Diff for /imach/src/imach.c between versions 1.48 and 1.159

version 1.48, 2002/06/10 13:12:49 version 1.159, 2014/09/01 10:34:10
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.159  2014/09/01 10:34:10  brouard
      Summary: WIN32
   This program computes Healthy Life Expectancies from    Author: Brouard
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a  
   first survey ("cross") where individuals from different ages are    Revision 1.158  2014/08/27 17:11:51  brouard
   interviewed on their health status or degree of disability (in the    *** empty log message ***
   case of a health survey which is our main interest) -2- at least a  
   second wave of interviews ("longitudinal") which measure each change    Revision 1.157  2014/08/27 16:26:55  brouard
   (if any) in individual health status.  Health expectancies are    Summary: Preparing windows Visual studio version
   computed from the time spent in each health state according to a    Author: Brouard
   model. More health states you consider, more time is necessary to reach the  
   Maximum Likelihood of the parameters involved in the model.  The    In order to compile on Visual studio, time.h is now correct and time_t
   simplest model is the multinomial logistic model where pij is the    and tm struct should be used. difftime should be used but sometimes I
   probability to be observed in state j at the second wave    just make the differences in raw time format (time(&now).
   conditional to be observed in state i at the first wave. Therefore    Trying to suppress #ifdef LINUX
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    Add xdg-open for __linux in order to open default browser.
   '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 1.156  2014/08/25 20:10:10  brouard
   where the markup *Covariates have to be included here again* invites    *** empty log message ***
   you to do it.  More covariates you add, slower the  
   convergence.    Revision 1.155  2014/08/25 18:32:34  brouard
     Summary: New compile, minor changes
   The advantage of this computer programme, compared to a simple    Author: Brouard
   multinomial logistic model, is clear when the delay between waves is not  
   identical for each individual. Also, if a individual missed an    Revision 1.154  2014/06/20 17:32:08  brouard
   intermediate interview, the information is lost, but taken into    Summary: Outputs now all graphs of convergence to period prevalence
   account using an interpolation or extrapolation.    
     Revision 1.153  2014/06/20 16:45:46  brouard
   hPijx is the probability to be observed in state i at age x+h    Summary: If 3 live state, convergence to period prevalence on same graph
   conditional to the observed state i at age x. The delay 'h' can be    Author: Brouard
   split into an exact number (nh*stepm) of unobserved intermediate  
   states. This elementary transition (by month or quarter trimester,    Revision 1.152  2014/06/18 17:54:09  brouard
   semester or year) is model as a multinomial logistic.  The hPx    Summary: open browser, use gnuplot on same dir than imach if not found in the path
   matrix is simply the matrix product of nh*stepm elementary matrices  
   and the contribution of each individual to the likelihood is simply    Revision 1.151  2014/06/18 16:43:30  brouard
   hPijx.    *** empty log message ***
   
   Also this programme outputs the covariance matrix of the parameters but also    Revision 1.150  2014/06/18 16:42:35  brouard
   of the life expectancies. It also computes the prevalence limits.    Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
      Author: brouard
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).  
            Institut national d'études démographiques, Paris.    Revision 1.149  2014/06/18 15:51:14  brouard
   This software have been partly granted by Euro-REVES, a concerted action    Summary: Some fixes in parameter files errors
   from the European Union.    Author: Nicolas Brouard
   It is copyrighted identically to a GNU software product, ie programme and  
   software can be distributed freely for non commercial use. Latest version    Revision 1.148  2014/06/17 17:38:48  brouard
   can be accessed at http://euroreves.ined.fr/imach .    Summary: Nothing new
   **********************************************************************/    Author: Brouard
    
 #include <math.h>    Just a new packaging for OS/X version 0.98nS
 #include <stdio.h>  
 #include <stdlib.h>    Revision 1.147  2014/06/16 10:33:11  brouard
 #include <unistd.h>    *** empty log message ***
   
 #define MAXLINE 256    Revision 1.146  2014/06/16 10:20:28  brouard
 #define GNUPLOTPROGRAM "gnuplot"    Summary: Merge
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/    Author: Brouard
 #define FILENAMELENGTH 80  
 /*#define DEBUG*/    Merge, before building revised version.
 #define windows  
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    Revision 1.145  2014/06/10 21:23:15  brouard
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    Summary: Debugging with valgrind
     Author: Nicolas Brouard
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */  
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    Lot of changes in order to output the results with some covariates
     After the Edimburgh REVES conference 2014, it seems mandatory to
 #define NINTERVMAX 8    improve the code.
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    No more memory valgrind error but a lot has to be done in order to
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    continue the work of splitting the code into subroutines.
 #define NCOVMAX 8 /* Maximum number of covariates */    Also, decodemodel has been improved. Tricode is still not
 #define MAXN 20000    optimal. nbcode should be improved. Documentation has been added in
 #define YEARM 12. /* Number of months per year */    the source code.
 #define AGESUP 130  
 #define AGEBASE 40    Revision 1.143  2014/01/26 09:45:38  brouard
 #ifdef windows    Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
 #define DIRSEPARATOR '\\'  
 #else    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
 #define DIRSEPARATOR '/'    (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
 #endif  
     Revision 1.142  2014/01/26 03:57:36  brouard
 char version[80]="Imach version 0.8h, May 2002, INED-EUROREVES ";    Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
 int erreur; /* Error number */  
 int nvar;    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;  
 int npar=NPARMAX;    Revision 1.141  2014/01/26 02:42:01  brouard
 int nlstate=2; /* Number of live states */    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
 int ndeath=1; /* Number of dead states */  
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    Revision 1.140  2011/09/02 10:37:54  brouard
 int popbased=0;    Summary: times.h is ok with mingw32 now.
   
 int *wav; /* Number of waves for this individuual 0 is possible */    Revision 1.139  2010/06/14 07:50:17  brouard
 int maxwav; /* Maxim number of waves */    After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
 int jmin, jmax; /* min, max spacing between 2 waves */    I remember having already fixed agemin agemax which are pointers now but not cvs saved.
 int mle, weightopt;  
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    Revision 1.138  2010/04/30 18:19:40  brouard
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    *** empty log message ***
 double jmean; /* Mean space between 2 waves */  
 double **oldm, **newm, **savm; /* Working pointers to matrices */    Revision 1.137  2010/04/29 18:11:38  brouard
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    (Module): Checking covariates for more complex models
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    than V1+V2. A lot of change to be done. Unstable.
 FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;  
 FILE *fichtm; /* Html File */    Revision 1.136  2010/04/26 20:30:53  brouard
 FILE *ficreseij;    (Module): merging some libgsl code. Fixing computation
 char filerese[FILENAMELENGTH];    of likelione (using inter/intrapolation if mle = 0) in order to
 FILE  *ficresvij;    get same likelihood as if mle=1.
 char fileresv[FILENAMELENGTH];    Some cleaning of code and comments added.
 FILE  *ficresvpl;  
 char fileresvpl[FILENAMELENGTH];    Revision 1.135  2009/10/29 15:33:14  brouard
 char title[MAXLINE];    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
 char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];  
 char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];    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.
 char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];  
     Revision 1.133  2009/07/06 10:21:25  brouard
 char filerest[FILENAMELENGTH];    just nforces
 char fileregp[FILENAMELENGTH];  
 char popfile[FILENAMELENGTH];    Revision 1.132  2009/07/06 08:22:05  brouard
     Many tings
 char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];  
     Revision 1.131  2009/06/20 16:22:47  brouard
 #define NR_END 1    Some dimensions resccaled
 #define FREE_ARG char*  
 #define FTOL 1.0e-10    Revision 1.130  2009/05/26 06:44:34  brouard
     (Module): Max Covariate is now set to 20 instead of 8. A
 #define NRANSI    lot of cleaning with variables initialized to 0. Trying to make
 #define ITMAX 200    V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
   
 #define TOL 2.0e-4    Revision 1.129  2007/08/31 13:49:27  lievre
     Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
 #define CGOLD 0.3819660  
 #define ZEPS 1.0e-10    Revision 1.128  2006/06/30 13:02:05  brouard
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    (Module): Clarifications on computing e.j
   
 #define GOLD 1.618034    Revision 1.127  2006/04/28 18:11:50  brouard
 #define GLIMIT 100.0    (Module): Yes the sum of survivors was wrong since
 #define TINY 1.0e-20    imach-114 because nhstepm was no more computed in the age
     loop. Now we define nhstepma in the age loop.
 static double maxarg1,maxarg2;    (Module): In order to speed up (in case of numerous covariates) we
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    compute health expectancies (without variances) in a first step
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    and then all the health expectancies with variances or standard
      deviation (needs data from the Hessian matrices) which slows the
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    computation.
 #define rint(a) floor(a+0.5)    In the future we should be able to stop the program is only health
     expectancies and graph are needed without standard deviations.
 static double sqrarg;  
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    Revision 1.126  2006/04/28 17:23:28  brouard
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    (Module): Yes the sum of survivors was wrong since
     imach-114 because nhstepm was no more computed in the age
 int imx;    loop. Now we define nhstepma in the age loop.
 int stepm;    Version 0.98h
 /* Stepm, step in month: minimum step interpolation*/  
     Revision 1.125  2006/04/04 15:20:31  lievre
 int estepm;    Errors in calculation of health expectancies. Age was not initialized.
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/    Forecasting file added.
   
 int m,nb;    Revision 1.124  2006/03/22 17:13:53  lievre
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    Parameters are printed with %lf instead of %f (more numbers after the comma).
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    The log-likelihood is printed in the log file
 double **pmmij, ***probs, ***mobaverage;  
 double dateintmean=0;    Revision 1.123  2006/03/20 10:52:43  brouard
     * imach.c (Module): <title> changed, corresponds to .htm file
 double *weight;    name. <head> headers where missing.
 int **s; /* Status */  
 double *agedc, **covar, idx;    * imach.c (Module): Weights can have a decimal point as for
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    English (a comma might work with a correct LC_NUMERIC environment,
     otherwise the weight is truncated).
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    Modification of warning when the covariates values are not 0 or
 double ftolhess; /* Tolerance for computing hessian */    1.
     Version 0.98g
 /**************** split *************************/  
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    Revision 1.122  2006/03/20 09:45:41  brouard
 {    (Module): Weights can have a decimal point as for
    char *s;                             /* pointer */    English (a comma might work with a correct LC_NUMERIC environment,
    int  l1, l2;                         /* length counters */    otherwise the weight is truncated).
     Modification of warning when the covariates values are not 0 or
    l1 = strlen( path );                 /* length of path */    1.
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    Version 0.98g
    s = strrchr( path,  DIRSEPARATOR );          /* find last / */  
    if ( s == NULL ) {                   /* no directory, so use current */    Revision 1.121  2006/03/16 17:45:01  lievre
 #if     defined(__bsd__)                /* get current working directory */    * imach.c (Module): Comments concerning covariates added
       extern char       *getwd( );  
     * imach.c (Module): refinements in the computation of lli if
       if ( getwd( dirc ) == NULL ) {    status=-2 in order to have more reliable computation if stepm is
 #else    not 1 month. Version 0.98f
       extern char       *getcwd( );  
     Revision 1.120  2006/03/16 15:10:38  lievre
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    (Module): refinements in the computation of lli if
 #endif    status=-2 in order to have more reliable computation if stepm is
          return( GLOCK_ERROR_GETCWD );    not 1 month. Version 0.98f
       }  
       strcpy( name, path );             /* we've got it */    Revision 1.119  2006/03/15 17:42:26  brouard
    } else {                             /* strip direcotry from path */    (Module): Bug if status = -2, the loglikelihood was
       s++;                              /* after this, the filename */    computed as likelihood omitting the logarithm. Version O.98e
       l2 = strlen( s );                 /* length of filename */  
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    Revision 1.118  2006/03/14 18:20:07  brouard
       strcpy( name, s );                /* save file name */    (Module): varevsij Comments added explaining the second
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    table of variances if popbased=1 .
       dirc[l1-l2] = 0;                  /* add zero */    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
    }    (Module): Function pstamp added
    l1 = strlen( dirc );                 /* length of directory */    (Module): Version 0.98d
 #ifdef windows  
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    Revision 1.117  2006/03/14 17:16:22  brouard
 #else    (Module): varevsij Comments added explaining the second
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }    table of variances if popbased=1 .
 #endif    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
    s = strrchr( name, '.' );            /* find last / */    (Module): Function pstamp added
    s++;    (Module): Version 0.98d
    strcpy(ext,s);                       /* save extension */  
    l1= strlen( name);    Revision 1.116  2006/03/06 10:29:27  brouard
    l2= strlen( s)+1;    (Module): Variance-covariance wrong links and
    strncpy( finame, name, l1-l2);    varian-covariance of ej. is needed (Saito).
    finame[l1-l2]= 0;  
    return( 0 );                         /* we're done */    Revision 1.115  2006/02/27 12:17:45  brouard
 }    (Module): One freematrix added in mlikeli! 0.98c
   
     Revision 1.114  2006/02/26 12:57:58  brouard
 /******************************************/    (Module): Some improvements in processing parameter
     filename with strsep.
 void replace(char *s, char*t)  
 {    Revision 1.113  2006/02/24 14:20:24  brouard
   int i;    (Module): Memory leaks checks with valgrind and:
   int lg=20;    datafile was not closed, some imatrix were not freed and on matrix
   i=0;    allocation too.
   lg=strlen(t);  
   for(i=0; i<= lg; i++) {    Revision 1.112  2006/01/30 09:55:26  brouard
     (s[i] = t[i]);    (Module): Back to gnuplot.exe instead of wgnuplot.exe
     if (t[i]== '\\') s[i]='/';  
   }    Revision 1.111  2006/01/25 20:38:18  brouard
 }    (Module): Lots of cleaning and bugs added (Gompertz)
     (Module): Comments can be added in data file. Missing date values
 int nbocc(char *s, char occ)    can be a simple dot '.'.
 {  
   int i,j=0;    Revision 1.110  2006/01/25 00:51:50  brouard
   int lg=20;    (Module): Lots of cleaning and bugs added (Gompertz)
   i=0;  
   lg=strlen(s);    Revision 1.109  2006/01/24 19:37:15  brouard
   for(i=0; i<= lg; i++) {    (Module): Comments (lines starting with a #) are allowed in data.
   if  (s[i] == occ ) j++;  
   }    Revision 1.108  2006/01/19 18:05:42  lievre
   return j;    Gnuplot problem appeared...
 }    To be fixed
   
 void cutv(char *u,char *v, char*t, char occ)    Revision 1.107  2006/01/19 16:20:37  brouard
 {    Test existence of gnuplot in imach path
   int i,lg,j,p=0;  
   i=0;    Revision 1.106  2006/01/19 13:24:36  brouard
   for(j=0; j<=strlen(t)-1; j++) {    Some cleaning and links added in html output
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  
   }    Revision 1.105  2006/01/05 20:23:19  lievre
     *** empty log message ***
   lg=strlen(t);  
   for(j=0; j<p; j++) {    Revision 1.104  2005/09/30 16:11:43  lievre
     (u[j] = t[j]);    (Module): sump fixed, loop imx fixed, and simplifications.
   }    (Module): If the status is missing at the last wave but we know
      u[p]='\0';    that the person is alive, then we can code his/her status as -2
     (instead of missing=-1 in earlier versions) and his/her
    for(j=0; j<= lg; j++) {    contributions to the likelihood is 1 - Prob of dying from last
     if (j>=(p+1))(v[j-p-1] = t[j]);    health status (= 1-p13= p11+p12 in the easiest case of somebody in
   }    the healthy state at last known wave). Version is 0.98
 }  
     Revision 1.103  2005/09/30 15:54:49  lievre
 /********************** nrerror ********************/    (Module): sump fixed, loop imx fixed, and simplifications.
   
 void nrerror(char error_text[])    Revision 1.102  2004/09/15 17:31:30  brouard
 {    Add the possibility to read data file including tab characters.
   fprintf(stderr,"ERREUR ...\n");  
   fprintf(stderr,"%s\n",error_text);    Revision 1.101  2004/09/15 10:38:38  brouard
   exit(1);    Fix on curr_time
 }  
 /*********************** vector *******************/    Revision 1.100  2004/07/12 18:29:06  brouard
 double *vector(int nl, int nh)    Add version for Mac OS X. Just define UNIX in Makefile
 {  
   double *v;    Revision 1.99  2004/06/05 08:57:40  brouard
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    *** empty log message ***
   if (!v) nrerror("allocation failure in vector");  
   return v-nl+NR_END;    Revision 1.98  2004/05/16 15:05:56  brouard
 }    New version 0.97 . First attempt to estimate force of mortality
     directly from the data i.e. without the need of knowing the health
 /************************ free vector ******************/    state at each age, but using a Gompertz model: log u =a + b*age .
 void free_vector(double*v, int nl, int nh)    This is the basic analysis of mortality and should be done before any
 {    other analysis, in order to test if the mortality estimated from the
   free((FREE_ARG)(v+nl-NR_END));    cross-longitudinal survey is different from the mortality estimated
 }    from other sources like vital statistic data.
   
 /************************ivector *******************************/    The same imach parameter file can be used but the option for mle should be -3.
 int *ivector(long nl,long nh)  
 {    Agnès, who wrote this part of the code, tried to keep most of the
   int *v;    former routines in order to include the new code within the former code.
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  
   if (!v) nrerror("allocation failure in ivector");    The output is very simple: only an estimate of the intercept and of
   return v-nl+NR_END;    the slope with 95% confident intervals.
 }  
     Current limitations:
 /******************free ivector **************************/    A) Even if you enter covariates, i.e. with the
 void free_ivector(int *v, long nl, long nh)    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
 {    B) There is no computation of Life Expectancy nor Life Table.
   free((FREE_ARG)(v+nl-NR_END));  
 }    Revision 1.97  2004/02/20 13:25:42  lievre
     Version 0.96d. Population forecasting command line is (temporarily)
 /******************* imatrix *******************************/    suppressed.
 int **imatrix(long nrl, long nrh, long ncl, long nch)  
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    Revision 1.96  2003/07/15 15:38:55  brouard
 {    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    rewritten within the same printf. Workaround: many printfs.
   int **m;  
      Revision 1.95  2003/07/08 07:54:34  brouard
   /* allocate pointers to rows */    * imach.c (Repository):
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    (Repository): Using imachwizard code to output a more meaningful covariance
   if (!m) nrerror("allocation failure 1 in matrix()");    matrix (cov(a12,c31) instead of numbers.
   m += NR_END;  
   m -= nrl;    Revision 1.94  2003/06/27 13:00:02  brouard
      Just cleaning
    
   /* allocate rows and set pointers to them */    Revision 1.93  2003/06/25 16:33:55  brouard
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    (Module): On windows (cygwin) function asctime_r doesn't
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    exist so I changed back to asctime which exists.
   m[nrl] += NR_END;    (Module): Version 0.96b
   m[nrl] -= ncl;  
      Revision 1.92  2003/06/25 16:30:45  brouard
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    (Module): On windows (cygwin) function asctime_r doesn't
      exist so I changed back to asctime which exists.
   /* return pointer to array of pointers to rows */  
   return m;    Revision 1.91  2003/06/25 15:30:29  brouard
 }    * imach.c (Repository): Duplicated warning errors corrected.
     (Repository): Elapsed time after each iteration is now output. It
 /****************** free_imatrix *************************/    helps to forecast when convergence will be reached. Elapsed time
 void free_imatrix(m,nrl,nrh,ncl,nch)    is stamped in powell.  We created a new html file for the graphs
       int **m;    concerning matrix of covariance. It has extension -cov.htm.
       long nch,ncl,nrh,nrl;  
      /* free an int matrix allocated by imatrix() */    Revision 1.90  2003/06/24 12:34:15  brouard
 {    (Module): Some bugs corrected for windows. Also, when
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    mle=-1 a template is output in file "or"mypar.txt with the design
   free((FREE_ARG) (m+nrl-NR_END));    of the covariance matrix to be input.
 }  
     Revision 1.89  2003/06/24 12:30:52  brouard
 /******************* matrix *******************************/    (Module): Some bugs corrected for windows. Also, when
 double **matrix(long nrl, long nrh, long ncl, long nch)    mle=-1 a template is output in file "or"mypar.txt with the design
 {    of the covariance matrix to be input.
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  
   double **m;    Revision 1.88  2003/06/23 17:54:56  brouard
     * imach.c (Repository): Create a sub-directory where all the secondary files are. Only imach, htm, gp and r(imach) are on the main directory. Correct time and other things.
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");    Revision 1.87  2003/06/18 12:26:01  brouard
   m += NR_END;    Version 0.96
   m -= nrl;  
     Revision 1.86  2003/06/17 20:04:08  brouard
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    (Module): Change position of html and gnuplot routines and added
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    routine fileappend.
   m[nrl] += NR_END;  
   m[nrl] -= ncl;    Revision 1.85  2003/06/17 13:12:43  brouard
     * imach.c (Repository): Check when date of death was earlier that
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    current date of interview. It may happen when the death was just
   return m;    prior to the death. In this case, dh was negative and likelihood
 }    was wrong (infinity). We still send an "Error" but patch by
     assuming that the date of death was just one stepm after the
 /*************************free matrix ************************/    interview.
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    (Repository): Because some people have very long ID (first column)
 {    we changed int to long in num[] and we added a new lvector for
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    memory allocation. But we also truncated to 8 characters (left
   free((FREE_ARG)(m+nrl-NR_END));    truncation)
 }    (Repository): No more line truncation errors.
   
 /******************* ma3x *******************************/    Revision 1.84  2003/06/13 21:44:43  brouard
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    * imach.c (Repository): Replace "freqsummary" at a correct
 {    place. It differs from routine "prevalence" which may be called
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    many times. Probs is memory consuming and must be used with
   double ***m;    parcimony.
     Version 0.95a3 (should output exactly the same maximization than 0.8a2)
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");    Revision 1.83  2003/06/10 13:39:11  lievre
   m += NR_END;    *** empty log message ***
   m -= nrl;  
     Revision 1.82  2003/06/05 15:57:20  brouard
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    Add log in  imach.c and  fullversion number is now printed.
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;  */
   m[nrl] -= ncl;  /*
      Interpolated Markov Chain
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  
     Short summary of the programme:
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    This program computes Healthy Life Expectancies from
   m[nrl][ncl] += NR_END;    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
   m[nrl][ncl] -= nll;    first survey ("cross") where individuals from different ages are
   for (j=ncl+1; j<=nch; j++)    interviewed on their health status or degree of disability (in the
     m[nrl][j]=m[nrl][j-1]+nlay;    case of a health survey which is our main interest) -2- at least a
      second wave of interviews ("longitudinal") which measure each change
   for (i=nrl+1; i<=nrh; i++) {    (if any) in individual health status.  Health expectancies are
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;    computed from the time spent in each health state according to a
     for (j=ncl+1; j<=nch; j++)    model. More health states you consider, more time is necessary to reach the
       m[i][j]=m[i][j-1]+nlay;    Maximum Likelihood of the parameters involved in the model.  The
   }    simplest model is the multinomial logistic model where pij is the
   return m;    probability to be observed in state j at the second wave
 }    conditional to be observed in state i at the first wave. Therefore
     the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
 /*************************free ma3x ************************/    'age' is age and 'sex' is a covariate. If you want to have a more
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    complex model than "constant and age", you should modify the program
 {    where the markup *Covariates have to be included here again* invites
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    you to do it.  More covariates you add, slower the
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    convergence.
   free((FREE_ARG)(m+nrl-NR_END));  
 }    The advantage of this computer programme, compared to a simple
     multinomial logistic model, is clear when the delay between waves is not
 /***************** f1dim *************************/    identical for each individual. Also, if a individual missed an
 extern int ncom;    intermediate interview, the information is lost, but taken into
 extern double *pcom,*xicom;    account using an interpolation or extrapolation.  
 extern double (*nrfunc)(double []);  
      hPijx is the probability to be observed in state i at age x+h
 double f1dim(double x)    conditional to the observed state i at age x. The delay 'h' can be
 {    split into an exact number (nh*stepm) of unobserved intermediate
   int j;    states. This elementary transition (by month, quarter,
   double f;    semester or year) is modelled as a multinomial logistic.  The hPx
   double *xt;    matrix is simply the matrix product of nh*stepm elementary matrices
      and the contribution of each individual to the likelihood is simply
   xt=vector(1,ncom);    hPijx.
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  
   f=(*nrfunc)(xt);    Also this programme outputs the covariance matrix of the parameters but also
   free_vector(xt,1,ncom);    of the life expectancies. It also computes the period (stable) prevalence. 
   return f;    
 }    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
              Institut national d'études démographiques, Paris.
 /*****************brent *************************/    This software have been partly granted by Euro-REVES, a concerted action
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    from the European Union.
 {    It is copyrighted identically to a GNU software product, ie programme and
   int iter;    software can be distributed freely for non commercial use. Latest version
   double a,b,d,etemp;    can be accessed at http://euroreves.ined.fr/imach .
   double fu,fv,fw,fx;  
   double ftemp;    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
   double p,q,r,tol1,tol2,u,v,w,x,xm;    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
   double e=0.0;    
      **********************************************************************/
   a=(ax < cx ? ax : cx);  /*
   b=(ax > cx ? ax : cx);    main
   x=w=v=bx;    read parameterfile
   fw=fv=fx=(*f)(x);    read datafile
   for (iter=1;iter<=ITMAX;iter++) {    concatwav
     xm=0.5*(a+b);    freqsummary
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    if (mle >= 1)
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/      mlikeli
     printf(".");fflush(stdout);    print results files
 #ifdef DEBUG    if mle==1 
     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);       computes hessian
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    read end of parameter file: agemin, agemax, bage, fage, estepm
 #endif        begin-prev-date,...
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    open gnuplot file
       *xmin=x;    open html file
       return fx;    period (stable) prevalence      | pl_nom    1-1 2-2 etc by covariate
     }     for age prevalim()             | #****** V1=0  V2=1  V3=1  V4=0 ******
     ftemp=fu;                                    | 65 1 0 2 1 3 1 4 0  0.96326 0.03674
     if (fabs(e) > tol1) {      freexexit2 possible for memory heap.
       r=(x-w)*(fx-fv);  
       q=(x-v)*(fx-fw);    h Pij x                         | pij_nom  ficrestpij
       p=(x-v)*q-(x-w)*r;     # Cov Agex agex+h hpijx with i,j= 1-1 1-2     1-3     2-1     2-2     2-3
       q=2.0*(q-r);         1  85   85    1.00000             0.00000 0.00000 0.00000 1.00000 0.00000
       if (q > 0.0) p = -p;         1  85   86    0.68299             0.22291 0.09410 0.71093 0.00000 0.28907
       q=fabs(q);  
       etemp=e;         1  65   99    0.00364             0.00322 0.99314 0.00350 0.00310 0.99340
       e=d;         1  65  100    0.00214             0.00204 0.99581 0.00206 0.00196 0.99597
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    variance of p one-step probabilities varprob  | prob_nom   ficresprob #One-step probabilities and stand. devi in ()
         d=CGOLD*(e=(x >= xm ? a-x : b-x));     Standard deviation of one-step probabilities | probcor_nom   ficresprobcor #One-step probabilities and correlation matrix
       else {     Matrix of variance covariance of one-step probabilities |  probcov_nom ficresprobcov #One-step probabilities and covariance matrix
         d=p/q;  
         u=x+d;    forecasting if prevfcast==1 prevforecast call prevalence()
         if (u-a < tol2 || b-u < tol2)    health expectancies
           d=SIGN(tol1,xm-x);    Variance-covariance of DFLE
       }    prevalence()
     } else {     movingaverage()
       d=CGOLD*(e=(x >= xm ? a-x : b-x));    varevsij() 
     }    if popbased==1 varevsij(,popbased)
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    total life expectancies
     fu=(*f)(u);    Variance of period (stable) prevalence
     if (fu <= fx) {   end
       if (u >= x) a=x; else b=x;  */
       SHFT(v,w,x,u)  
         SHFT(fv,fw,fx,fu)  
         } else {  
           if (u < x) a=u; else b=u;   
           if (fu <= fw || w == x) {  #include <math.h>
             v=w;  #include <stdio.h>
             w=u;  #include <stdlib.h>
             fv=fw;  #include <string.h>
             fw=fu;  
           } else if (fu <= fv || v == x || v == w) {  #ifdef _WIN32
             v=u;  #include <io.h>
             fv=fu;  #else
           }  #include <unistd.h>
         }  #endif
   }  
   nrerror("Too many iterations in brent");  #include <limits.h>
   *xmin=x;  #include <sys/types.h>
   return fx;  #include <sys/stat.h>
 }  #include <errno.h>
   /* extern int errno; */
 /****************** mnbrak ***********************/  
   /* #ifdef LINUX */
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  /* #include <time.h> */
             double (*func)(double))  /* #include "timeval.h" */
 {  /* #else */
   double ulim,u,r,q, dum;  /* #include <sys/time.h> */
   double fu;  /* #endif */
    
   *fa=(*func)(*ax);  #include <time.h>
   *fb=(*func)(*bx);  
   if (*fb > *fa) {  #ifdef GSL
     SHFT(dum,*ax,*bx,dum)  #include <gsl/gsl_errno.h>
       SHFT(dum,*fb,*fa,dum)  #include <gsl/gsl_multimin.h>
       }  #endif
   *cx=(*bx)+GOLD*(*bx-*ax);  
   *fc=(*func)(*cx);  /* #include <libintl.h> */
   while (*fb > *fc) {  /* #define _(String) gettext (String) */
     r=(*bx-*ax)*(*fb-*fc);  
     q=(*bx-*cx)*(*fb-*fa);  #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  #define GNUPLOTPROGRAM "gnuplot"
     ulim=(*bx)+GLIMIT*(*cx-*bx);  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
     if ((*bx-u)*(u-*cx) > 0.0) {  #define FILENAMELENGTH 132
       fu=(*func)(u);  
     } else if ((*cx-u)*(u-ulim) > 0.0) {  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
       fu=(*func)(u);  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
       if (fu < *fc) {  
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
           SHFT(*fb,*fc,fu,(*func)(u))  #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
           }  
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  #define NINTERVMAX 8
       u=ulim;  #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
       fu=(*func)(u);  #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
     } else {  #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
       u=(*cx)+GOLD*(*cx-*bx);  #define codtabm(h,k)  1 & (h-1) >> (k-1) ;
       fu=(*func)(u);  #define MAXN 20000
     }  #define YEARM 12. /**< Number of months per year */
     SHFT(*ax,*bx,*cx,u)  #define AGESUP 130
       SHFT(*fa,*fb,*fc,fu)  #define AGEBASE 40
       }  #define AGEGOMP 10. /**< Minimal age for Gompertz adjustment */
 }  #ifdef _WIN32
   #define DIRSEPARATOR '\\'
 /*************** linmin ************************/  #define CHARSEPARATOR "\\"
   #define ODIRSEPARATOR '/'
 int ncom;  #else
 double *pcom,*xicom;  #define DIRSEPARATOR '/'
 double (*nrfunc)(double []);  #define CHARSEPARATOR "/"
    #define ODIRSEPARATOR '\\'
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  #endif
 {  
   double brent(double ax, double bx, double cx,  /* $Id$ */
                double (*f)(double), double tol, double *xmin);  /* $State$ */
   double f1dim(double x);  
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  char version[]="Imach version 0.98nX, August 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121)";
               double *fc, double (*func)(double));  char fullversion[]="$Revision$ $Date$"; 
   int j;  char strstart[80];
   double xx,xmin,bx,ax;  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
   double fx,fb,fa;  int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
    int nvar=0, nforce=0; /* Number of variables, number of forces */
   ncom=n;  /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
   pcom=vector(1,n);  int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
   xicom=vector(1,n);  int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
   nrfunc=func;  int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
   for (j=1;j<=n;j++) {  int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
     pcom[j]=p[j];  int cptcovprodnoage=0; /**< Number of covariate products without age */   
     xicom[j]=xi[j];  int cptcoveff=0; /* Total number of covariates to vary for printing results */
   }  int cptcov=0; /* Working variable */
   ax=0.0;  int npar=NPARMAX;
   xx=1.0;  int nlstate=2; /* Number of live states */
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  int ndeath=1; /* Number of dead states */
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
 #ifdef DEBUG  int popbased=0;
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  
 #endif  int *wav; /* Number of waves for this individuual 0 is possible */
   for (j=1;j<=n;j++) {  int maxwav=0; /* Maxim number of waves */
     xi[j] *= xmin;  int jmin=0, jmax=0; /* min, max spacing between 2 waves */
     p[j] += xi[j];  int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
   }  int gipmx=0, gsw=0; /* Global variables on the number of contributions 
   free_vector(xicom,1,n);                     to the likelihood and the sum of weights (done by funcone)*/
   free_vector(pcom,1,n);  int mle=1, weightopt=0;
 }  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
   int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
 /*************** powell ************************/  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,             * wave mi and wave mi+1 is not an exact multiple of stepm. */
             double (*func)(double []))  double jmean=1; /* Mean space between 2 waves */
 {  double **matprod2(); /* test */
   void linmin(double p[], double xi[], int n, double *fret,  double **oldm, **newm, **savm; /* Working pointers to matrices */
               double (*func)(double []));  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   int i,ibig,j;  /*FILE *fic ; */ /* Used in readdata only */
   double del,t,*pt,*ptt,*xit;  FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   double fp,fptt;  FILE *ficlog, *ficrespow;
   double *xits;  int globpr=0; /* Global variable for printing or not */
   pt=vector(1,n);  double fretone; /* Only one call to likelihood */
   ptt=vector(1,n);  long ipmx=0; /* Number of contributions */
   xit=vector(1,n);  double sw; /* Sum of weights */
   xits=vector(1,n);  char filerespow[FILENAMELENGTH];
   *fret=(*func)(p);  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
   for (j=1;j<=n;j++) pt[j]=p[j];  FILE *ficresilk;
   for (*iter=1;;++(*iter)) {  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
     fp=(*fret);  FILE *ficresprobmorprev;
     ibig=0;  FILE *fichtm, *fichtmcov; /* Html File */
     del=0.0;  FILE *ficreseij;
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  char filerese[FILENAMELENGTH];
     for (i=1;i<=n;i++)  FILE *ficresstdeij;
       printf(" %d %.12f",i, p[i]);  char fileresstde[FILENAMELENGTH];
     printf("\n");  FILE *ficrescveij;
     for (i=1;i<=n;i++) {  char filerescve[FILENAMELENGTH];
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  FILE  *ficresvij;
       fptt=(*fret);  char fileresv[FILENAMELENGTH];
 #ifdef DEBUG  FILE  *ficresvpl;
       printf("fret=%lf \n",*fret);  char fileresvpl[FILENAMELENGTH];
 #endif  char title[MAXLINE];
       printf("%d",i);fflush(stdout);  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
       linmin(p,xit,n,fret,func);  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
       if (fabs(fptt-(*fret)) > del) {  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
         del=fabs(fptt-(*fret));  char command[FILENAMELENGTH];
         ibig=i;  int  outcmd=0;
       }  
 #ifdef DEBUG  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
       printf("%d %.12e",i,(*fret));  
       for (j=1;j<=n;j++) {  char filelog[FILENAMELENGTH]; /* Log file */
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  char filerest[FILENAMELENGTH];
         printf(" x(%d)=%.12e",j,xit[j]);  char fileregp[FILENAMELENGTH];
       }  char popfile[FILENAMELENGTH];
       for(j=1;j<=n;j++)  
         printf(" p=%.12e",p[j]);  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
       printf("\n");  
 #endif  /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
     }  /* struct timezone tzp; */
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  /* extern int gettimeofday(); */
 #ifdef DEBUG  struct tm tml, *gmtime(), *localtime();
       int k[2],l;  
       k[0]=1;  extern time_t time();
       k[1]=-1;  
       printf("Max: %.12e",(*func)(p));  struct tm start_time, end_time, curr_time, last_time, forecast_time;
       for (j=1;j<=n;j++)  time_t  rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
         printf(" %.12e",p[j]);  struct tm tm;
       printf("\n");  
       for(l=0;l<=1;l++) {  char strcurr[80], strfor[80];
         for (j=1;j<=n;j++) {  
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  char *endptr;
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  long lval;
         }  double dval;
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  
       }  #define NR_END 1
 #endif  #define FREE_ARG char*
   #define FTOL 1.0e-10
   
       free_vector(xit,1,n);  #define NRANSI 
       free_vector(xits,1,n);  #define ITMAX 200 
       free_vector(ptt,1,n);  
       free_vector(pt,1,n);  #define TOL 2.0e-4 
       return;  
     }  #define CGOLD 0.3819660 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  #define ZEPS 1.0e-10 
     for (j=1;j<=n;j++) {  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
       ptt[j]=2.0*p[j]-pt[j];  
       xit[j]=p[j]-pt[j];  #define GOLD 1.618034 
       pt[j]=p[j];  #define GLIMIT 100.0 
     }  #define TINY 1.0e-20 
     fptt=(*func)(ptt);  
     if (fptt < fp) {  static double maxarg1,maxarg2;
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
       if (t < 0.0) {  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
         linmin(p,xit,n,fret,func);    
         for (j=1;j<=n;j++) {  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
           xi[j][ibig]=xi[j][n];  #define rint(a) floor(a+0.5)
           xi[j][n]=xit[j];  
         }  static double sqrarg;
 #ifdef DEBUG  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
         for(j=1;j<=n;j++)  int agegomp= AGEGOMP;
           printf(" %.12e",xit[j]);  
         printf("\n");  int imx; 
 #endif  int stepm=1;
       }  /* Stepm, step in month: minimum step interpolation*/
     }  
   }  int estepm;
 }  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
   
 /**** Prevalence limit ****************/  int m,nb;
   long *num;
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
 {  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit  double **pmmij, ***probs;
      matrix by transitions matrix until convergence is reached */  double *ageexmed,*agecens;
   double dateintmean=0;
   int i, ii,j,k;  
   double min, max, maxmin, maxmax,sumnew=0.;  double *weight;
   double **matprod2();  int **s; /* Status */
   double **out, cov[NCOVMAX], **pmij();  double *agedc;
   double **newm;  double  **covar; /**< covar[j,i], value of jth covariate for individual i,
   double agefin, delaymax=50 ; /* Max number of years to converge */                    * covar=matrix(0,NCOVMAX,1,n); 
                     * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
   for (ii=1;ii<=nlstate+ndeath;ii++)  double  idx; 
     for (j=1;j<=nlstate+ndeath;j++){  int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);  int *Ndum; /** Freq of modality (tricode */
     }  int **codtab; /**< codtab=imatrix(1,100,1,10); */
   int **Tvard, *Tprod, cptcovprod, *Tvaraff;
    cov[1]=1.;  double *lsurv, *lpop, *tpop;
    
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */  double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){  double ftolhess; /**< Tolerance for computing hessian */
     newm=savm;  
     /* Covariates have to be included here again */  /**************** split *************************/
      cov[2]=agefin;  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
    {
       for (k=1; k<=cptcovn;k++) {    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];       the name of the file (name), its extension only (ext) and its first part of the name (finame)
         /*      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]]);*/    */ 
       }    char  *ss;                            /* pointer */
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    int   l1, l2;                         /* length counters */
       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]]];    l1 = strlen(path );                   /* length of path */
     if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/    if ( ss == NULL ) {                   /* no directory, so determine current directory */
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/      strcpy( name, path );               /* we got the fullname name because no directory */
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
         printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
     savm=oldm;      /* get current working directory */
     oldm=newm;      /*    extern  char* getcwd ( char *buf , int len);*/
     maxmax=0.;      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
     for(j=1;j<=nlstate;j++){        return( GLOCK_ERROR_GETCWD );
       min=1.;      }
       max=0.;      /* got dirc from getcwd*/
       for(i=1; i<=nlstate; i++) {      printf(" DIRC = %s \n",dirc);
         sumnew=0;    } else {                              /* strip direcotry from path */
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];      ss++;                               /* after this, the filename */
         prlim[i][j]= newm[i][j]/(1-sumnew);      l2 = strlen( ss );                  /* length of filename */
         max=FMAX(max,prlim[i][j]);      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
         min=FMIN(min,prlim[i][j]);      strcpy( name, ss );         /* save file name */
       }      strncpy( dirc, path, l1 - l2 );     /* now the directory */
       maxmin=max-min;      dirc[l1-l2] = 0;                    /* add zero */
       maxmax=FMAX(maxmax,maxmin);      printf(" DIRC2 = %s \n",dirc);
     }    }
     if(maxmax < ftolpl){    /* We add a separator at the end of dirc if not exists */
       return prlim;    l1 = strlen( dirc );                  /* length of directory */
     }    if( dirc[l1-1] != DIRSEPARATOR ){
   }      dirc[l1] =  DIRSEPARATOR;
 }      dirc[l1+1] = 0; 
       printf(" DIRC3 = %s \n",dirc);
 /*************** transition probabilities ***************/    }
     ss = strrchr( name, '.' );            /* find last / */
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )    if (ss >0){
 {      ss++;
   double s1, s2;      strcpy(ext,ss);                     /* save extension */
   /*double t34;*/      l1= strlen( name);
   int i,j,j1, nc, ii, jj;      l2= strlen(ss)+1;
       strncpy( finame, name, l1-l2);
     for(i=1; i<= nlstate; i++){      finame[l1-l2]= 0;
     for(j=1; j<i;j++){    }
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  
         /*s2 += param[i][j][nc]*cov[nc];*/    return( 0 );                          /* we're done */
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  }
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/  
       }  
       ps[i][j]=s2;  /******************************************/
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/  
     }  void replace_back_to_slash(char *s, char*t)
     for(j=i+1; j<=nlstate+ndeath;j++){  {
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    int i;
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    int lg=0;
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/    i=0;
       }    lg=strlen(t);
       ps[i][j]=s2;    for(i=0; i<= lg; i++) {
     }      (s[i] = t[i]);
   }      if (t[i]== '\\') s[i]='/';
     /*ps[3][2]=1;*/    }
   }
   for(i=1; i<= nlstate; i++){  
      s1=0;  char *trimbb(char *out, char *in)
     for(j=1; j<i; j++)  { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
       s1+=exp(ps[i][j]);    char *s;
     for(j=i+1; j<=nlstate+ndeath; j++)    s=out;
       s1+=exp(ps[i][j]);    while (*in != '\0'){
     ps[i][i]=1./(s1+1.);      while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
     for(j=1; j<i; j++)        in++;
       ps[i][j]= exp(ps[i][j])*ps[i][i];      }
     for(j=i+1; j<=nlstate+ndeath; j++)      *out++ = *in++;
       ps[i][j]= exp(ps[i][j])*ps[i][i];    }
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */    *out='\0';
   } /* end i */    return s;
   }
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){  
     for(jj=1; jj<= nlstate+ndeath; jj++){  char *cutl(char *blocc, char *alocc, char *in, char occ)
       ps[ii][jj]=0;  {
       ps[ii][ii]=1;    /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ' 
     }       and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
   }       gives blocc="abcdef2ghi" and alocc="j".
        If occ is not found blocc is null and alocc is equal to in. Returns blocc
     */
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){    char *s, *t, *bl;
     for(jj=1; jj<= nlstate+ndeath; jj++){    t=in;s=in;
      printf("%lf ",ps[ii][jj]);    while ((*in != occ) && (*in != '\0')){
    }      *alocc++ = *in++;
     printf("\n ");    }
     }    if( *in == occ){
     printf("\n ");printf("%lf ",cov[2]);*/      *(alocc)='\0';
 /*      s=++in;
   for(i=1; i<= npar; i++) printf("%f ",x[i]);    }
   goto end;*/   
     return ps;    if (s == t) {/* occ not found */
 }      *(alocc-(in-s))='\0';
       in=s;
 /**************** Product of 2 matrices ******************/    }
     while ( *in != '\0'){
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)      *blocc++ = *in++;
 {    }
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times  
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */    *blocc='\0';
   /* in, b, out are matrice of pointers which should have been initialized    return t;
      before: only the contents of out is modified. The function returns  }
      a pointer to pointers identical to out */  char *cutv(char *blocc, char *alocc, char *in, char occ)
   long i, j, k;  {
   for(i=nrl; i<= nrh; i++)    /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ' 
     for(k=ncolol; k<=ncoloh; k++)       and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
       for(j=ncl,out[i][k]=0.; j<=nch; j++)       gives blocc="abcdef2ghi" and alocc="j".
         out[i][k] +=in[i][j]*b[j][k];       If occ is not found blocc is null and alocc is equal to in. Returns alocc
     */
   return out;    char *s, *t;
 }    t=in;s=in;
     while (*in != '\0'){
       while( *in == occ){
 /************* Higher Matrix Product ***************/        *blocc++ = *in++;
         s=in;
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )      }
 {      *blocc++ = *in++;
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month    }
      duration (i.e. until    if (s == t) /* occ not found */
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.      *(blocc-(in-s))='\0';
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step    else
      (typically every 2 years instead of every month which is too big).      *(blocc-(in-s)-1)='\0';
      Model is determined by parameters x and covariates have to be    in=s;
      included manually here.    while ( *in != '\0'){
       *alocc++ = *in++;
      */    }
   
   int i, j, d, h, k;    *alocc='\0';
   double **out, cov[NCOVMAX];    return s;
   double **newm;  }
   
   /* Hstepm could be zero and should return the unit matrix */  int nbocc(char *s, char occ)
   for (i=1;i<=nlstate+ndeath;i++)  {
     for (j=1;j<=nlstate+ndeath;j++){    int i,j=0;
       oldm[i][j]=(i==j ? 1.0 : 0.0);    int lg=20;
       po[i][j][0]=(i==j ? 1.0 : 0.0);    i=0;
     }    lg=strlen(s);
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    for(i=0; i<= lg; i++) {
   for(h=1; h <=nhstepm; h++){    if  (s[i] == occ ) j++;
     for(d=1; d <=hstepm; d++){    }
       newm=savm;    return j;
       /* Covariates have to be included here again */  }
       cov[1]=1.;  
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;  /* void cutv(char *u,char *v, char*t, char occ) */
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  /* { */
       for (k=1; k<=cptcovage;k++)  /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
       for (k=1; k<=cptcovprod;k++)  /*      gives u="abcdef2ghi" and v="j" *\/ */
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  /*   int i,lg,j,p=0; */
   /*   i=0; */
   /*   lg=strlen(t); */
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/  /*   for(j=0; j<=lg-1; j++) { */
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/  /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,  /*   } */
                    pmij(pmmij,cov,ncovmodel,x,nlstate));  
       savm=oldm;  /*   for(j=0; j<p; j++) { */
       oldm=newm;  /*     (u[j] = t[j]); */
     }  /*   } */
     for(i=1; i<=nlstate+ndeath; i++)  /*      u[p]='\0'; */
       for(j=1;j<=nlstate+ndeath;j++) {  
         po[i][j][h]=newm[i][j];  /*    for(j=0; j<= lg; j++) { */
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);  /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
          */  /*   } */
       }  /* } */
   } /* end h */  
   return po;  /********************** nrerror ********************/
 }  
   void nrerror(char error_text[])
   {
 /*************** log-likelihood *************/    fprintf(stderr,"ERREUR ...\n");
 double func( double *x)    fprintf(stderr,"%s\n",error_text);
 {    exit(EXIT_FAILURE);
   int i, ii, j, k, mi, d, kk;  }
   double l, ll[NLSTATEMAX], cov[NCOVMAX];  /*********************** vector *******************/
   double **out;  double *vector(int nl, int nh)
   double sw; /* Sum of weights */  {
   double lli; /* Individual log likelihood */    double *v;
   long ipmx;    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
   /*extern weight */    if (!v) nrerror("allocation failure in vector");
   /* We are differentiating ll according to initial status */    return v-nl+NR_END;
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/  }
   /*for(i=1;i<imx;i++)  
     printf(" %d\n",s[4][i]);  /************************ free vector ******************/
   */  void free_vector(double*v, int nl, int nh)
   cov[1]=1.;  {
     free((FREE_ARG)(v+nl-NR_END));
   for(k=1; k<=nlstate; k++) ll[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];  /************************ivector *******************************/
     for(mi=1; mi<= wav[i]-1; mi++){  int *ivector(long nl,long nh)
       for (ii=1;ii<=nlstate+ndeath;ii++)  {
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);    int *v;
       for(d=0; d<dh[mi][i]; d++){    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
         newm=savm;    if (!v) nrerror("allocation failure in ivector");
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;    return v-nl+NR_END;
         for (kk=1; kk<=cptcovage;kk++) {  }
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];  
         }  /******************free ivector **************************/
          void free_ivector(int *v, long nl, long nh)
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,  {
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));    free((FREE_ARG)(v+nl-NR_END));
         savm=oldm;  }
         oldm=newm;  
          /************************lvector *******************************/
          long *lvector(long nl,long nh)
       } /* end mult */  {
          long *v;
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/    if (!v) nrerror("allocation failure in ivector");
       ipmx +=1;    return v-nl+NR_END;
       sw += weight[i];  }
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;  
     } /* end of wave */  /******************free lvector **************************/
   } /* end of individual */  void free_lvector(long *v, long nl, long nh)
   {
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];    free((FREE_ARG)(v+nl-NR_END));
   /* 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;  /******************* imatrix *******************************/
 }  int **imatrix(long nrl, long nrh, long ncl, long nch) 
        /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
   { 
 /*********** Maximum Likelihood Estimation ***************/    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
     int **m; 
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))    
 {    /* allocate pointers to rows */ 
   int i,j, iter;    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
   double **xi,*delti;    if (!m) nrerror("allocation failure 1 in matrix()"); 
   double fret;    m += NR_END; 
   xi=matrix(1,npar,1,npar);    m -= nrl; 
   for (i=1;i<=npar;i++)    
     for (j=1;j<=npar;j++)    
       xi[i][j]=(i==j ? 1.0 : 0.0);    /* allocate rows and set pointers to them */ 
   printf("Powell\n");    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
   powell(p,xi,npar,ftol,&iter,&fret,func);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
     m[nrl] += NR_END; 
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));    m[nrl] -= ncl; 
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));    
     for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
 }    
     /* return pointer to array of pointers to rows */ 
 /**** Computes Hessian and covariance matrix ***/    return m; 
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))  } 
 {  
   double  **a,**y,*x,pd;  /****************** free_imatrix *************************/
   double **hess;  void free_imatrix(m,nrl,nrh,ncl,nch)
   int i, j,jk;        int **m;
   int *indx;        long nch,ncl,nrh,nrl; 
        /* free an int matrix allocated by imatrix() */ 
   double hessii(double p[], double delta, int theta, double delti[]);  { 
   double hessij(double p[], double delti[], int i, int j);    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
   void lubksb(double **a, int npar, int *indx, double b[]) ;    free((FREE_ARG) (m+nrl-NR_END)); 
   void ludcmp(double **a, int npar, int *indx, double *d) ;  } 
   
   hess=matrix(1,npar,1,npar);  /******************* matrix *******************************/
   double **matrix(long nrl, long nrh, long ncl, long nch)
   printf("\nCalculation of the hessian matrix. Wait...\n");  {
   for (i=1;i<=npar;i++){    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
     printf("%d",i);fflush(stdout);    double **m;
     hess[i][i]=hessii(p,ftolhess,i,delti);  
     /*printf(" %f ",p[i]);*/    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     /*printf(" %lf ",hess[i][i]);*/    if (!m) nrerror("allocation failure 1 in matrix()");
   }    m += NR_END;
      m -= nrl;
   for (i=1;i<=npar;i++) {  
     for (j=1;j<=npar;j++)  {    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       if (j>i) {    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
         printf(".%d%d",i,j);fflush(stdout);    m[nrl] += NR_END;
         hess[i][j]=hessij(p,delti,i,j);    m[nrl] -= ncl;
         hess[j][i]=hess[i][j];      
         /*printf(" %lf ",hess[i][j]);*/    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
       }    return m;
     }    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
   }  m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
   printf("\n");  that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
      */
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");  }
    
   a=matrix(1,npar,1,npar);  /*************************free matrix ************************/
   y=matrix(1,npar,1,npar);  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   x=vector(1,npar);  {
   indx=ivector(1,npar);    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   for (i=1;i<=npar;i++)    free((FREE_ARG)(m+nrl-NR_END));
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];  }
   ludcmp(a,npar,indx,&pd);  
   /******************* ma3x *******************************/
   for (j=1;j<=npar;j++) {  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
     for (i=1;i<=npar;i++) x[i]=0;  {
     x[j]=1;    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
     lubksb(a,npar,indx,x);    double ***m;
     for (i=1;i<=npar;i++){  
       matcov[i][j]=x[i];    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     }    if (!m) nrerror("allocation failure 1 in matrix()");
   }    m += NR_END;
     m -= nrl;
   printf("\n#Hessian matrix#\n");  
   for (i=1;i<=npar;i++) {    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     for (j=1;j<=npar;j++) {    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
       printf("%.3e ",hess[i][j]);    m[nrl] += NR_END;
     }    m[nrl] -= ncl;
     printf("\n");  
   }    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   
   /* Recompute Inverse */    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
   for (i=1;i<=npar;i++)    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];    m[nrl][ncl] += NR_END;
   ludcmp(a,npar,indx,&pd);    m[nrl][ncl] -= nll;
     for (j=ncl+1; j<=nch; j++) 
   /*  printf("\n#Hessian matrix recomputed#\n");      m[nrl][j]=m[nrl][j-1]+nlay;
     
   for (j=1;j<=npar;j++) {    for (i=nrl+1; i<=nrh; i++) {
     for (i=1;i<=npar;i++) x[i]=0;      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
     x[j]=1;      for (j=ncl+1; j<=nch; j++) 
     lubksb(a,npar,indx,x);        m[i][j]=m[i][j-1]+nlay;
     for (i=1;i<=npar;i++){    }
       y[i][j]=x[i];    return m; 
       printf("%.3e ",y[i][j]);    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
     }             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
     printf("\n");    */
   }  }
   */  
   /*************************free ma3x ************************/
   free_matrix(a,1,npar,1,npar);  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
   free_matrix(y,1,npar,1,npar);  {
   free_vector(x,1,npar);    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
   free_ivector(indx,1,npar);    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   free_matrix(hess,1,npar,1,npar);    free((FREE_ARG)(m+nrl-NR_END));
   }
   
 }  /*************** function subdirf ***********/
   char *subdirf(char fileres[])
 /*************** hessian matrix ****************/  {
 double hessii( double x[], double delta, int theta, double delti[])    /* Caution optionfilefiname is hidden */
 {    strcpy(tmpout,optionfilefiname);
   int i;    strcat(tmpout,"/"); /* Add to the right */
   int l=1, lmax=20;    strcat(tmpout,fileres);
   double k1,k2;    return tmpout;
   double p2[NPARMAX+1];  }
   double res;  
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;  /*************** function subdirf2 ***********/
   double fx;  char *subdirf2(char fileres[], char *preop)
   int k=0,kmax=10;  {
   double l1;    
     /* Caution optionfilefiname is hidden */
   fx=func(x);    strcpy(tmpout,optionfilefiname);
   for (i=1;i<=npar;i++) p2[i]=x[i];    strcat(tmpout,"/");
   for(l=0 ; l <=lmax; l++){    strcat(tmpout,preop);
     l1=pow(10,l);    strcat(tmpout,fileres);
     delts=delt;    return tmpout;
     for(k=1 ; k <kmax; k=k+1){  }
       delt = delta*(l1*k);  
       p2[theta]=x[theta] +delt;  /*************** function subdirf3 ***********/
       k1=func(p2)-fx;  char *subdirf3(char fileres[], char *preop, char *preop2)
       p2[theta]=x[theta]-delt;  {
       k2=func(p2)-fx;    
       /*res= (k1-2.0*fx+k2)/delt/delt; */    /* Caution optionfilefiname is hidden */
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */    strcpy(tmpout,optionfilefiname);
          strcat(tmpout,"/");
 #ifdef DEBUG    strcat(tmpout,preop);
       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);    strcat(tmpout,preop2);
 #endif    strcat(tmpout,fileres);
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */    return tmpout;
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){  }
         k=kmax;  
       }  /***************** f1dim *************************/
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */  extern int ncom; 
         k=kmax; l=lmax*10.;  extern double *pcom,*xicom;
       }  extern double (*nrfunc)(double []); 
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){   
         delts=delt;  double f1dim(double x) 
       }  { 
     }    int j; 
   }    double f;
   delti[theta]=delts;    double *xt; 
   return res;   
      xt=vector(1,ncom); 
 }    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
     f=(*nrfunc)(xt); 
 double hessij( double x[], double delti[], int thetai,int thetaj)    free_vector(xt,1,ncom); 
 {    return f; 
   int i;  } 
   int l=1, l1, lmax=20;  
   double k1,k2,k3,k4,res,fx;  /*****************brent *************************/
   double p2[NPARMAX+1];  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
   int k;  { 
     int iter; 
   fx=func(x);    double a,b,d,etemp;
   for (k=1; k<=2; k++) {    double fu=0,fv,fw,fx;
     for (i=1;i<=npar;i++) p2[i]=x[i];    double ftemp;
     p2[thetai]=x[thetai]+delti[thetai]/k;    double p,q,r,tol1,tol2,u,v,w,x,xm; 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    double e=0.0; 
     k1=func(p2)-fx;   
      a=(ax < cx ? ax : cx); 
     p2[thetai]=x[thetai]+delti[thetai]/k;    b=(ax > cx ? ax : cx); 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    x=w=v=bx; 
     k2=func(p2)-fx;    fw=fv=fx=(*f)(x); 
      for (iter=1;iter<=ITMAX;iter++) { 
     p2[thetai]=x[thetai]-delti[thetai]/k;      xm=0.5*(a+b); 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
     k3=func(p2)-fx;      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
        printf(".");fflush(stdout);
     p2[thetai]=x[thetai]-delti[thetai]/k;      fprintf(ficlog,".");fflush(ficlog);
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;  #ifdef DEBUG
     k4=func(p2)-fx;      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);
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */      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);
 #ifdef DEBUG      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);  #endif
 #endif      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
   }        *xmin=x; 
   return res;        return fx; 
 }      } 
       ftemp=fu;
 /************** Inverse of matrix **************/      if (fabs(e) > tol1) { 
 void ludcmp(double **a, int n, int *indx, double *d)        r=(x-w)*(fx-fv); 
 {        q=(x-v)*(fx-fw); 
   int i,imax,j,k;        p=(x-v)*q-(x-w)*r; 
   double big,dum,sum,temp;        q=2.0*(q-r); 
   double *vv;        if (q > 0.0) p = -p; 
          q=fabs(q); 
   vv=vector(1,n);        etemp=e; 
   *d=1.0;        e=d; 
   for (i=1;i<=n;i++) {        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
     big=0.0;          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
     for (j=1;j<=n;j++)        else { 
       if ((temp=fabs(a[i][j])) > big) big=temp;          d=p/q; 
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");          u=x+d; 
     vv[i]=1.0/big;          if (u-a < tol2 || b-u < tol2) 
   }            d=SIGN(tol1,xm-x); 
   for (j=1;j<=n;j++) {        } 
     for (i=1;i<j;i++) {      } else { 
       sum=a[i][j];        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];      } 
       a[i][j]=sum;      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
     }      fu=(*f)(u); 
     big=0.0;      if (fu <= fx) { 
     for (i=j;i<=n;i++) {        if (u >= x) a=x; else b=x; 
       sum=a[i][j];        SHFT(v,w,x,u) 
       for (k=1;k<j;k++)          SHFT(fv,fw,fx,fu) 
         sum -= a[i][k]*a[k][j];          } else { 
       a[i][j]=sum;            if (u < x) a=u; else b=u; 
       if ( (dum=vv[i]*fabs(sum)) >= big) {            if (fu <= fw || w == x) { 
         big=dum;              v=w; 
         imax=i;              w=u; 
       }              fv=fw; 
     }              fw=fu; 
     if (j != imax) {            } else if (fu <= fv || v == x || v == w) { 
       for (k=1;k<=n;k++) {              v=u; 
         dum=a[imax][k];              fv=fu; 
         a[imax][k]=a[j][k];            } 
         a[j][k]=dum;          } 
       }    } 
       *d = -(*d);    nrerror("Too many iterations in brent"); 
       vv[imax]=vv[j];    *xmin=x; 
     }    return fx; 
     indx[j]=imax;  } 
     if (a[j][j] == 0.0) a[j][j]=TINY;  
     if (j != n) {  /****************** mnbrak ***********************/
       dum=1.0/(a[j][j]);  
       for (i=j+1;i<=n;i++) a[i][j] *= dum;  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
     }              double (*func)(double)) 
   }  { 
   free_vector(vv,1,n);  /* Doesn't work */    double ulim,u,r,q, dum;
 ;    double fu; 
 }   
     *fa=(*func)(*ax); 
 void lubksb(double **a, int n, int *indx, double b[])    *fb=(*func)(*bx); 
 {    if (*fb > *fa) { 
   int i,ii=0,ip,j;      SHFT(dum,*ax,*bx,dum) 
   double sum;        SHFT(dum,*fb,*fa,dum) 
          } 
   for (i=1;i<=n;i++) {    *cx=(*bx)+GOLD*(*bx-*ax); 
     ip=indx[i];    *fc=(*func)(*cx); 
     sum=b[ip];    while (*fb > *fc) { 
     b[ip]=b[i];      r=(*bx-*ax)*(*fb-*fc); 
     if (ii)      q=(*bx-*cx)*(*fb-*fa); 
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
     else if (sum) ii=i;        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
     b[i]=sum;      ulim=(*bx)+GLIMIT*(*cx-*bx); 
   }      if ((*bx-u)*(u-*cx) > 0.0) { 
   for (i=n;i>=1;i--) {        fu=(*func)(u); 
     sum=b[i];      } else if ((*cx-u)*(u-ulim) > 0.0) { 
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];        fu=(*func)(u); 
     b[i]=sum/a[i][i];        if (fu < *fc) { 
   }          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
 }            SHFT(*fb,*fc,fu,(*func)(u)) 
             } 
 /************ Frequencies ********************/      } else if ((u-ulim)*(ulim-*cx) >= 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)        u=ulim; 
 {  /* Some frequencies */        fu=(*func)(u); 
        } else { 
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;        u=(*cx)+GOLD*(*cx-*bx); 
   double ***freq; /* Frequencies */        fu=(*func)(u); 
   double *pp;      } 
   double pos, k2, dateintsum=0,k2cpt=0;      SHFT(*ax,*bx,*cx,u) 
   FILE *ficresp;        SHFT(*fa,*fb,*fc,fu) 
   char fileresp[FILENAMELENGTH];        } 
    } 
   pp=vector(1,nlstate);  
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);  /*************** linmin ************************/
   strcpy(fileresp,"p");  
   strcat(fileresp,fileres);  int ncom; 
   if((ficresp=fopen(fileresp,"w"))==NULL) {  double *pcom,*xicom;
     printf("Problem with prevalence resultfile: %s\n", fileresp);  double (*nrfunc)(double []); 
     exit(0);   
   }  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);  { 
   j1=0;    double brent(double ax, double bx, double cx, 
                   double (*f)(double), double tol, double *xmin); 
   j=cptcoveff;    double f1dim(double x); 
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
                  double *fc, double (*func)(double)); 
   for(k1=1; k1<=j;k1++){    int j; 
     for(i1=1; i1<=ncodemax[k1];i1++){    double xx,xmin,bx,ax; 
       j1++;    double fx,fb,fa;
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);   
         scanf("%d", i);*/    ncom=n; 
       for (i=-1; i<=nlstate+ndeath; i++)      pcom=vector(1,n); 
         for (jk=-1; jk<=nlstate+ndeath; jk++)      xicom=vector(1,n); 
           for(m=agemin; m <= agemax+3; m++)    nrfunc=func; 
             freq[i][jk][m]=0;    for (j=1;j<=n;j++) { 
            pcom[j]=p[j]; 
       dateintsum=0;      xicom[j]=xi[j]; 
       k2cpt=0;    } 
       for (i=1; i<=imx; i++) {    ax=0.0; 
         bool=1;    xx=1.0; 
         if  (cptcovn>0) {    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
           for (z1=1; z1<=cptcoveff; z1++)    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])  #ifdef DEBUG
               bool=0;    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
         }    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
         if (bool==1) {  #endif
           for(m=firstpass; m<=lastpass; m++){    for (j=1;j<=n;j++) { 
             k2=anint[m][i]+(mint[m][i]/12.);      xi[j] *= xmin; 
             if ((k2>=dateprev1) && (k2<=dateprev2)) {      p[j] += xi[j]; 
               if(agev[m][i]==0) agev[m][i]=agemax+1;    } 
               if(agev[m][i]==1) agev[m][i]=agemax+2;    free_vector(xicom,1,n); 
               if (m<lastpass) {    free_vector(pcom,1,n); 
                 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];  
               }  char *asc_diff_time(long time_sec, char ascdiff[])
                {
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {    long sec_left, days, hours, minutes;
                 dateintsum=dateintsum+k2;    days = (time_sec) / (60*60*24);
                 k2cpt++;    sec_left = (time_sec) % (60*60*24);
               }    hours = (sec_left) / (60*60) ;
             }    sec_left = (sec_left) %(60*60);
           }    minutes = (sec_left) /60;
         }    sec_left = (sec_left) % (60);
       }    sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);  
            return ascdiff;
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);  }
   
       if  (cptcovn>0) {  /*************** powell ************************/
         fprintf(ficresp, "\n#********** Variable ");  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);              double (*func)(double [])) 
         fprintf(ficresp, "**********\n#");  { 
       }    void linmin(double p[], double xi[], int n, double *fret, 
       for(i=1; i<=nlstate;i++)                double (*func)(double [])); 
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);    int i,ibig,j; 
       fprintf(ficresp, "\n");    double del,t,*pt,*ptt,*xit;
          double fp,fptt;
       for(i=(int)agemin; i <= (int)agemax+3; i++){    double *xits;
         if(i==(int)agemax+3)    int niterf, itmp;
           printf("Total");  
         else    pt=vector(1,n); 
           printf("Age %d", i);    ptt=vector(1,n); 
         for(jk=1; jk <=nlstate ; jk++){    xit=vector(1,n); 
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    xits=vector(1,n); 
             pp[jk] += freq[jk][m][i];    *fret=(*func)(p); 
         }    for (j=1;j<=n;j++) pt[j]=p[j]; 
         for(jk=1; jk <=nlstate ; jk++){      rcurr_time = time(NULL);  
           for(m=-1, pos=0; m <=0 ; m++)    for (*iter=1;;++(*iter)) { 
             pos += freq[jk][m][i];      fp=(*fret); 
           if(pp[jk]>=1.e-10)      ibig=0; 
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);      del=0.0; 
           else      rlast_time=rcurr_time;
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);      /* (void) gettimeofday(&curr_time,&tzp); */
         }      rcurr_time = time(NULL);  
       curr_time = *localtime(&rcurr_time);
         for(jk=1; jk <=nlstate ; jk++){      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
             pp[jk] += freq[jk][m][i];  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
         }     for (i=1;i<=n;i++) {
         printf(" %d %.12f",i, p[i]);
         for(jk=1,pos=0; jk <=nlstate ; jk++)        fprintf(ficlog," %d %.12lf",i, p[i]);
           pos += pp[jk];        fprintf(ficrespow," %.12lf", p[i]);
         for(jk=1; jk <=nlstate ; jk++){      }
           if(pos>=1.e-5)      printf("\n");
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);      fprintf(ficlog,"\n");
           else      fprintf(ficrespow,"\n");fflush(ficrespow);
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);      if(*iter <=3){
           if( i <= (int) agemax){        tml = *localtime(&rcurr_time);
             if(pos>=1.e-5){        strcpy(strcurr,asctime(&tml));
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);  /*       asctime_r(&tm,strcurr); */
               probs[i][jk][j1]= pp[jk]/pos;        rforecast_time=rcurr_time; 
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/        itmp = strlen(strcurr);
             }        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
             else          strcurr[itmp-1]='\0';
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
           }        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
         }        for(niterf=10;niterf<=30;niterf+=10){
                  rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
         for(jk=-1; jk <=nlstate+ndeath; jk++)          forecast_time = *localtime(&rforecast_time);
           for(m=-1; m <=nlstate+ndeath; m++)  /*      asctime_r(&tmf,strfor); */
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);          strcpy(strfor,asctime(&forecast_time));
         if(i <= (int) agemax)          itmp = strlen(strfor);
           fprintf(ficresp,"\n");          if(strfor[itmp-1]=='\n')
         printf("\n");          strfor[itmp-1]='\0';
       }          printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
     }          fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
   }        }
   dateintmean=dateintsum/k2cpt;      }
        for (i=1;i<=n;i++) { 
   fclose(ficresp);        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);        fptt=(*fret); 
   free_vector(pp,1,nlstate);  #ifdef DEBUG
          printf("fret=%lf \n",*fret);
   /* End of Freq */        fprintf(ficlog,"fret=%lf \n",*fret);
 }  #endif
         printf("%d",i);fflush(stdout);
 /************ Prevalence ********************/        fprintf(ficlog,"%d",i);fflush(ficlog);
 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)        linmin(p,xit,n,fret,func); 
 {  /* Some frequencies */        if (fabs(fptt-(*fret)) > del) { 
            del=fabs(fptt-(*fret)); 
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;          ibig=i; 
   double ***freq; /* Frequencies */        } 
   double *pp;  #ifdef DEBUG
   double pos, k2;        printf("%d %.12e",i,(*fret));
         fprintf(ficlog,"%d %.12e",i,(*fret));
   pp=vector(1,nlstate);        for (j=1;j<=n;j++) {
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
            printf(" x(%d)=%.12e",j,xit[j]);
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
   j1=0;        }
          for(j=1;j<=n;j++) {
   j=cptcoveff;          printf(" p=%.12e",p[j]);
   if (cptcovn<1) {j=1;ncodemax[1]=1;}          fprintf(ficlog," p=%.12e",p[j]);
          }
   for(k1=1; k1<=j;k1++){        printf("\n");
     for(i1=1; i1<=ncodemax[k1];i1++){        fprintf(ficlog,"\n");
       j1++;  #endif
            } 
       for (i=-1; i<=nlstate+ndeath; i++)        if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
         for (jk=-1; jk<=nlstate+ndeath; jk++)    #ifdef DEBUG
           for(m=agemin; m <= agemax+3; m++)        int k[2],l;
             freq[i][jk][m]=0;        k[0]=1;
              k[1]=-1;
       for (i=1; i<=imx; i++) {        printf("Max: %.12e",(*func)(p));
         bool=1;        fprintf(ficlog,"Max: %.12e",(*func)(p));
         if  (cptcovn>0) {        for (j=1;j<=n;j++) {
           for (z1=1; z1<=cptcoveff; z1++)          printf(" %.12e",p[j]);
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])          fprintf(ficlog," %.12e",p[j]);
               bool=0;        }
         }        printf("\n");
         if (bool==1) {        fprintf(ficlog,"\n");
           for(m=firstpass; m<=lastpass; m++){        for(l=0;l<=1;l++) {
             k2=anint[m][i]+(mint[m][i]/12.);          for (j=1;j<=n;j++) {
             if ((k2>=dateprev1) && (k2<=dateprev2)) {            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
               if(agev[m][i]==0) agev[m][i]=agemax+1;            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
               if(agev[m][i]==1) agev[m][i]=agemax+2;            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
               if (m<lastpass) {          }
                 if (calagedate>0)          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
                   freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
                 else        }
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];  #endif
                 freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];  
               }  
             }        free_vector(xit,1,n); 
           }        free_vector(xits,1,n); 
         }        free_vector(ptt,1,n); 
       }        free_vector(pt,1,n); 
       for(i=(int)agemin; i <= (int)agemax+3; i++){        return; 
         for(jk=1; jk <=nlstate ; jk++){      } 
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
             pp[jk] += freq[jk][m][i];      for (j=1;j<=n;j++) { 
         }        ptt[j]=2.0*p[j]-pt[j]; 
         for(jk=1; jk <=nlstate ; jk++){        xit[j]=p[j]-pt[j]; 
           for(m=-1, pos=0; m <=0 ; m++)        pt[j]=p[j]; 
             pos += freq[jk][m][i];      } 
         }      fptt=(*func)(ptt); 
              if (fptt < fp) { 
         for(jk=1; jk <=nlstate ; jk++){        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)        if (t < 0.0) { 
             pp[jk] += freq[jk][m][i];          linmin(p,xit,n,fret,func); 
         }          for (j=1;j<=n;j++) { 
                    xi[j][ibig]=xi[j][n]; 
         for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];            xi[j][n]=xit[j]; 
                  }
         for(jk=1; jk <=nlstate ; jk++){      #ifdef DEBUG
           if( i <= (int) agemax){          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
             if(pos>=1.e-5){          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
               probs[i][jk][j1]= pp[jk]/pos;          for(j=1;j<=n;j++){
             }            printf(" %.12e",xit[j]);
           }            fprintf(ficlog," %.12e",xit[j]);
         }          }
                  printf("\n");
       }          fprintf(ficlog,"\n");
     }  #endif
   }        }
       } 
      } 
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);  } 
   free_vector(pp,1,nlstate);  
    /**** Prevalence limit (stable or period prevalence)  ****************/
 }  /* End of Freq */  
   double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
 /************* Waves Concatenation ***************/  {
     /* Computes the prevalence limit in each live state at age x by left multiplying the unit
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)       matrix by transitions matrix until convergence is reached */
 {  
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.    int i, ii,j,k;
      Death is a valid wave (if date is known).    double min, max, maxmin, maxmax,sumnew=0.;
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i    /* double **matprod2(); */ /* test */
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]    double **out, cov[NCOVMAX+1], **pmij();
      and mw[mi+1][i]. dh depends on stepm.    double **newm;
      */    double agefin, delaymax=50 ; /* Max number of years to converge */
   
   int i, mi, m;    for (ii=1;ii<=nlstate+ndeath;ii++)
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;      for (j=1;j<=nlstate+ndeath;j++){
      double sum=0., jmean=0.;*/        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       }
   int j, k=0,jk, ju, jl;  
   double sum=0.;     cov[1]=1.;
   jmin=1e+5;   
   jmax=-1;   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   jmean=0.;    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
   for(i=1; i<=imx; i++){      newm=savm;
     mi=0;      /* Covariates have to be included here again */
     m=firstpass;      cov[2]=agefin;
     while(s[m][i] <= nlstate){      
       if(s[m][i]>=1)      for (k=1; k<=cptcovn;k++) {
         mw[++mi][i]=m;        cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
       if(m >=lastpass)        /*printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtab[%d][Tvar[%d]]=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], ij, k, codtab[ij][Tvar[k]]);*/
         break;      }
       else      /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
         m++;      /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
     }/* end while */      /*   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] > nlstate){      
       mi++;     /* Death is another wave */      /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
       /* if(mi==0)  never been interviewed correctly before death */      /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
          /* Only death is a correct wave */      /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
       mw[mi][i]=m;      /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
     }      /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
       out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
     wav[i]=mi;      
     if(mi==0)      savm=oldm;
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);      oldm=newm;
   }      maxmax=0.;
       for(j=1;j<=nlstate;j++){
   for(i=1; i<=imx; i++){        min=1.;
     for(mi=1; mi<wav[i];mi++){        max=0.;
       if (stepm <=0)        for(i=1; i<=nlstate; i++) {
         dh[mi][i]=1;          sumnew=0;
       else{          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
         if (s[mw[mi+1][i]][i] > nlstate) {          prlim[i][j]= newm[i][j]/(1-sumnew);
           if (agedc[i] < 2*AGESUP) {          /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);          max=FMAX(max,prlim[i][j]);
           if(j==0) j=1;  /* Survives at least one month after exam */          min=FMIN(min,prlim[i][j]);
           k=k+1;        }
           if (j >= jmax) jmax=j;        maxmin=max-min;
           if (j <= jmin) jmin=j;        maxmax=FMAX(maxmax,maxmin);
           sum=sum+j;      }
           /*if (j<0) printf("j=%d num=%d \n",j,i); */      if(maxmax < ftolpl){
           }        return prlim;
         }      }
         else{    }
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));  }
           k=k+1;  
           if (j >= jmax) jmax=j;  /*************** transition probabilities ***************/ 
           else if (j <= jmin)jmin=j;  
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
           sum=sum+j;  {
         }    /* According to parameters values stored in x and the covariate's values stored in cov,
         jk= j/stepm;       computes the probability to be observed in state j being in state i by appying the
         jl= j -jk*stepm;       model to the ncovmodel covariates (including constant and age).
         ju= j -(jk+1)*stepm;       lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
         if(jl <= -ju)       and, according on how parameters are entered, the position of the coefficient xij(nc) of the
           dh[mi][i]=jk;       ncth covariate in the global vector x is given by the formula:
         else       j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
           dh[mi][i]=jk+1;       j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
         if(dh[mi][i]==0)       Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
           dh[mi][i]=1; /* At least one step */       sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
       }       Outputs ps[i][j] the probability to be observed in j being in j according to
     }       the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
   }    */
   jmean=sum/k;    double s1, lnpijopii;
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);    /*double t34;*/
  }    int i,j,j1, nc, ii, jj;
 /*********** Tricode ****************************/  
 void tricode(int *Tvar, int **nbcode, int imx)      for(i=1; i<= nlstate; i++){
 {        for(j=1; j<i;j++){
   int Ndum[20],ij=1, k, j, i;          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
   int cptcode=0;            /*lnpijopii += param[i][j][nc]*cov[nc];*/
   cptcoveff=0;            lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
    /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
   for (k=0; k<19; k++) Ndum[k]=0;          }
   for (k=1; k<=7; k++) ncodemax[k]=0;          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
   /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {        }
     for (i=1; i<=imx; i++) {        for(j=i+1; j<=nlstate+ndeath;j++){
       ij=(int)(covar[Tvar[j]][i]);          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
       Ndum[ij]++;            /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/            lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
       if (ij > cptcode) cptcode=ij;  /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
     }          }
           ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
     for (i=0; i<=cptcode; i++) {        }
       if(Ndum[i]!=0) ncodemax[j]++;      }
     }      
     ij=1;      for(i=1; i<= nlstate; i++){
         s1=0;
         for(j=1; j<i; j++){
     for (i=1; i<=ncodemax[j]; i++) {          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
       for (k=0; k<=19; k++) {          /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
         if (Ndum[k] != 0) {        }
           nbcode[Tvar[j]][ij]=k;        for(j=i+1; j<=nlstate+ndeath; j++){
                    s1+=exp(ps[i][j]); /* In fact sums pij/pii */
           ij++;          /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
         }        }
         if (ij > ncodemax[j]) break;        /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
       }          ps[i][i]=1./(s1+1.);
     }        /* Computing other pijs */
   }          for(j=1; j<i; j++)
           ps[i][j]= exp(ps[i][j])*ps[i][i];
  for (k=0; k<19; k++) Ndum[k]=0;        for(j=i+1; j<=nlstate+ndeath; j++)
           ps[i][j]= exp(ps[i][j])*ps[i][i];
  for (i=1; i<=ncovmodel-2; i++) {        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
       ij=Tvar[i];      } /* end i */
       Ndum[ij]++;      
     }      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
         for(jj=1; jj<= nlstate+ndeath; jj++){
  ij=1;          ps[ii][jj]=0;
  for (i=1; i<=10; i++) {          ps[ii][ii]=1;
    if((Ndum[i]!=0) && (i<=ncovcol)){        }
      Tvaraff[ij]=i;      }
      ij++;      
    }      
  }      /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
        /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
     cptcoveff=ij-1;      /*  printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
 }      /*   } */
       /*   printf("\n "); */
 /*********** Health Expectancies ****************/      /* } */
       /* printf("\n ");printf("%lf ",cov[2]);*/
 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 )      /*
         for(i=1; i<= npar; i++) printf("%f ",x[i]);
 {        goto end;*/
   /* Health expectancies */      return ps;
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;  }
   double age, agelim, hf;  
   double ***p3mat,***varhe;  /**************** Product of 2 matrices ******************/
   double **dnewm,**doldm;  
   double *xp;  double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
   double **gp, **gm;  {
   double ***gradg, ***trgradg;    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
   int theta;       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
     /* in, b, out are matrice of pointers which should have been initialized 
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);       before: only the contents of out is modified. The function returns
   xp=vector(1,npar);       a pointer to pointers identical to out */
   dnewm=matrix(1,nlstate*2,1,npar);    int i, j, k;
   doldm=matrix(1,nlstate*2,1,nlstate*2);    for(i=nrl; i<= nrh; i++)
        for(k=ncolol; k<=ncoloh; k++){
   fprintf(ficreseij,"# Health expectancies\n");        out[i][k]=0.;
   fprintf(ficreseij,"# Age");        for(j=ncl; j<=nch; j++)
   for(i=1; i<=nlstate;i++)          out[i][k] +=in[i][j]*b[j][k];
     for(j=1; j<=nlstate;j++)      }
       fprintf(ficreseij," %1d-%1d (SE)",i,j);    return out;
   fprintf(ficreseij,"\n");  }
   
   if(estepm < stepm){  
     printf ("Problem %d lower than %d\n",estepm, stepm);  /************* Higher Matrix Product ***************/
   }  
   else  hstepm=estepm;    double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
   /* We compute the life expectancy from trapezoids spaced every estepm months  {
    * This is mainly to measure the difference between two models: for example    /* Computes the transition matrix starting at age 'age' over 
    * if stepm=24 months pijx are given only every 2 years and by summing them       'nhstepm*hstepm*stepm' months (i.e. until
    * we are calculating an estimate of the Life Expectancy assuming a linear       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
    * progression inbetween and thus overestimating or underestimating according       nhstepm*hstepm matrices. 
    * to the curvature of the survival function. If, for the same date, we       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
    * estimate the model with stepm=1 month, we can keep estepm to 24 months       (typically every 2 years instead of every month which is too big 
    * to compare the new estimate of Life expectancy with the same linear       for the memory).
    * hypothesis. A more precise result, taking into account a more precise       Model is determined by parameters x and covariates have to be 
    * curvature will be obtained if estepm is as small as stepm. */       included manually here. 
   
   /* 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, d, h, k;
      nstepm is the number of stepm from age to agelin.    double **out, cov[NCOVMAX+1];
      Look at hpijx to understand the reason of that which relies in memory size    double **newm;
      and note for a fixed period like estepm months */  
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the    /* Hstepm could be zero and should return the unit matrix */
      survival function given by stepm (the optimization length). Unfortunately it    for (i=1;i<=nlstate+ndeath;i++)
      means that if the survival funtion is printed only each two years of age and if      for (j=1;j<=nlstate+ndeath;j++){
      you sum them up and add 1 year (area under the trapezoids) you won't get the same        oldm[i][j]=(i==j ? 1.0 : 0.0);
      results. So we changed our mind and took the option of the best precision.        po[i][j][0]=(i==j ? 1.0 : 0.0);
   */      }
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     for(h=1; h <=nhstepm; h++){
   agelim=AGESUP;      for(d=1; d <=hstepm; d++){
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        newm=savm;
     /* nhstepm age range expressed in number of stepm */        /* Covariates have to be included here again */
     nstepm=(int) rint((agelim-age)*YEARM/stepm);        cov[1]=1.;
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
     /* if (stepm >= YEARM) hstepm=1;*/        for (k=1; k<=cptcovn;k++) 
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        for (k=1; k<=cptcovage;k++)
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     gp=matrix(0,nhstepm,1,nlstate*2);        for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
     gm=matrix(0,nhstepm,1,nlstate*2);          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   
     /* Computed by stepm unit matrices, product of hstepm matrices, stored  
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);          /*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, 
                      pmij(pmmij,cov,ncovmodel,x,nlstate));
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */        savm=oldm;
         oldm=newm;
     /* Computing Variances of health expectancies */      }
       for(i=1; i<=nlstate+ndeath; i++)
      for(theta=1; theta <=npar; theta++){        for(j=1;j<=nlstate+ndeath;j++) {
       for(i=1; i<=npar; i++){          po[i][j][h]=newm[i][j];
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
       }        }
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        /*printf("h=%d ",h);*/
      } /* end h */
       cptj=0;  /*     printf("\n H=%d \n",h); */
       for(j=1; j<= nlstate; j++){    return po;
         for(i=1; i<=nlstate; i++){  }
           cptj=cptj+1;  
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){  
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;  /*************** log-likelihood *************/
           }  double func( double *x)
         }  {
       }    int i, ii, j, k, mi, d, kk;
          double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
          double **out;
       for(i=1; i<=npar; i++)    double sw; /* Sum of weights */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    double lli; /* Individual log likelihood */
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      int s1, s2;
          double bbh, survp;
       cptj=0;    long ipmx;
       for(j=1; j<= nlstate; j++){    /*extern weight */
         for(i=1;i<=nlstate;i++){    /* We are differentiating ll according to initial status */
           cptj=cptj+1;    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){    /*for(i=1;i<imx;i++) 
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;      printf(" %d\n",s[4][i]);
           }    */
         }    cov[1]=1.;
       }  
       for(j=1; j<= nlstate*2; j++)    for(k=1; k<=nlstate; k++) ll[k]=0.;
         for(h=0; h<=nhstepm-1; h++){  
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    if(mle==1){
         }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
      }        /* Computes the values of the ncovmodel covariates of the model
               depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
 /* End theta */           Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
            to be observed in j being in i according to the model.
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);         */
         for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
      for(h=0; h<=nhstepm-1; h++)          cov[2+k]=covar[Tvar[k]][i];
       for(j=1; j<=nlstate*2;j++)        }
         for(theta=1; theta <=npar; theta++)        /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 
           trgradg[h][j][theta]=gradg[h][theta][j];           is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] 
                 has been calculated etc */
         for(mi=1; mi<= wav[i]-1; mi++){
      for(i=1;i<=nlstate*2;i++)          for (ii=1;ii<=nlstate+ndeath;ii++)
       for(j=1;j<=nlstate*2;j++)            for (j=1;j<=nlstate+ndeath;j++){
         varhe[i][j][(int)age] =0.;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               savm[ii][j]=(ii==j ? 1.0 : 0.0);
      printf("%d|",(int)age);fflush(stdout);            }
      for(h=0;h<=nhstepm-1;h++){          for(d=0; d<dh[mi][i]; d++){
       for(k=0;k<=nhstepm-1;k++){            newm=savm;
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);            for (kk=1; kk<=cptcovage;kk++) {
         for(i=1;i<=nlstate*2;i++)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
           for(j=1;j<=nlstate*2;j++)            }
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     }            savm=oldm;
     /* Computing expectancies */            oldm=newm;
     for(i=1; i<=nlstate;i++)          } /* end mult */
       for(j=1; j<=nlstate;j++)        
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;          /* But now since version 0.9 we anticipate for bias at large stepm.
                     * If stepm is larger than one month (smallest stepm) and if the exact delay 
 /* 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]);*/           * (in months) between two waves is not a multiple of stepm, we rounded to 
            * the nearest (and in case of equal distance, to the lowest) interval but now
         }           * we keep into memory the bias bh[mi][i] and also the previous matrix product
            * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
     fprintf(ficreseij,"%3.0f",age );           * probability in order to take into account the bias as a fraction of the way
     cptj=0;           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
     for(i=1; i<=nlstate;i++)           * -stepm/2 to stepm/2 .
       for(j=1; j<=nlstate;j++){           * For stepm=1 the results are the same as for previous versions of Imach.
         cptj++;           * For stepm > 1 the results are less biased than in previous versions. 
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );           */
       }          s1=s[mw[mi][i]][i];
     fprintf(ficreseij,"\n");          s2=s[mw[mi+1][i]][i];
              bbh=(double)bh[mi][i]/(double)stepm; 
     free_matrix(gm,0,nhstepm,1,nlstate*2);          /* bias bh is positive if real duration
     free_matrix(gp,0,nhstepm,1,nlstate*2);           * is higher than the multiple of stepm and negative otherwise.
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);           */
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          if( s2 > nlstate){ 
   }            /* i.e. if s2 is a death state and if the date of death is known 
   printf("\n");               then the contribution to the likelihood is the probability to 
                die between last step unit time and current  step unit time, 
   free_vector(xp,1,npar);               which is also equal to probability to die before dh 
   free_matrix(dnewm,1,nlstate*2,1,npar);               minus probability to die before dh-stepm . 
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);               In version up to 0.92 likelihood was computed
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);          as if date of death was unknown. Death was treated as any other
 }          health state: the date of the interview describes the actual state
           and not the date of a change in health state. The former idea was
 /************ Variance ******************/          to consider that at each interview the state was recorded
 void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm)          (healthy, disable or death) and IMaCh was corrected; but when we
 {          introduced the exact date of death then we should have modified
   /* Variance of health expectancies */          the contribution of an exact death to the likelihood. This new
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/          contribution is smaller and very dependent of the step unit
   double **newm;          stepm. It is no more the probability to die between last interview
   double **dnewm,**doldm;          and month of death but the probability to survive from last
   int i, j, nhstepm, hstepm, h, nstepm ;          interview up to one month before death multiplied by the
   int k, cptcode;          probability to die within a month. Thanks to Chris
   double *xp;          Jackson for correcting this bug.  Former versions increased
   double **gp, **gm;          mortality artificially. The bad side is that we add another loop
   double ***gradg, ***trgradg;          which slows down the processing. The difference can be up to 10%
   double ***p3mat;          lower mortality.
   double age,agelim, hf;            */
   int theta;            lli=log(out[s1][s2] - savm[s1][s2]);
   
   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");          } else if  (s2==-2) {
   for(i=1; i<=nlstate;i++)            for (j=1,survp=0. ; j<=nlstate; j++) 
     for(j=1; j<=nlstate;j++)              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);            /*survp += out[s1][j]; */
   fprintf(ficresvij,"\n");            lli= log(survp);
           }
   xp=vector(1,npar);          
   dnewm=matrix(1,nlstate,1,npar);          else if  (s2==-4) { 
   doldm=matrix(1,nlstate,1,nlstate);            for (j=3,survp=0. ; j<=nlstate; j++)  
                survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   if(estepm < stepm){            lli= log(survp); 
     printf ("Problem %d lower than %d\n",estepm, stepm);          } 
   }  
   else  hstepm=estepm;            else if  (s2==-5) { 
   /* For example we decided to compute the life expectancy with the smallest unit */            for (j=1,survp=0. ; j<=2; j++)  
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
      nhstepm is the number of hstepm from age to agelim            lli= log(survp); 
      nstepm is the number of stepm from age to agelin.          } 
      Look at hpijx to understand the reason of that which relies in memory size          
      and note for a fixed period like k years */          else{
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
      survival function given by stepm (the optimization length). Unfortunately it            /*  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 */
      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          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
      results. So we changed our mind and took the option of the best precision.          /*if(lli ==000.0)*/
   */          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */          ipmx +=1;
   agelim = AGESUP;          sw += weight[i];
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        } /* end of wave */
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */      } /* end of individual */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    }  else if(mle==2){
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     gp=matrix(0,nhstepm,1,nlstate);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     gm=matrix(0,nhstepm,1,nlstate);        for(mi=1; mi<= wav[i]-1; mi++){
           for (ii=1;ii<=nlstate+ndeath;ii++)
     for(theta=1; theta <=npar; theta++){            for (j=1;j<=nlstate+ndeath;j++){
       for(i=1; i<=npar; i++){ /* Computes gradient */              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         xp[i] = x[i] + (i==theta ?delti[theta]:0);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       }            }
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            for(d=0; d<=dh[mi][i]; d++){
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);            newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       if (popbased==1) {            for (kk=1; kk<=cptcovage;kk++) {
         for(i=1; i<=nlstate;i++)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
           prlim[i][i]=probs[(int)age][i][ij];            }
       }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       for(j=1; j<= nlstate; j++){            savm=oldm;
         for(h=0; h<=nhstepm; h++){            oldm=newm;
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)          } /* end mult */
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];        
         }          s1=s[mw[mi][i]][i];
       }          s2=s[mw[mi+1][i]][i];
              bbh=(double)bh[mi][i]/(double)stepm; 
       for(i=1; i<=npar; i++) /* Computes gradient */          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 */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          ipmx +=1;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            sw += weight[i];
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
          } /* end of wave */
       if (popbased==1) {      } /* end of individual */
         for(i=1; i<=nlstate;i++)    }  else if(mle==3){  /* exponential inter-extrapolation */
           prlim[i][i]=probs[(int)age][i][ij];      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for(mi=1; mi<= wav[i]-1; mi++){
       for(j=1; j<= nlstate; j++){          for (ii=1;ii<=nlstate+ndeath;ii++)
         for(h=0; h<=nhstepm; h++){            for (j=1;j<=nlstate+ndeath;j++){
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         }            }
       }          for(d=0; d<dh[mi][i]; d++){
             newm=savm;
       for(j=1; j<= nlstate; j++)            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         for(h=0; h<=nhstepm; h++){            for (kk=1; kk<=cptcovage;kk++) {
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         }            }
     } /* End theta */            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);            savm=oldm;
             oldm=newm;
     for(h=0; h<=nhstepm; h++)          } /* end mult */
       for(j=1; j<=nlstate;j++)        
         for(theta=1; theta <=npar; theta++)          s1=s[mw[mi][i]][i];
           trgradg[h][j][theta]=gradg[h][theta][j];          s2=s[mw[mi+1][i]][i];
           bbh=(double)bh[mi][i]/(double)stepm; 
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */          lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
     for(i=1;i<=nlstate;i++)          ipmx +=1;
       for(j=1;j<=nlstate;j++)          sw += weight[i];
         vareij[i][j][(int)age] =0.;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         } /* end of wave */
     for(h=0;h<=nhstepm;h++){      } /* end of individual */
       for(k=0;k<=nhstepm;k++){    }else if (mle==4){  /* ml=4 no inter-extrapolation */
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for(i=1;i<=nlstate;i++)        for(mi=1; mi<= wav[i]-1; mi++){
           for(j=1;j<=nlstate;j++)          for (ii=1;ii<=nlstate+ndeath;ii++)
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;            for (j=1;j<=nlstate+ndeath;j++){
       }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             }
     fprintf(ficresvij,"%.0f ",age );          for(d=0; d<dh[mi][i]; d++){
     for(i=1; i<=nlstate;i++)            newm=savm;
       for(j=1; j<=nlstate;j++){            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);            for (kk=1; kk<=cptcovage;kk++) {
       }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     fprintf(ficresvij,"\n");            }
     free_matrix(gp,0,nhstepm,1,nlstate);          
     free_matrix(gm,0,nhstepm,1,nlstate);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);            savm=oldm;
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            oldm=newm;
   } /* End age */          } /* end mult */
          
   free_vector(xp,1,npar);          s1=s[mw[mi][i]][i];
   free_matrix(doldm,1,nlstate,1,npar);          s2=s[mw[mi+1][i]][i];
   free_matrix(dnewm,1,nlstate,1,nlstate);          if( s2 > nlstate){ 
             lli=log(out[s1][s2] - savm[s1][s2]);
 }          }else{
             lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
 /************ Variance of prevlim ******************/          }
 void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)          ipmx +=1;
 {          sw += weight[i];
   /* Variance of prevalence limit */          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/  /*      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 **newm;        } /* end of wave */
   double **dnewm,**doldm;      } /* end of individual */
   int i, j, nhstepm, hstepm;    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
   int k, cptcode;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   double *xp;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   double *gp, *gm;        for(mi=1; mi<= wav[i]-1; mi++){
   double **gradg, **trgradg;          for (ii=1;ii<=nlstate+ndeath;ii++)
   double age,agelim;            for (j=1;j<=nlstate+ndeath;j++){
   int theta;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                  savm[ii][j]=(ii==j ? 1.0 : 0.0);
   fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n");            }
   fprintf(ficresvpl,"# Age");          for(d=0; d<dh[mi][i]; d++){
   for(i=1; i<=nlstate;i++)            newm=savm;
       fprintf(ficresvpl," %1d-%1d",i,i);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   fprintf(ficresvpl,"\n");            for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   xp=vector(1,npar);            }
   dnewm=matrix(1,nlstate,1,npar);          
   doldm=matrix(1,nlstate,1,nlstate);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   hstepm=1*YEARM; /* Every year of age */            savm=oldm;
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */            oldm=newm;
   agelim = AGESUP;          } /* end mult */
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          s1=s[mw[mi][i]][i];
     if (stepm >= YEARM) hstepm=1;          s2=s[mw[mi+1][i]][i];
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
     gradg=matrix(1,npar,1,nlstate);          ipmx +=1;
     gp=vector(1,nlstate);          sw += weight[i];
     gm=vector(1,nlstate);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
     for(theta=1; theta <=npar; theta++){        } /* end of wave */
       for(i=1; i<=npar; i++){ /* Computes gradient */      } /* end of individual */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    } /* End of if */
       }    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
       for(i=1;i<=nlstate;i++)    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
         gp[i] = prlim[i][i];    return -l;
      }
       for(i=1; i<=npar; i++) /* Computes gradient */  
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  /*************** log-likelihood *************/
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  double funcone( double *x)
       for(i=1;i<=nlstate;i++)  {
         gm[i] = prlim[i][i];    /* Same as likeli but slower because of a lot of printf and if */
     int i, ii, j, k, mi, d, kk;
       for(i=1;i<=nlstate;i++)    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];    double **out;
     } /* End theta */    double lli; /* Individual log likelihood */
     double llt;
     trgradg =matrix(1,nlstate,1,npar);    int s1, s2;
     double bbh, survp;
     for(j=1; j<=nlstate;j++)    /*extern weight */
       for(theta=1; theta <=npar; theta++)    /* We are differentiating ll according to initial status */
         trgradg[j][theta]=gradg[theta][j];    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     /*for(i=1;i<imx;i++) 
     for(i=1;i<=nlstate;i++)      printf(" %d\n",s[4][i]);
       varpl[i][(int)age] =0.;    */
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);    cov[1]=1.;
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);  
     for(i=1;i<=nlstate;i++)    for(k=1; k<=nlstate; k++) ll[k]=0.;
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */  
     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     fprintf(ficresvpl,"%.0f ",age );      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     for(i=1; i<=nlstate;i++)      for(mi=1; mi<= wav[i]-1; mi++){
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));        for (ii=1;ii<=nlstate+ndeath;ii++)
     fprintf(ficresvpl,"\n");          for (j=1;j<=nlstate+ndeath;j++){
     free_vector(gp,1,nlstate);            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     free_vector(gm,1,nlstate);            savm[ii][j]=(ii==j ? 1.0 : 0.0);
     free_matrix(gradg,1,npar,1,nlstate);          }
     free_matrix(trgradg,1,nlstate,1,npar);        for(d=0; d<dh[mi][i]; d++){
   } /* End age */          newm=savm;
           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   free_vector(xp,1,npar);          for (kk=1; kk<=cptcovage;kk++) {
   free_matrix(doldm,1,nlstate,1,npar);            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   free_matrix(dnewm,1,nlstate,1,nlstate);          }
           /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
 }          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                        1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 /************ Variance of one-step probabilities  ******************/          /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
 void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)          /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
 {          savm=oldm;
   int i, j,  i1, k1, l1;          oldm=newm;
   int k2, l2, j1,  z1;        } /* end mult */
   int k=0,l, cptcode;        
   int first=1;        s1=s[mw[mi][i]][i];
   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2;        s2=s[mw[mi+1][i]][i];
   double **dnewm,**doldm;        bbh=(double)bh[mi][i]/(double)stepm; 
   double *xp;        /* bias is positive if real duration
   double *gp, *gm;         * is higher than the multiple of stepm and negative otherwise.
   double **gradg, **trgradg;         */
   double **mu;        if( s2 > nlstate && (mle <5) ){  /* Jackson */
   double age,agelim, cov[NCOVMAX];          lli=log(out[s1][s2] - savm[s1][s2]);
   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */        } else if  (s2==-2) {
   int theta;          for (j=1,survp=0. ; j<=nlstate; j++) 
   char fileresprob[FILENAMELENGTH];            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   char fileresprobcov[FILENAMELENGTH];          lli= log(survp);
   char fileresprobcor[FILENAMELENGTH];        }else if (mle==1){
           lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   double ***varpij;        } 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 */
   strcpy(fileresprob,"prob");        } else if(mle==3){  /* exponential inter-extrapolation */
   strcat(fileresprob,fileres);          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 */
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {        } else if (mle==4){  /* mle=4 no inter-extrapolation */
     printf("Problem with resultfile: %s\n", fileresprob);          lli=log(out[s1][s2]); /* Original formula */
   }        } else{  /* mle=0 back to 1 */
   strcpy(fileresprobcov,"probcov");          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   strcat(fileresprobcov,fileres);          /*lli=log(out[s1][s2]); */ /* Original formula */
   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {        } /* End of if */
     printf("Problem with resultfile: %s\n", fileresprobcov);        ipmx +=1;
   }        sw += weight[i];
   strcpy(fileresprobcor,"probcor");        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   strcat(fileresprobcor,fileres);        /*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]); */
   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {        if(globpr){
     printf("Problem with resultfile: %s\n", fileresprobcor);          fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
   }   %11.6f %11.6f %11.6f ", \
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
              llt +=ll[k]*gipmx/gsw;
   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
   fprintf(ficresprob,"# Age");          }
   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");          fprintf(ficresilk," %10.6f\n", -llt);
   fprintf(ficresprobcov,"# Age");        }
   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");      } /* end of wave */
   fprintf(ficresprobcov,"# Age");    } /* end of individual */
     for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   for(i=1; i<=nlstate;i++)    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     for(j=1; j<=(nlstate+ndeath);j++){    if(globpr==0){ /* First time we count the contributions and weights */
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);      gipmx=ipmx;
       fprintf(ficresprobcov," p%1d-%1d ",i,j);      gsw=sw;
       fprintf(ficresprobcor," p%1d-%1d ",i,j);    }
     }      return -l;
   fprintf(ficresprob,"\n");  }
   fprintf(ficresprobcov,"\n");  
   fprintf(ficresprobcor,"\n");  
   xp=vector(1,npar);  /*************** function likelione ***********/
   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));  {
   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);    /* This routine should help understanding what is done with 
   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);       the selection of individuals/waves and
   first=1;       to check the exact contribution to the likelihood.
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {       Plotting could be done.
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);     */
     exit(0);    int k;
   }  
   else{    if(*globpri !=0){ /* Just counts and sums, no printings */
     fprintf(ficgp,"\n# Routine varprob");      strcpy(fileresilk,"ilk"); 
   }      strcat(fileresilk,fileres);
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
     printf("Problem with html file: %s\n", optionfilehtm);        printf("Problem with resultfile: %s\n", fileresilk);
     exit(0);        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
   }      }
   else{      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(fichtm,"\n<H2> Computing matrix of variance-covariance of step probabilities</h2>\n");      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
     fprintf(fichtm,"\n<br> We 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");      /*  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(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");      for(k=1; k<=nlstate; k++) 
         fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
   }      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
   cov[1]=1;    }
   j=cptcoveff;  
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    *fretone=(*funcone)(p);
   j1=0;    if(*globpri !=0){
   for(k1=1; k1<=1;k1++){      fclose(ficresilk);
     for(i1=1; i1<=ncodemax[k1];i1++){      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
     j1++;      fflush(fichtm); 
     } 
     if  (cptcovn>0) {    return;
       fprintf(ficresprob, "\n#********** Variable ");  }
       fprintf(ficresprobcov, "\n#********** Variable ");  
       fprintf(ficgp, "\n#********** Variable ");  
       fprintf(fichtm, "\n<h4>********** Variable</h4>\n ");  /*********** Maximum Likelihood Estimation ***************/
       fprintf(ficresprobcor, "\n#********** Variable ");  
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
       fprintf(ficresprob, "**********\n#");  {
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    int i,j, iter;
       fprintf(ficresprobcov, "**********\n#");    double **xi;
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    double fret;
       fprintf(ficgp, "**********\n#");    double fretone; /* Only one call to likelihood */
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    /*  char filerespow[FILENAMELENGTH];*/
       fprintf(ficgp, "**********\n#");    xi=matrix(1,npar,1,npar);
       for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    for (i=1;i<=npar;i++)
       fprintf(fichtm, "**********\n#");      for (j=1;j<=npar;j++)
     }        xi[i][j]=(i==j ? 1.0 : 0.0);
        printf("Powell\n");  fprintf(ficlog,"Powell\n");
       for (age=bage; age<=fage; age ++){    strcpy(filerespow,"pow"); 
         cov[2]=age;    strcat(filerespow,fileres);
         for (k=1; k<=cptcovn;k++) {    if((ficrespow=fopen(filerespow,"w"))==NULL) {
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];      printf("Problem with resultfile: %s\n", filerespow);
         }      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    }
         for (k=1; k<=cptcovprod;k++)    fprintf(ficrespow,"# Powell\n# iter -2*LL");
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    for (i=1;i<=nlstate;i++)
              for(j=1;j<=nlstate+ndeath;j++)
         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);    fprintf(ficrespow,"\n");
         gp=vector(1,(nlstate)*(nlstate+ndeath));  
         gm=vector(1,(nlstate)*(nlstate+ndeath));    powell(p,xi,npar,ftol,&iter,&fret,func);
      
         for(theta=1; theta <=npar; theta++){    free_matrix(xi,1,npar,1,npar);
           for(i=1; i<=npar; i++)    fclose(ficrespow);
             xp[i] = x[i] + (i==theta ?delti[theta]:0);    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
              fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
           pmij(pmmij,cov,ncovmodel,xp,nlstate);    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
            
           k=0;  }
           for(i=1; i<= (nlstate); i++){  
             for(j=1; j<=(nlstate+ndeath);j++){  /**** Computes Hessian and covariance matrix ***/
               k=k+1;  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
               gp[k]=pmmij[i][j];  {
             }    double  **a,**y,*x,pd;
           }    double **hess;
              int i, j,jk;
           for(i=1; i<=npar; i++)    int *indx;
             xp[i] = x[i] - (i==theta ?delti[theta]:0);  
        double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
           pmij(pmmij,cov,ncovmodel,xp,nlstate);    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
           k=0;    void lubksb(double **a, int npar, int *indx, double b[]) ;
           for(i=1; i<=(nlstate); i++){    void ludcmp(double **a, int npar, int *indx, double *d) ;
             for(j=1; j<=(nlstate+ndeath);j++){    double gompertz(double p[]);
               k=k+1;    hess=matrix(1,npar,1,npar);
               gm[k]=pmmij[i][j];  
             }    printf("\nCalculation of the hessian matrix. Wait...\n");
           }    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
          for (i=1;i<=npar;i++){
           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)      printf("%d",i);fflush(stdout);
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];        fprintf(ficlog,"%d",i);fflush(ficlog);
         }     
        hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)      
           for(theta=1; theta <=npar; theta++)      /*  printf(" %f ",p[i]);
             trgradg[j][theta]=gradg[theta][j];          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
            }
         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);    
         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);    for (i=1;i<=npar;i++) {
              for (j=1;j<=npar;j++)  {
         pmij(pmmij,cov,ncovmodel,x,nlstate);        if (j>i) { 
                  printf(".%d%d",i,j);fflush(stdout);
         k=0;          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
         for(i=1; i<=(nlstate); i++){          hess[i][j]=hessij(p,delti,i,j,func,npar);
           for(j=1; j<=(nlstate+ndeath);j++){          
             k=k+1;          hess[j][i]=hess[i][j];    
             mu[k][(int) age]=pmmij[i][j];          /*printf(" %lf ",hess[i][j]);*/
           }        }
         }      }
         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)    }
           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)    printf("\n");
             varpij[i][j][(int)age] = doldm[i][j];    fprintf(ficlog,"\n");
   
         /*printf("\n%d ",(int)age);    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
      for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));    
      }*/    a=matrix(1,npar,1,npar);
     y=matrix(1,npar,1,npar);
         fprintf(ficresprob,"\n%d ",(int)age);    x=vector(1,npar);
         fprintf(ficresprobcov,"\n%d ",(int)age);    indx=ivector(1,npar);
         fprintf(ficresprobcor,"\n%d ",(int)age);    for (i=1;i<=npar;i++)
       for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)    ludcmp(a,npar,indx,&pd);
           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));  
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){    for (j=1;j<=npar;j++) {
           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);      for (i=1;i<=npar;i++) x[i]=0;
           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);      x[j]=1;
         }      lubksb(a,npar,indx,x);
         i=0;      for (i=1;i<=npar;i++){ 
         for (k=1; k<=(nlstate);k++){        matcov[i][j]=x[i];
           for (l=1; l<=(nlstate+ndeath);l++){      }
             i=i++;    }
             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);  
             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);    printf("\n#Hessian matrix#\n");
             for (j=1; j<=i;j++){    fprintf(ficlog,"\n#Hessian matrix#\n");
               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);    for (i=1;i<=npar;i++) { 
               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));      for (j=1;j<=npar;j++) { 
             }        printf("%.3e ",hess[i][j]);
           }        fprintf(ficlog,"%.3e ",hess[i][j]);
         }/* end of loop for state */      }
       } /* end of loop for age */      printf("\n");
         /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/      fprintf(ficlog,"\n");
       for (k1=1; k1<=(nlstate);k1++){    }
         for (l1=1; l1<=(nlstate+ndeath);l1++){  
           if(l1==k1) continue;    /* Recompute Inverse */
           i=(k1-1)*(nlstate+ndeath)+l1;    for (i=1;i<=npar;i++)
           for (k2=1; k2<=(nlstate);k2++){      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
             for (l2=1; l2<=(nlstate+ndeath);l2++){    ludcmp(a,npar,indx,&pd);
               if(l2==k2) continue;  
               j=(k2-1)*(nlstate+ndeath)+l2;    /*  printf("\n#Hessian matrix recomputed#\n");
               if(j<=i) continue;  
               for (age=bage; age<=fage; age ++){    for (j=1;j<=npar;j++) {
                 if ((int)age %5==0){      for (i=1;i<=npar;i++) x[i]=0;
                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;      x[j]=1;
                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;      lubksb(a,npar,indx,x);
                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;      for (i=1;i<=npar;i++){ 
                   mu1=mu[i][(int) age]/stepm*YEARM ;        y[i][j]=x[i];
                   mu2=mu[j][(int) age]/stepm*YEARM;        printf("%.3e ",y[i][j]);
                   /* Computing eigen value of matrix of covariance */        fprintf(ficlog,"%.3e ",y[i][j]);
                   lc1=(v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12));      }
                   lc2=(v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12));      printf("\n");
                   printf("Var %.4e %.4e cov %.4e Eigen %.3e %.3e\n",v1,v2,cv12,lc1,lc2);      fprintf(ficlog,"\n");
                   /* Eigen vectors */    }
                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));    */
                   v21=sqrt(1.-v11*v11);  
                   v12=-v21;    free_matrix(a,1,npar,1,npar);
                   v22=v11;    free_matrix(y,1,npar,1,npar);
                   /*printf(fignu*/    free_vector(x,1,npar);
                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */    free_ivector(indx,1,npar);
                   /* mu2+ v21*lc1*cost + v21*lc2*sin(t) */    free_matrix(hess,1,npar,1,npar);
                   if(first==1){  
                     first=0;  
                     fprintf(ficgp,"\nset parametric;set nolabel");  }
                     fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k2,l2,k1,l1);  
                     fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");  /*************** hessian matrix ****************/
                     fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%1d%1d-%1d%1d.png\">varpijgr%s%1d%1d-%1d%1d.png</A>, ",k2,l2,k1,l1,optionfilefiname,k2,l2,k1,l1,optionfilefiname,k2,l2,k1,l1);  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
                     fprintf(fichtm,"\n<br><img src=\"varpijgr%s%1d%1d-%1d%1d.png\">, ",optionfilefiname,k2,l2,k1,l1);  {
                     fprintf(ficgp,"\nset out \"varpijgr%s%1d%1d-%1d%1d.png\"",optionfilefiname,k2,l2,k1,l1);    int i;
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);    int l=1, lmax=20;
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);    double k1,k2;
                     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)) t \"%d\"",\    double p2[MAXPARM+1]; /* identical to x */
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \    double res;
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
                   }else{    double fx;
                     first=0;    int k=0,kmax=10;
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);    double l1;
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);  
                     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)) t \"%d\"",\    fx=func(x);
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \    for (i=1;i<=npar;i++) p2[i]=x[i];
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);    for(l=0 ; l <=lmax; l++){  /* Enlarging the zone around the Maximum */
                   }/* if first */      l1=pow(10,l);
                 } /* age mod 5 */      delts=delt;
               } /* end loop age */      for(k=1 ; k <kmax; k=k+1){
               fprintf(ficgp,"\nset out \"varpijgr%s%1d%1d-%1d%1d.png\";replot;",optionfilefiname,k2,l2,k1,l1);        delt = delta*(l1*k);
               first=1;        p2[theta]=x[theta] +delt;
             } /*l12 */        k1=func(p2)-fx;   /* Might be negative if too close to the theoretical maximum */
           } /* k12 */        p2[theta]=x[theta]-delt;
         } /*l1 */        k2=func(p2)-fx;
       }/* k1 */        /*res= (k1-2.0*fx+k2)/delt/delt; */
     } /* loop covariates */        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);        
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));  #ifdef DEBUGHESS
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));        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);
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);        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_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);  #endif
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
   }        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
   free_vector(xp,1,npar);          k=kmax;
   fclose(ficresprob);        }
   fclose(ficresprobcov);        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
   fclose(ficresprobcor);          k=kmax; l=lmax*10.;
   fclose(ficgp);        }
   fclose(fichtm);        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
 }          delts=delt;
         }
       }
 /******************* Printing html file ***********/    }
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \    delti[theta]=delts;
                   int lastpass, int stepm, int weightopt, char model[],\    return res; 
                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\    
                   int popforecast, int estepm ,\  }
                   double jprev1, double mprev1,double anprev1, \  
                   double jprev2, double mprev2,double anprev2){  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
   int jj1, k1, i1, cpt;  {
   /*char optionfilehtm[FILENAMELENGTH];*/    int i;
   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {    int l=1, l1, lmax=20;
     printf("Problem with %s \n",optionfilehtm), exit(0);    double k1,k2,k3,k4,res,fx;
   }    double p2[MAXPARM+1];
     int k;
    fprintf(fichtm,"<ul><li>Result files (first order: no variance)<br>\n  
  - 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    fx=func(x);
  - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n    for (k=1; k<=2; k++) {
  - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n      for (i=1;i<=npar;i++) p2[i]=x[i];
  - Life expectancies by age and initial health status (estepm=%2d months):      p2[thetai]=x[thetai]+delti[thetai]/k;
    <a href=\"e%s\">e%s</a> <br>\n</li>", \      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);      k1=func(p2)-fx;
     
  fprintf(fichtm,"\n<li> Result files (second order: variances)<br>\n      p2[thetai]=x[thetai]+delti[thetai]/k;
  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
  - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n      k2=func(p2)-fx;
  - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n    
  - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n      p2[thetai]=x[thetai]-delti[thetai]/k;
  - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
  - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n      k3=func(p2)-fx;
  - 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);    
       p2[thetai]=x[thetai]-delti[thetai]/k;
  if(popforecast==1) fprintf(fichtm,"\n      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n      k4=func(p2)-fx;
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
         <br>",fileres,fileres,fileres,fileres);  #ifdef DEBUG
  else      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(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(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);
 fprintf(fichtm," <li>Graphs</li><p>");  #endif
     }
  m=cptcoveff;    return res;
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}  }
   
  jj1=0;  /************** Inverse of matrix **************/
  for(k1=1; k1<=m;k1++){  void ludcmp(double **a, int n, int *indx, double *d) 
    for(i1=1; i1<=ncodemax[k1];i1++){  { 
      jj1++;    int i,imax,j,k; 
      if (cptcovn > 0) {    double big,dum,sum,temp; 
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");    double *vv; 
        for (cpt=1; cpt<=cptcoveff;cpt++)   
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);    vv=vector(1,n); 
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");    *d=1.0; 
      }    for (i=1;i<=n;i++) { 
      /* Pij */      big=0.0; 
      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>      for (j=1;j<=n;j++) 
 <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);            if ((temp=fabs(a[i][j])) > big) big=temp; 
      /* Quasi-incidences */      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
      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>      vv[i]=1.0/big; 
 <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);    } 
        /* Stable prevalence in each health state */    for (j=1;j<=n;j++) { 
        for(cpt=1; cpt<nlstate;cpt++){      for (i=1;i<j;i++) { 
          fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>        sum=a[i][j]; 
 <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
        }        a[i][j]=sum; 
     for(cpt=1; cpt<=nlstate;cpt++) {      } 
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident      big=0.0; 
 interval) in state (%d): v%s%d%d.png <br>      for (i=j;i<=n;i++) { 
 <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);          sum=a[i][j]; 
      }        for (k=1;k<j;k++) 
      for(cpt=1; cpt<=nlstate;cpt++) {          sum -= a[i][k]*a[k][j]; 
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>        a[i][j]=sum; 
 <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);        if ( (dum=vv[i]*fabs(sum)) >= big) { 
      }          big=dum; 
      fprintf(fichtm,"\n<br>- Total life expectancy by age and          imax=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);      } 
    }      if (j != imax) { 
  }        for (k=1;k<=n;k++) { 
 fclose(fichtm);          dum=a[imax][k]; 
 }          a[imax][k]=a[j][k]; 
           a[j][k]=dum; 
 /******************* Gnuplot file **************/        } 
 void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){        *d = -(*d); 
         vv[imax]=vv[j]; 
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;      } 
   int ng;      indx[j]=imax; 
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {      if (a[j][j] == 0.0) a[j][j]=TINY; 
     printf("Problem with file %s",optionfilegnuplot);      if (j != n) { 
   }        dum=1.0/(a[j][j]); 
         for (i=j+1;i<=n;i++) a[i][j] *= dum; 
 #ifdef windows      } 
     fprintf(ficgp,"cd \"%s\" \n",pathc);    } 
 #endif    free_vector(vv,1,n);  /* Doesn't work */
 m=pow(2,cptcoveff);  ;
    } 
  /* 1eme*/  
   for (cpt=1; cpt<= nlstate ; cpt ++) {  void lubksb(double **a, int n, int *indx, double b[]) 
    for (k1=1; k1<= m ; k1 ++) {  { 
     int i,ii=0,ip,j; 
 #ifdef windows    double sum; 
      fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);   
      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);    for (i=1;i<=n;i++) { 
 #endif      ip=indx[i]; 
 #ifdef unix      sum=b[ip]; 
 fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);      b[ip]=b[i]; 
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);      if (ii) 
 #endif        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
       else if (sum) ii=i; 
 for (i=1; i<= nlstate ; i ++) {      b[i]=sum; 
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    } 
   else fprintf(ficgp," \%%*lf (\%%*lf)");    for (i=n;i>=1;i--) { 
 }      sum=b[i]; 
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
     for (i=1; i<= nlstate ; i ++) {      b[i]=sum/a[i][i]; 
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    } 
   else fprintf(ficgp," \%%*lf (\%%*lf)");  } 
 }  
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);  void pstamp(FILE *fichier)
      for (i=1; i<= nlstate ; i ++) {  {
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
   else fprintf(ficgp," \%%*lf (\%%*lf)");  }
 }    
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));  /************ Frequencies ********************/
 #ifdef unix  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[])
 fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");  {  /* Some frequencies */
 #endif    
    }    int i, m, jk, k1,i1, j1, bool, z1,j;
   }    int first;
   /*2 eme*/    double ***freq; /* Frequencies */
     double *pp, **prop;
   for (k1=1; k1<= m ; k1 ++) {    double pos,posprop, k2, dateintsum=0,k2cpt=0;
     fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);    char fileresp[FILENAMELENGTH];
     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);    
        pp=vector(1,nlstate);
     for (i=1; i<= nlstate+1 ; i ++) {    prop=matrix(1,nlstate,iagemin,iagemax+3);
       k=2*i;    strcpy(fileresp,"p");
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);    strcat(fileresp,fileres);
       for (j=1; j<= nlstate+1 ; j ++) {    if((ficresp=fopen(fileresp,"w"))==NULL) {
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      printf("Problem with prevalence resultfile: %s\n", fileresp);
   else fprintf(ficgp," \%%*lf (\%%*lf)");      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
 }        exit(0);
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");    }
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);    j1=0;
       for (j=1; j<= nlstate+1 ; j ++) {    
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    j=cptcoveff;
         else fprintf(ficgp," \%%*lf (\%%*lf)");    if (cptcovn<1) {j=1;ncodemax[1]=1;}
 }    
       fprintf(ficgp,"\" t\"\" w l 0,");    first=1;
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);  
       for (j=1; j<= nlstate+1 ; j ++) {    /* for(k1=1; k1<=j ; k1++){   /* Loop on covariates */
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    /*  for(i1=1; i1<=ncodemax[k1];i1++){ /* Now it is 2 */
   else fprintf(ficgp," \%%*lf (\%%*lf)");    /*    j1++;
 }    */
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");    for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
       else fprintf(ficgp,"\" t\"\" w l 0,");        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
     }          scanf("%d", i);*/
   }        for (i=-5; i<=nlstate+ndeath; i++)  
            for (jk=-5; jk<=nlstate+ndeath; jk++)  
   /*3eme*/            for(m=iagemin; m <= iagemax+3; m++)
               freq[i][jk][m]=0;
   for (k1=1; k1<= m ; k1 ++) {        
     for (cpt=1; cpt<= nlstate ; cpt ++) {        for (i=1; i<=nlstate; i++)  
       k=2+nlstate*(2*cpt-2);          for(m=iagemin; m <= iagemax+3; m++)
       fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);            prop[i][m]=0;
       fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);        
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);        dateintsum=0;
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");        k2cpt=0;
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);        for (i=1; i<=imx; i++) {
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);          bool=1;
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");          if  (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);            for (z1=1; z1<=cptcoveff; z1++)       
               if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
 */                  /* Tests if the value of each of the covariates of i is equal to filter j1 */
       for (i=1; i< nlstate ; i ++) {                bool=0;
         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);                /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtab[%d][%d]=%d, nbcode[Tvaraff][codtab[%d][%d]=%d, j1=%d\n", 
                   bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
       }                  j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
     }                /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
   }              } 
            }
   /* CV preval stat */   
     for (k1=1; k1<= m ; k1 ++) {          if (bool==1){
     for (cpt=1; cpt<nlstate ; cpt ++) {            for(m=firstpass; m<=lastpass; m++){
       k=3;              k2=anint[m][i]+(mint[m][i]/12.);
       fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
       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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
                 if(agev[m][i]==1) agev[m][i]=iagemax+2;
       for (i=1; i< nlstate ; i ++)                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
         fprintf(ficgp,"+$%d",k+i+1);                if (m<lastpass) {
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
                        freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
       l=3+(nlstate+ndeath)*cpt;                }
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);                
       for (i=1; i< nlstate ; i ++) {                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
         l=3+(nlstate+ndeath)*cpt;                  dateintsum=dateintsum+k2;
         fprintf(ficgp,"+$%d",l+i+1);                  k2cpt++;
       }                }
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);                  /*}*/
     }            }
   }            }
          } /* end i */
   /* proba elementaires */         
    for(i=1,jk=1; i <=nlstate; i++){        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
     for(k=1; k <=(nlstate+ndeath); k++){        pstamp(ficresp);
       if (k != i) {        if  (cptcovn>0) {
         for(j=1; j <=ncovmodel; j++){          fprintf(ficresp, "\n#********** Variable "); 
                  for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);          fprintf(ficresp, "**********\n#");
           jk++;          fprintf(ficlog, "\n#********** Variable "); 
           fprintf(ficgp,"\n");          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         }          fprintf(ficlog, "**********\n#");
       }        }
     }        for(i=1; i<=nlstate;i++) 
    }          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
         fprintf(ficresp, "\n");
    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/        
      for(jk=1; jk <=m; jk++) {        for(i=iagemin; i <= iagemax+3; i++){
        fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);          if(i==iagemax+3){
        if (ng==2)            fprintf(ficlog,"Total");
          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");          }else{
        else            if(first==1){
          fprintf(ficgp,"\nset title \"Probability\"\n");              first=0;
        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);              printf("See log file for details...\n");
        i=1;            }
        for(k2=1; k2<=nlstate; k2++) {            fprintf(ficlog,"Age %d", i);
          k3=i;          }
          for(k=1; k<=(nlstate+ndeath); k++) {          for(jk=1; jk <=nlstate ; jk++){
            if (k != k2){            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
              if(ng==2)              pp[jk] += freq[jk][m][i]; 
                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);          }
              else          for(jk=1; jk <=nlstate ; jk++){
                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);            for(m=-1, pos=0; m <=0 ; m++)
              ij=1;              pos += freq[jk][m][i];
              for(j=3; j <=ncovmodel; j++) {            if(pp[jk]>=1.e-10){
                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {              if(first==1){
                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);                printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
                  ij++;              }
                }              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
                else            }else{
                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);              if(first==1)
              }                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
              fprintf(ficgp,")/(1");              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
                          }
              for(k1=1; k1 <=nlstate; k1++){            }
                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);  
                ij=1;          for(jk=1; jk <=nlstate ; jk++){
                for(j=3; j <=ncovmodel; j++){            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {              pp[jk] += freq[jk][m][i];
                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);          }       
                    ij++;          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
                  }            pos += pp[jk];
                  else            posprop += prop[jk][i];
                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);          }
                }          for(jk=1; jk <=nlstate ; jk++){
                fprintf(ficgp,")");            if(pos>=1.e-5){
              }              if(first==1)
              fprintf(ficgp,") t \"p%d%d\" ", k2,k);                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
              i=i+ncovmodel;            }else{
            }              if(first==1)
          }                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
        }              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
      }            }
    }            if( i <= iagemax){
    fclose(ficgp);              if(pos>=1.e-5){
 }  /* end gnuplot */                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
                 /*probs[i][jk][j1]= pp[jk]/pos;*/
                 /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
 /*************** Moving average **************/              }
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){              else
                 fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
   int i, cpt, cptcod;            }
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)          }
       for (i=1; i<=nlstate;i++)          
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)          for(jk=-1; jk <=nlstate+ndeath; jk++)
           mobaverage[(int)agedeb][i][cptcod]=0.;            for(m=-1; m <=nlstate+ndeath; m++)
                  if(freq[jk][m][i] !=0 ) {
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){              if(first==1)
       for (i=1; i<=nlstate;i++){                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
           for (cpt=0;cpt<=4;cpt++){              }
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];          if(i <= iagemax)
           }            fprintf(ficresp,"\n");
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;          if(first==1)
         }            printf("Others in log...\n");
       }          fprintf(ficlog,"\n");
     }        }
            /*}*/
 }    }
     dateintmean=dateintsum/k2cpt; 
    
 /************** Forecasting ******************/    fclose(ficresp);
 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){    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
      free_vector(pp,1,nlstate);
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
   int *popage;    /* End of Freq */
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;  }
   double *popeffectif,*popcount;  
   double ***p3mat;  /************ Prevalence ********************/
   char fileresf[FILENAMELENGTH];  void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
   {  
  agelim=AGESUP;    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;       in each health status at the date of interview (if between dateprev1 and dateprev2).
        We still use firstpass and lastpass as another selection.
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    */
     
      int i, m, jk, k1, i1, j1, bool, z1,j;
   strcpy(fileresf,"f");    double ***freq; /* Frequencies */
   strcat(fileresf,fileres);    double *pp, **prop;
   if((ficresf=fopen(fileresf,"w"))==NULL) {    double pos,posprop; 
     printf("Problem with forecast resultfile: %s\n", fileresf);    double  y2; /* in fractional years */
   }    int iagemin, iagemax;
   printf("Computing forecasting: result on file '%s' \n", fileresf);    int first; /** to stop verbosity which is redirected to log file */
   
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    iagemin= (int) agemin;
     iagemax= (int) agemax;
   if (mobilav==1) {    /*pp=vector(1,nlstate);*/
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    prop=matrix(1,nlstate,iagemin,iagemax+3); 
     movingaverage(agedeb, fage, ageminpar, mobaverage);    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
   }    j1=0;
     
   stepsize=(int) (stepm+YEARM-1)/YEARM;    /*j=cptcoveff;*/
   if (stepm<=12) stepsize=1;    if (cptcovn<1) {j=1;ncodemax[1]=1;}
      
   agelim=AGESUP;    first=1;
      for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
   hstepm=1;      /*for(i1=1; i1<=ncodemax[k1];i1++){
   hstepm=hstepm/stepm;        j1++;*/
   yp1=modf(dateintmean,&yp);        
   anprojmean=yp;        for (i=1; i<=nlstate; i++)  
   yp2=modf((yp1*12),&yp);          for(m=iagemin; m <= iagemax+3; m++)
   mprojmean=yp;            prop[i][m]=0.0;
   yp1=modf((yp2*30.5),&yp);       
   jprojmean=yp;        for (i=1; i<=imx; i++) { /* Each individual */
   if(jprojmean==0) jprojmean=1;          bool=1;
   if(mprojmean==0) jprojmean=1;          if  (cptcovn>0) {
              for (z1=1; z1<=cptcoveff; z1++) 
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
                  bool=0;
   for(cptcov=1;cptcov<=i2;cptcov++){          } 
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){          if (bool==1) { 
       k=k+1;            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
       fprintf(ficresf,"\n#******");              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
       for(j=1;j<=cptcoveff;j++) {              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
       }                if(agev[m][i]==1) agev[m][i]=iagemax+2;
       fprintf(ficresf,"******\n");                if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
       fprintf(ficresf,"# StartingAge FinalAge");                if (s[m][i]>0 && s[m][i]<=nlstate) { 
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);                  /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
                        prop[s[m][i]][(int)agev[m][i]] += weight[i];
                        prop[s[m][i]][iagemax+3] += weight[i]; 
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {                } 
         fprintf(ficresf,"\n");              }
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);              } /* end selection of waves */
           }
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){        }
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);        for(i=iagemin; i <= iagemax+3; i++){  
           nhstepm = nhstepm/hstepm;          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
                      posprop += prop[jk][i]; 
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          } 
           oldm=oldms;savm=savms;          
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            for(jk=1; jk <=nlstate ; jk++){     
                    if( i <=  iagemax){ 
           for (h=0; h<=nhstepm; h++){              if(posprop>=1.e-5){ 
             if (h==(int) (calagedate+YEARM*cpt)) {                probs[i][jk][j1]= prop[jk][i]/posprop;
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);              } else{
             }                if(first==1){
             for(j=1; j<=nlstate+ndeath;j++) {                  first=0;
               kk1=0.;kk2=0;                  printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others on log file...\n",jk,i,j1,probs[i][jk][j1]);
               for(i=1; i<=nlstate;i++) {                              }
                 if (mobilav==1)              }
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];            } 
                 else {          }/* end jk */ 
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];        }/* end i */ 
                 }      /*} *//* end i1 */
                    } /* end j1 */
               }    
               if (h==(int)(calagedate+12*cpt)){    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
                 fprintf(ficresf," %.3f", kk1);    /*free_vector(pp,1,nlstate);*/
                            free_matrix(prop,1,nlstate, iagemin,iagemax+3);
               }  }  /* End of prevalence */
             }  
           }  /************* Waves Concatenation ***************/
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
         }  void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
       }  {
     }    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
   }       Death is a valid wave (if date is known).
               mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
        and mw[mi+1][i]. dh depends on stepm.
   fclose(ficresf);       */
 }  
 /************** Forecasting ******************/    int i, mi, m;
 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 j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
         double sum=0., jmean=0.;*/
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;    int first;
   int *popage;    int j, k=0,jk, ju, jl;
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;    double sum=0.;
   double *popeffectif,*popcount;    first=0;
   double ***p3mat,***tabpop,***tabpopprev;    jmin=1e+5;
   char filerespop[FILENAMELENGTH];    jmax=-1;
     jmean=0.;
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    for(i=1; i<=imx; i++){
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      mi=0;
   agelim=AGESUP;      m=firstpass;
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;      while(s[m][i] <= nlstate){
          if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);          mw[++mi][i]=m;
          if(m >=lastpass)
            break;
   strcpy(filerespop,"pop");        else
   strcat(filerespop,fileres);          m++;
   if((ficrespop=fopen(filerespop,"w"))==NULL) {      }/* end while */
     printf("Problem with forecast resultfile: %s\n", filerespop);      if (s[m][i] > nlstate){
   }        mi++;     /* Death is another wave */
   printf("Computing forecasting: result on file '%s' \n", filerespop);        /* if(mi==0)  never been interviewed correctly before death */
            /* Only death is a correct wave */
   if (cptcoveff==0) ncodemax[cptcoveff]=1;        mw[mi][i]=m;
       }
   if (mobilav==1) {  
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      wav[i]=mi;
     movingaverage(agedeb, fage, ageminpar, mobaverage);      if(mi==0){
   }        nbwarn++;
         if(first==0){
   stepsize=(int) (stepm+YEARM-1)/YEARM;          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
   if (stepm<=12) stepsize=1;          first=1;
          }
   agelim=AGESUP;        if(first==1){
            fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
   hstepm=1;        }
   hstepm=hstepm/stepm;      } /* end mi==0 */
      } /* End individuals */
   if (popforecast==1) {  
     if((ficpop=fopen(popfile,"r"))==NULL) {    for(i=1; i<=imx; i++){
       printf("Problem with population file : %s\n",popfile);exit(0);      for(mi=1; mi<wav[i];mi++){
     }        if (stepm <=0)
     popage=ivector(0,AGESUP);          dh[mi][i]=1;
     popeffectif=vector(0,AGESUP);        else{
     popcount=vector(0,AGESUP);          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
                if (agedc[i] < 2*AGESUP) {
     i=1;                j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;              if(j==0) j=1;  /* Survives at least one month after exam */
                  else if(j<0){
     imx=i;                nberr++;
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];                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]);
   }                j=1; /* Temporary Dangerous patch */
                 printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
   for(cptcov=1;cptcov<=i2;cptcov++){                fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){                fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
       k=k+1;              }
       fprintf(ficrespop,"\n#******");              k=k+1;
       for(j=1;j<=cptcoveff;j++) {              if (j >= jmax){
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                jmax=j;
       }                ijmax=i;
       fprintf(ficrespop,"******\n");              }
       fprintf(ficrespop,"# Age");              if (j <= jmin){
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);                jmin=j;
       if (popforecast==1)  fprintf(ficrespop," [Population]");                ijmin=i;
                    }
       for (cpt=0; cpt<=0;cpt++) {              sum=sum+j;
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);                /*if (j<0) printf("j=%d num=%d \n",j,i);*/
                      /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){            }
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);          }
           nhstepm = nhstepm/hstepm;          else{
                      j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  /*        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]); */
           oldm=oldms;savm=savms;  
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);              k=k+1;
                    if (j >= jmax) {
           for (h=0; h<=nhstepm; h++){              jmax=j;
             if (h==(int) (calagedate+YEARM*cpt)) {              ijmax=i;
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);            }
             }            else if (j <= jmin){
             for(j=1; j<=nlstate+ndeath;j++) {              jmin=j;
               kk1=0.;kk2=0;              ijmin=i;
               for(i=1; i<=nlstate;i++) {                          }
                 if (mobilav==1)            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];            /*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]);*/
                 else {            if(j<0){
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];              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(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
               if (h==(int)(calagedate+12*cpt)){            }
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;            sum=sum+j;
                   /*fprintf(ficrespop," %.3f", kk1);          }
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/          jk= j/stepm;
               }          jl= j -jk*stepm;
             }          ju= j -(jk+1)*stepm;
             for(i=1; i<=nlstate;i++){          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
               kk1=0.;            if(jl==0){
                 for(j=1; j<=nlstate;j++){              dh[mi][i]=jk;
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];              bh[mi][i]=0;
                 }            }else{ /* We want a negative bias in order to only have interpolation ie
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];                    * to avoid the price of an extra matrix product in likelihood */
             }              dh[mi][i]=jk+1;
               bh[mi][i]=ju;
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)            }
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);          }else{
           }            if(jl <= -ju){
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              dh[mi][i]=jk;
         }              bh[mi][i]=jl;       /* bias is positive if real duration
       }                                   * is higher than the multiple of stepm and negative otherwise.
                                     */
   /******/            }
             else{
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {              dh[mi][i]=jk+1;
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);                bh[mi][i]=ju;
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){            }
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);            if(dh[mi][i]==0){
           nhstepm = nhstepm/hstepm;              dh[mi][i]=1; /* At least one step */
                        bh[mi][i]=ju; /* At least one step */
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              /*  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);*/
           oldm=oldms;savm=savms;            }
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            } /* end if mle */
           for (h=0; h<=nhstepm; h++){        }
             if (h==(int) (calagedate+YEARM*cpt)) {      } /* end wave */
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);    }
             }    jmean=sum/k;
             for(j=1; j<=nlstate+ndeath;j++) {    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);
               kk1=0.;kk2=0;    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);
               for(i=1; i<=nlstate;i++) {                 }
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];      
               }  /*********** Tricode ****************************/
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);  void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
             }  {
           }    /**< Uses cptcovn+2*cptcovprod as the number of covariates */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    /*      Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 
         }    /* Boring subroutine which should only output nbcode[Tvar[j]][k]
       }     * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
    }    /* nbcode[Tvar[j]][1]= 
   }    */
    
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
     int modmaxcovj=0; /* Modality max of covariates j */
   if (popforecast==1) {    int cptcode=0; /* Modality max of covariates j */
     free_ivector(popage,0,AGESUP);    int modmincovj=0; /* Modality min of covariates j */
     free_vector(popeffectif,0,AGESUP);  
     free_vector(popcount,0,AGESUP);  
   }    cptcoveff=0; 
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);   
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    for (k=-1; k < maxncov; k++) Ndum[k]=0;
   fclose(ficrespop);    for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
 }  
     /* Loop on covariates without age and products */
 /***********************************************/    for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */
 /**************** Main Program *****************/      for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the 
 /***********************************************/                                 modality of this covariate Vj*/ 
         ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
 int main(int argc, char *argv[])                                      * If product of Vn*Vm, still boolean *:
 {                                      * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
                                       * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;        /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
   double agedeb, agefin,hf;                                        modality of the nth covariate of individual i. */
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;        if (ij > modmaxcovj)
           modmaxcovj=ij; 
   double fret;        else if (ij < modmincovj) 
   double **xi,tmp,delta;          modmincovj=ij; 
         if ((ij < -1) && (ij > NCOVMAX)){
   double dum; /* Dummy variable */          printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
   double ***p3mat;          exit(1);
   int *indx;        }else
   char line[MAXLINE], linepar[MAXLINE];        Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];        /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
   int firstobs=1, lastobs=10;        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
   int sdeb, sfin; /* Status at beginning and end */        /* getting the maximum value of the modality of the covariate
   int c,  h , cpt,l;           (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
   int ju,jl, mi;           female is 1, then modmaxcovj=1.*/
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;      }
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;      printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
   int mobilav=0,popforecast=0;      cptcode=modmaxcovj;
   int hstepm, nhstepm;      /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;     /*for (i=0; i<=cptcode; i++) {*/
       for (i=modmincovj;  i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
   double bage, fage, age, agelim, agebase;        printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
   double ftolpl=FTOL;        if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
   double **prlim;          ncodemax[j]++;  /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
   double *severity;        }
   double ***param; /* Matrix of parameters */        /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for
   double  *p;           historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
   double **matcov; /* Matrix of covariance */      } /* Ndum[-1] number of undefined modalities */
   double ***delti3; /* Scale */  
   double *delti; /* Scale */      /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
   double ***eij, ***vareij;      /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
   double **varpl; /* Variances of prevalence limits by age */      /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
   double *epj, vepp;         modmincovj=3; modmaxcovj = 7;
   double kk1, kk2;         There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;         which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy 
           variables V1_1 and V1_2.
          nbcode[Tvar[j]][ij]=k;
   char *alph[]={"a","a","b","c","d","e"}, str[4];         nbcode[Tvar[j]][1]=0;
          nbcode[Tvar[j]][2]=1;
          nbcode[Tvar[j]][3]=2;
   char z[1]="c", occ;      */
 #include <sys/time.h>      ij=1; /* ij is similar to i but can jumps over null modalities */
 #include <time.h>      for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];        for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
            /*recode from 0 */
   /* long total_usecs;          if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
   struct timeval start_time, end_time;            nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode. 
                                         k is a modality. If we have model=V1+V1*sex 
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */                                       then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
   getcwd(pathcd, size);            ij++;
           }
   printf("\n%s",version);          if (ij > ncodemax[j]) break; 
   if(argc <=1){        }  /* end of loop on */
     printf("\nEnter the parameter file name: ");      } /* end of loop on modality */ 
     scanf("%s",pathtot);    } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/  
   }    
   else{   for (k=-1; k< maxncov; k++) Ndum[k]=0; 
     strcpy(pathtot,argv[1]);    
   }    for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */ 
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/ 
   /*cygwin_split_path(pathtot,path,optionfile);     ij=Tvar[i]; /* Tvar might be -1 if status was unknown */ 
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/     Ndum[ij]++; 
   /* cutv(path,optionfile,pathtot,'\\');*/   } 
   
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);   ij=1;
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);   for (i=0; i<=  maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
   chdir(path);     /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
   replace(pathc,path);     if((Ndum[i]!=0) && (i<=ncovcol)){
        /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
 /*-------- arguments in the command line --------*/       Tvaraff[ij]=i; /*For printing (unclear) */
        ij++;
   strcpy(fileres,"r");     }else
   strcat(fileres, optionfilefiname);         Tvaraff[ij]=0;
   strcat(fileres,".txt");    /* Other files have txt extension */   }
    ij--;
   /*---------arguments file --------*/   cptcoveff=ij; /*Number of total covariates*/
   
   if((ficpar=fopen(optionfile,"r"))==NULL)    {  }
     printf("Problem with optionfile %s\n",optionfile);  
     goto end;  
   }  /*********** Health Expectancies ****************/
   
   strcpy(filereso,"o");  void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
   strcat(filereso,fileres);  
   if((ficparo=fopen(filereso,"w"))==NULL) {  {
     printf("Problem with Output resultfile: %s\n", filereso);goto end;    /* Health expectancies, no variances */
   }    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
     int nhstepma, nstepma; /* Decreasing with age */
   /* Reads comments: lines beginning with '#' */    double age, agelim, hf;
   while((c=getc(ficpar))=='#' && c!= EOF){    double ***p3mat;
     ungetc(c,ficpar);    double eip;
     fgets(line, MAXLINE, ficpar);  
     puts(line);    pstamp(ficreseij);
     fputs(line,ficparo);    fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
   }    fprintf(ficreseij,"# Age");
   ungetc(c,ficpar);    for(i=1; i<=nlstate;i++){
       for(j=1; j<=nlstate;j++){
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);        fprintf(ficreseij," e%1d%1d ",i,j);
   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(ficreseij," e%1d. ",i);
 while((c=getc(ficpar))=='#' && c!= EOF){    }
     ungetc(c,ficpar);    fprintf(ficreseij,"\n");
     fgets(line, MAXLINE, ficpar);  
     puts(line);    
     fputs(line,ficparo);    if(estepm < stepm){
   }      printf ("Problem %d lower than %d\n",estepm, stepm);
   ungetc(c,ficpar);    }
      else  hstepm=estepm;   
        /* We compute the life expectancy from trapezoids spaced every estepm months
   covar=matrix(0,NCOVMAX,1,n);     * This is mainly to measure the difference between two models: for example
   cptcovn=0;     * if stepm=24 months pijx are given only every 2 years and by summing them
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;     * we are calculating an estimate of the Life Expectancy assuming a linear 
      * progression in between and thus overestimating or underestimating according
   ncovmodel=2+cptcovn;     * to the curvature of the survival function. If, for the same date, we 
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */     * estimate the model with stepm=1 month, we can keep estepm to 24 months
       * to compare the new estimate of Life expectancy with the same linear 
   /* Read guess parameters */     * hypothesis. A more precise result, taking into account a more precise
   /* Reads comments: lines beginning with '#' */     * curvature will be obtained if estepm is as small as stepm. */
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);    /* For example we decided to compute the life expectancy with the smallest unit */
     fgets(line, MAXLINE, ficpar);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
     puts(line);       nhstepm is the number of hstepm from age to agelim 
     fputs(line,ficparo);       nstepm is the number of stepm from age to agelin. 
   }       Look at hpijx to understand the reason of that which relies in memory size
   ungetc(c,ficpar);       and note for a fixed period like estepm months */
      /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);       survival function given by stepm (the optimization length). Unfortunately it
     for(i=1; i <=nlstate; i++)       means that if the survival funtion is printed only each two years of age and if
     for(j=1; j <=nlstate+ndeath-1; j++){       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
       fscanf(ficpar,"%1d%1d",&i1,&j1);       results. So we changed our mind and took the option of the best precision.
       fprintf(ficparo,"%1d%1d",i1,j1);    */
       printf("%1d%1d",i,j);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
       for(k=1; k<=ncovmodel;k++){  
         fscanf(ficpar," %lf",&param[i][j][k]);    agelim=AGESUP;
         printf(" %lf",param[i][j][k]);    /* If stepm=6 months */
         fprintf(ficparo," %lf",param[i][j][k]);      /* Computed by stepm unit matrices, product of hstepm matrices, stored
       }         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
       fscanf(ficpar,"\n");      
       printf("\n");  /* nhstepm age range expressed in number of stepm */
       fprintf(ficparo,"\n");    nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
     }    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
      /* if (stepm >= YEARM) hstepm=1;*/
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   p=param[1][1];  
      for (age=bage; age<=fage; age ++){ 
   /* Reads comments: lines beginning with '#' */      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
   while((c=getc(ficpar))=='#' && c!= EOF){      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     ungetc(c,ficpar);      /* if (stepm >= YEARM) hstepm=1;*/
     fgets(line, MAXLINE, ficpar);      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
     puts(line);  
     fputs(line,ficparo);      /* If stepm=6 months */
   }      /* Computed by stepm unit matrices, product of hstepma matrices, stored
   ungetc(c,ficpar);         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
       
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);      hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */      
   for(i=1; i <=nlstate; i++){      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     for(j=1; j <=nlstate+ndeath-1; j++){      
       fscanf(ficpar,"%1d%1d",&i1,&j1);      printf("%d|",(int)age);fflush(stdout);
       printf("%1d%1d",i,j);      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
       fprintf(ficparo,"%1d%1d",i1,j1);      
       for(k=1; k<=ncovmodel;k++){      /* Computing expectancies */
         fscanf(ficpar,"%le",&delti3[i][j][k]);      for(i=1; i<=nlstate;i++)
         printf(" %le",delti3[i][j][k]);        for(j=1; j<=nlstate;j++)
         fprintf(ficparo," %le",delti3[i][j][k]);          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
       }            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
       fscanf(ficpar,"\n");            
       printf("\n");            /* 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(ficparo,"\n");  
     }          }
   }  
   delti=delti3[1][1];      fprintf(ficreseij,"%3.0f",age );
        for(i=1; i<=nlstate;i++){
   /* Reads comments: lines beginning with '#' */        eip=0;
   while((c=getc(ficpar))=='#' && c!= EOF){        for(j=1; j<=nlstate;j++){
     ungetc(c,ficpar);          eip +=eij[i][j][(int)age];
     fgets(line, MAXLINE, ficpar);          fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
     puts(line);        }
     fputs(line,ficparo);        fprintf(ficreseij,"%9.4f", eip );
   }      }
   ungetc(c,ficpar);      fprintf(ficreseij,"\n");
        
   matcov=matrix(1,npar,1,npar);    }
   for(i=1; i <=npar; i++){    free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     fscanf(ficpar,"%s",&str);    printf("\n");
     printf("%s",str);    fprintf(ficlog,"\n");
     fprintf(ficparo,"%s",str);    
     for(j=1; j <=i; j++){  }
       fscanf(ficpar," %le",&matcov[i][j]);  
       printf(" %.5le",matcov[i][j]);  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[] )
       fprintf(ficparo," %.5le",matcov[i][j]);  
     }  {
     fscanf(ficpar,"\n");    /* Covariances of health expectancies eij and of total life expectancies according
     printf("\n");     to initial status i, ei. .
     fprintf(ficparo,"\n");    */
   }    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
   for(i=1; i <=npar; i++)    int nhstepma, nstepma; /* Decreasing with age */
     for(j=i+1;j<=npar;j++)    double age, agelim, hf;
       matcov[i][j]=matcov[j][i];    double ***p3matp, ***p3matm, ***varhe;
        double **dnewm,**doldm;
   printf("\n");    double *xp, *xm;
     double **gp, **gm;
     double ***gradg, ***trgradg;
     /*-------- Rewriting paramater file ----------*/    int theta;
      strcpy(rfileres,"r");    /* "Rparameterfile */  
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/    double eip, vip;
      strcat(rfileres,".");    /* */  
      strcat(rfileres,optionfilext);    /* Other files have txt extension */    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
     if((ficres =fopen(rfileres,"w"))==NULL) {    xp=vector(1,npar);
       printf("Problem writing new parameter file: %s\n", fileres);goto end;    xm=vector(1,npar);
     }    dnewm=matrix(1,nlstate*nlstate,1,npar);
     fprintf(ficres,"#%s\n",version);    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
        
     /*-------- data file ----------*/    pstamp(ficresstdeij);
     if((fic=fopen(datafile,"r"))==NULL)    {    fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
       printf("Problem with datafile: %s\n", datafile);goto end;    fprintf(ficresstdeij,"# Age");
     }    for(i=1; i<=nlstate;i++){
       for(j=1; j<=nlstate;j++)
     n= lastobs;        fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
     severity = vector(1,maxwav);      fprintf(ficresstdeij," e%1d. ",i);
     outcome=imatrix(1,maxwav+1,1,n);    }
     num=ivector(1,n);    fprintf(ficresstdeij,"\n");
     moisnais=vector(1,n);  
     annais=vector(1,n);    pstamp(ficrescveij);
     moisdc=vector(1,n);    fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
     andc=vector(1,n);    fprintf(ficrescveij,"# Age");
     agedc=vector(1,n);    for(i=1; i<=nlstate;i++)
     cod=ivector(1,n);      for(j=1; j<=nlstate;j++){
     weight=vector(1,n);        cptj= (j-1)*nlstate+i;
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */        for(i2=1; i2<=nlstate;i2++)
     mint=matrix(1,maxwav,1,n);          for(j2=1; j2<=nlstate;j2++){
     anint=matrix(1,maxwav,1,n);            cptj2= (j2-1)*nlstate+i2;
     s=imatrix(1,maxwav+1,1,n);            if(cptj2 <= cptj)
     adl=imatrix(1,maxwav+1,1,n);                  fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
     tab=ivector(1,NCOVMAX);          }
     ncodemax=ivector(1,8);      }
     fprintf(ficrescveij,"\n");
     i=1;    
     while (fgets(line, MAXLINE, fic) != NULL)    {    if(estepm < stepm){
       if ((i >= firstobs) && (i <=lastobs)) {      printf ("Problem %d lower than %d\n",estepm, stepm);
            }
         for (j=maxwav;j>=1;j--){    else  hstepm=estepm;   
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);    /* We compute the life expectancy from trapezoids spaced every estepm months
           strcpy(line,stra);     * This is mainly to measure the difference between two models: for example
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);     * if stepm=24 months pijx are given only every 2 years and by summing them
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);     * 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 
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);     * estimate the model with stepm=1 month, we can keep estepm to 24 months
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);     * to compare the new estimate of Life expectancy with the same linear 
      * hypothesis. A more precise result, taking into account a more precise
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);     * curvature will be obtained if estepm is as small as stepm. */
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);  
     /* For example we decided to compute the life expectancy with the smallest unit */
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
         for (j=ncovcol;j>=1;j--){       nhstepm is the number of hstepm from age to agelim 
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);       nstepm is the number of stepm from age to agelin. 
         }       Look at hpijx to understand the reason of that which relies in memory size
         num[i]=atol(stra);       and note for a fixed period like estepm months */
            /* We decided (b) to get a life expectancy respecting the most precise curvature of the
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){       survival function given by stepm (the optimization length). Unfortunately it
           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;}*/       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 
         i=i+1;       results. So we changed our mind and took the option of the best precision.
       }    */
     }    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     /* printf("ii=%d", ij);  
        scanf("%d",i);*/    /* If stepm=6 months */
   imx=i-1; /* Number of individuals */    /* nhstepm age range expressed in number of stepm */
     agelim=AGESUP;
   /* for (i=1; i<=imx; i++){    nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;    /* if (stepm >= YEARM) hstepm=1;*/
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     }*/    
    /*  for (i=1; i<=imx; i++){    p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
      if (s[4][i]==9)  s[4][i]=-1;    p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
      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]));}*/    gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
      trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
      gp=matrix(0,nhstepm,1,nlstate*nlstate);
   /* Calculation of the number of parameter from char model*/    gm=matrix(0,nhstepm,1,nlstate*nlstate);
   Tvar=ivector(1,15);  
   Tprod=ivector(1,15);    for (age=bage; age<=fage; age ++){ 
   Tvaraff=ivector(1,15);      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
   Tvard=imatrix(1,15,1,2);      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   Tage=ivector(1,15);            /* if (stepm >= YEARM) hstepm=1;*/
          nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
   if (strlen(model) >1){  
     j=0, j1=0, k1=1, k2=1;      /* If stepm=6 months */
     j=nbocc(model,'+');      /* Computed by stepm unit matrices, product of hstepma matrices, stored
     j1=nbocc(model,'*');         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
     cptcovn=j+1;      
     cptcovprod=j1;      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
      
     strcpy(modelsav,model);      /* Computing  Variances of health expectancies */
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
       printf("Error. Non available option model=%s ",model);         decrease memory allocation */
       goto end;      for(theta=1; theta <=npar; theta++){
     }        for(i=1; i<=npar; i++){ 
              xp[i] = x[i] + (i==theta ?delti[theta]:0);
     for(i=(j+1); i>=1;i--){          xm[i] = x[i] - (i==theta ?delti[theta]:0);
       cutv(stra,strb,modelsav,'+');        }
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);        hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/        hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
       /*scanf("%d",i);*/    
       if (strchr(strb,'*')) {        for(j=1; j<= nlstate; j++){
         cutv(strd,strc,strb,'*');          for(i=1; i<=nlstate; i++){
         if (strcmp(strc,"age")==0) {            for(h=0; h<=nhstepm-1; h++){
           cptcovprod--;              gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
           cutv(strb,stre,strd,'V');              gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
           Tvar[i]=atoi(stre);            }
           cptcovage++;          }
             Tage[cptcovage]=i;        }
             /*printf("stre=%s ", stre);*/       
         }        for(ij=1; ij<= nlstate*nlstate; ij++)
         else if (strcmp(strd,"age")==0) {          for(h=0; h<=nhstepm-1; h++){
           cptcovprod--;            gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
           cutv(strb,stre,strc,'V');          }
           Tvar[i]=atoi(stre);      }/* End theta */
           cptcovage++;      
           Tage[cptcovage]=i;      
         }      for(h=0; h<=nhstepm-1; h++)
         else {        for(j=1; j<=nlstate*nlstate;j++)
           cutv(strb,stre,strc,'V');          for(theta=1; theta <=npar; theta++)
           Tvar[i]=ncovcol+k1;            trgradg[h][j][theta]=gradg[h][theta][j];
           cutv(strb,strc,strd,'V');      
           Tprod[k1]=i;  
           Tvard[k1][1]=atoi(strc);       for(ij=1;ij<=nlstate*nlstate;ij++)
           Tvard[k1][2]=atoi(stre);        for(ji=1;ji<=nlstate*nlstate;ji++)
           Tvar[cptcovn+k2]=Tvard[k1][1];          varhe[ij][ji][(int)age] =0.;
           Tvar[cptcovn+k2+1]=Tvard[k1][2];  
           for (k=1; k<=lastobs;k++)       printf("%d|",(int)age);fflush(stdout);
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
           k1++;       for(h=0;h<=nhstepm-1;h++){
           k2=k2+2;        for(k=0;k<=nhstepm-1;k++){
         }          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
       }          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
       else {          for(ij=1;ij<=nlstate*nlstate;ij++)
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/            for(ji=1;ji<=nlstate*nlstate;ji++)
        /*  scanf("%d",i);*/              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
       cutv(strd,strc,strb,'V');        }
       Tvar[i]=atoi(strc);      }
       }  
       strcpy(modelsav,stra);        /* Computing expectancies */
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);      hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
         scanf("%d",i);*/      for(i=1; i<=nlstate;i++)
     }        for(j=1; j<=nlstate;j++)
 }          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
              eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);            
   printf("cptcovprod=%d ", cptcovprod);            /* 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]);*/
   scanf("%d ",i);*/  
     fclose(fic);          }
   
     /*  if(mle==1){*/      fprintf(ficresstdeij,"%3.0f",age );
     if (weightopt != 1) { /* Maximisation without weights*/      for(i=1; i<=nlstate;i++){
       for(i=1;i<=n;i++) weight[i]=1.0;        eip=0.;
     }        vip=0.;
     /*-calculation of age at interview from date of interview and age at death -*/        for(j=1; j<=nlstate;j++){
     agev=matrix(1,maxwav,1,imx);          eip += eij[i][j][(int)age];
           for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
     for (i=1; i<=imx; i++) {            vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
       for(m=2; (m<= maxwav); m++) {          fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){        }
          anint[m][i]=9999;        fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
          s[m][i]=-1;      }
        }      fprintf(ficresstdeij,"\n");
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;  
       }      fprintf(ficrescveij,"%3.0f",age );
     }      for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
     for (i=1; i<=imx; i++)  {          cptj= (j-1)*nlstate+i;
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);          for(i2=1; i2<=nlstate;i2++)
       for(m=1; (m<= maxwav); m++){            for(j2=1; j2<=nlstate;j2++){
         if(s[m][i] >0){              cptj2= (j2-1)*nlstate+i2;
           if (s[m][i] >= nlstate+1) {              if(cptj2 <= cptj)
             if(agedc[i]>0)                fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
               if(moisdc[i]!=99 && andc[i]!=9999)            }
                 agev[m][i]=agedc[i];        }
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/      fprintf(ficrescveij,"\n");
            else {     
               if (andc[i]!=9999){    }
               printf("Warning negative age at death: %d line:%d\n",num[i],i);    free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
               agev[m][i]=-1;    free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
               }    free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
             }    free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
           }    free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           else if(s[m][i] !=9){ /* Should no more exist */    free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);    printf("\n");
             if(mint[m][i]==99 || anint[m][i]==9999)    fprintf(ficlog,"\n");
               agev[m][i]=1;  
             else if(agev[m][i] <agemin){    free_vector(xm,1,npar);
               agemin=agev[m][i];    free_vector(xp,1,npar);
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
             }    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
             else if(agev[m][i] >agemax){    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
               agemax=agev[m][i];  }
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/  
             }  /************ Variance ******************/
             /*agev[m][i]=anint[m][i]-annais[i];*/  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[])
             /*   agev[m][i] = age[i]+2*m;*/  {
           }    /* Variance of health expectancies */
           else { /* =9 */    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
             agev[m][i]=1;    /* double **newm;*/
             s[m][i]=-1;    double **dnewm,**doldm;
           }    double **dnewmp,**doldmp;
         }    int i, j, nhstepm, hstepm, h, nstepm ;
         else /*= 0 Unknown */    int k, cptcode;
           agev[m][i]=1;    double *xp;
       }    double **gp, **gm;  /* for var eij */
        double ***gradg, ***trgradg; /*for var eij */
     }    double **gradgp, **trgradgp; /* for var p point j */
     for (i=1; i<=imx; i++)  {    double *gpp, *gmp; /* for var p point j */
       for(m=1; (m<= maxwav); m++){    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
         if (s[m][i] > (nlstate+ndeath)) {    double ***p3mat;
           printf("Error: Wrong value in nlstate or ndeath\n");      double age,agelim, hf;
           goto end;    double ***mobaverage;
         }    int theta;
       }    char digit[4];
     }    char digitp[25];
   
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);    char fileresprobmorprev[FILENAMELENGTH];
   
     free_vector(severity,1,maxwav);    if(popbased==1){
     free_imatrix(outcome,1,maxwav+1,1,n);      if(mobilav!=0)
     free_vector(moisnais,1,n);        strcpy(digitp,"-populbased-mobilav-");
     free_vector(annais,1,n);      else strcpy(digitp,"-populbased-nomobil-");
     /* free_matrix(mint,1,maxwav,1,n);    }
        free_matrix(anint,1,maxwav,1,n);*/    else 
     free_vector(moisdc,1,n);      strcpy(digitp,"-stablbased-");
     free_vector(andc,1,n);  
     if (mobilav!=0) {
          mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     wav=ivector(1,imx);      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
     dh=imatrix(1,lastpass-firstpass+1,1,imx);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);        printf(" Error in movingaverage mobilav=%d\n",mobilav);
          }
     /* Concatenates waves */    }
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);  
     strcpy(fileresprobmorprev,"prmorprev"); 
     sprintf(digit,"%-d",ij);
       Tcode=ivector(1,100);    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);    strcat(fileresprobmorprev,digit); /* Tvar to be done */
       ncodemax[1]=1;    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);    strcat(fileresprobmorprev,fileres);
          if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
    codtab=imatrix(1,100,1,10);      printf("Problem with resultfile: %s\n", fileresprobmorprev);
    h=0;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
    m=pow(2,cptcoveff);    }
      printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
    for(k=1;k<=cptcoveff; k++){   
      for(i=1; i <=(m/pow(2,k));i++){    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
        for(j=1; j <= ncodemax[k]; j++){    pstamp(ficresprobmorprev);
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){    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);
            h++;    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/      fprintf(ficresprobmorprev," p.%-d SE",j);
          }      for(i=1; i<=nlstate;i++)
        }        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
      }    }  
    }    fprintf(ficresprobmorprev,"\n");
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);    fprintf(ficgp,"\n# Routine varevsij");
       codtab[1][2]=1;codtab[2][2]=2; */    /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
    /* for(i=1; i <=m ;i++){    fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
       for(k=1; k <=cptcovn; k++){    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);  /*   } */
       }    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
       printf("\n");    pstamp(ficresvij);
       }    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
       scanf("%d",i);*/    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);
    /* Calculates basic frequencies. Computes observed prevalence at single age    else
        and prints on file fileres'p'. */      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++)
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    fprintf(ficresvij,"\n");
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    xp=vector(1,npar);
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    dnewm=matrix(1,nlstate,1,npar);
          doldm=matrix(1,nlstate,1,nlstate);
     /* For Powell, parameters are in a vector p[] starting at p[1]    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */  
     gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
     if(mle==1){    gpp=vector(nlstate+1,nlstate+ndeath);
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);    gmp=vector(nlstate+1,nlstate+ndeath);
     }    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
        
     /*--------- results files --------------*/    if(estepm < stepm){
     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);      printf ("Problem %d lower than %d\n",estepm, stepm);
      }
     else  hstepm=estepm;   
    jk=1;    /* For example we decided to compute the life expectancy with the smallest unit */
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");       nhstepm is the number of hstepm from age to agelim 
    for(i=1,jk=1; i <=nlstate; i++){       nstepm is the number of stepm from age to agelin. 
      for(k=1; k <=(nlstate+ndeath); k++){       Look at function hpijx to understand why (it is linked to memory size questions) */
        if (k != i)    /* 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
            printf("%d%d ",i,k);       means that if the survival funtion is printed every two years of age and if
            fprintf(ficres,"%1d%1d ",i,k);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
            for(j=1; j <=ncovmodel; j++){       results. So we changed our mind and took the option of the best precision.
              printf("%f ",p[jk]);    */
              fprintf(ficres,"%f ",p[jk]);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
              jk++;    agelim = AGESUP;
            }    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
            printf("\n");      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
            fprintf(ficres,"\n");      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
          }      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
      }      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
    }      gp=matrix(0,nhstepm,1,nlstate);
  if(mle==1){      gm=matrix(0,nhstepm,1,nlstate);
     /* Computing hessian and covariance matrix */  
     ftolhess=ftol; /* Usually correct */  
     hesscov(matcov, p, npar, delti, ftolhess, func);      for(theta=1; theta <=npar; theta++){
  }        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");          xp[i] = x[i] + (i==theta ?delti[theta]:0);
     printf("# Scales (for hessian or gradient estimation)\n");        }
      for(i=1,jk=1; i <=nlstate; i++){        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
       for(j=1; j <=nlstate+ndeath; j++){        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         if (j!=i) {  
           fprintf(ficres,"%1d%1d",i,j);        if (popbased==1) {
           printf("%1d%1d",i,j);          if(mobilav ==0){
           for(k=1; k<=ncovmodel;k++){            for(i=1; i<=nlstate;i++)
             printf(" %.5e",delti[jk]);              prlim[i][i]=probs[(int)age][i][ij];
             fprintf(ficres," %.5e",delti[jk]);          }else{ /* mobilav */ 
             jk++;            for(i=1; i<=nlstate;i++)
           }              prlim[i][i]=mobaverage[(int)age][i][ij];
           printf("\n");          }
           fprintf(ficres,"\n");        }
         }    
       }        for(j=1; j<= nlstate; j++){
      }          for(h=0; h<=nhstepm; h++){
                for(i=1, gp[h][j]=0.;i<=nlstate;i++)
     k=1;              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");          }
     printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");        }
     for(i=1;i<=npar;i++){        /* This for computing probability of death (h=1 means
       /*  if (k>nlstate) k=1;           computed over hstepm matrices product = hstepm*stepm months) 
       i1=(i-1)/(ncovmodel*nlstate)+1;           as a weighted average of prlim.
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);        */
       printf("%s%d%d",alph[k],i1,tab[i]);*/        for(j=nlstate+1;j<=nlstate+ndeath;j++){
       fprintf(ficres,"%3d",i);          for(i=1,gpp[j]=0.; i<= nlstate; i++)
       printf("%3d",i);            gpp[j] += prlim[i][i]*p3mat[i][j][1];
       for(j=1; j<=i;j++){        }    
         fprintf(ficres," %.5e",matcov[i][j]);        /* end probability of death */
         printf(" %.5e",matcov[i][j]);  
       }        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
       fprintf(ficres,"\n");          xp[i] = x[i] - (i==theta ?delti[theta]:0);
       printf("\n");        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
       k++;        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     }   
            if (popbased==1) {
     while((c=getc(ficpar))=='#' && c!= EOF){          if(mobilav ==0){
       ungetc(c,ficpar);            for(i=1; i<=nlstate;i++)
       fgets(line, MAXLINE, ficpar);              prlim[i][i]=probs[(int)age][i][ij];
       puts(line);          }else{ /* mobilav */ 
       fputs(line,ficparo);            for(i=1; i<=nlstate;i++)
     }              prlim[i][i]=mobaverage[(int)age][i][ij];
     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;        for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
     if (fage <= 2) {          for(h=0; h<=nhstepm; h++){
       bage = ageminpar;            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
       fage = agemaxpar;              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
     }          }
            }
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");        /* This for computing probability of death (h=1 means
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);           computed over hstepm matrices product = hstepm*stepm months) 
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);           as a weighted average of prlim.
          */
     while((c=getc(ficpar))=='#' && c!= EOF){        for(j=nlstate+1;j<=nlstate+ndeath;j++){
     ungetc(c,ficpar);          for(i=1,gmp[j]=0.; i<= nlstate; i++)
     fgets(line, MAXLINE, ficpar);           gmp[j] += prlim[i][i]*p3mat[i][j][1];
     puts(line);        }    
     fputs(line,ficparo);        /* end probability of death */
   }  
   ungetc(c,ficpar);        for(j=1; j<= nlstate; j++) /* vareij */
            for(h=0; h<=nhstepm; h++){
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
   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);  
              for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
   while((c=getc(ficpar))=='#' && c!= EOF){          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
     ungetc(c,ficpar);        }
     fgets(line, MAXLINE, ficpar);  
     puts(line);      } /* End theta */
     fputs(line,ficparo);  
   }      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   ungetc(c,ficpar);  
        for(h=0; h<=nhstepm; h++) /* veij */
         for(j=1; j<=nlstate;j++)
    dateprev1=anprev1+mprev1/12.+jprev1/365.;          for(theta=1; theta <=npar; theta++)
    dateprev2=anprev2+mprev2/12.+jprev2/365.;            trgradg[h][j][theta]=gradg[h][theta][j];
   
   fscanf(ficpar,"pop_based=%d\n",&popbased);      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
   fprintf(ficparo,"pop_based=%d\n",popbased);          for(theta=1; theta <=npar; theta++)
   fprintf(ficres,"pop_based=%d\n",popbased);            trgradgp[j][theta]=gradgp[theta][j];
      
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     fgets(line, MAXLINE, ficpar);      for(i=1;i<=nlstate;i++)
     puts(line);        for(j=1;j<=nlstate;j++)
     fputs(line,ficparo);          vareij[i][j][(int)age] =0.;
   }  
   ungetc(c,ficpar);      for(h=0;h<=nhstepm;h++){
         for(k=0;k<=nhstepm;k++){
   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);          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
 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);          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
 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);          for(i=1;i<=nlstate;i++)
             for(j=1;j<=nlstate;j++)
               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++)
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);          varppt[j][i]=doldmp[j][i];
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);      /* end ppptj */
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);      /*  x centered again */
       hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
    
 /*------------ gnuplot -------------*/      if (popbased==1) {
   strcpy(optionfilegnuplot,optionfilefiname);        if(mobilav ==0){
   strcat(optionfilegnuplot,".gp");          for(i=1; i<=nlstate;i++)
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {            prlim[i][i]=probs[(int)age][i][ij];
     printf("Problem with file %s",optionfilegnuplot);        }else{ /* mobilav */ 
   }          for(i=1; i<=nlstate;i++)
   fclose(ficgp);            prlim[i][i]=mobaverage[(int)age][i][ij];
  printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);        }
 /*--------- index.htm --------*/      }
                
   strcpy(optionfilehtm,optionfile);      /* This for computing probability of death (h=1 means
   strcat(optionfilehtm,".htm");         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {         as a weighted average of prlim.
     printf("Problem with %s \n",optionfilehtm), exit(0);      */
   }      for(j=nlstate+1;j<=nlstate+ndeath;j++){
         for(i=1,gmp[j]=0.;i<= nlstate; i++) 
   fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n      }    
 \n      /* end probability of death */
 Total number of observations=%d <br>\n  
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
 <hr  size=\"2\" color=\"#EC5E5E\">      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
  <ul><li>Parameter files<br>\n        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n        for(i=1; i<=nlstate;i++){
  - Gnuplot file name: <a href=\"%s\">%s</a><br></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot);          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
   fclose(fichtm);        }
       } 
  printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);      fprintf(ficresprobmorprev,"\n");
    
 /*------------ free_vector  -------------*/      fprintf(ficresvij,"%.0f ",age );
  chdir(path);      for(i=1; i<=nlstate;i++)
          for(j=1; j<=nlstate;j++){
  free_ivector(wav,1,imx);          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);        }
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);        fprintf(ficresvij,"\n");
  free_ivector(num,1,n);      free_matrix(gp,0,nhstepm,1,nlstate);
  free_vector(agedc,1,n);      free_matrix(gm,0,nhstepm,1,nlstate);
  /*free_matrix(covar,1,NCOVMAX,1,n);*/      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
  fclose(ficparo);      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
  fclose(ficres);      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     } /* End age */
     free_vector(gpp,nlstate+1,nlstate+ndeath);
   /*--------------- Prevalence limit --------------*/    free_vector(gmp,nlstate+1,nlstate+ndeath);
      free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
   strcpy(filerespl,"pl");    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
   strcat(filerespl,fileres);    fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
   if((ficrespl=fopen(filerespl,"w"))==NULL) {    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;    fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
   }  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
   fprintf(ficrespl,"#Prevalence limit\n");  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
   fprintf(ficrespl,"#Age ");    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
   fprintf(ficrespl,"\n");    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
      fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
   prlim=matrix(1,nlstate,1,nlstate);    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);
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    /*  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);
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  */
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */  
   k=0;    free_vector(xp,1,npar);
   agebase=ageminpar;    free_matrix(doldm,1,nlstate,1,nlstate);
   agelim=agemaxpar;    free_matrix(dnewm,1,nlstate,1,npar);
   ftolpl=1.e-10;    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   i1=cptcoveff;    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
   if (cptcovn < 1){i1=1;}    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   for(cptcov=1;cptcov<=i1;cptcov++){    fclose(ficresprobmorprev);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    fflush(ficgp);
         k=k+1;    fflush(fichtm); 
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/  }  /* end varevsij */
         fprintf(ficrespl,"\n#******");  
         for(j=1;j<=cptcoveff;j++)  /************ Variance of prevlim ******************/
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, char strstart[])
         fprintf(ficrespl,"******\n");  {
            /* Variance of prevalence limit */
         for (age=agebase; age<=agelim; age++){    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    double **newm;
           fprintf(ficrespl,"%.0f",age );    double **dnewm,**doldm;
           for(i=1; i<=nlstate;i++)    int i, j, nhstepm, hstepm;
           fprintf(ficrespl," %.5f", prlim[i][i]);    int k, cptcode;
           fprintf(ficrespl,"\n");    double *xp;
         }    double *gp, *gm;
       }    double **gradg, **trgradg;
     }    double age,agelim;
   fclose(ficrespl);    int theta;
     
   /*------------- h Pij x at various ages ------------*/    pstamp(ficresvpl);
      fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);    fprintf(ficresvpl,"# Age");
   if((ficrespij=fopen(filerespij,"w"))==NULL) {    for(i=1; i<=nlstate;i++)
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;        fprintf(ficresvpl," %1d-%1d",i,i);
   }    fprintf(ficresvpl,"\n");
   printf("Computing pij: result on file '%s' \n", filerespij);  
      xp=vector(1,npar);
   stepsize=(int) (stepm+YEARM-1)/YEARM;    dnewm=matrix(1,nlstate,1,npar);
   /*if (stepm<=24) stepsize=2;*/    doldm=matrix(1,nlstate,1,nlstate);
     
   agelim=AGESUP;    hstepm=1*YEARM; /* Every year of age */
   hstepm=stepsize*YEARM; /* Every year of age */    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */    agelim = AGESUP;
      for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   k=0;      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
   for(cptcov=1;cptcov<=i1;cptcov++){      if (stepm >= YEARM) hstepm=1;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
       k=k+1;      gradg=matrix(1,npar,1,nlstate);
         fprintf(ficrespij,"\n#****** ");      gp=vector(1,nlstate);
         for(j=1;j<=cptcoveff;j++)      gm=vector(1,nlstate);
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
         fprintf(ficrespij,"******\n");      for(theta=1; theta <=npar; theta++){
                for(i=1; i<=npar; i++){ /* Computes gradient */
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */          xp[i] = x[i] + (i==theta ?delti[theta]:0);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        }
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        for(i=1;i<=nlstate;i++)
           oldm=oldms;savm=savms;          gp[i] = prlim[i][i];
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        
           fprintf(ficrespij,"# Age");        for(i=1; i<=npar; i++) /* Computes gradient */
           for(i=1; i<=nlstate;i++)          xp[i] = x[i] - (i==theta ?delti[theta]:0);
             for(j=1; j<=nlstate+ndeath;j++)        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
               fprintf(ficrespij," %1d-%1d",i,j);        for(i=1;i<=nlstate;i++)
           fprintf(ficrespij,"\n");          gm[i] = prlim[i][i];
            for (h=0; h<=nhstepm; h++){  
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );        for(i=1;i<=nlstate;i++)
             for(i=1; i<=nlstate;i++)          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
               for(j=1; j<=nlstate+ndeath;j++)      } /* End theta */
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);  
             fprintf(ficrespij,"\n");      trgradg =matrix(1,nlstate,1,npar);
              }  
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      for(j=1; j<=nlstate;j++)
           fprintf(ficrespij,"\n");        for(theta=1; theta <=npar; theta++)
         }          trgradg[j][theta]=gradg[theta][j];
     }  
   }      for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] =0.;
   varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
       matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
   fclose(ficrespij);      for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   
   /*---------- Forecasting ------------------*/      fprintf(ficresvpl,"%.0f ",age );
   if((stepm == 1) && (strcmp(model,".")==0)){      for(i=1; i<=nlstate;i++)
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);      fprintf(ficresvpl,"\n");
   }      free_vector(gp,1,nlstate);
   else{      free_vector(gm,1,nlstate);
     erreur=108;      free_matrix(gradg,1,npar,1,nlstate);
     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);      free_matrix(trgradg,1,nlstate,1,npar);
   }    } /* End age */
    
     free_vector(xp,1,npar);
   /*---------- Health expectancies and variances ------------*/    free_matrix(doldm,1,nlstate,1,npar);
     free_matrix(dnewm,1,nlstate,1,nlstate);
   strcpy(filerest,"t");  
   strcat(filerest,fileres);  }
   if((ficrest=fopen(filerest,"w"))==NULL) {  
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;  /************ Variance of one-step probabilities  ******************/
   }  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
   printf("Computing Total LEs with variances: file '%s' \n", filerest);  {
     int i, j=0,  i1, k1, l1, t, tj;
     int k2, l2, j1,  z1;
   strcpy(filerese,"e");    int k=0,l, cptcode;
   strcat(filerese,fileres);    int first=1, first1, first2;
   if((ficreseij=fopen(filerese,"w"))==NULL) {    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);    double **dnewm,**doldm;
   }    double *xp;
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);    double *gp, *gm;
     double **gradg, **trgradg;
  strcpy(fileresv,"v");    double **mu;
   strcat(fileresv,fileres);    double age,agelim, cov[NCOVMAX+1];
   if((ficresvij=fopen(fileresv,"w"))==NULL) {    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);    int theta;
   }    char fileresprob[FILENAMELENGTH];
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    char fileresprobcov[FILENAMELENGTH];
   calagedate=-1;    char fileresprobcor[FILENAMELENGTH];
 prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    double ***varpij;
   
   k=0;    strcpy(fileresprob,"prob"); 
   for(cptcov=1;cptcov<=i1;cptcov++){    strcat(fileresprob,fileres);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
       k=k+1;      printf("Problem with resultfile: %s\n", fileresprob);
       fprintf(ficrest,"\n#****** ");      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
       for(j=1;j<=cptcoveff;j++)    }
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    strcpy(fileresprobcov,"probcov"); 
       fprintf(ficrest,"******\n");    strcat(fileresprobcov,fileres);
     if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
       fprintf(ficreseij,"\n#****** ");      printf("Problem with resultfile: %s\n", fileresprobcov);
       for(j=1;j<=cptcoveff;j++)      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    }
       fprintf(ficreseij,"******\n");    strcpy(fileresprobcor,"probcor"); 
     strcat(fileresprobcor,fileres);
       fprintf(ficresvij,"\n#****** ");    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
       for(j=1;j<=cptcoveff;j++)      printf("Problem with resultfile: %s\n", fileresprobcor);
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
       fprintf(ficresvij,"******\n");    }
     printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
       oldm=oldms;savm=savms;    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);      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);
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
       oldm=oldms;savm=savms;    pstamp(ficresprob);
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
        fprintf(ficresprob,"# Age");
     pstamp(ficresprobcov);
      fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");    fprintf(ficresprobcov,"# Age");
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);    pstamp(ficresprobcor);
       fprintf(ficrest,"\n");    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
     fprintf(ficresprobcor,"# Age");
       epj=vector(1,nlstate+1);  
       for(age=bage; age <=fage ;age++){  
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    for(i=1; i<=nlstate;i++)
         if (popbased==1) {      for(j=1; j<=(nlstate+ndeath);j++){
           for(i=1; i<=nlstate;i++)        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
             prlim[i][i]=probs[(int)age][i][k];        fprintf(ficresprobcov," p%1d-%1d ",i,j);
         }        fprintf(ficresprobcor," p%1d-%1d ",i,j);
              }  
         fprintf(ficrest," %4.0f",age);   /* fprintf(ficresprob,"\n");
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){    fprintf(ficresprobcov,"\n");
           for(i=1, epj[j]=0.;i <=nlstate;i++) {    fprintf(ficresprobcor,"\n");
             epj[j] += prlim[i][i]*eij[i][j][(int)age];   */
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/    xp=vector(1,npar);
           }    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
           epj[nlstate+1] +=epj[j];    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
         }    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
     varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
         for(i=1, vepp=0.;i <=nlstate;i++)    first=1;
           for(j=1;j <=nlstate;j++)    fprintf(ficgp,"\n# Routine varprob");
             vepp += vareij[i][j][(int)age];    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));    fprintf(fichtm,"\n");
         for(j=1;j <=nlstate;j++){  
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
         }    fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
         fprintf(ficrest,"\n");    file %s<br>\n",optionfilehtmcov);
       }    fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
     }  and drawn. It helps understanding how is the covariance between two incidences.\
   }   They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
 free_matrix(mint,1,maxwav,1,n);    fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);  It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
     free_vector(weight,1,n);  would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
   fclose(ficreseij);  standard deviations wide on each axis. <br>\
   fclose(ficresvij);   Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
   fclose(ficrest);   and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
   fclose(ficpar);  To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
   free_vector(epj,1,nlstate+1);  
      cov[1]=1;
   /*------- Variance limit prevalence------*/      /* tj=cptcoveff; */
     tj = (int) pow(2,cptcoveff);
   strcpy(fileresvpl,"vpl");    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
   strcat(fileresvpl,fileres);    j1=0;
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {    for(j1=1; j1<=tj;j1++){
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);      /*for(i1=1; i1<=ncodemax[t];i1++){ */
     exit(0);      /*j1++;*/
   }        if  (cptcovn>0) {
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);          fprintf(ficresprob, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   k=0;          fprintf(ficresprob, "**********\n#\n");
   for(cptcov=1;cptcov<=i1;cptcov++){          fprintf(ficresprobcov, "\n#********** Variable "); 
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       k=k+1;          fprintf(ficresprobcov, "**********\n#\n");
       fprintf(ficresvpl,"\n#****** ");          
       for(j=1;j<=cptcoveff;j++)          fprintf(ficgp, "\n#********** Variable "); 
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       fprintf(ficresvpl,"******\n");          fprintf(ficgp, "**********\n#\n");
                
       varpl=matrix(1,nlstate,(int) bage, (int) fage);          
       oldm=oldms;savm=savms;          fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     }          fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
  }          
           fprintf(ficresprobcor, "\n#********** Variable ");    
   fclose(ficresvpl);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcor, "**********\n#");    
   /*---------- End : free ----------------*/        }
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);        
          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);        trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);        gp=vector(1,(nlstate)*(nlstate+ndeath));
          gm=vector(1,(nlstate)*(nlstate+ndeath));
          for (age=bage; age<=fage; age ++){ 
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);          cov[2]=age;
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);          for (k=1; k<=cptcovn;k++) {
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);                                                           * 1  1 1 1 1
                                                             * 2  2 1 1 1
   free_matrix(matcov,1,npar,1,npar);                                                           * 3  1 2 1 1
   free_vector(delti,1,npar);                                                           */
   free_matrix(agev,1,maxwav,1,imx);            /* nbcode[1][1]=0 nbcode[1][2]=1;*/
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);          }
           for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   fprintf(fichtm,"\n</body>");          for (k=1; k<=cptcovprod;k++)
   fclose(fichtm);            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   fclose(ficgp);          
        
           for(theta=1; theta <=npar; theta++){
   if(erreur >0)            for(i=1; i<=npar; i++)
     printf("End of Imach with error or warning %d\n",erreur);              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
   else   printf("End of Imach\n");            
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */            pmij(pmmij,cov,ncovmodel,xp,nlstate);
              
   /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/            k=0;
   /*printf("Total time was %d uSec.\n", total_usecs);*/            for(i=1; i<= (nlstate); i++){
   /*------ End -----------*/              for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gp[k]=pmmij[i][j];
  end:              }
 #ifdef windows            }
   /* chdir(pathcd);*/            
 #endif            for(i=1; i<=npar; i++)
  /*system("wgnuplot graph.plt");*/              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
  /*system("../gp37mgw/wgnuplot graph.plt");*/      
  /*system("cd ../gp37mgw");*/            pmij(pmmij,cov,ncovmodel,xp,nlstate);
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/            k=0;
  strcpy(plotcmd,GNUPLOTPROGRAM);            for(i=1; i<=(nlstate); i++){
  strcat(plotcmd," ");              for(j=1; j<=(nlstate+ndeath);j++){
  strcat(plotcmd,optionfilegnuplot);                k=k+1;
  system(plotcmd);                gm[k]=pmmij[i][j];
               }
 #ifdef windows            }
   while (z[0] != 'q') {       
     /* chdir(path); */            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
     scanf("%s",z);          }
     if (z[0] == 'c') system("./imach");  
     else if (z[0] == 'e') system(optionfilehtm);          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
     else if (z[0] == 'g') system(plotcmd);            for(theta=1; theta <=npar; theta++)
     else if (z[0] == 'q') exit(0);              trgradg[j][theta]=gradg[theta][j];
   }          
 #endif          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
 }          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
   
           pmij(pmmij,cov,ncovmodel,x,nlstate);
           
           k=0;
           for(i=1; i<=(nlstate); i++){
             for(j=1; j<=(nlstate+ndeath);j++){
               k=k+1;
               mu[k][(int) age]=pmmij[i][j];
             }
           }
           for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
             for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
               varpij[i][j][(int)age] = doldm[i][j];
   
           /*printf("\n%d ",(int)age);
             for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             }*/
   
           fprintf(ficresprob,"\n%d ",(int)age);
           fprintf(ficresprobcov,"\n%d ",(int)age);
           fprintf(ficresprobcor,"\n%d ",(int)age);
   
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
             fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
             fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
           }
           i=0;
           for (k=1; k<=(nlstate);k++){
             for (l=1; l<=(nlstate+ndeath);l++){ 
               i++;
               fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
               fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
               for (j=1; j<=i;j++){
                 /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
                 fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
                 fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
               }
             }
           }/* end of loop for state */
         } /* end of loop for age */
         free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
         free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
         free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
         free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
         
         /* Confidence intervalle of pij  */
         /*
           fprintf(ficgp,"\nunset parametric;unset label");
           fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
           fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
           fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
           fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
           fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
           fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
         */
   
         /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
         first1=1;first2=2;
         for (k2=1; k2<=(nlstate);k2++){
           for (l2=1; l2<=(nlstate+ndeath);l2++){ 
             if(l2==k2) continue;
             j=(k2-1)*(nlstate+ndeath)+l2;
             for (k1=1; k1<=(nlstate);k1++){
               for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                 if(l1==k1) continue;
                 i=(k1-1)*(nlstate+ndeath)+l1;
                 if(i<=j) continue;
                 for (age=bage; age<=fage; age ++){ 
                   if ((int)age %5==0){
                     v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                     v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     mu1=mu[i][(int) age]/stepm*YEARM ;
                     mu2=mu[j][(int) age]/stepm*YEARM;
                     c12=cv12/sqrt(v1*v2);
                     /* Computing eigen value of matrix of covariance */
                     lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     if ((lc2 <0) || (lc1 <0) ){
                       if(first2==1){
                         first1=0;
                       printf("Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS. See log file for details...\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);
                       }
                       fprintf(ficlog,"Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS.\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);fflush(ficlog);
                       /* lc1=fabs(lc1); */ /* If we want to have them positive */
                       /* lc2=fabs(lc2); */
                     }
   
                     /* Eigen vectors */
                     v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                     /*v21=sqrt(1.-v11*v11); *//* error */
                     v21=(lc1-v1)/cv12*v11;
                     v12=-v21;
                     v22=v11;
                     tnalp=v21/v11;
                     if(first1==1){
                       first1=0;
                       printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     }
                     fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     /*printf(fignu*/
                     /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                     /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                     if(first==1){
                       first=0;
                       fprintf(ficgp,"\nset parametric;unset label");
                       fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
                       fprintf(ficgp,"\nset ter png small size 320, 240");
                       fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
    :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
   %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }else{
                       first=0;
                       fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }/* if first */
                   } /* age mod 5 */
                 } /* end loop age */
                 fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                 first=1;
               } /*l12 */
             } /* k12 */
           } /*l1 */
         }/* k1 */
         /* } /* loop covariates */
     }
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
     free_vector(xp,1,npar);
     fclose(ficresprob);
     fclose(ficresprobcov);
     fclose(ficresprobcor);
     fflush(ficgp);
     fflush(fichtmcov);
   }
   
   
   /******************* Printing html file ***********/
   void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                     int popforecast, int estepm ,\
                     double jprev1, double mprev1,double anprev1, \
                     double jprev2, double mprev2,double anprev2){
     int jj1, k1, i1, cpt;
   
      fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
      <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
   </ul>");
      fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
    - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
              jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
      fprintf(fichtm,"\
    - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
              stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
      fprintf(fichtm,"\
    - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
              subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
      fprintf(fichtm,"\
    - (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n",
              estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
      fprintf(fichtm,"\
    - Population projections by age and states: \
      <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
   
   fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
    m=pow(2,cptcoveff);
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        /* Pij */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d_1.png\">%s%d_1.png</a><br> \
   <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
        /* Quasi-incidences */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
    before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d_2.png\">%s%d_2.png</a><br> \
   <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
          /* Period (stable) prevalence in each health state */
          for(cpt=1; cpt<=nlstate;cpt++){
            fprintf(fichtm,"<br>- Convergence from each state (1 to %d) to period (stable) prevalence in state %d <a href=\"%s%d_%d.png\">%s%d_%d.png</a><br> \
   <img src=\"%s%d_%d.png\">",nlstate, cpt, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
          }
        for(cpt=1; cpt<=nlstate;cpt++) {
           fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
   <img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
        }
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
   
   
    fprintf(fichtm,"\
   \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
    - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
   
    fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
    fprintf(fichtm,"\
    - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
   
    fprintf(fichtm,"\
    - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
    fprintf(fichtm,"\
    - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
            estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
    fprintf(fichtm,"\
    - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",
            estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
    fprintf(fichtm,"\
    - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
            subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   
   /*  if(popforecast==1) fprintf(fichtm,"\n */
   /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
   /*      <br>",fileres,fileres,fileres,fileres); */
   /*  else  */
   /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
    fflush(fichtm);
    fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   
    m=pow(2,cptcoveff);
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        for(cpt=1; cpt<=nlstate;cpt++) {
          fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
   prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
   <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
        }
        fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
   true period expectancies (those weighted with period prevalences are also\
    drawn in addition to the population based expectancies computed using\
    observed and cahotic prevalences: %s%d.png<br>\
   <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
    fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m0,cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
     int ng=0;
   /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   /*     printf("Problem with file %s",optionfilegnuplot); */
   /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   /*   } */
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
     m=pow(2,cptcoveff);
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
    /* 1eme*/
     fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
     for (cpt=1; cpt<= nlstate ; cpt ++) {
       for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
        fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
        fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
        fprintf(ficgp,"set xlabel \"Age\" \n\
   set ylabel \"Probability\" \n\
   set ter png small size 320, 240\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else        fprintf(ficgp," \%%*lf (\%%*lf)");
        }
        fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        } 
        fprintf(ficgp,"\" t\"95\%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }  
        fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
      }
     }
     /*2 eme*/
     fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
     for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
       fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
       
       for (i=1; i<= nlstate+1 ; i ++) {
         k=2*i;
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         fprintf(ficgp,"\" t\"\" w l lt 0,");
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
         else fprintf(ficgp,"\" t\"\" w l lt 0,");
       }
     }
     
     /*3eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<= nlstate ; cpt ++) {
         /*       k=2+nlstate*(2*cpt-2); */
         k=2+(nlstate+1)*(cpt-1);
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
         fprintf(ficgp,"set ter png small size 320, 240\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           
         */
         for (i=1; i< nlstate ; i ++) {
           fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1);
           /*      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
           
         } 
         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
       }
     }
     
     /* CV preval stable (period) */
     for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
         k=3;
         fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
         fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   set ter png small size 320, 240\n\
   unset log y\n\
   plot [%.f:%.f]  ", ageminpar, agemaxpar);
         for (i=1; i<= nlstate ; i ++){
           if(i==1)
             fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
           else
             fprintf(ficgp,", '' ");
           l=(nlstate+ndeath)*(i-1)+1;
           fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
           for (j=1; j<= (nlstate-1) ; j ++)
             fprintf(ficgp,"+$%d",k+l+j);
           fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
         } /* nlstate */
         fprintf(ficgp,"\n");
       } /* end cpt state*/ 
     } /* end covariate */  
     
     /* proba elementaires */
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             jk++; 
             fprintf(ficgp,"\n");
           }
         }
       }
      }
     /*goto avoid;*/
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        for(jk=1; jk <=m; jk++) {
          fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
          if (ng==2)
            fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
          else
            fprintf(ficgp,"\nset title \"Probability\"\n");
          fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
          for(k2=1; k2<=nlstate; k2++) {
            k3=i;
            for(k=1; k<=(nlstate+ndeath); k++) {
              if (k != k2){
                if(ng==2)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                else
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;/* To be checked else nbcode[0][0] wrong */
                for(j=3; j <=ncovmodel; j++) {
                  /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /\* Bug valgrind *\/ */
                  /*        /\*fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);*\/ */
                  /*        ij++; */
                  /* } */
                  /* else */
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
                fprintf(ficgp,")/(1");
                
                for(k1=1; k1 <=nlstate; k1++){   
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
                  for(j=3; j <=ncovmodel; j++){
                    /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { */
                    /*   fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); */
                    /*   ij++; */
                    /* } */
                    /* else */
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                  }
                  fprintf(ficgp,")");
                }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
              }
            } /* end k */
          } /* end k2 */
        } /* end jk */
      } /* end ng */
    avoid:
      fflush(ficgp); 
   }  /* end gnuplot */
   
   
   /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
     int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
     double age;
   
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          we use a 5 terms etc. until the borders are no more concerned. 
       */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
           }
         }/* end age */
       }/* end mob */
     }else return -1;
     return 0;
   }/* End movingaverage */
   
   
   /************** Forecasting ******************/
   prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
     int *popage;
     double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   
   
   /**************** function prwizard **********************/
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     /* Wizard to print covariance matrix template */
   
     char ca[32], cb[32], cc[32];
     int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
   } /* end of prwizard */
   /******************* Gompertz Likelihood ******************************/
   double gompertz(double x[])
   { 
     double A,B,L=0.0,sump=0.,num=0.;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
   
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
                +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           L=L+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
    
     return -2*L*num/sump;
   }
   
   #ifdef GSL
   /******************* Gompertz_f Likelihood ******************************/
   double gompertz_f(const gsl_vector *v, void *params)
   { 
     double A,B,LL=0.0,sump=0.,num=0.;
     double *x= (double *) v->data;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
     printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
                +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           LL=LL+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
     printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
    
     return -2*LL*num/sump;
   }
   #endif
   
   /******************* Printing html file ***********/
   void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,  double p[],double **matcov,double agemortsup){
     int i,k;
   
     fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
     fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
     for (i=1;i<=2;i++) 
       fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
     fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
     fprintf(fichtm,"</ul>");
   
   fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
   
    fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
   
    for (k=agegomp;k<(agemortsup-2);k++) 
      fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
   
    
     fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
     fprintf(ficgp,"set out \"graphmort.png\"\n "); 
     fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
     fprintf(ficgp, "set ter png small size 320, 240\n set log y\n"); 
     /* fprintf(ficgp, "set size 0.65,0.65\n"); */
     fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
   
   } 
   
   int readdata(char datafile[], int firstobs, int lastobs, int *imax)
   {
   
     /*-------- data file ----------*/
     FILE *fic;
     char dummy[]="                         ";
     int i, j, n;
     int linei, month, year,iout;
     char line[MAXLINE], linetmp[MAXLINE];
     char stra[80], strb[80];
     char *stratrunc;
     int lstra;
   
   
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem while opening datafile: %s\n", datafile);return 1;
       fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
     }
   
     i=1;
     linei=0;
     while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
       linei=linei+1;
       for(j=strlen(line); j>=0;j--){  /* Untabifies line */
         if(line[j] == '\t')
           line[j] = ' ';
       }
       for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
         ;
       };
       line[j+1]=0;  /* Trims blanks at end of line */
       if(line[0]=='#'){
         fprintf(ficlog,"Comment line\n%s\n",line);
         printf("Comment line\n%s\n",line);
         continue;
       }
       trimbb(linetmp,line); /* Trims multiple blanks in line */
       for (j=0; line[j]!='\0';j++){
         line[j]=linetmp[j];
       }
     
   
       for (j=maxwav;j>=1;j--){
         cutv(stra, strb, line, ' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
         /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
             fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);
             return 1;
           }
         }
         s[j][i]=lval;
         
         strcpy(line,stra);
         cutv(stra, strb,line,' ');
         if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
         }
         else  if(iout=sscanf(strb,"%s.",dummy) != 0){
           month=99;
           year=9999;
         }else{
           printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);fflush(ficlog);
           return 1;
         }
         anint[j][i]= (double) year; 
         mint[j][i]= (double)month; 
         strcpy(line,stra);
       } /* ENd Waves */
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.",dummy) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
       }
       andc[i]=(double) year; 
       moisdc[i]=(double) month; 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.", dummy) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
       }
       if (year==9999) {
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given.  Exiting.\n",strb, linei,i,line);
         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
   
       }
       annais[i]=(double)(year);
       moisnais[i]=(double)(month); 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       errno=0;
       dval=strtod(strb,&endptr); 
       if( strb[0]=='\0' || (*endptr != '\0')){
         printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fprintf(ficlog,"Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fflush(ficlog);
         return 1;
       }
       weight[i]=dval; 
       strcpy(line,stra);
       
       for (j=ncovcol;j>=1;j--){
         cutv(stra, strb,line,' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);
             fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);fflush(ficlog);
             return 1;
           }
         }
         if(lval <-1 || lval >1){
           printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);
           fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
           return 1;
         }
         covar[j][i]=(double)(lval);
         strcpy(line,stra);
       }  
       lstra=strlen(stra);
        
       if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
         stratrunc = &(stra[lstra-9]);
         num[i]=atol(stratrunc);
       }
       else
         num[i]=atol(stra);
       /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
         printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
       
       i=i+1;
     } /* End loop reading  data */
   
     *imax=i-1; /* Number of individuals */
     fclose(fic);
    
     return (0);
     endread:
       printf("Exiting readdata: ");
       fclose(fic);
       return (1);
   
   
   
   }
   void removespace(char *str) {
     char *p1 = str, *p2 = str;
     do
       while (*p2 == ' ')
         p2++;
     while (*p1++ = *p2++);
   }
   
   int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
      * Model  V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age
      * - cptcovt total number of covariates of the model nbocc(+)+1 = 8
      * - cptcovn or number of covariates k of the models excluding age*products =6
      * - cptcovage number of covariates with age*products =2
      * - cptcovs number of simple covariates
      * - Tvar[k] is the id of the kth covariate Tvar[1]@12 {1, 2, 3, 8, 10, 11, 8, 3, 7, 8, 5, 6}, thus Tvar[5=V7*V8]=10
      *     which is a new column after the 9 (ncovcol) variables. 
      * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
      * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
      *    Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
      * - Tvard[k]  p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
    */
   {
     int i, j, k, ks;
     int i1, j1, k1, k2;
     char modelsav[80];
     char stra[80], strb[80], strc[80], strd[80],stre[80];
   
     /*removespace(model);*/
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
       j=nbocc(model,'+'); /**< j=Number of '+' */
       j1=nbocc(model,'*'); /**< j1=Number of '*' */
       cptcovs=j+1-j1; /**<  Number of simple covariates V1+V2*age+V3 +V3*V4=> V1 + V3 =2  */
       cptcovt= j+1; /* Number of total covariates in the model V1 + V2*age+ V3 + V3*V4=> 4*/
                     /* including age products which are counted in cptcovage.
                     /* but the covariates which are products must be treated separately: ncovn=4- 2=2 (V1+V3). */
       cptcovprod=j1; /**< Number of products  V1*V2 +v3*age = 2 */
       cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1  */
       strcpy(modelsav,model); 
       if (strstr(model,"AGE") !=0){
         printf("Error. AGE must be in lower case 'age' model=%s ",model);
         fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
         return 1;
       }
       if (strstr(model,"v") !=0){
         printf("Error. 'v' must be in upper case 'V' model=%s ",model);
         fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
         return 1;
       }
       
       /*   Design
        *  V1   V2   V3   V4  V5  V6  V7  V8  V9 Weight
        *  <          ncovcol=8                >
        * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
        *   k=  1    2      3       4     5       6      7        8
        *  cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
        *  covar[k,i], value of kth covariate if not including age for individual i:
        *       covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
        *  Tvar[k] # of the kth covariate:  Tvar[1]=2  Tvar[4]=3 Tvar[8]=8
        *       if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and 
        *  Tage[++cptcovage]=k
        *       if products, new covar are created after ncovcol with k1
        *  Tvar[k]=ncovcol+k1; # of the kth covariate product:  Tvar[5]=ncovcol+1=10  Tvar[6]=ncovcol+1=11
        *  Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
        *  Tvard[k1][1]=m Tvard[k1][2]=m; Tvard[1][1]=5 (V5) Tvard[1][2]=6 Tvard[2][1]=7 (V7) Tvard[2][2]=8
        *  Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
        *  Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
        *  V1   V2   V3   V4  V5  V6  V7  V8  V9  V10  V11
        *  <          ncovcol=8                >
        *       Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8    d1   d1   d2  d2
        *          k=  1    2      3       4     5       6      7        8    9   10   11  12
        *     Tvar[k]= 2    1      3       3    10      11      8        8    5    6    7   8
        * p Tvar[1]@12={2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
        * p Tprod[1]@2={                         6, 5}
        *p Tvard[1][1]@4= {7, 8, 5, 6}
        * covar[k][i]= V2   V1      ?      V3    V5*V6?   V7*V8?  ?       V8   
        *  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
        *How to reorganize?
        * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
        * Tvars {2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
        *       {2,   1,     4,      8,    5,      6,     3,       7}
        * Struct []
        */
   
       /* This loop fills the array Tvar from the string 'model'.*/
       /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
       /*   modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4  */
       /*  k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
       /*  k=3 V4 Tvar[k=3]= 4 (from V4) */
       /*  k=2 V1 Tvar[k=2]= 1 (from V1) */
       /*  k=1 Tvar[1]=2 (from V2) */
       /*  k=5 Tvar[5] */
       /* for (k=1; k<=cptcovn;k++) { */
       /*  cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
       /*  } */
       /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
       /*
        * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
       for(k=cptcovt; k>=1;k--) /**< Number of covariates */
           Tvar[k]=0;
       cptcovage=0;
       for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
         cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' 
                                        modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
           cutl(strc,strd,strb,'*'); /**< strd*strc  Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
           if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
             /* covar is not filled and then is empty */
             cptcovprod--;
             cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
             Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2 */
             cptcovage++; /* Sums the number of covariates which include age as a product */
             Tage[cptcovage]=k;  /* Tage[1] = 4 */
             /*printf("stre=%s ", stre);*/
           } else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutl(stre,strb,strc,'V');
             Tvar[k]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=k;
           } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/
             /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
             cptcovn++;
             cptcovprodnoage++;k1++;
             cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
             Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
                                     because this model-covariate is a construction we invent a new column
                                     ncovcol + k1
                                     If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
                                     Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
             cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */
             Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
             Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
             k2=k2+2;
             Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
             Tvar[cptcovt+k2+1]=Tvard[k1][2];  /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
             for (i=1; i<=lastobs;i++){
               /* Computes the new covariate which is a product of
                  covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
               covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
             }
           } /* End age is not in the model */
         } /* End if model includes a product */
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
           cutl(strd,strc,strb,'V');
           ks++; /**< Number of simple covariates */
           cptcovn++;
           Tvar[k]=atoi(strd);
         }
         strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+V1+V4 */ 
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);*/
   
   
     return (0); /* with covar[new additional covariate if product] and Tage if age */ 
     endread:
       printf("Exiting decodemodel: ");
       return (1);
   }
   
   calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
   {
     int i, m;
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           *nberr++;
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           *nberr++;
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if ((int)andc[i]!=9999){
                   nbwarn++;
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] < *agemin){ 
               *agemin=agev[m][i];
               printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
             }
             else if(agev[m][i] >*agemax){
               *agemax=agev[m][i];
               /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           *nberr++;
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           return 1;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax); 
   
     return (0);
     endread:
       printf("Exiting calandcheckages: ");
       return (1);
   }
   
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
   #ifdef GSL
     const gsl_multimin_fminimizer_type *T;
     size_t iteri = 0, it;
     int rval = GSL_CONTINUE;
     int status = GSL_SUCCESS;
     double ssval;
   #endif
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
     int linei, month, year,iout;
     int jj, ll, li, lj, lk, imk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int itimes;
     int NDIM=2;
     int vpopbased=0;
   
     char ca[32], cb[32], cc[32];
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     struct stat info;
     double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE], pathimach[MAXLINE]; 
     char **bp, *tok, *val; /* pathtot */
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,*tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     int agemortsup;
     float  sumlpop=0.;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
     double **ximort;
     char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
     int *dcwave;
   
     char z[1]="c", occ;
   
     /*char  *strt;*/
     char strtend[80];
   
     long total_usecs;
    
   /*   setlocale (LC_ALL, ""); */
   /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   /*   textdomain (PACKAGE); */
   /*   setlocale (LC_CTYPE, ""); */
   /*   setlocale (LC_MESSAGES, ""); */
   
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     rstart_time = time(NULL);  
     /*  (void) gettimeofday(&start_time,&tzp);*/
     start_time = *localtime(&rstart_time);
     curr_time=start_time;
     /*tml = *localtime(&start_time.tm_sec);*/
     /* strcpy(strstart,asctime(&tml)); */
     strcpy(strstart,asctime(&start_time));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tm_sec = tp.tm_sec +86400; */
   /*  tm = *localtime(&start_time.tm_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tm_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     nberr=0; /* Number of errors and warnings */
     nbwarn=0;
     getcwd(pathcd, size);
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       fgets(pathr,FILENAMELENGTH,stdin);
       i=strlen(pathr);
       if(pathr[i-1]=='\n')
         pathr[i-1]='\0';
       i=strlen(pathr);
       if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
         pathr[i-1]='\0';
      for (tok = pathr; tok != NULL; ){
         printf("Pathr |%s|\n",pathr);
         while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
         printf("val= |%s| pathr=%s\n",val,pathr);
         strcpy (pathtot, val);
         if(pathr[0] == '\0') break; /* Dirty */
       }
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     /* Split argv[0], imach program to get pathimach */
     printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
     split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
     printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
    /*   strcpy(pathimach,argv[0]); */
     /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path); /* Can be a relative path */
     if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
       printf("Current directory %s!\n",pathcd);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s\n%s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: \n");
     fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     printf("Local time (at start):%s",strstart);
     fprintf(ficlog,"Local time (at start): %s",strstart);
     fflush(ficlog);
   /*   (void) gettimeofday(&curr_time,&tzp); */
   /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
       fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
       fflush(ficlog);
       /* goto end; */
       exit(70); 
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       fputs(line,stdout);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       fputs(line, stdout);
       //puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n);  /**< used in readdata */
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
     /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
        v1+v2*age+v2*v3 makes cptcovn = 3
     */
     if (strlen(model)>1) 
       ncovmodel=2+nbocc(model,'+')+1; /*Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7*/
     else
       ncovmodel=2;
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
     npar= nforce*ncovmodel; /* Number of parameters like aij*/
     if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
       printf("Too complex model for current IMaCh: npar=(nlstate+ndeath-1)*nlstate*ncovmodel=%d >= %d(MAXPARM) or nlstate=%d >= %d(NLSTATEMAX) or ndeath=%d >= %d(NDEATHMAX) or ncovmodel=(k+age+#of+signs)=%d(NCOVMAX) >= %d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fprintf(ficlog,"Too complex model for current IMaCh: %d >=%d(MAXPARM) or %d >=%d(NLSTATEMAX) or %d >=%d(NDEATHMAX) or %d(NCOVMAX) >=%d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fflush(stdout);
       fclose (ficlog);
       goto end;
     }
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     delti=delti3[1][1];
     /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
     if(mle==-1){ /* Print a wizard for help writing covariance matrix */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       fclose (ficparo);
       fclose (ficlog);
       goto end;
       exit(0);
     }
     else if(mle==-3) {
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       matcov=matrix(1,npar,1,npar);
     }
     else{
       /* Read guessed parameters */
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
       
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       for(i=1; i <=nlstate; i++){
         j=0;
         for(jj=1; jj <=nlstate+ndeath; jj++){
           if(jj==i) continue;
           j++;
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1 != i) && (j1 != j)){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
   It might be a problem of design; if ncovcol and the model are correct\n \
   run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           fprintf(ficparo,"%1d%1d",i1,j1);
           if(mle==1)
             printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar," %lf",&param[i][j][k]);
             if(mle==1){
               printf(" %lf",param[i][j][k]);
               fprintf(ficlog," %lf",param[i][j][k]);
             }
             else
               fprintf(ficlog," %lf",param[i][j][k]);
             fprintf(ficparo," %lf",param[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           if(mle==1)
             printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficparo,"\n");
         }
       }  
       fflush(ficlog);
   
       /* Reads scales values */
       p=param[1][1];
       
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
   
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath-1; j++){
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1-i)*(j1-j)!=0){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           printf("%1d%1d",i,j);
           fprintf(ficparo,"%1d%1d",i1,j1);
           fprintf(ficlog,"%1d%1d",i1,j1);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar,"%le",&delti3[i][j][k]);
             printf(" %le",delti3[i][j][k]);
             fprintf(ficparo," %le",delti3[i][j][k]);
             fprintf(ficlog," %le",delti3[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           printf("\n");
           fprintf(ficparo,"\n");
           fprintf(ficlog,"\n");
         }
       }
       fflush(ficlog);
   
       /* Reads covariance matrix */
       delti=delti3[1][1];
   
   
       /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
     
       matcov=matrix(1,npar,1,npar);
       for(i=1; i <=npar; i++)
         for(j=1; j <=npar; j++) matcov[i][j]=0.;
         
       for(i=1; i <=npar; i++){
         fscanf(ficpar,"%s",str);
         if(mle==1)
           printf("%s",str);
         fprintf(ficlog,"%s",str);
         fprintf(ficparo,"%s",str);
         for(j=1; j <=i; j++){
           fscanf(ficpar," %le",&matcov[i][j]);
           if(mle==1){
             printf(" %.5le",matcov[i][j]);
           }
           fprintf(ficlog," %.5le",matcov[i][j]);
           fprintf(ficparo," %.5le",matcov[i][j]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
       for(i=1; i <=npar; i++)
         for(j=i+1;j<=npar;j++)
           matcov[i][j]=matcov[j][i];
       
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       
       fflush(ficlog);
       
       /*-------- Rewriting parameter file ----------*/
       strcpy(rfileres,"r");    /* "Rparameterfile */
       strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
       strcat(rfileres,".");    /* */
       strcat(rfileres,optionfilext);    /* Other files have txt extension */
       if((ficres =fopen(rfileres,"w"))==NULL) {
         printf("Problem writing new parameter file: %s\n", fileres);goto end;
         fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
       }
       fprintf(ficres,"#%s\n",version);
     }    /* End of mle != -3 */
   
   
     n= lastobs;
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */ 
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
   
     /* Reads data from file datafile */
     if (readdata(datafile, firstobs, lastobs, &imx)==1)
       goto end;
   
     /* Calculation of the number of parameters from char model */
       /*    modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 
           k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
           k=3 V4 Tvar[k=3]= 4 (from V4)
           k=2 V1 Tvar[k=2]= 1 (from V1)
           k=1 Tvar[1]=2 (from V2)
       */
     Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
     /*  V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs). 
         For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4, 
         Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
     */
     /* For model-covariate k tells which data-covariate to use but
       because this model-covariate is a construction we invent a new column
       ncovcol + k1
       If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
       Tvar[3=V1*V4]=4+1 etc */
     Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
     /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
        if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2)
     */
     Tvaraff=ivector(1,NCOVMAX); /* Unclear */
     Tvard=imatrix(1,NCOVMAX,1,2); /* n=Tvard[k1][1]  and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm
                               * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd. 
                               * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
     Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
                            4 covariates (3 plus signs)
                            Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
                         */  
   
     if(decodemodel(model, lastobs) == 1)
       goto end;
   
     if((double)(lastobs-imx)/(double)imx > 1.10){
       nbwarn++;
       printf("Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
       fprintf(ficlog,"Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
     }
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
       for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
     }
   
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
       goto end;
   
   
     agegomp=(int)agemin;
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
     /* */
     
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
     /* */
    
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     Ndum =ivector(-1,NCOVMAX);  
     if (ncovmodel > 2)
       tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
   
     codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
     /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
     h=0;
   
   
     /*if (cptcovn > 0) */
         
    
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
       for(i=1; i <=pow(2,cptcoveff-k);i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */ 
         for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
           for(cpt=1; cpt <=pow(2,k-1); cpt++){  /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */ 
             h++;
             if (h>m) 
               h=1;
             /**< codtab(h,k)  k   = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
              *     h     1     2     3     4
              *______________________________  
              *     1 i=1 1 i=1 1 i=1 1 i=1 1
              *     2     2     1     1     1
              *     3 i=2 1     2     1     1
              *     4     2     2     1     1
              *     5 i=3 1 i=2 1     2     1
              *     6     2     1     2     1
              *     7 i=4 1     2     2     1
              *     8     2     2     2     1
              *     9 i=5 1 i=3 1 i=2 1     1
              *    10     2     1     1     1
              *    11 i=6 1     2     1     1
              *    12     2     2     1     1
              *    13 i=7 1 i=4 1     2     1    
              *    14     2     1     2     1
              *    15 i=8 1     2     2     1
              *    16     2     2     2     1
              */
             codtab[h][k]=j;
             /*codtab[h][Tvar[k]]=j;*/
             printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]);
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
          printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
   
    free_ivector(Ndum,-1,NCOVMAX);
   
   
       
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     if(mle==-3)
       strcat(optionfilegnuplot,"-mort");
     strcat(optionfilegnuplot,".gp");
   
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       //fprintf(ficgp,"set missing 'NaNq'\n");
       fprintf(ficgp,"set datafile missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname); /* Main html file */
     if(mle==-3)
       strcat(optionfilehtm,"-mort");
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm);
       exit(0);
     }
   
     strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
     strcat(optionfilehtmcov,"-cov.htm");
     if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtmcov), exit(0);
     }
     else{
     fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
             optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
    - Log file of the run: <a href=\"%s\">%s</a><br>\n\
    - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
    - Date and time at start: %s</ul>\n",\
             optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
             optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
             fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
     chdir(optionfilefiname); /* Move to directory named optionfile */
     
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
   
     fprintf(fichtm,"\n");
     fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
             imx,agemin,agemax,jmin,jmax,jmean);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
   
     if (mle==-3){
       ximort=matrix(1,NDIM,1,NDIM); 
   /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
       cens=ivector(1,n);
       ageexmed=vector(1,n);
       agecens=vector(1,n);
       dcwave=ivector(1,n);
    
       for (i=1; i<=imx; i++){
         dcwave[i]=-1;
         for (m=firstpass; m<=lastpass; m++)
           if (s[m][i]>nlstate) {
             dcwave[i]=m;
             /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
             break;
           }
       }
   
       for (i=1; i<=imx; i++) {
         if (wav[i]>0){
           ageexmed[i]=agev[mw[1][i]][i];
           j=wav[i];
           agecens[i]=1.; 
   
           if (ageexmed[i]> 1 && wav[i] > 0){
             agecens[i]=agev[mw[j][i]][i];
             cens[i]= 1;
           }else if (ageexmed[i]< 1) 
             cens[i]= -1;
           if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
             cens[i]=0 ;
         }
         else cens[i]=-1;
       }
       
       for (i=1;i<=NDIM;i++) {
         for (j=1;j<=NDIM;j++)
           ximort[i][j]=(i == j ? 1.0 : 0.0);
       }
       
       /*p[1]=0.0268; p[NDIM]=0.083;*/
       /*printf("%lf %lf", p[1], p[2]);*/
       
       
   #ifdef GSL
       printf("GSL optimization\n");  fprintf(ficlog,"Powell\n");
   #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) --------------*/
   #include "prevlim.h"  /* Use ficrespl, ficlog */
       fclose(ficrespl);
   
   #ifdef FREEEXIT2
   #include "freeexit2.h"
   #endif
   
       /*------------- h Pij x at various ages ------------*/
   #include "hpijx.h"
       fclose(ficrespij);
   
     /*-------------- Variance of one-step probabilities---*/
       k=1;
       varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
   
   
       probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for(i=1;i<=AGESUP;i++)
         for(j=1;j<=NCOVMAX;j++)
           for(k=1;k<=NCOVMAX;k++)
             probs[i][j][k]=0.;
   
       /*---------- Forecasting ------------------*/
       /*if((stepm == 1) && (strcmp(model,".")==0)){*/
       if(prevfcast==1){
         /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
         /*      }  */
         /*      else{ */
         /*        erreur=108; */
         /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*      } */
       }
     
   
       /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
   
       prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
       /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
           ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
       */
   
       if (mobilav!=0) {
         mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
           fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
           printf(" Error in movingaverage mobilav=%d\n",mobilav);
         }
       }
   
   
       /*---------- Health expectancies, no variances ------------*/
   
       strcpy(filerese,"e");
       strcat(filerese,fileres);
       if((ficreseij=fopen(filerese,"w"))==NULL) {
         printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
         fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       }
       printf("Computing Health Expectancies: result on file '%s' \n", filerese);
       fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficreseij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficreseij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);  
         
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         /*}*/
       }
       fclose(ficreseij);
   
   
       /*---------- Health expectancies and variances ------------*/
   
   
       strcpy(filerest,"t");
       strcat(filerest,fileres);
       if((ficrest=fopen(filerest,"w"))==NULL) {
         printf("Problem with total LE resultfile: %s\n", filerest);goto end;
         fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
       }
       printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
       fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
   
   
       strcpy(fileresstde,"stde");
       strcat(fileresstde,fileres);
       if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
         printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
         fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
       }
       printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
       fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
   
       strcpy(filerescve,"cve");
       strcat(filerescve,fileres);
       if((ficrescveij=fopen(filerescve,"w"))==NULL) {
         printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
         fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
       }
       printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
       fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
   
       strcpy(fileresv,"v");
       strcat(fileresv,fileres);
       if((ficresvij=fopen(fileresv,"w"))==NULL) {
         printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
         fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
       }
       printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
       fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficrest,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrest,"******\n");
   
           fprintf(ficresstdeij,"\n#****** ");
           fprintf(ficrescveij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficresstdeij,"******\n");
           fprintf(ficrescveij,"******\n");
   
           fprintf(ficresvij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);  
           /*
            */
           /* goto endfree; */
    
           vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           pstamp(ficrest);
   
   
           for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
             oldm=oldms;savm=savms; /* Segmentation fault */
             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,NCOVMAX,1,2);
       free_imatrix(s,1,maxwav+1,1,n);
       free_matrix(anint,1,maxwav,1,n); 
       free_matrix(mint,1,maxwav,1,n);
       free_ivector(cod,1,n);
       free_ivector(tab,1,NCOVMAX);
       fclose(ficresstdeij);
       fclose(ficrescveij);
       fclose(ficresvij);
       fclose(ficrest);
       fclose(ficpar);
     
       /*------- Variance of period (stable) prevalence------*/   
   
       strcpy(fileresvpl,"vpl");
       strcat(fileresvpl,fileres);
       if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
         printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
         exit(0);
       }
       printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
   
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficresvpl,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvpl,"******\n");
         
           varpl=matrix(1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
           free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
         /*}*/
       }
   
       fclose(ficresvpl);
   
       /*---------- End : free ----------------*/
       if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
     }  /* mle==-3 arrives here for freeing */
    endfree:
       free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
       free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(covar,0,NCOVMAX,1,n);
       free_matrix(matcov,1,npar,1,npar);
       /*free_vector(delti,1,npar);*/
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       free_matrix(agev,1,maxwav,1,imx);
       free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   
       free_ivector(ncodemax,1,NCOVMAX);
       free_ivector(Tvar,1,NCOVMAX);
       free_ivector(Tprod,1,NCOVMAX);
       free_ivector(Tvaraff,1,NCOVMAX);
       free_ivector(Tage,1,NCOVMAX);
   
       free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
       free_imatrix(codtab,1,100,1,10);
     fflush(fichtm);
     fflush(ficgp);
     
   
     if((nberr >0) || (nbwarn>0)){
       printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
       fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
     }else{
       printf("End of Imach\n");
       fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     /*(void) gettimeofday(&end_time,&tzp);*/
     rend_time = time(NULL);  
     end_time = *localtime(&rend_time);
     /* tml = *localtime(&end_time.tm_sec); */
     strcpy(strtend,asctime(&end_time));
     printf("Local time at start %s\nLocal time at end   %s",strstart, strtend); 
     fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
     printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
   
     printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
     fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
     fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
     /*  printf("Total time was %d uSec.\n", total_usecs);*/
   /*   if(fileappend(fichtm,optionfilehtm)){ */
     fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtm);
     fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtmcov);
     fclose(ficgp);
     fclose(ficlog);
     /*------ End -----------*/
   
   
      printf("Before Current directory %s!\n",pathcd);
      if(chdir(pathcd) != 0)
       printf("Can't move to directory %s!\n",path);
     if(getcwd(pathcd,MAXLINE) > 0)
       printf("Current directory %s!\n",pathcd);
     /*strcat(plotcmd,CHARSEPARATOR);*/
     sprintf(plotcmd,"gnuplot");
   #ifdef _WIN32
     sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
   #endif
     if(!stat(plotcmd,&info)){
       printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
       if(!stat(getenv("GNUPLOTBIN"),&info)){
         printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #ifdef __unix
       strcpy(plotcmd,GNUPLOTPROGRAM);
       if(!stat(plotcmd,&info)){
         printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #endif
     }else
       strcpy(pplotcmd,plotcmd);
     
     sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
     printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
   
     if((outcmd=system(plotcmd)) != 0){
       printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
       printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
       sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
       if((outcmd=system(plotcmd)) != 0)
         printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
     }
     printf(" Successful, please wait...");
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
       scanf("%s",z);
   /*     if (z[0] == 'c') system("./imach"); */
       if (z[0] == 'e') {
   #ifdef __APPLE__
         sprintf(pplotcmd, "open %s", optionfilehtm);
   #elif __linux
         sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
   #else
         sprintf(pplotcmd, "%s", optionfilehtm);
   #endif
         printf("Starting browser with: %s",pplotcmd);fflush(stdout);
         system(pplotcmd);
       }
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     end:
     while (z[0] != 'q') {
       printf("\nType  q for exiting: ");
       scanf("%s",z);
     }
   }

Removed from v.1.48  
changed lines
  Added in v.1.159


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