvar[cptcovn+k2]=Tvard[k1][1]; /* Tvar[(cptcovn=4+k2=1)=5]= 1 (V1) */
             Tvar[cptcovn+k2+1]=Tvard[k1][2];  /* Tvar[(cptcovn=4+(k2=1)+1)=6]= 4 (V4) */
             for (i=1; i<=lastobs;i++){
               /* Computes the new covariate which is a product of
                  covar[n][i]* covar[m][i] and stores it at ncovol+k1 */
               covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
             }
             k1++;
             k2=k2+2;
           } /* End age is not in the model */
         } /* End if model includes a product */
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
           cutv(strd,strc,strb,'V');
           Tvar[k]=atoi(strc);
         }
         strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+V1+V4 */ 
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);*/
   
   
     return (0); /* with covar[new additional covariate if product] and Tage if age */ 
     endread:
       printf("Exiting decodemodel: ");
       return (1);
   }
   
   calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
   {
     int i, m;
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           *nberr++;
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           *nberr++;
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if ((int)andc[i]!=9999){
                   nbwarn++;
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] < *agemin){ 
               *agemin=agev[m][i];
               printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
             }
             else if(agev[m][i] >*agemax){
               *agemax=agev[m][i];
               printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           *nberr++;
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           return 1;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax); 
   
     return (0);
     endread:
       printf("Exiting calandcheckages: ");
       return (1);
   }
   
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
   #ifdef GSL
     const gsl_multimin_fminimizer_type *T;
     size_t iteri = 0, it;
     int rval = GSL_CONTINUE;
     int status = GSL_SUCCESS;
     double ssval;
   #endif
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
     int linei, month, year,iout;
     int jj, ll, li, lj, lk, imk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int itimes;
     int NDIM=2;
     int vpopbased=0;
   
     char ca[32], cb[32], cc[32];
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     struct stat info;
     double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE], pathimach[MAXLINE]; 
     char **bp, *tok, *val; /* pathtot */
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,*tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     int agemortsup;
     float  sumlpop=0.;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
     double **ximort;
     char *alph[]={"a","a","b","c","d","e"}, str[4];
     int *dcwave;
   
     char z[1]="c", occ;
   
     /*char  *strt;*/
     char strtend[80];
   
     long total_usecs;
    
   /*   setlocale (LC_ALL, ""); */
   /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   /*   textdomain (PACKAGE); */
   /*   setlocale (LC_CTYPE, ""); */
   /*   setlocale (LC_MESSAGES, ""); */
   
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     (void) gettimeofday(&start_time,&tzp);
     curr_time=start_time;
     tm = *localtime(&start_time.tv_sec);
     tmg = *gmtime(&start_time.tv_sec);
     strcpy(strstart,asctime(&tm));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tv_sec = tp.tv_sec +86400; */
   /*  tm = *localtime(&start_time.tv_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tv_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     nberr=0; /* Number of errors and warnings */
     nbwarn=0;
     getcwd(pathcd, size);
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       fgets(pathr,FILENAMELENGTH,stdin);
       i=strlen(pathr);
       if(pathr[i-1]=='\n')
         pathr[i-1]='\0';
      for (tok = pathr; tok != NULL; ){
         printf("Pathr |%s|\n",pathr);
         while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
         printf("val= |%s| pathr=%s\n",val,pathr);
         strcpy (pathtot, val);
         if(pathr[0] == '\0') break; /* Dirty */
       }
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     /* Split argv[0], imach program to get pathimach */
     printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
     split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
     printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
    /*   strcpy(pathimach,argv[0]); */
     /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path); /* Can be a relative path */
     if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
       printf("Current directory %s!\n",pathcd);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s\n%s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: \n");
     fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     printf("Local time (at start):%s",strstart);
     fprintf(ficlog,"Local time (at start): %s",strstart);
     fflush(ficlog);
   /*   (void) gettimeofday(&curr_time,&tzp); */
   /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile %s\n",optionfile);
       fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       fflush(ficlog);
       goto end;
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       fputs(line,stdout);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       fputs(line, stdout);
       //puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n); 
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
     /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
        v1+v2*age+v2*v3 makes cptcovn = 3
     */
     if (strlen(model)>1) 
       cptcovn=nbocc(model,'+')+1;
     /* ncovprod */
     ncovmodel=2+cptcovn; /*Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7*/
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
     npar= nforce*ncovmodel; /* Number of parameters like aij*/
     if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
       printf("Too complex model for current IMaCh: npar=(nlstate+ndeath-1)*nlstate*ncovmodel=%d >= %d(MAXPARM) or nlstate=%d >= %d(NLSTATEMAX) or ndeath=%d >= %d(NDEATHMAX) or ncovmodel=(k+age+#of+signs)=%d(NCOVMAX) >= %d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fprintf(ficlog,"Too complex model for current IMaCh: %d >=%d(MAXPARM) or %d >=%d(NLSTATEMAX) or %d >=%d(NDEATHMAX) or %d(NCOVMAX) >=%d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fflush(stdout);
       fclose (ficlog);
       goto end;
     }
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     delti=delti3[1][1];
     /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
     if(mle==-1){ /* Print a wizard for help writing covariance matrix */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       fclose (ficparo);
       fclose (ficlog);
       goto end;
       exit(0);
     }
     else if(mle==-3) {
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       matcov=matrix(1,npar,1,npar);
     }
     else{
       /* Read guess parameters */
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
       
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       for(i=1; i <=nlstate; i++){
         j=0;
         for(jj=1; jj <=nlstate+ndeath; jj++){
           if(jj==i) continue;
           j++;
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1 != i) && (j1 != j)){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
   It might be a problem of design; if ncovcol and the model are correct\n \
   run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           fprintf(ficparo,"%1d%1d",i1,j1);
           if(mle==1)
             printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar," %lf",&param[i][j][k]);
             if(mle==1){
               printf(" %lf",param[i][j][k]);
               fprintf(ficlog," %lf",param[i][j][k]);
             }
             else
               fprintf(ficlog," %lf",param[i][j][k]);
             fprintf(ficparo," %lf",param[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           if(mle==1)
             printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficparo,"\n");
         }
       }  
       fflush(ficlog);
   
       p=param[1][1];
       
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
   
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath-1; j++){
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1-i)*(j1-j)!=0){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           printf("%1d%1d",i,j);
           fprintf(ficparo,"%1d%1d",i1,j1);
           fprintf(ficlog,"%1d%1d",i1,j1);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar,"%le",&delti3[i][j][k]);
             printf(" %le",delti3[i][j][k]);
             fprintf(ficparo," %le",delti3[i][j][k]);
             fprintf(ficlog," %le",delti3[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           printf("\n");
           fprintf(ficparo,"\n");
           fprintf(ficlog,"\n");
         }
       }
       fflush(ficlog);
   
       delti=delti3[1][1];
   
   
       /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
     
       matcov=matrix(1,npar,1,npar);
       for(i=1; i <=npar; i++)
         for(j=1; j <=npar; j++) matcov[i][j]=0.;
         
       for(i=1; i <=npar; i++){
         fscanf(ficpar,"%s",&str);
         if(mle==1)
           printf("%s",str);
         fprintf(ficlog,"%s",str);
         fprintf(ficparo,"%s",str);
         for(j=1; j <=i; j++){
           fscanf(ficpar," %le",&matcov[i][j]);
           if(mle==1){
             printf(" %.5le",matcov[i][j]);
           }
           fprintf(ficlog," %.5le",matcov[i][j]);
           fprintf(ficparo," %.5le",matcov[i][j]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
       for(i=1; i <=npar; i++)
         for(j=i+1;j<=npar;j++)
           matcov[i][j]=matcov[j][i];
       
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       
       fflush(ficlog);
       
       /*-------- Rewriting parameter file ----------*/
       strcpy(rfileres,"r");    /* "Rparameterfile */
       strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
       strcat(rfileres,".");    /* */
       strcat(rfileres,optionfilext);    /* Other files have txt extension */
       if((ficres =fopen(rfileres,"w"))==NULL) {
         printf("Problem writing new parameter file: %s\n", fileres);goto end;
         fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
       }
       fprintf(ficres,"#%s\n",version);
     }    /* End of mle != -3 */
   
   
     n= lastobs;
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */ 
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,8); /* hard coded ? */
   
     /* Reads data from file datafile */
     if (readdata(datafile, firstobs, lastobs, &imx)==1)
       goto end;
   
     /* Calculation of the number of parameters from char model */
       /*    modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 
           k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
           k=3 V4 Tvar[k=3]= 4 (from V4)
           k=2 V1 Tvar[k=2]= 1 (from V1)
           k=1 Tvar[1]=2 (from V2)
       */
     Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
     /*  V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs). 
         For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4, 
         Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
     */
     /* For model-covariate k tells which data-covariate to use but
       because this model-covariate is a construction we invent a new column
       ncovcol + k1
       If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
       Tvar[3=V1*V4]=4+1 etc */
     Tprod=ivector(1,15); /* Gives the position of a product */
     /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
        if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2)
     */
     Tvaraff=ivector(1,15); 
     Tvard=imatrix(1,15,1,2); /* n=Tvard[k1][1]  and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm
                               * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd. 
                               * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
     Tage=ivector(1,15); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
                            4 covariates (3 plus signs)
                            Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
                         */  
   
     if(decodemodel(model, lastobs) == 1)
       goto end;
   
     if((double)(lastobs-imx)/(double)imx > 1.10){
       nbwarn++;
       printf("Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
       fprintf(ficlog,"Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
     }
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
       for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
     }
   
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
       goto end;
   
   
     agegomp=(int)agemin;
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
   
      
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     if (cptcovn > 0) tricode(Tvar,nbcode,imx);
         
     codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
                                    the estimations*/
     h=0;
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
       for(i=1; i <=(m/pow(2,k));i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */ 
         for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate */
           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){  /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */ 
             h++;
             if (h>m) 
               h=1;
             codtab[h][k]=j;
             codtab[h][Tvar[k]]=j;
             printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]);
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
          printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
       
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     if(mle==-3)
       strcat(optionfilegnuplot,"-mort");
     strcat(optionfilegnuplot,".gp");
   
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       //fprintf(ficgp,"set missing 'NaNq'\n");
       fprintf(ficgp,"set datafile missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname); /* Main html file */
     if(mle==-3)
       strcat(optionfilehtm,"-mort");
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm);
       exit(0);
     }
   
     strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
     strcat(optionfilehtmcov,"-cov.htm");
     if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtmcov), exit(0);
     }
     else{
     fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
             optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
    - Log file of the run: <a href=\"%s\">%s</a><br>\n\
    - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
    - Date and time at start: %s</ul>\n",\
             optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
             optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
             fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
     chdir(optionfilefiname); /* Move to directory named optionfile */
     
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
   
     fprintf(fichtm,"\n");
     fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
             imx,agemin,agemax,jmin,jmax,jmean);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
   
     if (mle==-3){
       ximort=matrix(1,NDIM,1,NDIM); 
   /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
       cens=ivector(1,n);
       ageexmed=vector(1,n);
       agecens=vector(1,n);
       dcwave=ivector(1,n);
    
       for (i=1; i<=imx; i++){
         dcwave[i]=-1;
         for (m=firstpass; m<=lastpass; m++)
           if (s[m][i]>nlstate) {
             dcwave[i]=m;
             /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
             break;
           }
       }
   
       for (i=1; i<=imx; i++) {
         if (wav[i]>0){
           ageexmed[i]=agev[mw[1][i]][i];
           j=wav[i];
           agecens[i]=1.; 
   
           if (ageexmed[i]> 1 && wav[i] > 0){
             agecens[i]=agev[mw[j][i]][i];
             cens[i]= 1;
           }else if (ageexmed[i]< 1) 
             cens[i]= -1;
           if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
             cens[i]=0 ;
         }
         else cens[i]=-1;
       }
       
       for (i=1;i<=NDIM;i++) {
         for (j=1;j<=NDIM;j++)
           ximort[i][j]=(i == j ? 1.0 : 0.0);
       }
       
       p[1]=0.0268; p[NDIM]=0.083;
       /*printf("%lf %lf", p[1], p[2]);*/
       
       
   #ifdef GSL
       printf("GSL optimization\n");  fprintf(ficlog,"Powell\n");
   #elsedef
       printf("Powell\n");  fprintf(ficlog,"Powell\n");
   #endif
       strcpy(filerespow,"pow-mort"); 
       strcat(filerespow,fileres);
       if((ficrespow=fopen(filerespow,"w"))==NULL) {
         printf("Problem with resultfile: %s\n", filerespow);
         fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
       }
   #ifdef GSL
       fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
   #elsedef
       fprintf(ficrespow,"# Powell\n# iter -2*LL");
   #endif
       /*  for (i=1;i<=nlstate;i++)
           for(j=1;j<=nlstate+ndeath;j++)
           if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       */
       fprintf(ficrespow,"\n");
   #ifdef GSL
       /* gsl starts here */ 
       T = gsl_multimin_fminimizer_nmsimplex;
       gsl_multimin_fminimizer *sfm = NULL;
       gsl_vector *ss, *x;
       gsl_multimin_function minex_func;
   
       /* Initial vertex size vector */
       ss = gsl_vector_alloc (NDIM);
       
       if (ss == NULL){
         GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
       }
       /* Set all step sizes to 1 */
       gsl_vector_set_all (ss, 0.001);
   
       /* Starting point */
       
       x = gsl_vector_alloc (NDIM);
       
       if (x == NULL){
         gsl_vector_free(ss);
         GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
       }
     
       /* Initialize method and iterate */
       /*     p[1]=0.0268; p[NDIM]=0.083; */
   /*     gsl_vector_set(x, 0, 0.0268); */
   /*     gsl_vector_set(x, 1, 0.083); */
       gsl_vector_set(x, 0, p[1]);
       gsl_vector_set(x, 1, p[2]);
   
       minex_func.f = &gompertz_f;
       minex_func.n = NDIM;
       minex_func.params = (void *)&p; /* ??? */
       
       sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
       gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
       
       printf("Iterations beginning .....\n\n");
       printf("Iter. #    Intercept       Slope     -Log Likelihood     Simplex size\n");
   
       iteri=0;
       while (rval == GSL_CONTINUE){
         iteri++;
         status = gsl_multimin_fminimizer_iterate(sfm);
         
         if (status) printf("error: %s\n", gsl_strerror (status));
         fflush(0);
         
         if (status) 
           break;
         
         rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
         ssval = gsl_multimin_fminimizer_size (sfm);
         
         if (rval == GSL_SUCCESS)
           printf ("converged to a local maximum at\n");
         
         printf("%5d ", iteri);
         for (it = 0; it < NDIM; it++){
           printf ("%10.5f ", gsl_vector_get (sfm->x, it));
         }
         printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
       }
       
       printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
       
       gsl_vector_free(x); /* initial values */
       gsl_vector_free(ss); /* inital step size */
       for (it=0; it<NDIM; it++){
         p[it+1]=gsl_vector_get(sfm->x,it);
         fprintf(ficrespow," %.12lf", p[it]);
       }
       gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1)  */
   #endif
   #ifdef POWELL
        powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
   #endif  
       fclose(ficrespow);
       
       hesscov(matcov, p, NDIM, delti, 1e-4, gompertz); 
   
       for(i=1; i <=NDIM; i++)
         for(j=i+1;j<=NDIM;j++)
           matcov[i][j]=matcov[j][i];
       
       printf("\nCovariance matrix\n ");
       for(i=1; i <=NDIM; i++) {
         for(j=1;j<=NDIM;j++){ 
           printf("%f ",matcov[i][j]);
         }
         printf("\n ");
       }
       
       printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
       for (i=1;i<=NDIM;i++) 
         printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
   
       lsurv=vector(1,AGESUP);
       lpop=vector(1,AGESUP);
       tpop=vector(1,AGESUP);
       lsurv[agegomp]=100000;
       
       for (k=agegomp;k<=AGESUP;k++) {
         agemortsup=k;
         if (p[1]*exp(p[2]*(k-agegomp))>1) break;
       }
       
       for (k=agegomp;k<agemortsup;k++)
         lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
       
       for (k=agegomp;k<agemortsup;k++){
         lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
         sumlpop=sumlpop+lpop[k];
       }
       
       tpop[agegomp]=sumlpop;
       for (k=agegomp;k<(agemortsup-3);k++){
         /*  tpop[k+1]=2;*/
         tpop[k+1]=tpop[k]-lpop[k];
       }
       
       
       printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
       for (k=agegomp;k<(agemortsup-2);k++) 
         printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
       
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
                        stepm, weightopt,\
                        model,imx,p,matcov,agemortsup);
       
       free_vector(lsurv,1,AGESUP);
       free_vector(lpop,1,AGESUP);
       free_vector(tpop,1,AGESUP);
   #ifdef GSL
       free_ivector(cens,1,n);
       free_vector(agecens,1,n);
       free_ivector(dcwave,1,n);
       free_matrix(ximort,1,NDIM,1,NDIM);
   #endif
     } /* Endof if mle==-3 */
     
     else{ /* For mle >=1 */
       globpr=0;/* debug */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       globpr=1; /* to print the contributions */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       if(mle>=1){ /* Could be 1 or 2 */
         mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
       }
       
       /*--------- results files --------------*/
       fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
       
       
       fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(k=1; k <=(nlstate+ndeath); k++){
           if (k != i) {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%lf ",p[jk]);
               fprintf(ficlog,"%lf ",p[jk]);
               fprintf(ficres,"%lf ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       if(mle!=0){
         /* Computing hessian and covariance matrix */
         ftolhess=ftol; /* Usually correct */
         hesscov(matcov, p, npar, delti, ftolhess, func);
       }
       fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
       printf("# Scales (for hessian or gradient estimation)\n");
       fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if (j!=i) {
             fprintf(ficres,"%1d%1d",i,j);
             printf("%1d%1d",i,j);
             fprintf(ficlog,"%1d%1d",i,j);
             for(k=1; k<=ncovmodel;k++){
               printf(" %.5e",delti[jk]);
               fprintf(ficlog," %.5e",delti[jk]);
               fprintf(ficres," %.5e",delti[jk]);
               jk++;
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       
       fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       if(mle>=1)
         printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       /* # 121 Var(a12)\n\ */
       /* # 122 Cov(b12,a12) Var(b12)\n\ */
       /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
       /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
       /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
       /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
       /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
       /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
       
       
       /* Just to have a covariance matrix which will be more understandable
          even is we still don't want to manage dictionary of variables
       */
       for(itimes=1;itimes<=2;itimes++){
         jj=0;
         for(i=1; i <=nlstate; i++){
           for(j=1; j <=nlstate+ndeath; j++){
             if(j==i) continue;
             for(k=1; k<=ncovmodel;k++){
               jj++;
               ca[0]= k+'a'-1;ca[1]='\0';
               if(itimes==1){
                 if(mle>=1)
                   printf("#%1d%1d%d",i,j,k);
                 fprintf(ficlog,"#%1d%1d%d",i,j,k);
                 fprintf(ficres,"#%1d%1d%d",i,j,k);
               }else{
                 if(mle>=1)
                   printf("%1d%1d%d",i,j,k);
                 fprintf(ficlog,"%1d%1d%d",i,j,k);
                 fprintf(ficres,"%1d%1d%d",i,j,k);
               }
               ll=0;
               for(li=1;li <=nlstate; li++){
                 for(lj=1;lj <=nlstate+ndeath; lj++){
                   if(lj==li) continue;
                   for(lk=1;lk<=ncovmodel;lk++){
                     ll++;
                     if(ll<=jj){
                       cb[0]= lk +'a'-1;cb[1]='\0';
                       if(ll<jj){
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }else{
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }
                     }
                   } /* end lk */
                 } /* end lj */
               } /* end li */
               if(mle>=1)
                 printf("\n");
               fprintf(ficlog,"\n");
               fprintf(ficres,"\n");
               numlinepar++;
             } /* end k*/
           } /*end j */
         } /* end i */
       } /* end itimes */
       
       fflush(ficlog);
       fflush(ficres);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       estepm=0;
       fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
       if (estepm==0 || estepm < stepm) estepm=stepm;
       if (fage <= 2) {
         bage = ageminpar;
         fage = agemaxpar;
       }
       
       fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
       fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
       fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       
       dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
       dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
       
       fscanf(ficpar,"pop_based=%d\n",&popbased);
       fprintf(ficparo,"pop_based=%d\n",popbased);   
       fprintf(ficres,"pop_based=%d\n",popbased);   
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
       fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       /* day and month of proj2 are not used but only year anproj2.*/
       
       
       
       /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
       /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                    model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                    jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
         
      /*------------ free_vector  -------------*/
      /*  chdir(path); */
    
       free_ivector(wav,1,imx);
       free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
       free_lvector(num,1,n);
       free_vector(agedc,1,n);
       /*free_matrix(covar,0,NCOVMAX,1,n);*/
       /*free_matrix(covar,1,NCOVMAX,1,n);*/
       fclose(ficparo);
       fclose(ficres);
   
   
       /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
     
       strcpy(filerespl,"pl");
       strcat(filerespl,fileres);
       if((ficrespl=fopen(filerespl,"w"))==NULL) {
         printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
         fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
       }
       printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
       fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
       pstamp(ficrespl);
       fprintf(ficrespl,"# Period (stable) prevalence \n");
       fprintf(ficrespl,"#Age ");
       for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
       fprintf(ficrespl,"\n");
     
       prlim=matrix(1,nlstate,1,nlstate);
   
       agebase=ageminpar;
       agelim=agemaxpar;
       ftolpl=1.e-10;
       i1=cptcoveff;
       if (cptcovn < 1){i1=1;}
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           /* to clean */
           printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,codtab[cptcod][cptcov],nbcode);
           fprintf(ficrespl,"\n#******");
           printf("\n#******");
           fprintf(ficlog,"\n#******");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficrespl,"******\n");
           printf("******\n");
           fprintf(ficlog,"******\n");
           
           for (age=agebase; age<=agelim; age++){
             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
             fprintf(ficrespl,"%.0f ",age );
             for(j=1;j<=cptcoveff;j++)
               fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             for(i=1; i<=nlstate;i++)
               fprintf(ficrespl," %.5f", prlim[i][i]);
             fprintf(ficrespl,"\n");
           }
         }
       }
       fclose(ficrespl);
   
       /*------------- h Pij x at various ages ------------*/
     
       strcpy(filerespij,"pij");  strcat(filerespij,fileres);
       if((ficrespij=fopen(filerespij,"w"))==NULL) {
         printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
         fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
       }
       printf("Computing pij: result on file '%s' \n", filerespij);
       fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
       stepsize=(int) (stepm+YEARM-1)/YEARM;
       /*if (stepm<=24) stepsize=2;*/
   
       agelim=AGESUP;
       hstepm=stepsize*YEARM; /* Every year of age */
       hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
       /* hstepm=1;   aff par mois*/
       pstamp(ficrespij);
       fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           fprintf(ficrespij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrespij,"******\n");
           
           for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
             nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   
             /*      nhstepm=nhstepm*YEARM; aff par mois*/
   
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %1d-%1d",i,j);
             fprintf(ficrespij,"\n");
             for (h=0; h<=nhstepm; h++){
               fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
               for(i=1; i<=nlstate;i++)
                 for(j=1; j<=nlstate+ndeath;j++)
                   fprintf(ficrespij," %.5f", p3mat[i][j][h]);
               fprintf(ficrespij,"\n");
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             fprintf(ficrespij,"\n");
           }
         }
       }
   
       varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
   
       fclose(ficrespij);
   
       probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for(i=1;i<=AGESUP;i++)
         for(j=1;j<=NCOVMAX;j++)
           for(k=1;k<=NCOVMAX;k++)
             probs[i][j][k]=0.;
   
       /*---------- Forecasting ------------------*/
       /*if((stepm == 1) && (strcmp(model,".")==0)){*/
       if(prevfcast==1){
         /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
         /*      }  */
         /*      else{ */
         /*        erreur=108; */
         /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*      } */
       }
     
   
       /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
   
       prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
       /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
           ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
       */
   
       if (mobilav!=0) {
         mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
           fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
           printf(" Error in movingaverage mobilav=%d\n",mobilav);
         }
       }
   
   
       /*---------- Health expectancies, no variances ------------*/
   
       strcpy(filerese,"e");
       strcat(filerese,fileres);
       if((ficreseij=fopen(filerese,"w"))==NULL) {
         printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
         fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       }
       printf("Computing Health Expectancies: result on file '%s' \n", filerese);
       fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1; 
           fprintf(ficreseij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficreseij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);  
         
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         }
       }
       fclose(ficreseij);
   
   
       /*---------- Health expectancies and variances ------------*/
   
   
       strcpy(filerest,"t");
       strcat(filerest,fileres);
       if((ficrest=fopen(filerest,"w"))==NULL) {
         printf("Problem with total LE resultfile: %s\n", filerest);goto end;
         fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
       }
       printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
       fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
   
   
       strcpy(fileresstde,"stde");
       strcat(fileresstde,fileres);
       if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
         printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
         fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
       }
       printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
       fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
   
       strcpy(filerescve,"cve");
       strcat(filerescve,fileres);
       if((ficrescveij=fopen(filerescve,"w"))==NULL) {
         printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
         fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
       }
       printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
       fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
   
       strcpy(fileresv,"v");
       strcat(fileresv,fileres);
       if((ficresvij=fopen(fileresv,"w"))==NULL) {
         printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
         fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
       }
       printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
       fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1; 
           fprintf(ficrest,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrest,"******\n");
   
           fprintf(ficresstdeij,"\n#****** ");
           fprintf(ficrescveij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficresstdeij,"******\n");
           fprintf(ficrescveij,"******\n");
   
           fprintf(ficresvij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);  
    
           vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           pstamp(ficrest);
           for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
             oldm=oldms;savm=savms;
             varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart);   fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");
             if(vpopbased==1)
               fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
             else
               fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
             fprintf(ficrest,"# Age e.. (std) ");
             for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
             fprintf(ficrest,"\n");
   
             epj=vector(1,nlstate+1);
             for(age=bage; age <=fage ;age++){
               prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
               if (vpopbased==1) {
                 if(mobilav ==0){
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=probs[(int)age][i][k];
                 }else{ /* mobilav */ 
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=mobaverage[(int)age][i][k];
                 }
               }
           
               fprintf(ficrest," %4.0f",age);
               for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
                 for(i=1, epj[j]=0.;i <=nlstate;i++) {
                   epj[j] += prlim[i][i]*eij[i][j][(int)age];
                   /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
                 }
                 epj[nlstate+1] +=epj[j];
               }
   
               for(i=1, vepp=0.;i <=nlstate;i++)
                 for(j=1;j <=nlstate;j++)
                   vepp += vareij[i][j][(int)age];
               fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
               for(j=1;j <=nlstate;j++){
                 fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
               }
               fprintf(ficrest,"\n");
             }
           }
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_vector(epj,1,nlstate+1);
         }
       }
       free_vector(weight,1,n);
       free_imatrix(Tvard,1,15,1,2);
       free_imatrix(s,1,maxwav+1,1,n);
       free_matrix(anint,1,maxwav,1,n); 
       free_matrix(mint,1,maxwav,1,n);
       free_ivector(cod,1,n);
       free_ivector(tab,1,NCOVMAX);
       fclose(ficresstdeij);
       fclose(ficrescveij);
       fclose(ficresvij);
       fclose(ficrest);
       fclose(ficpar);
     
       /*------- Variance of period (stable) prevalence------*/   
   
       strcpy(fileresvpl,"vpl");
       strcat(fileresvpl,fileres);
       if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
         printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
         exit(0);
       }
       printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           fprintf(ficresvpl,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvpl,"******\n");
         
           varpl=matrix(1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
           free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
         }
       }
   
       fclose(ficresvpl);
   
       /*---------- End : free ----------------*/
       if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
     }  /* mle==-3 arrives here for freeing */
    endfree:
       free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
       free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(covar,0,NCOVMAX,1,n);
       free_matrix(matcov,1,npar,1,npar);
       /*free_vector(delti,1,npar);*/
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       free_matrix(agev,1,maxwav,1,imx);
       free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   
       free_ivector(ncodemax,1,8);
       free_ivector(Tvar,1,15);
       free_ivector(Tprod,1,15);
       free_ivector(Tvaraff,1,15);
       free_ivector(Tage,1,15);
   
       free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
       free_imatrix(codtab,1,100,1,10);
     fflush(fichtm);
     fflush(ficgp);
     
   
     if((nberr >0) || (nbwarn>0)){
       printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
       fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
     }else{
       printf("End of Imach\n");
       fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     (void) gettimeofday(&end_time,&tzp);
     tm = *localtime(&end_time.tv_sec);
     tmg = *gmtime(&end_time.tv_sec);
     strcpy(strtend,asctime(&tm));
     printf("Local time at start %s\nLocal time at end   %s",strstart, strtend); 
     fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
     printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
   
     printf("Total time was %ld Sec.\n", end_time.tv_sec -start_time.tv_sec);
     fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
     fprintf(ficlog,"Total time was %ld Sec.\n", end_time.tv_sec -start_time.tv_sec);
     /*  printf("Total time was %d uSec.\n", total_usecs);*/
   /*   if(fileappend(fichtm,optionfilehtm)){ */
     fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtm);
     fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtmcov);
     fclose(ficgp);
     fclose(ficlog);
     /*------ End -----------*/
   
   
      printf("Before Current directory %s!\n",pathcd);
      if(chdir(pathcd) != 0)
       printf("Can't move to directory %s!\n",path);
     if(getcwd(pathcd,MAXLINE) > 0)
       printf("Current directory %s!\n",pathcd);
     /*strcat(plotcmd,CHARSEPARATOR);*/
     sprintf(plotcmd,"gnuplot");
   #ifndef UNIX
     sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
   #endif
     if(!stat(plotcmd,&info)){
       printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
       if(!stat(getenv("GNUPLOTBIN"),&info)){
         printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #ifdef UNIX
       strcpy(plotcmd,GNUPLOTPROGRAM);
       if(!stat(plotcmd,&info)){
         printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #endif
     }else
       strcpy(pplotcmd,plotcmd);
     
     sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
     printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
   
     if((outcmd=system(plotcmd)) != 0){
       printf("\n Problem with gnuplot\n");
     }
     printf(" Wait...");
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again and q for exiting: ");
       scanf("%s",z);
   /*     if (z[0] == 'c') system("./imach"); */
       if (z[0] == 'e') {
         printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
         system(optionfilehtm);
       }
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     end:
     while (z[0] != 'q') {
       printf("\nType  q for exiting: ");
       scanf("%s",z);
     }
   }
   
   
   
Removed from v.1.52  
changed lines
  Added in v.1.141

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