Diff for /imach/src/imach.c between versions 1.50 and 1.163

version 1.50, 2002/06/26 23:25:02 version 1.163, 2014/12/16 10:30:11
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.163  2014/12/16 10:30:11  brouard
      * imach.c (Module): Merging 1.61 to 1.162
   This program computes Healthy Life Expectancies from  
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    Revision 1.162  2014/09/25 11:43:39  brouard
   first survey ("cross") where individuals from different ages are    Summary: temporary backup 0.99!
   interviewed on their health status or degree of disability (in the  
   case of a health survey which is our main interest) -2- at least a    Revision 1.1  2014/09/16 11:06:58  brouard
   second wave of interviews ("longitudinal") which measure each change    Summary: With some code (wrong) for nlopt
   (if any) in individual health status.  Health expectancies are  
   computed from the time spent in each health state according to a    Author:
   model. More health states you consider, more time is necessary to reach the  
   Maximum Likelihood of the parameters involved in the model.  The    Revision 1.161  2014/09/15 20:41:41  brouard
   simplest model is the multinomial logistic model where pij is the    Summary: Problem with macro SQR on Intel compiler
   probability to be observed in state j at the second wave  
   conditional to be observed in state i at the first wave. Therefore    Revision 1.160  2014/09/02 09:24:05  brouard
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    *** empty log message ***
   '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 1.159  2014/09/01 10:34:10  brouard
   where the markup *Covariates have to be included here again* invites    Summary: WIN32
   you to do it.  More covariates you add, slower the    Author: Brouard
   convergence.  
     Revision 1.158  2014/08/27 17:11:51  brouard
   The advantage of this computer programme, compared to a simple    *** empty log message ***
   multinomial logistic model, is clear when the delay between waves is not  
   identical for each individual. Also, if a individual missed an    Revision 1.157  2014/08/27 16:26:55  brouard
   intermediate interview, the information is lost, but taken into    Summary: Preparing windows Visual studio version
   account using an interpolation or extrapolation.      Author: Brouard
   
   hPijx is the probability to be observed in state i at age x+h    In order to compile on Visual studio, time.h is now correct and time_t
   conditional to the observed state i at age x. The delay 'h' can be    and tm struct should be used. difftime should be used but sometimes I
   split into an exact number (nh*stepm) of unobserved intermediate    just make the differences in raw time format (time(&now).
   states. This elementary transition (by month or quarter trimester,    Trying to suppress #ifdef LINUX
   semester or year) is model as a multinomial logistic.  The hPx    Add xdg-open for __linux in order to open default browser.
   matrix is simply the matrix product of nh*stepm elementary matrices  
   and the contribution of each individual to the likelihood is simply    Revision 1.156  2014/08/25 20:10:10  brouard
   hPijx.    *** empty log message ***
   
   Also this programme outputs the covariance matrix of the parameters but also    Revision 1.155  2014/08/25 18:32:34  brouard
   of the life expectancies. It also computes the prevalence limits.    Summary: New compile, minor changes
      Author: Brouard
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).  
            Institut national d'études démographiques, Paris.    Revision 1.154  2014/06/20 17:32:08  brouard
   This software have been partly granted by Euro-REVES, a concerted action    Summary: Outputs now all graphs of convergence to period prevalence
   from the European Union.  
   It is copyrighted identically to a GNU software product, ie programme and    Revision 1.153  2014/06/20 16:45:46  brouard
   software can be distributed freely for non commercial use. Latest version    Summary: If 3 live state, convergence to period prevalence on same graph
   can be accessed at http://euroreves.ined.fr/imach .    Author: Brouard
   **********************************************************************/  
      Revision 1.152  2014/06/18 17:54:09  brouard
 #include <math.h>    Summary: open browser, use gnuplot on same dir than imach if not found in the path
 #include <stdio.h>  
 #include <stdlib.h>    Revision 1.151  2014/06/18 16:43:30  brouard
 #include <unistd.h>    *** empty log message ***
   
 #define MAXLINE 256    Revision 1.150  2014/06/18 16:42:35  brouard
 #define GNUPLOTPROGRAM "gnuplot"    Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/    Author: brouard
 #define FILENAMELENGTH 80  
 /*#define DEBUG*/    Revision 1.149  2014/06/18 15:51:14  brouard
 #define windows    Summary: Some fixes in parameter files errors
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    Author: Nicolas Brouard
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */  
     Revision 1.148  2014/06/17 17:38:48  brouard
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    Summary: Nothing new
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    Author: Brouard
   
 #define NINTERVMAX 8    Just a new packaging for OS/X version 0.98nS
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */  
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    Revision 1.147  2014/06/16 10:33:11  brouard
 #define NCOVMAX 8 /* Maximum number of covariates */    *** empty log message ***
 #define MAXN 20000  
 #define YEARM 12. /* Number of months per year */    Revision 1.146  2014/06/16 10:20:28  brouard
 #define AGESUP 130    Summary: Merge
 #define AGEBASE 40    Author: Brouard
 #ifdef windows  
 #define DIRSEPARATOR '\\'    Merge, before building revised version.
 #define ODIRSEPARATOR '/'  
 #else    Revision 1.145  2014/06/10 21:23:15  brouard
 #define DIRSEPARATOR '/'    Summary: Debugging with valgrind
 #define ODIRSEPARATOR '\\'    Author: Nicolas Brouard
 #endif  
     Lot of changes in order to output the results with some covariates
 char version[80]="Imach version 0.8i, June 2002, INED-EUROREVES ";    After the Edimburgh REVES conference 2014, it seems mandatory to
 int erreur; /* Error number */    improve the code.
 int nvar;    No more memory valgrind error but a lot has to be done in order to
 int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;    continue the work of splitting the code into subroutines.
 int npar=NPARMAX;    Also, decodemodel has been improved. Tricode is still not
 int nlstate=2; /* Number of live states */    optimal. nbcode should be improved. Documentation has been added in
 int ndeath=1; /* Number of dead states */    the source code.
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  
 int popbased=0;    Revision 1.143  2014/01/26 09:45:38  brouard
     Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
 int *wav; /* Number of waves for this individuual 0 is possible */  
 int maxwav; /* Maxim number of waves */    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
 int jmin, jmax; /* min, max spacing between 2 waves */    (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
 int mle, weightopt;  
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    Revision 1.142  2014/01/26 03:57:36  brouard
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
 double jmean; /* Mean space between 2 waves */  
 double **oldm, **newm, **savm; /* Working pointers to matrices */    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    Revision 1.141  2014/01/26 02:42:01  brouard
 FILE *ficlog;    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
 FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;  
 FILE *ficresprobmorprev;    Revision 1.140  2011/09/02 10:37:54  brouard
 FILE *fichtm; /* Html File */    Summary: times.h is ok with mingw32 now.
 FILE *ficreseij;  
 char filerese[FILENAMELENGTH];    Revision 1.139  2010/06/14 07:50:17  brouard
 FILE  *ficresvij;    After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
 char fileresv[FILENAMELENGTH];    I remember having already fixed agemin agemax which are pointers now but not cvs saved.
 FILE  *ficresvpl;  
 char fileresvpl[FILENAMELENGTH];    Revision 1.138  2010/04/30 18:19:40  brouard
 char title[MAXLINE];    *** empty log message ***
 char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];  
 char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];    Revision 1.137  2010/04/29 18:11:38  brouard
     (Module): Checking covariates for more complex models
 char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];    than V1+V2. A lot of change to be done. Unstable.
 char filelog[FILENAMELENGTH]; /* Log file */  
 char filerest[FILENAMELENGTH];    Revision 1.136  2010/04/26 20:30:53  brouard
 char fileregp[FILENAMELENGTH];    (Module): merging some libgsl code. Fixing computation
 char popfile[FILENAMELENGTH];    of likelione (using inter/intrapolation if mle = 0) in order to
     get same likelihood as if mle=1.
 char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];    Some cleaning of code and comments added.
   
 #define NR_END 1    Revision 1.135  2009/10/29 15:33:14  brouard
 #define FREE_ARG char*    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
 #define FTOL 1.0e-10  
     Revision 1.134  2009/10/29 13:18:53  brouard
 #define NRANSI    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
 #define ITMAX 200  
     Revision 1.133  2009/07/06 10:21:25  brouard
 #define TOL 2.0e-4    just nforces
   
 #define CGOLD 0.3819660    Revision 1.132  2009/07/06 08:22:05  brouard
 #define ZEPS 1.0e-10    Many tings
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  
     Revision 1.131  2009/06/20 16:22:47  brouard
 #define GOLD 1.618034    Some dimensions resccaled
 #define GLIMIT 100.0  
 #define TINY 1.0e-20    Revision 1.130  2009/05/26 06:44:34  brouard
     (Module): Max Covariate is now set to 20 instead of 8. A
 static double maxarg1,maxarg2;    lot of cleaning with variables initialized to 0. Trying to make
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  
      Revision 1.129  2007/08/31 13:49:27  lievre
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    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 rint(a) floor(a+0.5)  
     Revision 1.128  2006/06/30 13:02:05  brouard
 static double sqrarg;    (Module): Clarifications on computing e.j
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    Revision 1.127  2006/04/28 18:11:50  brouard
     (Module): Yes the sum of survivors was wrong since
 int imx;    imach-114 because nhstepm was no more computed in the age
 int stepm;    loop. Now we define nhstepma in the age loop.
 /* Stepm, step in month: minimum step interpolation*/    (Module): In order to speed up (in case of numerous covariates) we
     compute health expectancies (without variances) in a first step
 int estepm;    and then all the health expectancies with variances or standard
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/    deviation (needs data from the Hessian matrices) which slows the
     computation.
 int m,nb;    In the future we should be able to stop the program is only health
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    expectancies and graph are needed without standard deviations.
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  
 double **pmmij, ***probs, ***mobaverage;    Revision 1.126  2006/04/28 17:23:28  brouard
 double dateintmean=0;    (Module): Yes the sum of survivors was wrong since
     imach-114 because nhstepm was no more computed in the age
 double *weight;    loop. Now we define nhstepma in the age loop.
 int **s; /* Status */    Version 0.98h
 double *agedc, **covar, idx;  
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    Revision 1.125  2006/04/04 15:20:31  lievre
     Errors in calculation of health expectancies. Age was not initialized.
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    Forecasting file added.
 double ftolhess; /* Tolerance for computing hessian */  
     Revision 1.124  2006/03/22 17:13:53  lievre
 /**************** split *************************/    Parameters are printed with %lf instead of %f (more numbers after the comma).
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    The log-likelihood is printed in the log file
 {  
    char *s;                             /* pointer */    Revision 1.123  2006/03/20 10:52:43  brouard
    int  l1, l2;                         /* length counters */    * imach.c (Module): <title> changed, corresponds to .htm file
     name. <head> headers where missing.
    l1 = strlen( path );                 /* length of path */  
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    * imach.c (Module): Weights can have a decimal point as for
    s= strrchr( path, DIRSEPARATOR );            /* find last / */    English (a comma might work with a correct LC_NUMERIC environment,
    if ( s == NULL ) {                   /* no directory, so use current */    otherwise the weight is truncated).
      /*if(strrchr(path, ODIRSEPARATOR )==NULL)    Modification of warning when the covariates values are not 0 or
        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/    1.
 #if     defined(__bsd__)                /* get current working directory */    Version 0.98g
       extern char       *getwd( );  
     Revision 1.122  2006/03/20 09:45:41  brouard
       if ( getwd( dirc ) == NULL ) {    (Module): Weights can have a decimal point as for
 #else    English (a comma might work with a correct LC_NUMERIC environment,
       extern char       *getcwd( );    otherwise the weight is truncated).
     Modification of warning when the covariates values are not 0 or
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    1.
 #endif    Version 0.98g
          return( GLOCK_ERROR_GETCWD );  
       }    Revision 1.121  2006/03/16 17:45:01  lievre
       strcpy( name, path );             /* we've got it */    * imach.c (Module): Comments concerning covariates added
    } else {                             /* strip direcotry from path */  
       s++;                              /* after this, the filename */    * imach.c (Module): refinements in the computation of lli if
       l2 = strlen( s );                 /* length of filename */    status=-2 in order to have more reliable computation if stepm is
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    not 1 month. Version 0.98f
       strcpy( name, s );                /* save file name */  
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    Revision 1.120  2006/03/16 15:10:38  lievre
       dirc[l1-l2] = 0;                  /* add zero */    (Module): refinements in the computation of lli if
    }    status=-2 in order to have more reliable computation if stepm is
    l1 = strlen( dirc );                 /* length of directory */    not 1 month. Version 0.98f
 #ifdef windows  
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    Revision 1.119  2006/03/15 17:42:26  brouard
 #else    (Module): Bug if status = -2, the loglikelihood was
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }    computed as likelihood omitting the logarithm. Version O.98e
 #endif  
    s = strrchr( name, '.' );            /* find last / */    Revision 1.118  2006/03/14 18:20:07  brouard
    s++;    (Module): varevsij Comments added explaining the second
    strcpy(ext,s);                       /* save extension */    table of variances if popbased=1 .
    l1= strlen( name);    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
    l2= strlen( s)+1;    (Module): Function pstamp added
    strncpy( finame, name, l1-l2);    (Module): Version 0.98d
    finame[l1-l2]= 0;  
    return( 0 );                         /* we're done */    Revision 1.117  2006/03/14 17:16:22  brouard
 }    (Module): varevsij Comments added explaining the second
     table of variances if popbased=1 .
     (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 /******************************************/    (Module): Function pstamp added
     (Module): Version 0.98d
 void replace(char *s, char*t)  
 {    Revision 1.116  2006/03/06 10:29:27  brouard
   int i;    (Module): Variance-covariance wrong links and
   int lg=20;    varian-covariance of ej. is needed (Saito).
   i=0;  
   lg=strlen(t);    Revision 1.115  2006/02/27 12:17:45  brouard
   for(i=0; i<= lg; i++) {    (Module): One freematrix added in mlikeli! 0.98c
     (s[i] = t[i]);  
     if (t[i]== '\\') s[i]='/';    Revision 1.114  2006/02/26 12:57:58  brouard
   }    (Module): Some improvements in processing parameter
 }    filename with strsep.
   
 int nbocc(char *s, char occ)    Revision 1.113  2006/02/24 14:20:24  brouard
 {    (Module): Memory leaks checks with valgrind and:
   int i,j=0;    datafile was not closed, some imatrix were not freed and on matrix
   int lg=20;    allocation too.
   i=0;  
   lg=strlen(s);    Revision 1.112  2006/01/30 09:55:26  brouard
   for(i=0; i<= lg; i++) {    (Module): Back to gnuplot.exe instead of wgnuplot.exe
   if  (s[i] == occ ) j++;  
   }    Revision 1.111  2006/01/25 20:38:18  brouard
   return j;    (Module): Lots of cleaning and bugs added (Gompertz)
 }    (Module): Comments can be added in data file. Missing date values
     can be a simple dot '.'.
 void cutv(char *u,char *v, char*t, char occ)  
 {    Revision 1.110  2006/01/25 00:51:50  brouard
   /* cuts string t into u and v where u is ended by char occ excluding it    (Module): Lots of cleaning and bugs added (Gompertz)
      and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)  
      gives u="abcedf" and v="ghi2j" */    Revision 1.109  2006/01/24 19:37:15  brouard
   int i,lg,j,p=0;    (Module): Comments (lines starting with a #) are allowed in data.
   i=0;  
   for(j=0; j<=strlen(t)-1; j++) {    Revision 1.108  2006/01/19 18:05:42  lievre
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    Gnuplot problem appeared...
   }    To be fixed
   
   lg=strlen(t);    Revision 1.107  2006/01/19 16:20:37  brouard
   for(j=0; j<p; j++) {    Test existence of gnuplot in imach path
     (u[j] = t[j]);  
   }    Revision 1.106  2006/01/19 13:24:36  brouard
      u[p]='\0';    Some cleaning and links added in html output
   
    for(j=0; j<= lg; j++) {    Revision 1.105  2006/01/05 20:23:19  lievre
     if (j>=(p+1))(v[j-p-1] = t[j]);    *** empty log message ***
   }  
 }    Revision 1.104  2005/09/30 16:11:43  lievre
     (Module): sump fixed, loop imx fixed, and simplifications.
 /********************** nrerror ********************/    (Module): If the status is missing at the last wave but we know
     that the person is alive, then we can code his/her status as -2
 void nrerror(char error_text[])    (instead of missing=-1 in earlier versions) and his/her
 {    contributions to the likelihood is 1 - Prob of dying from last
   fprintf(stderr,"ERREUR ...\n");    health status (= 1-p13= p11+p12 in the easiest case of somebody in
   fprintf(stderr,"%s\n",error_text);    the healthy state at last known wave). Version is 0.98
   exit(1);  
 }    Revision 1.103  2005/09/30 15:54:49  lievre
 /*********************** vector *******************/    (Module): sump fixed, loop imx fixed, and simplifications.
 double *vector(int nl, int nh)  
 {    Revision 1.102  2004/09/15 17:31:30  brouard
   double *v;    Add the possibility to read data file including tab characters.
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  
   if (!v) nrerror("allocation failure in vector");    Revision 1.101  2004/09/15 10:38:38  brouard
   return v-nl+NR_END;    Fix on curr_time
 }  
     Revision 1.100  2004/07/12 18:29:06  brouard
 /************************ free vector ******************/    Add version for Mac OS X. Just define UNIX in Makefile
 void free_vector(double*v, int nl, int nh)  
 {    Revision 1.99  2004/06/05 08:57:40  brouard
   free((FREE_ARG)(v+nl-NR_END));    *** empty log message ***
 }  
     Revision 1.98  2004/05/16 15:05:56  brouard
 /************************ivector *******************************/    New version 0.97 . First attempt to estimate force of mortality
 int *ivector(long nl,long nh)    directly from the data i.e. without the need of knowing the health
 {    state at each age, but using a Gompertz model: log u =a + b*age .
   int *v;    This is the basic analysis of mortality and should be done before any
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    other analysis, in order to test if the mortality estimated from the
   if (!v) nrerror("allocation failure in ivector");    cross-longitudinal survey is different from the mortality estimated
   return v-nl+NR_END;    from other sources like vital statistic data.
 }  
     The same imach parameter file can be used but the option for mle should be -3.
 /******************free ivector **************************/  
 void free_ivector(int *v, long nl, long nh)    Agnès, who wrote this part of the code, tried to keep most of the
 {    former routines in order to include the new code within the former code.
   free((FREE_ARG)(v+nl-NR_END));  
 }    The output is very simple: only an estimate of the intercept and of
     the slope with 95% confident intervals.
 /******************* imatrix *******************************/  
 int **imatrix(long nrl, long nrh, long ncl, long nch)    Current limitations:
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    A) Even if you enter covariates, i.e. with the
 {    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    B) There is no computation of Life Expectancy nor Life Table.
   int **m;  
      Revision 1.97  2004/02/20 13:25:42  lievre
   /* allocate pointers to rows */    Version 0.96d. Population forecasting command line is (temporarily)
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    suppressed.
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;    Revision 1.96  2003/07/15 15:38:55  brouard
   m -= nrl;    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
      rewritten within the same printf. Workaround: many printfs.
    
   /* allocate rows and set pointers to them */    Revision 1.95  2003/07/08 07:54:34  brouard
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    * imach.c (Repository):
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    (Repository): Using imachwizard code to output a more meaningful covariance
   m[nrl] += NR_END;    matrix (cov(a12,c31) instead of numbers.
   m[nrl] -= ncl;  
      Revision 1.94  2003/06/27 13:00:02  brouard
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    Just cleaning
    
   /* return pointer to array of pointers to rows */    Revision 1.93  2003/06/25 16:33:55  brouard
   return m;    (Module): On windows (cygwin) function asctime_r doesn't
 }    exist so I changed back to asctime which exists.
     (Module): Version 0.96b
 /****************** free_imatrix *************************/  
 void free_imatrix(m,nrl,nrh,ncl,nch)    Revision 1.92  2003/06/25 16:30:45  brouard
       int **m;    (Module): On windows (cygwin) function asctime_r doesn't
       long nch,ncl,nrh,nrl;    exist so I changed back to asctime which exists.
      /* free an int matrix allocated by imatrix() */  
 {    Revision 1.91  2003/06/25 15:30:29  brouard
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    * imach.c (Repository): Duplicated warning errors corrected.
   free((FREE_ARG) (m+nrl-NR_END));    (Repository): Elapsed time after each iteration is now output. It
 }    helps to forecast when convergence will be reached. Elapsed time
     is stamped in powell.  We created a new html file for the graphs
 /******************* matrix *******************************/    concerning matrix of covariance. It has extension -cov.htm.
 double **matrix(long nrl, long nrh, long ncl, long nch)  
 {    Revision 1.90  2003/06/24 12:34:15  brouard
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    (Module): Some bugs corrected for windows. Also, when
   double **m;    mle=-1 a template is output in file "or"mypar.txt with the design
     of the covariance matrix to be input.
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");    Revision 1.89  2003/06/24 12:30:52  brouard
   m += NR_END;    (Module): Some bugs corrected for windows. Also, when
   m -= nrl;    mle=-1 a template is output in file "or"mypar.txt with the design
     of the covariance matrix to be input.
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    Revision 1.88  2003/06/23 17:54:56  brouard
   m[nrl] += NR_END;    * imach.c (Repository): Create a sub-directory where all the secondary files are. Only imach, htm, gp and r(imach) are on the main directory. Correct time and other things.
   m[nrl] -= ncl;  
     Revision 1.87  2003/06/18 12:26:01  brouard
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    Version 0.96
   return m;  
 }    Revision 1.86  2003/06/17 20:04:08  brouard
     (Module): Change position of html and gnuplot routines and added
 /*************************free matrix ************************/    routine fileappend.
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  
 {    Revision 1.85  2003/06/17 13:12:43  brouard
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    * imach.c (Repository): Check when date of death was earlier that
   free((FREE_ARG)(m+nrl-NR_END));    current date of interview. It may happen when the death was just
 }    prior to the death. In this case, dh was negative and likelihood
     was wrong (infinity). We still send an "Error" but patch by
 /******************* ma3x *******************************/    assuming that the date of death was just one stepm after the
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    interview.
 {    (Repository): Because some people have very long ID (first column)
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    we changed int to long in num[] and we added a new lvector for
   double ***m;    memory allocation. But we also truncated to 8 characters (left
     truncation)
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    (Repository): No more line truncation errors.
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;    Revision 1.84  2003/06/13 21:44:43  brouard
   m -= nrl;    * imach.c (Repository): Replace "freqsummary" at a correct
     place. It differs from routine "prevalence" which may be called
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    many times. Probs is memory consuming and must be used with
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    parcimony.
   m[nrl] += NR_END;    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
   m[nrl] -= ncl;  
     Revision 1.83  2003/06/10 13:39:11  lievre
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    *** empty log message ***
   
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    Revision 1.82  2003/06/05 15:57:20  brouard
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    Add log in  imach.c and  fullversion number is now printed.
   m[nrl][ncl] += NR_END;  
   m[nrl][ncl] -= nll;  */
   for (j=ncl+1; j<=nch; j++)  /*
     m[nrl][j]=m[nrl][j-1]+nlay;     Interpolated Markov Chain
    
   for (i=nrl+1; i<=nrh; i++) {    Short summary of the programme:
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;    
     for (j=ncl+1; j<=nch; j++)    This program computes Healthy Life Expectancies from
       m[i][j]=m[i][j-1]+nlay;    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
   }    first survey ("cross") where individuals from different ages are
   return m;    interviewed on their health status or degree of disability (in the
 }    case of a health survey which is our main interest) -2- at least a
     second wave of interviews ("longitudinal") which measure each change
 /*************************free ma3x ************************/    (if any) in individual health status.  Health expectancies are
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    computed from the time spent in each health state according to a
 {    model. More health states you consider, more time is necessary to reach the
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    Maximum Likelihood of the parameters involved in the model.  The
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    simplest model is the multinomial logistic model where pij is the
   free((FREE_ARG)(m+nrl-NR_END));    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
 /***************** f1dim *************************/    'age' is age and 'sex' is a covariate. If you want to have a more
 extern int ncom;    complex model than "constant and age", you should modify the program
 extern double *pcom,*xicom;    where the markup *Covariates have to be included here again* invites
 extern double (*nrfunc)(double []);    you to do it.  More covariates you add, slower the
      convergence.
 double f1dim(double x)  
 {    The advantage of this computer programme, compared to a simple
   int j;    multinomial logistic model, is clear when the delay between waves is not
   double f;    identical for each individual. Also, if a individual missed an
   double *xt;    intermediate interview, the information is lost, but taken into
      account using an interpolation or extrapolation.  
   xt=vector(1,ncom);  
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    hPijx is the probability to be observed in state i at age x+h
   f=(*nrfunc)(xt);    conditional to the observed state i at age x. The delay 'h' can be
   free_vector(xt,1,ncom);    split into an exact number (nh*stepm) of unobserved intermediate
   return f;    states. This elementary transition (by month, quarter,
 }    semester or year) is modelled as a multinomial logistic.  The hPx
     matrix is simply the matrix product of nh*stepm elementary matrices
 /*****************brent *************************/    and the contribution of each individual to the likelihood is simply
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    hPijx.
 {  
   int iter;    Also this programme outputs the covariance matrix of the parameters but also
   double a,b,d,etemp;    of the life expectancies. It also computes the period (stable) prevalence. 
   double fu,fv,fw,fx;    
   double ftemp;    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
   double p,q,r,tol1,tol2,u,v,w,x,xm;             Institut national d'études démographiques, Paris.
   double e=0.0;    This software have been partly granted by Euro-REVES, a concerted action
      from the European Union.
   a=(ax < cx ? ax : cx);    It is copyrighted identically to a GNU software product, ie programme and
   b=(ax > cx ? ax : cx);    software can be distributed freely for non commercial use. Latest version
   x=w=v=bx;    can be accessed at http://euroreves.ined.fr/imach .
   fw=fv=fx=(*f)(x);  
   for (iter=1;iter<=ITMAX;iter++) {    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
     xm=0.5*(a+b);    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    **********************************************************************/
     printf(".");fflush(stdout);  /*
     fprintf(ficlog,".");fflush(ficlog);    main
 #ifdef DEBUG    read parameterfile
     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);    read datafile
     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);    concatwav
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    freqsummary
 #endif    if (mle >= 1)
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){      mlikeli
       *xmin=x;    print results files
       return fx;    if mle==1 
     }       computes hessian
     ftemp=fu;    read end of parameter file: agemin, agemax, bage, fage, estepm
     if (fabs(e) > tol1) {        begin-prev-date,...
       r=(x-w)*(fx-fv);    open gnuplot file
       q=(x-v)*(fx-fw);    open html file
       p=(x-v)*q-(x-w)*r;    period (stable) prevalence      | pl_nom    1-1 2-2 etc by covariate
       q=2.0*(q-r);     for age prevalim()             | #****** V1=0  V2=1  V3=1  V4=0 ******
       if (q > 0.0) p = -p;                                    | 65 1 0 2 1 3 1 4 0  0.96326 0.03674
       q=fabs(q);      freexexit2 possible for memory heap.
       etemp=e;  
       e=d;    h Pij x                         | pij_nom  ficrestpij
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))     # Cov Agex agex+h hpijx with i,j= 1-1 1-2     1-3     2-1     2-2     2-3
         d=CGOLD*(e=(x >= xm ? a-x : b-x));         1  85   85    1.00000             0.00000 0.00000 0.00000 1.00000 0.00000
       else {         1  85   86    0.68299             0.22291 0.09410 0.71093 0.00000 0.28907
         d=p/q;  
         u=x+d;         1  65   99    0.00364             0.00322 0.99314 0.00350 0.00310 0.99340
         if (u-a < tol2 || b-u < tol2)         1  65  100    0.00214             0.00204 0.99581 0.00206 0.00196 0.99597
           d=SIGN(tol1,xm-x);    variance of p one-step probabilities varprob  | prob_nom   ficresprob #One-step probabilities and stand. devi in ()
       }     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=CGOLD*(e=(x >= xm ? a-x : b-x));  
     }    forecasting if prevfcast==1 prevforecast call prevalence()
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    health expectancies
     fu=(*f)(u);    Variance-covariance of DFLE
     if (fu <= fx) {    prevalence()
       if (u >= x) a=x; else b=x;     movingaverage()
       SHFT(v,w,x,u)    varevsij() 
         SHFT(fv,fw,fx,fu)    if popbased==1 varevsij(,popbased)
         } else {    total life expectancies
           if (u < x) a=u; else b=u;    Variance of period (stable) prevalence
           if (fu <= fw || w == x) {   end
             v=w;  */
             w=u;  
             fv=fw;  
             fw=fu;  
           } else if (fu <= fv || v == x || v == w) {   
             v=u;  #include <math.h>
             fv=fu;  #include <stdio.h>
           }  #include <stdlib.h>
         }  #include <string.h>
   }  
   nrerror("Too many iterations in brent");  #ifdef _WIN32
   *xmin=x;  #include <io.h>
   return fx;  #else
 }  #include <unistd.h>
   #endif
 /****************** mnbrak ***********************/  
   #include <limits.h>
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  #include <sys/types.h>
             double (*func)(double))  #include <sys/stat.h>
 {  #include <errno.h>
   double ulim,u,r,q, dum;  /* extern int errno; */
   double fu;  
    /* #ifdef LINUX */
   *fa=(*func)(*ax);  /* #include <time.h> */
   *fb=(*func)(*bx);  /* #include "timeval.h" */
   if (*fb > *fa) {  /* #else */
     SHFT(dum,*ax,*bx,dum)  /* #include <sys/time.h> */
       SHFT(dum,*fb,*fa,dum)  /* #endif */
       }  
   *cx=(*bx)+GOLD*(*bx-*ax);  #include <time.h>
   *fc=(*func)(*cx);  
   while (*fb > *fc) {  #ifdef GSL
     r=(*bx-*ax)*(*fb-*fc);  #include <gsl/gsl_errno.h>
     q=(*bx-*cx)*(*fb-*fa);  #include <gsl/gsl_multimin.h>
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  #endif
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  
     ulim=(*bx)+GLIMIT*(*cx-*bx);  #ifdef NLOPT
     if ((*bx-u)*(u-*cx) > 0.0) {  #include <nlopt.h>
       fu=(*func)(u);  typedef struct {
     } else if ((*cx-u)*(u-ulim) > 0.0) {    double (* function)(double [] );
       fu=(*func)(u);  } myfunc_data ;
       if (fu < *fc) {  #endif
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  
           SHFT(*fb,*fc,fu,(*func)(u))  /* #include <libintl.h> */
           }  /* #define _(String) gettext (String) */
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  
       u=ulim;  #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
       fu=(*func)(u);  
     } else {  #define GNUPLOTPROGRAM "gnuplot"
       u=(*cx)+GOLD*(*cx-*bx);  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
       fu=(*func)(u);  #define FILENAMELENGTH 132
     }  
     SHFT(*ax,*bx,*cx,u)  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
       SHFT(*fa,*fb,*fc,fu)  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
       }  
 }  #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
   #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
 /*************** linmin ************************/  
   #define NINTERVMAX 8
 int ncom;  #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
 double *pcom,*xicom;  #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
 double (*nrfunc)(double []);  #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
    #define codtabm(h,k)  1 & (h-1) >> (k-1) ;
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  #define MAXN 20000
 {  #define YEARM 12. /**< Number of months per year */
   double brent(double ax, double bx, double cx,  #define AGESUP 130
                double (*f)(double), double tol, double *xmin);  #define AGEBASE 40
   double f1dim(double x);  #define AGEGOMP 10. /**< Minimal age for Gompertz adjustment */
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  #ifdef _WIN32
               double *fc, double (*func)(double));  #define DIRSEPARATOR '\\'
   int j;  #define CHARSEPARATOR "\\"
   double xx,xmin,bx,ax;  #define ODIRSEPARATOR '/'
   double fx,fb,fa;  #else
    #define DIRSEPARATOR '/'
   ncom=n;  #define CHARSEPARATOR "/"
   pcom=vector(1,n);  #define ODIRSEPARATOR '\\'
   xicom=vector(1,n);  #endif
   nrfunc=func;  
   for (j=1;j<=n;j++) {  /* $Id$ */
     pcom[j]=p[j];  /* $State$ */
     xicom[j]=xi[j];  
   }  char version[]="Imach version 0.99, September 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121)";
   ax=0.0;  char fullversion[]="$Revision$ $Date$"; 
   xx=1.0;  char strstart[80];
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
 #ifdef DEBUG  int nvar=0, nforce=0; /* Number of variables, number of forces */
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
 #endif  int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
   for (j=1;j<=n;j++) {  int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
     xi[j] *= xmin;  int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
     p[j] += xi[j];  int cptcovprodnoage=0; /**< Number of covariate products without age */   
   }  int cptcoveff=0; /* Total number of covariates to vary for printing results */
   free_vector(xicom,1,n);  int cptcov=0; /* Working variable */
   free_vector(pcom,1,n);  int npar=NPARMAX;
 }  int nlstate=2; /* Number of live states */
   int ndeath=1; /* Number of dead states */
 /*************** powell ************************/  int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  int popbased=0;
             double (*func)(double []))  
 {  int *wav; /* Number of waves for this individuual 0 is possible */
   void linmin(double p[], double xi[], int n, double *fret,  int maxwav=0; /* Maxim number of waves */
               double (*func)(double []));  int jmin=0, jmax=0; /* min, max spacing between 2 waves */
   int i,ibig,j;  int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
   double del,t,*pt,*ptt,*xit;  int gipmx=0, gsw=0; /* Global variables on the number of contributions 
   double fp,fptt;                     to the likelihood and the sum of weights (done by funcone)*/
   double *xits;  int mle=1, weightopt=0;
   pt=vector(1,n);  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
   ptt=vector(1,n);  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
   xit=vector(1,n);  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
   xits=vector(1,n);             * wave mi and wave mi+1 is not an exact multiple of stepm. */
   *fret=(*func)(p);  int countcallfunc=0;  /* Count the number of calls to func */
   for (j=1;j<=n;j++) pt[j]=p[j];  double jmean=1; /* Mean space between 2 waves */
   for (*iter=1;;++(*iter)) {  double **matprod2(); /* test */
     fp=(*fret);  double **oldm, **newm, **savm; /* Working pointers to matrices */
     ibig=0;  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
     del=0.0;  /*FILE *fic ; */ /* Used in readdata only */
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  FILE *ficlog, *ficrespow;
     for (i=1;i<=n;i++)  int globpr=0; /* Global variable for printing or not */
       printf(" %d %.12f",i, p[i]);  double fretone; /* Only one call to likelihood */
     fprintf(ficlog," %d %.12f",i, p[i]);  long ipmx=0; /* Number of contributions */
     printf("\n");  double sw; /* Sum of weights */
     fprintf(ficlog,"\n");  char filerespow[FILENAMELENGTH];
     for (i=1;i<=n;i++) {  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  FILE *ficresilk;
       fptt=(*fret);  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
 #ifdef DEBUG  FILE *ficresprobmorprev;
       printf("fret=%lf \n",*fret);  FILE *fichtm, *fichtmcov; /* Html File */
       fprintf(ficlog,"fret=%lf \n",*fret);  FILE *ficreseij;
 #endif  char filerese[FILENAMELENGTH];
       printf("%d",i);fflush(stdout);  FILE *ficresstdeij;
       fprintf(ficlog,"%d",i);fflush(ficlog);  char fileresstde[FILENAMELENGTH];
       linmin(p,xit,n,fret,func);  FILE *ficrescveij;
       if (fabs(fptt-(*fret)) > del) {  char filerescve[FILENAMELENGTH];
         del=fabs(fptt-(*fret));  FILE  *ficresvij;
         ibig=i;  char fileresv[FILENAMELENGTH];
       }  FILE  *ficresvpl;
 #ifdef DEBUG  char fileresvpl[FILENAMELENGTH];
       printf("%d %.12e",i,(*fret));  char title[MAXLINE];
       fprintf(ficlog,"%d %.12e",i,(*fret));  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
       for (j=1;j<=n;j++) {  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
         printf(" x(%d)=%.12e",j,xit[j]);  char command[FILENAMELENGTH];
         fprintf(ficlog," x(%d)=%.12e",j,xit[j]);  int  outcmd=0;
       }  
       for(j=1;j<=n;j++) {  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
         printf(" p=%.12e",p[j]);  
         fprintf(ficlog," p=%.12e",p[j]);  char filelog[FILENAMELENGTH]; /* Log file */
       }  char filerest[FILENAMELENGTH];
       printf("\n");  char fileregp[FILENAMELENGTH];
       fprintf(ficlog,"\n");  char popfile[FILENAMELENGTH];
 #endif  
     }  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  
 #ifdef DEBUG  /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
       int k[2],l;  /* struct timezone tzp; */
       k[0]=1;  /* extern int gettimeofday(); */
       k[1]=-1;  struct tm tml, *gmtime(), *localtime();
       printf("Max: %.12e",(*func)(p));  
       fprintf(ficlog,"Max: %.12e",(*func)(p));  extern time_t time();
       for (j=1;j<=n;j++) {  
         printf(" %.12e",p[j]);  struct tm start_time, end_time, curr_time, last_time, forecast_time;
         fprintf(ficlog," %.12e",p[j]);  time_t  rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
       }  struct tm tm;
       printf("\n");  
       fprintf(ficlog,"\n");  char strcurr[80], strfor[80];
       for(l=0;l<=1;l++) {  
         for (j=1;j<=n;j++) {  char *endptr;
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  long lval;
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  double dval;
           fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  
         }  #define NR_END 1
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  #define FREE_ARG char*
         fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  #define FTOL 1.0e-10
       }  
 #endif  #define NRANSI 
   #define ITMAX 200 
   
       free_vector(xit,1,n);  #define TOL 2.0e-4 
       free_vector(xits,1,n);  
       free_vector(ptt,1,n);  #define CGOLD 0.3819660 
       free_vector(pt,1,n);  #define ZEPS 1.0e-10 
       return;  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
     }  
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  #define GOLD 1.618034 
     for (j=1;j<=n;j++) {  #define GLIMIT 100.0 
       ptt[j]=2.0*p[j]-pt[j];  #define TINY 1.0e-20 
       xit[j]=p[j]-pt[j];  
       pt[j]=p[j];  static double maxarg1,maxarg2;
     }  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
     fptt=(*func)(ptt);  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
     if (fptt < fp) {    
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
       if (t < 0.0) {  #define rint(a) floor(a+0.5)
         linmin(p,xit,n,fret,func);  
         for (j=1;j<=n;j++) {  static double sqrarg;
           xi[j][ibig]=xi[j][n];  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
           xi[j][n]=xit[j];  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
         }  int agegomp= AGEGOMP;
 #ifdef DEBUG  
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  int imx; 
         fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  int stepm=1;
         for(j=1;j<=n;j++){  /* Stepm, step in month: minimum step interpolation*/
           printf(" %.12e",xit[j]);  
           fprintf(ficlog," %.12e",xit[j]);  int estepm;
         }  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
         printf("\n");  
         fprintf(ficlog,"\n");  int m,nb;
 #endif  long *num;
       }  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
     }  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
   }  double **pmmij, ***probs;
 }  double *ageexmed,*agecens;
   double dateintmean=0;
 /**** Prevalence limit ****************/  
   double *weight;
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  int **s; /* Status */
 {  double *agedc;
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit  double  **covar; /**< covar[j,i], value of jth covariate for individual i,
      matrix by transitions matrix until convergence is reached */                    * covar=matrix(0,NCOVMAX,1,n); 
                     * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
   int i, ii,j,k;  double  idx; 
   double min, max, maxmin, maxmax,sumnew=0.;  int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
   double **matprod2();  int *Ndum; /** Freq of modality (tricode */
   double **out, cov[NCOVMAX], **pmij();  int **codtab; /**< codtab=imatrix(1,100,1,10); */
   double **newm;  int **Tvard, *Tprod, cptcovprod, *Tvaraff;
   double agefin, delaymax=50 ; /* Max number of years to converge */  double *lsurv, *lpop, *tpop;
   
   for (ii=1;ii<=nlstate+ndeath;ii++)  double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
     for (j=1;j<=nlstate+ndeath;j++){  double ftolhess; /**< Tolerance for computing hessian */
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);  
     }  /**************** split *************************/
   static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
    cov[1]=1.;  {
      /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */       the name of the file (name), its extension only (ext) and its first part of the name (finame)
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){    */ 
     newm=savm;    char  *ss;                            /* pointer */
     /* Covariates have to be included here again */    int   l1, l2;                         /* length counters */
      cov[2]=agefin;  
      l1 = strlen(path );                   /* length of path */
       for (k=1; k<=cptcovn;k++) {    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
         /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/    if ( ss == NULL ) {                   /* no directory, so determine current directory */
       }      strcpy( name, path );               /* we got the fullname name because no directory */
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
       for (k=1; k<=cptcovprod;k++)        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];      /* get current working directory */
       /*    extern  char* getcwd ( char *buf , int len);*/
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/        return( GLOCK_ERROR_GETCWD );
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/      }
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);      /* got dirc from getcwd*/
       printf(" DIRC = %s \n",dirc);
     savm=oldm;    } else {                              /* strip direcotry from path */
     oldm=newm;      ss++;                               /* after this, the filename */
     maxmax=0.;      l2 = strlen( ss );                  /* length of filename */
     for(j=1;j<=nlstate;j++){      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
       min=1.;      strcpy( name, ss );         /* save file name */
       max=0.;      strncpy( dirc, path, l1 - l2 );     /* now the directory */
       for(i=1; i<=nlstate; i++) {      dirc[l1-l2] = 0;                    /* add zero */
         sumnew=0;      printf(" DIRC2 = %s \n",dirc);
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];    }
         prlim[i][j]= newm[i][j]/(1-sumnew);    /* We add a separator at the end of dirc if not exists */
         max=FMAX(max,prlim[i][j]);    l1 = strlen( dirc );                  /* length of directory */
         min=FMIN(min,prlim[i][j]);    if( dirc[l1-1] != DIRSEPARATOR ){
       }      dirc[l1] =  DIRSEPARATOR;
       maxmin=max-min;      dirc[l1+1] = 0; 
       maxmax=FMAX(maxmax,maxmin);      printf(" DIRC3 = %s \n",dirc);
     }    }
     if(maxmax < ftolpl){    ss = strrchr( name, '.' );            /* find last / */
       return prlim;    if (ss >0){
     }      ss++;
   }      strcpy(ext,ss);                     /* save extension */
 }      l1= strlen( name);
       l2= strlen(ss)+1;
 /*************** transition probabilities ***************/      strncpy( finame, name, l1-l2);
       finame[l1-l2]= 0;
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )    }
 {  
   double s1, s2;    return( 0 );                          /* we're done */
   /*double t34;*/  }
   int i,j,j1, nc, ii, jj;  
   
     for(i=1; i<= nlstate; i++){  /******************************************/
     for(j=1; j<i;j++){  
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  void replace_back_to_slash(char *s, char*t)
         /*s2 += param[i][j][nc]*cov[nc];*/  {
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    int i;
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/    int lg=0;
       }    i=0;
       ps[i][j]=s2;    lg=strlen(t);
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/    for(i=0; i<= lg; i++) {
     }      (s[i] = t[i]);
     for(j=i+1; j<=nlstate+ndeath;j++){      if (t[i]== '\\') s[i]='/';
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    }
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  }
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/  
       }  char *trimbb(char *out, char *in)
       ps[i][j]=s2;  { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
     }    char *s;
   }    s=out;
     /*ps[3][2]=1;*/    while (*in != '\0'){
       while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
   for(i=1; i<= nlstate; i++){        in++;
      s1=0;      }
     for(j=1; j<i; j++)      *out++ = *in++;
       s1+=exp(ps[i][j]);    }
     for(j=i+1; j<=nlstate+ndeath; j++)    *out='\0';
       s1+=exp(ps[i][j]);    return s;
     ps[i][i]=1./(s1+1.);  }
     for(j=1; j<i; j++)  
       ps[i][j]= exp(ps[i][j])*ps[i][i];  char *cutl(char *blocc, char *alocc, char *in, char occ)
     for(j=i+1; j<=nlstate+ndeath; j++)  {
       ps[i][j]= exp(ps[i][j])*ps[i][i];    /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ' 
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */       and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
   } /* end i */       gives blocc="abcdef2ghi" and alocc="j".
        If occ is not found blocc is null and alocc is equal to in. Returns blocc
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){    */
     for(jj=1; jj<= nlstate+ndeath; jj++){    char *s, *t;
       ps[ii][jj]=0;    t=in;s=in;
       ps[ii][ii]=1;    while ((*in != occ) && (*in != '\0')){
     }      *alocc++ = *in++;
   }    }
     if( *in == occ){
       *(alocc)='\0';
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){      s=++in;
     for(jj=1; jj<= nlstate+ndeath; jj++){    }
      printf("%lf ",ps[ii][jj]);   
    }    if (s == t) {/* occ not found */
     printf("\n ");      *(alocc-(in-s))='\0';
     }      in=s;
     printf("\n ");printf("%lf ",cov[2]);*/    }
 /*    while ( *in != '\0'){
   for(i=1; i<= npar; i++) printf("%f ",x[i]);      *blocc++ = *in++;
   goto end;*/    }
     return ps;  
 }    *blocc='\0';
     return t;
 /**************** Product of 2 matrices ******************/  }
   char *cutv(char *blocc, char *alocc, char *in, char occ)
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)  {
 {    /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ' 
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times       and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */       gives blocc="abcdef2ghi" and alocc="j".
   /* in, b, out are matrice of pointers which should have been initialized       If occ is not found blocc is null and alocc is equal to in. Returns alocc
      before: only the contents of out is modified. The function returns    */
      a pointer to pointers identical to out */    char *s, *t;
   long i, j, k;    t=in;s=in;
   for(i=nrl; i<= nrh; i++)    while (*in != '\0'){
     for(k=ncolol; k<=ncoloh; k++)      while( *in == occ){
       for(j=ncl,out[i][k]=0.; j<=nch; j++)        *blocc++ = *in++;
         out[i][k] +=in[i][j]*b[j][k];        s=in;
       }
   return out;      *blocc++ = *in++;
 }    }
     if (s == t) /* occ not found */
       *(blocc-(in-s))='\0';
 /************* Higher Matrix Product ***************/    else
       *(blocc-(in-s)-1)='\0';
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )    in=s;
 {    while ( *in != '\0'){
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month      *alocc++ = *in++;
      duration (i.e. until    }
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.  
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step    *alocc='\0';
      (typically every 2 years instead of every month which is too big).    return s;
      Model is determined by parameters x and covariates have to be  }
      included manually here.  
   int nbocc(char *s, char occ)
      */  {
     int i,j=0;
   int i, j, d, h, k;    int lg=20;
   double **out, cov[NCOVMAX];    i=0;
   double **newm;    lg=strlen(s);
     for(i=0; i<= lg; i++) {
   /* Hstepm could be zero and should return the unit matrix */    if  (s[i] == occ ) j++;
   for (i=1;i<=nlstate+ndeath;i++)    }
     for (j=1;j<=nlstate+ndeath;j++){    return j;
       oldm[i][j]=(i==j ? 1.0 : 0.0);  }
       po[i][j][0]=(i==j ? 1.0 : 0.0);  
     }  /* void cutv(char *u,char *v, char*t, char occ) */
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */  /* { */
   for(h=1; h <=nhstepm; h++){  /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
     for(d=1; d <=hstepm; d++){  /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
       newm=savm;  /*      gives u="abcdef2ghi" and v="j" *\/ */
       /* Covariates have to be included here again */  /*   int i,lg,j,p=0; */
       cov[1]=1.;  /*   i=0; */
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;  /*   lg=strlen(t); */
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  /*   for(j=0; j<=lg-1; j++) { */
       for (k=1; k<=cptcovage;k++)  /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  /*   } */
       for (k=1; k<=cptcovprod;k++)  
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  /*   for(j=0; j<p; j++) { */
   /*     (u[j] = t[j]); */
   /*   } */
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/  /*      u[p]='\0'; */
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/  
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,  /*    for(j=0; j<= lg; j++) { */
                    pmij(pmmij,cov,ncovmodel,x,nlstate));  /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
       savm=oldm;  /*   } */
       oldm=newm;  /* } */
     }  
     for(i=1; i<=nlstate+ndeath; i++)  #ifdef _WIN32
       for(j=1;j<=nlstate+ndeath;j++) {  char * strsep(char **pp, const char *delim)
         po[i][j][h]=newm[i][j];  {
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);    char *p, *q;
          */           
       }    if ((p = *pp) == NULL)
   } /* end h */      return 0;
   return po;    if ((q = strpbrk (p, delim)) != NULL)
 }    {
       *pp = q + 1;
       *q = '\0';
 /*************** log-likelihood *************/    }
 double func( double *x)    else
 {      *pp = 0;
   int i, ii, j, k, mi, d, kk;    return p;
   double l, ll[NLSTATEMAX], cov[NCOVMAX];  }
   double **out;  #endif
   double sw; /* Sum of weights */  
   double lli; /* Individual log likelihood */  /********************** nrerror ********************/
   long ipmx;  
   /*extern weight */  void nrerror(char error_text[])
   /* We are differentiating ll according to initial status */  {
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    fprintf(stderr,"ERREUR ...\n");
   /*for(i=1;i<imx;i++)    fprintf(stderr,"%s\n",error_text);
     printf(" %d\n",s[4][i]);    exit(EXIT_FAILURE);
   */  }
   cov[1]=1.;  /*********************** vector *******************/
   double *vector(int nl, int nh)
   for(k=1; k<=nlstate; k++) ll[k]=0.;  {
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){    double *v;
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
     for(mi=1; mi<= wav[i]-1; mi++){    if (!v) nrerror("allocation failure in vector");
       for (ii=1;ii<=nlstate+ndeath;ii++)    return v-nl+NR_END;
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);  }
       for(d=0; d<dh[mi][i]; d++){  
         newm=savm;  /************************ free vector ******************/
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;  void free_vector(double*v, int nl, int nh)
         for (kk=1; kk<=cptcovage;kk++) {  {
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];    free((FREE_ARG)(v+nl-NR_END));
         }  }
          
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,  /************************ivector *******************************/
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));  int *ivector(long nl,long nh)
         savm=oldm;  {
         oldm=newm;    int *v;
            v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
            if (!v) nrerror("allocation failure in ivector");
       } /* end mult */    return v-nl+NR_END;
        }
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);  
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/  /******************free ivector **************************/
       ipmx +=1;  void free_ivector(int *v, long nl, long nh)
       sw += weight[i];  {
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;    free((FREE_ARG)(v+nl-NR_END));
     } /* end of wave */  }
   } /* end of individual */  
   /************************lvector *******************************/
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];  long *lvector(long nl,long nh)
   /* 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 */    long *v;
   return -l;    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
 }    if (!v) nrerror("allocation failure in ivector");
     return v-nl+NR_END;
   }
 /*********** Maximum Likelihood Estimation ***************/  
   /******************free lvector **************************/
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))  void free_lvector(long *v, long nl, long nh)
 {  {
   int i,j, iter;    free((FREE_ARG)(v+nl-NR_END));
   double **xi,*delti;  }
   double fret;  
   xi=matrix(1,npar,1,npar);  /******************* imatrix *******************************/
   for (i=1;i<=npar;i++)  int **imatrix(long nrl, long nrh, long ncl, long nch) 
     for (j=1;j<=npar;j++)       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
       xi[i][j]=(i==j ? 1.0 : 0.0);  { 
   printf("Powell\n");  fprintf(ficlog,"Powell\n");    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
   powell(p,xi,npar,ftol,&iter,&fret,func);    int **m; 
     
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));    /* allocate pointers to rows */ 
   fprintf(ficlog,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));    if (!m) nrerror("allocation failure 1 in matrix()"); 
     m += NR_END; 
 }    m -= nrl; 
     
 /**** Computes Hessian and covariance matrix ***/    
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))    /* allocate rows and set pointers to them */ 
 {    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
   double  **a,**y,*x,pd;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
   double **hess;    m[nrl] += NR_END; 
   int i, j,jk;    m[nrl] -= ncl; 
   int *indx;    
     for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
   double hessii(double p[], double delta, int theta, double delti[]);    
   double hessij(double p[], double delti[], int i, int j);    /* return pointer to array of pointers to rows */ 
   void lubksb(double **a, int npar, int *indx, double b[]) ;    return m; 
   void ludcmp(double **a, int npar, int *indx, double *d) ;  } 
   
   hess=matrix(1,npar,1,npar);  /****************** free_imatrix *************************/
   void free_imatrix(m,nrl,nrh,ncl,nch)
   printf("\nCalculation of the hessian matrix. Wait...\n");        int **m;
   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");        long nch,ncl,nrh,nrl; 
   for (i=1;i<=npar;i++){       /* free an int matrix allocated by imatrix() */ 
     printf("%d",i);fflush(stdout);  { 
     fprintf(ficlog,"%d",i);fflush(ficlog);    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
     hess[i][i]=hessii(p,ftolhess,i,delti);    free((FREE_ARG) (m+nrl-NR_END)); 
     /*printf(" %f ",p[i]);*/  } 
     /*printf(" %lf ",hess[i][i]);*/  
   }  /******************* matrix *******************************/
    double **matrix(long nrl, long nrh, long ncl, long nch)
   for (i=1;i<=npar;i++) {  {
     for (j=1;j<=npar;j++)  {    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
       if (j>i) {    double **m;
         printf(".%d%d",i,j);fflush(stdout);  
         fprintf(ficlog,".%d%d",i,j);fflush(ficlog);    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
         hess[i][j]=hessij(p,delti,i,j);    if (!m) nrerror("allocation failure 1 in matrix()");
         hess[j][i]=hess[i][j];        m += NR_END;
         /*printf(" %lf ",hess[i][j]);*/    m -= nrl;
       }  
     }    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   }    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   printf("\n");    m[nrl] += NR_END;
   fprintf(ficlog,"\n");    m[nrl] -= ncl;
   
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");    return m;
      /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
   a=matrix(1,npar,1,npar);  m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
   y=matrix(1,npar,1,npar);  that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
   x=vector(1,npar);     */
   indx=ivector(1,npar);  }
   for (i=1;i<=npar;i++)  
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];  /*************************free matrix ************************/
   ludcmp(a,npar,indx,&pd);  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   {
   for (j=1;j<=npar;j++) {    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     for (i=1;i<=npar;i++) x[i]=0;    free((FREE_ARG)(m+nrl-NR_END));
     x[j]=1;  }
     lubksb(a,npar,indx,x);  
     for (i=1;i<=npar;i++){  /******************* ma3x *******************************/
       matcov[i][j]=x[i];  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
     }  {
   }    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
     double ***m;
   printf("\n#Hessian matrix#\n");  
   fprintf(ficlog,"\n#Hessian matrix#\n");    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   for (i=1;i<=npar;i++) {    if (!m) nrerror("allocation failure 1 in matrix()");
     for (j=1;j<=npar;j++) {    m += NR_END;
       printf("%.3e ",hess[i][j]);    m -= nrl;
       fprintf(ficlog,"%.3e ",hess[i][j]);  
     }    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     printf("\n");    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     fprintf(ficlog,"\n");    m[nrl] += NR_END;
   }    m[nrl] -= ncl;
   
   /* Recompute Inverse */    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   for (i=1;i<=npar;i++)  
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
   ludcmp(a,npar,indx,&pd);    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
     m[nrl][ncl] += NR_END;
   /*  printf("\n#Hessian matrix recomputed#\n");    m[nrl][ncl] -= nll;
     for (j=ncl+1; j<=nch; j++) 
   for (j=1;j<=npar;j++) {      m[nrl][j]=m[nrl][j-1]+nlay;
     for (i=1;i<=npar;i++) x[i]=0;    
     x[j]=1;    for (i=nrl+1; i<=nrh; i++) {
     lubksb(a,npar,indx,x);      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
     for (i=1;i<=npar;i++){      for (j=ncl+1; j<=nch; j++) 
       y[i][j]=x[i];        m[i][j]=m[i][j-1]+nlay;
       printf("%.3e ",y[i][j]);    }
       fprintf(ficlog,"%.3e ",y[i][j]);    return m; 
     }    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
     printf("\n");             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
     fprintf(ficlog,"\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);
       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);    strcat(tmpout,fileres);
 #endif    return tmpout;
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */  }
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){  
         k=kmax;  char *asc_diff_time(long time_sec, char ascdiff[])
       }  {
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */    long sec_left, days, hours, minutes;
         k=kmax; l=lmax*10.;    days = (time_sec) / (60*60*24);
       }    sec_left = (time_sec) % (60*60*24);
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){    hours = (sec_left) / (60*60) ;
         delts=delt;    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);  
   delti[theta]=delts;    return ascdiff;
   return res;  }
    
 }  /***************** f1dim *************************/
   extern int ncom; 
 double hessij( double x[], double delti[], int thetai,int thetaj)  extern double *pcom,*xicom;
 {  extern double (*nrfunc)(double []); 
   int i;   
   int l=1, l1, lmax=20;  double f1dim(double x) 
   double k1,k2,k3,k4,res,fx;  { 
   double p2[NPARMAX+1];    int j; 
   int k;    double f;
     double *xt; 
   fx=func(x);   
   for (k=1; k<=2; k++) {    xt=vector(1,ncom); 
     for (i=1;i<=npar;i++) p2[i]=x[i];    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
     p2[thetai]=x[thetai]+delti[thetai]/k;    f=(*nrfunc)(xt); 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    free_vector(xt,1,ncom); 
     k1=func(p2)-fx;    return f; 
    } 
     p2[thetai]=x[thetai]+delti[thetai]/k;  
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;  /*****************brent *************************/
     k2=func(p2)-fx;  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
    { 
     p2[thetai]=x[thetai]-delti[thetai]/k;    int iter; 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    double a,b,d,etemp;
     k3=func(p2)-fx;    double fu=0,fv,fw,fx;
      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; 
     k4=func(p2)-fx;   
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */    a=(ax < cx ? ax : cx); 
 #ifdef DEBUG    b=(ax > cx ? ax : cx); 
     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);    x=w=v=bx; 
     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);    fw=fv=fx=(*f)(x); 
 #endif    for (iter=1;iter<=ITMAX;iter++) { 
   }      xm=0.5*(a+b); 
   return res;      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
 }      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
       printf(".");fflush(stdout);
 /************** Inverse of matrix **************/      fprintf(ficlog,".");fflush(ficlog);
 void ludcmp(double **a, int n, int *indx, double *d)  #ifdef DEBUGBRENT
 {      printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
   int i,imax,j,k;      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);
   double big,dum,sum,temp;      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
   double *vv;  #endif
        if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
   vv=vector(1,n);        *xmin=x; 
   *d=1.0;        return fx; 
   for (i=1;i<=n;i++) {      } 
     big=0.0;      ftemp=fu;
     for (j=1;j<=n;j++)      if (fabs(e) > tol1) { 
       if ((temp=fabs(a[i][j])) > big) big=temp;        r=(x-w)*(fx-fv); 
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");        q=(x-v)*(fx-fw); 
     vv[i]=1.0/big;        p=(x-v)*q-(x-w)*r; 
   }        q=2.0*(q-r); 
   for (j=1;j<=n;j++) {        if (q > 0.0) p = -p; 
     for (i=1;i<j;i++) {        q=fabs(q); 
       sum=a[i][j];        etemp=e; 
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];        e=d; 
       a[i][j]=sum;        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
     }          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
     big=0.0;        else { 
     for (i=j;i<=n;i++) {          d=p/q; 
       sum=a[i][j];          u=x+d; 
       for (k=1;k<j;k++)          if (u-a < tol2 || b-u < tol2) 
         sum -= a[i][k]*a[k][j];            d=SIGN(tol1,xm-x); 
       a[i][j]=sum;        } 
       if ( (dum=vv[i]*fabs(sum)) >= big) {      } else { 
         big=dum;        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
         imax=i;      } 
       }      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
     }      fu=(*f)(u); 
     if (j != imax) {      if (fu <= fx) { 
       for (k=1;k<=n;k++) {        if (u >= x) a=x; else b=x; 
         dum=a[imax][k];        SHFT(v,w,x,u) 
         a[imax][k]=a[j][k];          SHFT(fv,fw,fx,fu) 
         a[j][k]=dum;          } else { 
       }            if (u < x) a=u; else b=u; 
       *d = -(*d);            if (fu <= fw || w == x) { 
       vv[imax]=vv[j];              v=w; 
     }              w=u; 
     indx[j]=imax;              fv=fw; 
     if (a[j][j] == 0.0) a[j][j]=TINY;              fw=fu; 
     if (j != n) {            } else if (fu <= fv || v == x || v == w) { 
       dum=1.0/(a[j][j]);              v=u; 
       for (i=j+1;i<=n;i++) a[i][j] *= dum;              fv=fu; 
     }            } 
   }          } 
   free_vector(vv,1,n);  /* Doesn't work */    } 
 ;    nrerror("Too many iterations in brent"); 
 }    *xmin=x; 
     return fx; 
 void lubksb(double **a, int n, int *indx, double b[])  } 
 {  
   int i,ii=0,ip,j;  /****************** mnbrak ***********************/
   double sum;  
    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
   for (i=1;i<=n;i++) {              double (*func)(double)) 
     ip=indx[i];  { 
     sum=b[ip];    double ulim,u,r,q, dum;
     b[ip]=b[i];    double fu; 
     if (ii)   
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];    *fa=(*func)(*ax); 
     else if (sum) ii=i;    *fb=(*func)(*bx); 
     b[i]=sum;    if (*fb > *fa) { 
   }      SHFT(dum,*ax,*bx,dum) 
   for (i=n;i>=1;i--) {        SHFT(dum,*fb,*fa,dum) 
     sum=b[i];        } 
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];    *cx=(*bx)+GOLD*(*bx-*ax); 
     b[i]=sum/a[i][i];    *fc=(*func)(*cx); 
   }    while (*fb > *fc) { /* Declining fa, fb, fc */
 }      r=(*bx-*ax)*(*fb-*fc); 
       q=(*bx-*cx)*(*fb-*fa); 
 /************ Frequencies ********************/      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
 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)        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscisse of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
 {  /* Some frequencies */      ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscisse where function can be evaluated */
        if ((*bx-u)*(u-*cx) > 0.0) { /* if u between b and c */
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;        fu=(*func)(u); 
   int first;  #ifdef DEBUG
   double ***freq; /* Frequencies */        /* f(x)=A(x-u)**2+f(u) */
   double *pp;        double A, fparabu; 
   double pos, k2, dateintsum=0,k2cpt=0;        A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
   FILE *ficresp;        fparabu= *fa - A*(*ax-u)*(*ax-u);
   char fileresp[FILENAMELENGTH];        printf("mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu);
          fprintf(ficlog, "mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu);
   pp=vector(1,nlstate);  #endif 
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);      } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
   strcpy(fileresp,"p");        fu=(*func)(u); 
   strcat(fileresp,fileres);        if (fu < *fc) { 
   if((ficresp=fopen(fileresp,"w"))==NULL) {          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
     printf("Problem with prevalence resultfile: %s\n", fileresp);            SHFT(*fb,*fc,fu,(*func)(u)) 
     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);            } 
     exit(0);      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
   }        u=ulim; 
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);        fu=(*func)(u); 
   j1=0;      } else { 
          u=(*cx)+GOLD*(*cx-*bx); 
   j=cptcoveff;        fu=(*func)(u); 
   if (cptcovn<1) {j=1;ncodemax[1]=1;}      } 
       SHFT(*ax,*bx,*cx,u) 
   first=1;        SHFT(*fa,*fb,*fc,fu) 
         } 
   for(k1=1; k1<=j;k1++){  } 
     for(i1=1; i1<=ncodemax[k1];i1++){  
       j1++;  /*************** linmin ************************/
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);  /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
         scanf("%d", i);*/  resets p to where the function func(p) takes on a minimum along the direction xi from p ,
       for (i=-1; i<=nlstate+ndeath; i++)    and replaces xi by the actual vector displacement that p was moved. Also returns as fret
         for (jk=-1; jk<=nlstate+ndeath; jk++)    the value of func at the returned location p . This is actually all accomplished by calling the
           for(m=agemin; m <= agemax+3; m++)  routines mnbrak and brent .*/
             freq[i][jk][m]=0;  int ncom; 
        double *pcom,*xicom;
       dateintsum=0;  double (*nrfunc)(double []); 
       k2cpt=0;   
       for (i=1; i<=imx; i++) {  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
         bool=1;  { 
         if  (cptcovn>0) {    double brent(double ax, double bx, double cx, 
           for (z1=1; z1<=cptcoveff; z1++)                 double (*f)(double), double tol, double *xmin); 
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])    double f1dim(double x); 
               bool=0;    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
         }                double *fc, double (*func)(double)); 
         if (bool==1) {    int j; 
           for(m=firstpass; m<=lastpass; m++){    double xx,xmin,bx,ax; 
             k2=anint[m][i]+(mint[m][i]/12.);    double fx,fb,fa;
             if ((k2>=dateprev1) && (k2<=dateprev2)) {   
               if(agev[m][i]==0) agev[m][i]=agemax+1;    ncom=n; 
               if(agev[m][i]==1) agev[m][i]=agemax+2;    pcom=vector(1,n); 
               if (m<lastpass) {    xicom=vector(1,n); 
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    nrfunc=func; 
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];    for (j=1;j<=n;j++) { 
               }      pcom[j]=p[j]; 
                    xicom[j]=xi[j]; 
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {    } 
                 dateintsum=dateintsum+k2;    ax=0.0; 
                 k2cpt++;    xx=1.0; 
               }    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Find a bracket a,x,b in direction n=xi ie xicom */
             }    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Find a minimum P+lambda n in that direction (lambdamin), with TOL between abscisses */
           }  #ifdef DEBUG
         }    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
       }    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
          #endif
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    for (j=1;j<=n;j++) { 
       xi[j] *= xmin; 
       if  (cptcovn>0) {      p[j] += xi[j]; 
         fprintf(ficresp, "\n#********** Variable ");    } 
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    free_vector(xicom,1,n); 
         fprintf(ficresp, "**********\n#");    free_vector(pcom,1,n); 
       }  } 
       for(i=1; i<=nlstate;i++)  
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);  
       fprintf(ficresp, "\n");  /*************** powell ************************/
        /*
       for(i=(int)agemin; i <= (int)agemax+3; i++){  Minimization of a function func of n variables. Input consists of an initial starting point
         if(i==(int)agemax+3){  p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
           fprintf(ficlog,"Total");  rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
         }else{  such that failure to decrease by more than this amount on one iteration signals doneness. On
           if(first==1){  output, p is set to the best point found, xi is the then-current direction set, fret is the returned
             first=0;  function value at p , and iter is the number of iterations taken. The routine linmin is used.
             printf("See log file for details...\n");   */
           }  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
           fprintf(ficlog,"Age %d", i);              double (*func)(double [])) 
         }  { 
         for(jk=1; jk <=nlstate ; jk++){    void linmin(double p[], double xi[], int n, double *fret, 
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)                double (*func)(double [])); 
             pp[jk] += freq[jk][m][i];    int i,ibig,j; 
         }    double del,t,*pt,*ptt,*xit;
         for(jk=1; jk <=nlstate ; jk++){    double fp,fptt;
           for(m=-1, pos=0; m <=0 ; m++)    double *xits;
             pos += freq[jk][m][i];    int niterf, itmp;
           if(pp[jk]>=1.e-10){  
             if(first==1){    pt=vector(1,n); 
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);    ptt=vector(1,n); 
             }    xit=vector(1,n); 
             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);    xits=vector(1,n); 
           }else{    *fret=(*func)(p); 
             if(first==1)    for (j=1;j<=n;j++) pt[j]=p[j]; 
               printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);      rcurr_time = time(NULL);  
             fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);    for (*iter=1;;++(*iter)) { 
           }      fp=(*fret); 
         }      ibig=0; 
       del=0.0; 
         for(jk=1; jk <=nlstate ; jk++){      rlast_time=rcurr_time;
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)      /* (void) gettimeofday(&curr_time,&tzp); */
             pp[jk] += freq[jk][m][i];      rcurr_time = time(NULL);  
         }      curr_time = *localtime(&rcurr_time);
       printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
         for(jk=1,pos=0; jk <=nlstate ; jk++)      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
           pos += pp[jk];  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
         for(jk=1; jk <=nlstate ; jk++){     for (i=1;i<=n;i++) {
           if(pos>=1.e-5){        printf(" %d %.12f",i, p[i]);
             if(first==1)        fprintf(ficlog," %d %.12lf",i, p[i]);
               printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);        fprintf(ficrespow," %.12lf", p[i]);
             fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);      }
           }else{      printf("\n");
             if(first==1)      fprintf(ficlog,"\n");
               printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);      fprintf(ficrespow,"\n");fflush(ficrespow);
             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);      if(*iter <=3){
           }        tml = *localtime(&rcurr_time);
           if( i <= (int) agemax){        strcpy(strcurr,asctime(&tml));
             if(pos>=1.e-5){        rforecast_time=rcurr_time; 
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);        itmp = strlen(strcurr);
               probs[i][jk][j1]= pp[jk]/pos;        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/          strcurr[itmp-1]='\0';
             }        printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
             else        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);        for(niterf=10;niterf<=30;niterf+=10){
           }          rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
         }          forecast_time = *localtime(&rforecast_time);
                  strcpy(strfor,asctime(&forecast_time));
         for(jk=-1; jk <=nlstate+ndeath; jk++)          itmp = strlen(strfor);
           for(m=-1; m <=nlstate+ndeath; m++)          if(strfor[itmp-1]=='\n')
             if(freq[jk][m][i] !=0 ) {          strfor[itmp-1]='\0';
             if(first==1)          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);
               printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);          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);
               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);        }
             }      }
         if(i <= (int) agemax)      for (i=1;i<=n;i++) { 
           fprintf(ficresp,"\n");        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
         if(first==1)        fptt=(*fret); 
           printf("Others in log...\n");  #ifdef DEBUG
         fprintf(ficlog,"\n");        printf("fret=%lf \n",*fret);
       }        fprintf(ficlog,"fret=%lf \n",*fret);
     }  #endif
   }        printf("%d",i);fflush(stdout);
   dateintmean=dateintsum/k2cpt;        fprintf(ficlog,"%d",i);fflush(ficlog);
          linmin(p,xit,n,fret,func); 
   fclose(ficresp);        if (fabs(fptt-(*fret)) > del) { 
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);          del=fabs(fptt-(*fret)); 
   free_vector(pp,1,nlstate);          ibig=i; 
          } 
   /* End of Freq */  #ifdef DEBUG
 }        printf("%d %.12e",i,(*fret));
         fprintf(ficlog,"%d %.12e",i,(*fret));
 /************ Prevalence ********************/        for (j=1;j<=n;j++) {
 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)          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
 {  /* Some frequencies */          printf(" x(%d)=%.12e",j,xit[j]);
            fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;        }
   double ***freq; /* Frequencies */        for(j=1;j<=n;j++) {
   double *pp;          printf(" p(%d)=%.12e",j,p[j]);
   double pos, k2;          fprintf(ficlog," p(%d)=%.12e",j,p[j]);
         }
   pp=vector(1,nlstate);        printf("\n");
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);        fprintf(ficlog,"\n");
    #endif
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);      } /* end i */
   j1=0;      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
    #ifdef DEBUG
   j=cptcoveff;        int k[2],l;
   if (cptcovn<1) {j=1;ncodemax[1]=1;}        k[0]=1;
          k[1]=-1;
   for(k1=1; k1<=j;k1++){        printf("Max: %.12e",(*func)(p));
     for(i1=1; i1<=ncodemax[k1];i1++){        fprintf(ficlog,"Max: %.12e",(*func)(p));
       j1++;        for (j=1;j<=n;j++) {
                printf(" %.12e",p[j]);
       for (i=-1; i<=nlstate+ndeath; i++)            fprintf(ficlog," %.12e",p[j]);
         for (jk=-1; jk<=nlstate+ndeath; jk++)          }
           for(m=agemin; m <= agemax+3; m++)        printf("\n");
             freq[i][jk][m]=0;        fprintf(ficlog,"\n");
              for(l=0;l<=1;l++) {
       for (i=1; i<=imx; i++) {          for (j=1;j<=n;j++) {
         bool=1;            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
         if  (cptcovn>0) {            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
           for (z1=1; z1<=cptcoveff; z1++)            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 (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])          }
               bool=0;          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
         }          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
         if (bool==1) {        }
           for(m=firstpass; m<=lastpass; m++){  #endif
             k2=anint[m][i]+(mint[m][i]/12.);  
             if ((k2>=dateprev1) && (k2<=dateprev2)) {  
               if(agev[m][i]==0) agev[m][i]=agemax+1;        free_vector(xit,1,n); 
               if(agev[m][i]==1) agev[m][i]=agemax+2;        free_vector(xits,1,n); 
               if (m<lastpass) {        free_vector(ptt,1,n); 
                 if (calagedate>0)        free_vector(pt,1,n); 
                   freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];        return; 
                 else      } 
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
                 freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];      for (j=1;j<=n;j++) { /* Computes an extrapolated point */
               }        ptt[j]=2.0*p[j]-pt[j]; 
             }        xit[j]=p[j]-pt[j]; 
           }        pt[j]=p[j]; 
         }      } 
       }      fptt=(*func)(ptt); 
       for(i=(int)agemin; i <= (int)agemax+3; i++){      if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
         for(jk=1; jk <=nlstate ; jk++){        /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        /* From x1 (P0) distance of x2 is at h and x3 is 2h */
             pp[jk] += freq[jk][m][i];        /* Let f"(x2) be the 2nd derivative equal everywhere.  */
         }        /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
         for(jk=1; jk <=nlstate ; jk++){        /* will reach at f3 = fm + h^2/2 f"m  ; f" = (f1 -2f2 +f3 ) / h**2 */
           for(m=-1, pos=0; m <=0 ; m++)        /* f1-f3 = delta(2h) = 2 h**2 f'' = 2(f1- 2f2 +f3) */
             pos += freq[jk][m][i];        /* Thus we compare delta(2h) with observed f1-f3 */
         }        /* or best gain on one ancient line 'del' with total  */
                /* gain f1-f2 = f1 - f2 - 'del' with del  */
         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++)  
             pp[jk] += freq[jk][m][i];        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del);
         }        t= t- del*SQR(fp-fptt);
                printf("t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t);
         for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];        fprintf(ficlog,"t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t);
          #ifdef DEBUG
         for(jk=1; jk <=nlstate ; jk++){            printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
           if( i <= (int) agemax){               (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
             if(pos>=1.e-5){        fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
               probs[i][jk][j1]= pp[jk]/pos;               (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
             }        printf("tt= %.12lf, t=%.12lf\n",2.0*(fp-2.0*(*fret)+fptt)*(fp-(*fret)-del)*(fp-(*fret)-del)-del*(fp-fptt)*(fp-fptt),t);
           }        fprintf(ficlog, "tt= %.12lf, t=%.12lf\n",2.0*(fp-2.0*(*fret)+fptt)*(fp-(*fret)-del)*(fp-(*fret)-del)-del*(fp-fptt)*(fp-fptt),t);
         }/* end jk */  #endif
       }/* end i */        if (t < 0.0) { /* Then we use it for last direction */
     } /* end i1 */          linmin(p,xit,n,fret,func); /* computes mean on the extrapolated direction.*/
   } /* end k1 */          for (j=1;j<=n;j++) { 
             xi[j][ibig]=xi[j][n]; /* Replace the direction with biggest decrease by n */
              xi[j][n]=xit[j];      /* and nth direction by the extrapolated */
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);          }
   free_vector(pp,1,nlstate);          printf("Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
            fprintf(ficlog,"Gaining to use average direction of P0 P%d instead of biggest increase direction :\n",n,ibig);
 }  /* End of Freq */  
   #ifdef DEBUG
 /************* Waves Concatenation ***************/          for(j=1;j<=n;j++){
             printf(" %.12e",xit[j]);
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)            fprintf(ficlog," %.12e",xit[j]);
 {          }
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.          printf("\n");
      Death is a valid wave (if date is known).          fprintf(ficlog,"\n");
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i  #endif
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]        } /* end of t negative */
      and mw[mi+1][i]. dh depends on stepm.      } /* end if (fptt < fp)  */
      */    } 
   } 
   int i, mi, m;  
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;  /**** Prevalence limit (stable or period prevalence)  ****************/
      double sum=0., jmean=0.;*/  
   int first;  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
   int j, k=0,jk, ju, jl;  {
   double sum=0.;    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
   first=0;       matrix by transitions matrix until convergence is reached */
   jmin=1e+5;  
   jmax=-1;    int i, ii,j,k;
   jmean=0.;    double min, max, maxmin, maxmax,sumnew=0.;
   for(i=1; i<=imx; i++){    /* double **matprod2(); */ /* test */
     mi=0;    double **out, cov[NCOVMAX+1], **pmij();
     m=firstpass;    double **newm;
     while(s[m][i] <= nlstate){    double agefin, delaymax=50 ; /* Max number of years to converge */
       if(s[m][i]>=1)  
         mw[++mi][i]=m;    for (ii=1;ii<=nlstate+ndeath;ii++)
       if(m >=lastpass)      for (j=1;j<=nlstate+ndeath;j++){
         break;        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       else      }
         m++;  
     }/* end while */     cov[1]=1.;
     if (s[m][i] > nlstate){   
       mi++;     /* Death is another wave */   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
       /* if(mi==0)  never been interviewed correctly before death */    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
          /* Only death is a correct wave */      newm=savm;
       mw[mi][i]=m;      /* Covariates have to be included here again */
     }      cov[2]=agefin;
       
     wav[i]=mi;      for (k=1; k<=cptcovn;k++) {
     if(mi==0){        cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
       if(first==0){        /*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]]);*/
         printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);      }
         first=1;      /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
       }      /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
       if(first==1){      /*   cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */
         fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i);      
       }      /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
     } /* end mi==0 */      /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
   }      /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
       /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
   for(i=1; i<=imx; i++){      /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
     for(mi=1; mi<wav[i];mi++){      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
       if (stepm <=0)      
         dh[mi][i]=1;      savm=oldm;
       else{      oldm=newm;
         if (s[mw[mi+1][i]][i] > nlstate) {      maxmax=0.;
           if (agedc[i] < 2*AGESUP) {      for(j=1;j<=nlstate;j++){
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);        min=1.;
           if(j==0) j=1;  /* Survives at least one month after exam */        max=0.;
           k=k+1;        for(i=1; i<=nlstate; i++) {
           if (j >= jmax) jmax=j;          sumnew=0;
           if (j <= jmin) jmin=j;          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
           sum=sum+j;          prlim[i][j]= newm[i][j]/(1-sumnew);
           /*if (j<0) printf("j=%d num=%d \n",j,i); */          /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
           }          max=FMAX(max,prlim[i][j]);
         }          min=FMIN(min,prlim[i][j]);
         else{        }
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));        maxmin=max-min;
           k=k+1;        maxmax=FMAX(maxmax,maxmin);
           if (j >= jmax) jmax=j;      }
           else if (j <= jmin)jmin=j;      if(maxmax < ftolpl){
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */        return prlim;
           sum=sum+j;      }
         }    }
         jk= j/stepm;  }
         jl= j -jk*stepm;  
         ju= j -(jk+1)*stepm;  /*************** transition probabilities ***************/ 
         if(jl <= -ju)  
           dh[mi][i]=jk;  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
         else  {
           dh[mi][i]=jk+1;    /* According to parameters values stored in x and the covariate's values stored in cov,
         if(dh[mi][i]==0)       computes the probability to be observed in state j being in state i by appying the
           dh[mi][i]=1; /* At least one step */       model to the ncovmodel covariates (including constant and age).
       }       lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
     }       and, according on how parameters are entered, the position of the coefficient xij(nc) of the
   }       ncth covariate in the global vector x is given by the formula:
   jmean=sum/k;       j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);       j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
   fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);       Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
  }       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
 /*********** Tricode ****************************/       the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
 void tricode(int *Tvar, int **nbcode, int imx)    */
 {    double s1, lnpijopii;
   int Ndum[20],ij=1, k, j, i;    /*double t34;*/
   int cptcode=0;    int i,j,j1, nc, ii, jj;
   cptcoveff=0;  
        for(i=1; i<= nlstate; i++){
   for (k=0; k<19; k++) Ndum[k]=0;        for(j=1; j<i;j++){
   for (k=1; k<=7; k++) ncodemax[k]=0;          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
             /*lnpijopii += param[i][j][nc]*cov[nc];*/
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {            lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
     for (i=1; i<=imx; i++) {  /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
       ij=(int)(covar[Tvar[j]][i]);          }
       Ndum[ij]++;          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/  /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
       if (ij > cptcode) cptcode=ij;        }
     }        for(j=i+1; j<=nlstate+ndeath;j++){
           for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
     for (i=0; i<=cptcode; i++) {            /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
       if(Ndum[i]!=0) ncodemax[j]++;            lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
     }  /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
     ij=1;          }
           ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
         }
     for (i=1; i<=ncodemax[j]; i++) {      }
       for (k=0; k<=19; k++) {      
         if (Ndum[k] != 0) {      for(i=1; i<= nlstate; i++){
           nbcode[Tvar[j]][ij]=k;        s1=0;
                  for(j=1; j<i; j++){
           ij++;          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
         }          /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
         if (ij > ncodemax[j]) break;        }
       }          for(j=i+1; j<=nlstate+ndeath; j++){
     }          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
   }            /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
         }
  for (k=0; k<19; k++) Ndum[k]=0;        /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
         ps[i][i]=1./(s1+1.);
  for (i=1; i<=ncovmodel-2; i++) {        /* Computing other pijs */
    ij=Tvar[i];        for(j=1; j<i; j++)
    Ndum[ij]++;          ps[i][j]= exp(ps[i][j])*ps[i][i];
  }        for(j=i+1; j<=nlstate+ndeath; j++)
           ps[i][j]= exp(ps[i][j])*ps[i][i];
  ij=1;        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
  for (i=1; i<=10; i++) {      } /* end i */
    if((Ndum[i]!=0) && (i<=ncovcol)){      
      Tvaraff[ij]=i;      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
      ij++;        for(jj=1; jj<= nlstate+ndeath; jj++){
    }          ps[ii][jj]=0;
  }          ps[ii][ii]=1;
          }
  cptcoveff=ij-1;      }
 }      
       
 /*********** Health Expectancies ****************/      /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
       /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
 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 )      /*  printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
       /*   } */
 {      /*   printf("\n "); */
   /* Health expectancies */      /* } */
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;      /* printf("\n ");printf("%lf ",cov[2]);*/
   double age, agelim, hf;      /*
   double ***p3mat,***varhe;        for(i=1; i<= npar; i++) printf("%f ",x[i]);
   double **dnewm,**doldm;        goto end;*/
   double *xp;      return ps;
   double **gp, **gm;  }
   double ***gradg, ***trgradg;  
   int theta;  /**************** Product of 2 matrices ******************/
   
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);  double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
   xp=vector(1,npar);  {
   dnewm=matrix(1,nlstate*2,1,npar);    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
   doldm=matrix(1,nlstate*2,1,nlstate*2);       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
      /* in, b, out are matrice of pointers which should have been initialized 
   fprintf(ficreseij,"# Health expectancies\n");       before: only the contents of out is modified. The function returns
   fprintf(ficreseij,"# Age");       a pointer to pointers identical to out */
   for(i=1; i<=nlstate;i++)    int i, j, k;
     for(j=1; j<=nlstate;j++)    for(i=nrl; i<= nrh; i++)
       fprintf(ficreseij," %1d-%1d (SE)",i,j);      for(k=ncolol; k<=ncoloh; k++){
   fprintf(ficreseij,"\n");        out[i][k]=0.;
         for(j=ncl; j<=nch; j++)
   if(estepm < stepm){          out[i][k] +=in[i][j]*b[j][k];
     printf ("Problem %d lower than %d\n",estepm, stepm);      }
   }    return out;
   else  hstepm=estepm;    }
   /* We compute the life expectancy from trapezoids spaced every estepm months  
    * This is mainly to measure the difference between two models: for example  
    * if stepm=24 months pijx are given only every 2 years and by summing them  /************* Higher Matrix Product ***************/
    * we are calculating an estimate of the Life Expectancy assuming a linear  
    * progression inbetween and thus overestimating or underestimating according  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
    * to the curvature of the survival function. If, for the same date, we  {
    * estimate the model with stepm=1 month, we can keep estepm to 24 months    /* Computes the transition matrix starting at age 'age' over 
    * to compare the new estimate of Life expectancy with the same linear       'nhstepm*hstepm*stepm' months (i.e. until
    * hypothesis. A more precise result, taking into account a more precise       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
    * curvature will be obtained if estepm is as small as stepm. */       nhstepm*hstepm matrices. 
        Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
   /* For example we decided to compute the life expectancy with the smallest unit */       (typically every 2 years instead of every month which is too big 
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.       for the memory).
      nhstepm is the number of hstepm from age to agelim       Model is determined by parameters x and covariates have to be 
      nstepm is the number of stepm from age to agelin.       included manually here. 
      Look at hpijx to understand the reason of that which relies in memory size  
      and note for a fixed period like estepm months */       */
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the  
      survival function given by stepm (the optimization length). Unfortunately it    int i, j, d, h, k;
      means that if the survival funtion is printed only each two years of age and if    double **out, cov[NCOVMAX+1];
      you sum them up and add 1 year (area under the trapezoids) you won't get the same    double **newm;
      results. So we changed our mind and took the option of the best precision.  
   */    /* Hstepm could be zero and should return the unit matrix */
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */    for (i=1;i<=nlstate+ndeath;i++)
       for (j=1;j<=nlstate+ndeath;j++){
   agelim=AGESUP;        oldm[i][j]=(i==j ? 1.0 : 0.0);
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        po[i][j][0]=(i==j ? 1.0 : 0.0);
     /* nhstepm age range expressed in number of stepm */      }
     nstepm=(int) rint((agelim-age)*YEARM/stepm);    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */    for(h=1; h <=nhstepm; h++){
     /* if (stepm >= YEARM) hstepm=1;*/      for(d=1; d <=hstepm; d++){
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */        newm=savm;
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        /* Covariates have to be included here again */
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);        cov[1]=1.;
     gp=matrix(0,nhstepm,1,nlstate*2);        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
     gm=matrix(0,nhstepm,1,nlstate*2);        for (k=1; k<=cptcovn;k++) 
           cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
     /* Computed by stepm unit matrices, product of hstepm matrices, stored        for (k=1; k<=cptcovage;k++)
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);          for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */  
         /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
     /* Computing Variances of health expectancies */        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
      for(theta=1; theta <=npar; theta++){                     pmij(pmmij,cov,ncovmodel,x,nlstate));
       for(i=1; i<=npar; i++){        savm=oldm;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        oldm=newm;
       }      }
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        for(i=1; i<=nlstate+ndeath; i++)
          for(j=1;j<=nlstate+ndeath;j++) {
       cptj=0;          po[i][j][h]=newm[i][j];
       for(j=1; j<= nlstate; j++){          /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
         for(i=1; i<=nlstate; i++){        }
           cptj=cptj+1;      /*printf("h=%d ",h);*/
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){    } /* end h */
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;  /*     printf("\n H=%d \n",h); */
           }    return po;
         }  }
       }  
        #ifdef NLOPT
          double  myfunc(unsigned n, const double *p1, double *grad, void *pd){
       for(i=1; i<=npar; i++)    double fret;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    double *xt;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      int j;
          myfunc_data *d2 = (myfunc_data *) pd;
       cptj=0;  /* xt = (p1-1); */
       for(j=1; j<= nlstate; j++){    xt=vector(1,n); 
         for(i=1;i<=nlstate;i++){    for (j=1;j<=n;j++)   xt[j]=p1[j-1]; /* xt[1]=p1[0] */
           cptj=cptj+1;  
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){    fret=(d2->function)(xt); /*  p xt[1]@8 is fine */
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;    /* fret=(*func)(xt); /\*  p xt[1]@8 is fine *\/ */
           }    printf("Function = %.12lf ",fret);
         }    for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]); 
       }    printf("\n");
       for(j=1; j<= nlstate*2; j++)   free_vector(xt,1,n);
         for(h=0; h<=nhstepm-1; h++){    return fret;
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];  }
         }  #endif
      }  
      /*************** log-likelihood *************/
 /* End theta */  double func( double *x)
   {
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);    int i, ii, j, k, mi, d, kk;
     double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
      for(h=0; h<=nhstepm-1; h++)    double **out;
       for(j=1; j<=nlstate*2;j++)    double sw; /* Sum of weights */
         for(theta=1; theta <=npar; theta++)    double lli; /* Individual log likelihood */
           trgradg[h][j][theta]=gradg[h][theta][j];    int s1, s2;
          double bbh, survp;
     long ipmx;
      for(i=1;i<=nlstate*2;i++)    /*extern weight */
       for(j=1;j<=nlstate*2;j++)    /* We are differentiating ll according to initial status */
         varhe[i][j][(int)age] =0.;    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     /*for(i=1;i<imx;i++) 
      printf("%d|",(int)age);fflush(stdout);      printf(" %d\n",s[4][i]);
      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);    */
      for(h=0;h<=nhstepm-1;h++){  
       for(k=0;k<=nhstepm-1;k++){    ++countcallfunc;
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);  
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);    cov[1]=1.;
         for(i=1;i<=nlstate*2;i++)  
           for(j=1;j<=nlstate*2;j++)    for(k=1; k<=nlstate; k++) ll[k]=0.;
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;  
       }    if(mle==1){
     }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     /* Computing expectancies */        /* Computes the values of the ncovmodel covariates of the model
     for(i=1; i<=nlstate;i++)           depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
       for(j=1; j<=nlstate;j++)           Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){           to be observed in j being in i according to the model.
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;         */
                  for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
 /* 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]);*/          cov[2+k]=covar[Tvar[k]][i];
         }
         }        /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 
            is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] 
     fprintf(ficreseij,"%3.0f",age );           has been calculated etc */
     cptj=0;        for(mi=1; mi<= wav[i]-1; mi++){
     for(i=1; i<=nlstate;i++)          for (ii=1;ii<=nlstate+ndeath;ii++)
       for(j=1; j<=nlstate;j++){            for (j=1;j<=nlstate+ndeath;j++){
         cptj++;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       }            }
     fprintf(ficreseij,"\n");          for(d=0; d<dh[mi][i]; d++){
                newm=savm;
     free_matrix(gm,0,nhstepm,1,nlstate*2);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     free_matrix(gp,0,nhstepm,1,nlstate*2);            for (kk=1; kk<=cptcovage;kk++) {
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);            }
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   printf("\n");            savm=oldm;
   fprintf(ficlog,"\n");            oldm=newm;
           } /* end mult */
   free_vector(xp,1,npar);        
   free_matrix(dnewm,1,nlstate*2,1,npar);          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);          /* But now since version 0.9 we anticipate for bias at large stepm.
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);           * If stepm is larger than one month (smallest stepm) and if the exact delay 
 }           * (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
 /************ Variance ******************/           * we keep into memory the bias bh[mi][i] and also the previous matrix product
 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)           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
 {           * probability in order to take into account the bias as a fraction of the way
   /* Variance of health expectancies */           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/           * -stepm/2 to stepm/2 .
   /* double **newm;*/           * For stepm=1 the results are the same as for previous versions of Imach.
   double **dnewm,**doldm;           * For stepm > 1 the results are less biased than in previous versions. 
   double **dnewmp,**doldmp;           */
   int i, j, nhstepm, hstepm, h, nstepm ;          s1=s[mw[mi][i]][i];
   int k, cptcode;          s2=s[mw[mi+1][i]][i];
   double *xp;          bbh=(double)bh[mi][i]/(double)stepm; 
   double **gp, **gm;  /* for var eij */          /* bias bh is positive if real duration
   double ***gradg, ***trgradg; /*for var eij */           * is higher than the multiple of stepm and negative otherwise.
   double **gradgp, **trgradgp; /* for var p point j */           */
   double *gpp, *gmp; /* for var p point j */          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
   double **varppt; /* for var p point j nlstate to nlstate+ndeath */          if( s2 > nlstate){ 
   double ***p3mat;            /* i.e. if s2 is a death state and if the date of death is known 
   double age,agelim, hf;               then the contribution to the likelihood is the probability to 
   int theta;               die between last step unit time and current  step unit time, 
   char digit[4];               which is also equal to probability to die before dh 
   char digitp[16];               minus probability to die before dh-stepm . 
                In version up to 0.92 likelihood was computed
   char fileresprobmorprev[FILENAMELENGTH];          as if date of death was unknown. Death was treated as any other
           health state: the date of the interview describes the actual state
   if(popbased==1)          and not the date of a change in health state. The former idea was
     strcpy(digitp,"-populbased-");          to consider that at each interview the state was recorded
   else          (healthy, disable or death) and IMaCh was corrected; but when we
     strcpy(digitp,"-stablbased-");          introduced the exact date of death then we should have modified
           the contribution of an exact death to the likelihood. This new
   strcpy(fileresprobmorprev,"prmorprev");          contribution is smaller and very dependent of the step unit
   sprintf(digit,"%-d",ij);          stepm. It is no more the probability to die between last interview
   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/          and month of death but the probability to survive from last
   strcat(fileresprobmorprev,digit); /* Tvar to be done */          interview up to one month before death multiplied by the
   strcat(fileresprobmorprev,digitp); /* Popbased or not */          probability to die within a month. Thanks to Chris
   strcat(fileresprobmorprev,fileres);          Jackson for correcting this bug.  Former versions increased
   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {          mortality artificially. The bad side is that we add another loop
     printf("Problem with resultfile: %s\n", fileresprobmorprev);          which slows down the processing. The difference can be up to 10%
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);          lower mortality.
   }            */
   printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);            lli=log(out[s1][s2] - savm[s1][s2]);
   fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);  
   fprintf(ficresprobmorprev,"# probabilities of dying during a year and weighted mean w1*p1j+w2*p2j+... stand dev in()\n");  
   fprintf(ficresprobmorprev,"# Age cov=%-d",ij);          } else if  (s2==-2) {
   for(j=nlstate+1; j<=(nlstate+ndeath);j++){            for (j=1,survp=0. ; j<=nlstate; j++) 
     fprintf(ficresprobmorprev," p.%-d SE",j);              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
     for(i=1; i<=nlstate;i++)            /*survp += out[s1][j]; */
       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);            lli= log(survp);
   }            }
   fprintf(ficresprobmorprev,"\n");          
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {          else if  (s2==-4) { 
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);            for (j=3,survp=0. ; j<=nlstate; j++)  
     fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
     exit(0);            lli= log(survp); 
   }          } 
   else{  
     fprintf(ficgp,"\n# Routine varevsij");          else if  (s2==-5) { 
   }            for (j=1,survp=0. ; j<=2; j++)  
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
     printf("Problem with html file: %s\n", optionfilehtm);            lli= log(survp); 
     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);          } 
     exit(0);          
   }          else{
   else{            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
     fprintf(fichtm,"\n<li><h4> Computing step probabilities of dying and weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");            /*  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 */
   }          } 
   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
           /*if(lli ==000.0)*/
   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");          /*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); */
   fprintf(ficresvij,"# Age");          ipmx +=1;
   for(i=1; i<=nlstate;i++)          sw += weight[i];
     for(j=1; j<=nlstate;j++)          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);        } /* end of wave */
   fprintf(ficresvij,"\n");      } /* end of individual */
     }  else if(mle==2){
   xp=vector(1,npar);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   dnewm=matrix(1,nlstate,1,npar);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   doldm=matrix(1,nlstate,1,nlstate);        for(mi=1; mi<= wav[i]-1; mi++){
   dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);          for (ii=1;ii<=nlstate+ndeath;ii++)
   doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);            for (j=1;j<=nlstate+ndeath;j++){
               oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   gpp=vector(nlstate+1,nlstate+ndeath);            }
   gmp=vector(nlstate+1,nlstate+ndeath);          for(d=0; d<=dh[mi][i]; d++){
   trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/            newm=savm;
              cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   if(estepm < stepm){            for (kk=1; kk<=cptcovage;kk++) {
     printf ("Problem %d lower than %d\n",estepm, stepm);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   }            }
   else  hstepm=estepm;              out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   /* For example we decided to compute the life expectancy with the smallest unit */                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.            savm=oldm;
      nhstepm is the number of hstepm from age to agelim            oldm=newm;
      nstepm is the number of stepm from age to agelin.          } /* end mult */
      Look at hpijx to understand the reason of that which relies in memory size        
      and note for a fixed period like k years */          s1=s[mw[mi][i]][i];
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the          s2=s[mw[mi+1][i]][i];
      survival function given by stepm (the optimization length). Unfortunately it          bbh=(double)bh[mi][i]/(double)stepm; 
      means that if the survival funtion is printed only each two years of age and if          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 */
      you sum them up and add 1 year (area under the trapezoids) you won't get the same          ipmx +=1;
      results. So we changed our mind and took the option of the best precision.          sw += weight[i];
   */          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */        } /* end of wave */
   agelim = AGESUP;      } /* end of individual */
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    }  else if(mle==3){  /* exponential inter-extrapolation */
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        for(mi=1; mi<= wav[i]-1; mi++){
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);          for (ii=1;ii<=nlstate+ndeath;ii++)
     gp=matrix(0,nhstepm,1,nlstate);            for (j=1;j<=nlstate+ndeath;j++){
     gm=matrix(0,nhstepm,1,nlstate);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               savm[ii][j]=(ii==j ? 1.0 : 0.0);
             }
     for(theta=1; theta <=npar; theta++){          for(d=0; d<dh[mi][i]; d++){
       for(i=1; i<=npar; i++){ /* Computes gradient */            newm=savm;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       }            for (kk=1; kk<=cptcovage;kk++) {
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);                cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);            }
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       if (popbased==1) {                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         for(i=1; i<=nlstate;i++)            savm=oldm;
           prlim[i][i]=probs[(int)age][i][ij];            oldm=newm;
       }          } /* end mult */
          
       for(j=1; j<= nlstate; j++){          s1=s[mw[mi][i]][i];
         for(h=0; h<=nhstepm; h++){          s2=s[mw[mi+1][i]][i];
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)          bbh=(double)bh[mi][i]/(double)stepm; 
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];          lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
         }          ipmx +=1;
       }          sw += weight[i];
       /* This for computing forces of mortality (h=1)as a weighted average */          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       for(j=nlstate+1,gpp[j]=0.;j<=nlstate+ndeath;j++){        } /* end of wave */
         for(i=1; i<= nlstate; i++)      } /* end of individual */
           gpp[j] += prlim[i][i]*p3mat[i][j][1];    }else if (mle==4){  /* ml=4 no inter-extrapolation */
       }          for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       /* end force of mortality */        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for(mi=1; mi<= wav[i]-1; mi++){
       for(i=1; i<=npar; i++) /* Computes gradient */          for (ii=1;ii<=nlstate+ndeath;ii++)
         xp[i] = x[i] - (i==theta ?delti[theta]:0);            for (j=1;j<=nlstate+ndeath;j++){
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);                oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
              }
       if (popbased==1) {          for(d=0; d<dh[mi][i]; d++){
         for(i=1; i<=nlstate;i++)            newm=savm;
           prlim[i][i]=probs[(int)age][i][ij];            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       }            for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       for(j=1; j<= nlstate; j++){            }
         for(h=0; h<=nhstepm; h++){          
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         }            savm=oldm;
       }            oldm=newm;
       /* This for computing force of mortality (h=1)as a weighted average */          } /* end mult */
       for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){        
         for(i=1; i<= nlstate; i++)          s1=s[mw[mi][i]][i];
           gmp[j] += prlim[i][i]*p3mat[i][j][1];          s2=s[mw[mi+1][i]][i];
       }              if( s2 > nlstate){ 
       /* end force of mortality */            lli=log(out[s1][s2] - savm[s1][s2]);
           }else{
       for(j=1; j<= nlstate; j++) /* vareij */            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
         for(h=0; h<=nhstepm; h++){          }
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];          ipmx +=1;
         }          sw += weight[i];
       for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];  /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
       }        } /* end of wave */
       } /* end of individual */
     } /* End theta */    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for(mi=1; mi<= wav[i]-1; mi++){
     for(h=0; h<=nhstepm; h++) /* veij */          for (ii=1;ii<=nlstate+ndeath;ii++)
       for(j=1; j<=nlstate;j++)            for (j=1;j<=nlstate+ndeath;j++){
         for(theta=1; theta <=npar; theta++)              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           trgradg[h][j][theta]=gradg[h][theta][j];              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             }
     for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */          for(d=0; d<dh[mi][i]; d++){
       for(theta=1; theta <=npar; theta++)            newm=savm;
         trgradgp[j][theta]=gradgp[theta][j];            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     for(i=1;i<=nlstate;i++)            }
       for(j=1;j<=nlstate;j++)          
         vareij[i][j][(int)age] =0.;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     for(h=0;h<=nhstepm;h++){            savm=oldm;
       for(k=0;k<=nhstepm;k++){            oldm=newm;
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);          } /* end mult */
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);        
         for(i=1;i<=nlstate;i++)          s1=s[mw[mi][i]][i];
           for(j=1;j<=nlstate;j++)          s2=s[mw[mi+1][i]][i];
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
       }          ipmx +=1;
     }          sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     /* pptj */          /*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]);*/
     matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);        } /* end of wave */
     matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);      } /* end of individual */
     for(j=nlstate+1;j<=nlstate+ndeath;j++)    } /* End of if */
       for(i=nlstate+1;i<=nlstate+ndeath;i++)    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
         varppt[j][i]=doldmp[j][i];    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     /* end ppptj */    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);      return -l;
     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);  }
    
     if (popbased==1) {  /*************** log-likelihood *************/
       for(i=1; i<=nlstate;i++)  double funcone( double *x)
         prlim[i][i]=probs[(int)age][i][ij];  {
     }    /* Same as likeli but slower because of a lot of printf and if */
        int i, ii, j, k, mi, d, kk;
     /* This for computing force of mortality (h=1)as a weighted average */    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
     for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){    double **out;
       for(i=1; i<= nlstate; i++)    double lli; /* Individual log likelihood */
         gmp[j] += prlim[i][i]*p3mat[i][j][1];    double llt;
     }        int s1, s2;
     /* end force of mortality */    double bbh, survp;
     /*extern weight */
     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);    /* We are differentiating ll according to initial status */
     for(j=nlstate+1; j<=(nlstate+ndeath);j++){    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
       fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));    /*for(i=1;i<imx;i++) 
       for(i=1; i<=nlstate;i++){      printf(" %d\n",s[4][i]);
         fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);    */
       }    cov[1]=1.;
     }  
     fprintf(ficresprobmorprev,"\n");    for(k=1; k<=nlstate; k++) ll[k]=0.;
   
     fprintf(ficresvij,"%.0f ",age );    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     for(i=1; i<=nlstate;i++)      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       for(j=1; j<=nlstate;j++){      for(mi=1; mi<= wav[i]-1; mi++){
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);        for (ii=1;ii<=nlstate+ndeath;ii++)
       }          for (j=1;j<=nlstate+ndeath;j++){
     fprintf(ficresvij,"\n");            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     free_matrix(gp,0,nhstepm,1,nlstate);            savm[ii][j]=(ii==j ? 1.0 : 0.0);
     free_matrix(gm,0,nhstepm,1,nlstate);          }
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);        for(d=0; d<dh[mi][i]; d++){
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);          newm=savm;
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   } /* End age */          for (kk=1; kk<=cptcovage;kk++) {
   free_vector(gpp,nlstate+1,nlstate+ndeath);            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   free_vector(gmp,nlstate+1,nlstate+ndeath);          }
   free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);          /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
   free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */          /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
   fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");          /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm);          savm=oldm;
   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm);          oldm=newm;
   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm);        } /* end mult */
   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);        
   fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months 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);        s1=s[mw[mi][i]][i];
   fprintf(ficgp,"\nset out \"varmuptjgr%s%s.png\";replot;",digitp,digit);        s2=s[mw[mi+1][i]][i];
         bbh=(double)bh[mi][i]/(double)stepm; 
   free_vector(xp,1,npar);        /* bias is positive if real duration
   free_matrix(doldm,1,nlstate,1,nlstate);         * is higher than the multiple of stepm and negative otherwise.
   free_matrix(dnewm,1,nlstate,1,npar);         */
   free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);        if( s2 > nlstate && (mle <5) ){  /* Jackson */
   free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);          lli=log(out[s1][s2] - savm[s1][s2]);
   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);        } else if  (s2==-2) {
   fclose(ficresprobmorprev);          for (j=1,survp=0. ; j<=nlstate; j++) 
   fclose(ficgp);            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   fclose(fichtm);          lli= log(survp);
         }else if (mle==1){
 }          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
         } else if(mle==2){
 /************ Variance of prevlim ******************/          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 */
 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)        } else if(mle==3){  /* exponential inter-extrapolation */
 {          lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
   /* Variance of prevalence limit */        } else if (mle==4){  /* mle=4 no inter-extrapolation */
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/          lli=log(out[s1][s2]); /* Original formula */
   double **newm;        } else{  /* mle=0 back to 1 */
   double **dnewm,**doldm;          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   int i, j, nhstepm, hstepm;          /*lli=log(out[s1][s2]); */ /* Original formula */
   int k, cptcode;        } /* End of if */
   double *xp;        ipmx +=1;
   double *gp, *gm;        sw += weight[i];
   double **gradg, **trgradg;        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   double age,agelim;        /*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]); */
   int theta;        if(globpr){
              fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
   fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n");   %11.6f %11.6f %11.6f ", \
   fprintf(ficresvpl,"# Age");                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
   for(i=1; i<=nlstate;i++)                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
       fprintf(ficresvpl," %1d-%1d",i,i);          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
   fprintf(ficresvpl,"\n");            llt +=ll[k]*gipmx/gsw;
             fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
   xp=vector(1,npar);          }
   dnewm=matrix(1,nlstate,1,npar);          fprintf(ficresilk," %10.6f\n", -llt);
   doldm=matrix(1,nlstate,1,nlstate);        }
        } /* end of wave */
   hstepm=1*YEARM; /* Every year of age */    } /* end of individual */
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   agelim = AGESUP;    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    if(globpr==0){ /* First time we count the contributions and weights */
     if (stepm >= YEARM) hstepm=1;      gipmx=ipmx;
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      gsw=sw;
     gradg=matrix(1,npar,1,nlstate);    }
     gp=vector(1,nlstate);    return -l;
     gm=vector(1,nlstate);  }
   
     for(theta=1; theta <=npar; theta++){  
       for(i=1; i<=npar; i++){ /* Computes gradient */  /*************** function likelione ***********/
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
       }  {
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    /* This routine should help understanding what is done with 
       for(i=1;i<=nlstate;i++)       the selection of individuals/waves and
         gp[i] = prlim[i][i];       to check the exact contribution to the likelihood.
           Plotting could be done.
       for(i=1; i<=npar; i++) /* Computes gradient */     */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    int k;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  
       for(i=1;i<=nlstate;i++)    if(*globpri !=0){ /* Just counts and sums, no printings */
         gm[i] = prlim[i][i];      strcpy(fileresilk,"ilk"); 
       strcat(fileresilk,fileres);
       for(i=1;i<=nlstate;i++)      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];        printf("Problem with resultfile: %s\n", fileresilk);
     } /* End theta */        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
       }
     trgradg =matrix(1,nlstate,1,npar);      fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
       fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
     for(j=1; j<=nlstate;j++)      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
       for(theta=1; theta <=npar; theta++)      for(k=1; k<=nlstate; k++) 
         trgradg[j][theta]=gradg[theta][j];        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
       fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
     for(i=1;i<=nlstate;i++)    }
       varpl[i][(int)age] =0.;  
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);    *fretone=(*funcone)(p);
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);    if(*globpri !=0){
     for(i=1;i<=nlstate;i++)      fclose(ficresilk);
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
       fflush(fichtm); 
     fprintf(ficresvpl,"%.0f ",age );    } 
     for(i=1; i<=nlstate;i++)    return;
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));  }
     fprintf(ficresvpl,"\n");  
     free_vector(gp,1,nlstate);  
     free_vector(gm,1,nlstate);  /*********** Maximum Likelihood Estimation ***************/
     free_matrix(gradg,1,npar,1,nlstate);  
     free_matrix(trgradg,1,nlstate,1,npar);  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   } /* End age */  {
     int i,j, iter;
   free_vector(xp,1,npar);    double **xi;
   free_matrix(doldm,1,nlstate,1,npar);    double fret;
   free_matrix(dnewm,1,nlstate,1,nlstate);    double fretone; /* Only one call to likelihood */
     /*  char filerespow[FILENAMELENGTH];*/
 }  
   #ifdef NLOPT
 /************ Variance of one-step probabilities  ******************/    int creturn;
 void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)    nlopt_opt opt;
 {    /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
   int i, j=0,  i1, k1, l1, t, tj;    double *lb;
   int k2, l2, j1,  z1;    double minf; /* the minimum objective value, upon return */
   int k=0,l, cptcode;    double * p1; /* Shifted parameters from 0 instead of 1 */
   int first=1, first1;    myfunc_data dinst, *d = &dinst;
   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2;  #endif
   double **dnewm,**doldm;  
   double *xp;  
   double *gp, *gm;    xi=matrix(1,npar,1,npar);
   double **gradg, **trgradg;    for (i=1;i<=npar;i++)
   double **mu;      for (j=1;j<=npar;j++)
   double age,agelim, cov[NCOVMAX];        xi[i][j]=(i==j ? 1.0 : 0.0);
   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */    printf("Powell\n");  fprintf(ficlog,"Powell\n");
   int theta;    strcpy(filerespow,"pow"); 
   char fileresprob[FILENAMELENGTH];    strcat(filerespow,fileres);
   char fileresprobcov[FILENAMELENGTH];    if((ficrespow=fopen(filerespow,"w"))==NULL) {
   char fileresprobcor[FILENAMELENGTH];      printf("Problem with resultfile: %s\n", filerespow);
       fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
   double ***varpij;    }
     fprintf(ficrespow,"# Powell\n# iter -2*LL");
   strcpy(fileresprob,"prob");    for (i=1;i<=nlstate;i++)
   strcat(fileresprob,fileres);      for(j=1;j<=nlstate+ndeath;j++)
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
     printf("Problem with resultfile: %s\n", fileresprob);    fprintf(ficrespow,"\n");
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);  #ifdef POWELL
   }    powell(p,xi,npar,ftol,&iter,&fret,func);
   strcpy(fileresprobcov,"probcov");  #endif
   strcat(fileresprobcov,fileres);  
   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {  #ifdef NLOPT
     printf("Problem with resultfile: %s\n", fileresprobcov);  #ifdef NEWUOA
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);    opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
   }  #else
   strcpy(fileresprobcor,"probcor");    opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
   strcat(fileresprobcor,fileres);  #endif
   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {    lb=vector(0,npar-1);
     printf("Problem with resultfile: %s\n", fileresprobcor);    for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);    nlopt_set_lower_bounds(opt, lb);
   }    nlopt_set_initial_step1(opt, 0.1);
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);    
   fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);    p1= (p+1); /*  p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);    d->function = func;
   fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);    printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);    nlopt_set_min_objective(opt, myfunc, d);
   fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);    nlopt_set_xtol_rel(opt, ftol);
      if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");      printf("nlopt failed! %d\n",creturn); 
   fprintf(ficresprob,"# Age");    }
   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");    else {
   fprintf(ficresprobcov,"# Age");      printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");      printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
   fprintf(ficresprobcov,"# Age");      iter=1; /* not equal */
     }
     nlopt_destroy(opt);
   for(i=1; i<=nlstate;i++)  #endif
     for(j=1; j<=(nlstate+ndeath);j++){    free_matrix(xi,1,npar,1,npar);
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);    fclose(ficrespow);
       fprintf(ficresprobcov," p%1d-%1d ",i,j);    printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
       fprintf(ficresprobcor," p%1d-%1d ",i,j);    fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
     }      fprintf(ficres,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
   fprintf(ficresprob,"\n");  
   fprintf(ficresprobcov,"\n");  }
   fprintf(ficresprobcor,"\n");  
   xp=vector(1,npar);  /**** Computes Hessian and covariance matrix ***/
   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));  {
   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);    double  **a,**y,*x,pd;
   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);    double **hess;
   first=1;    int i, j,jk;
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {    int *indx;
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);  
     fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
     exit(0);    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
   }    void lubksb(double **a, int npar, int *indx, double b[]) ;
   else{    void ludcmp(double **a, int npar, int *indx, double *d) ;
     fprintf(ficgp,"\n# Routine varprob");    double gompertz(double p[]);
   }    hess=matrix(1,npar,1,npar);
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {  
     printf("Problem with html file: %s\n", optionfilehtm);    printf("\nCalculation of the hessian matrix. Wait...\n");
     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
     exit(0);    for (i=1;i<=npar;i++){
   }      printf("%d",i);fflush(stdout);
   else{      fprintf(ficlog,"%d",i);fflush(ficlog);
     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");     
     fprintf(fichtm,"\n");       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
       
     fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");      /*  printf(" %f ",p[i]);
     fprintf(fichtm,"\nWe have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
     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 (i=1;i<=npar;i++) {
       for (j=1;j<=npar;j++)  {
          if (j>i) { 
   cov[1]=1;          printf(".%d%d",i,j);fflush(stdout);
   tj=cptcoveff;          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
   if (cptcovn<1) {tj=1;ncodemax[1]=1;}          hess[i][j]=hessij(p,delti,i,j,func,npar);
   j1=0;          
   for(t=1; t<=tj;t++){          hess[j][i]=hess[i][j];    
     for(i1=1; i1<=ncodemax[t];i1++){          /*printf(" %lf ",hess[i][j]);*/
       j1++;        }
            }
       if  (cptcovn>0) {    }
         fprintf(ficresprob, "\n#********** Variable ");    printf("\n");
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    fprintf(ficlog,"\n");
         fprintf(ficresprob, "**********\n#");  
         fprintf(ficresprobcov, "\n#********** Variable ");    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
         fprintf(ficresprobcov, "**********\n#");    
            a=matrix(1,npar,1,npar);
         fprintf(ficgp, "\n#********** Variable ");    y=matrix(1,npar,1,npar);
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    x=vector(1,npar);
         fprintf(ficgp, "**********\n#");    indx=ivector(1,npar);
            for (i=1;i<=npar;i++)
              for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
         fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");    ludcmp(a,npar,indx,&pd);
         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  
         fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");    for (j=1;j<=npar;j++) {
              for (i=1;i<=npar;i++) x[i]=0;
         fprintf(ficresprobcor, "\n#********** Variable ");          x[j]=1;
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);      lubksb(a,npar,indx,x);
         fprintf(ficgp, "**********\n#");          for (i=1;i<=npar;i++){ 
       }        matcov[i][j]=x[i];
            }
       for (age=bage; age<=fage; age ++){    }
         cov[2]=age;  
         for (k=1; k<=cptcovn;k++) {    printf("\n#Hessian matrix#\n");
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];    fprintf(ficlog,"\n#Hessian matrix#\n");
         }    for (i=1;i<=npar;i++) { 
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];      for (j=1;j<=npar;j++) { 
         for (k=1; k<=cptcovprod;k++)        printf("%.3e ",hess[i][j]);
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];        fprintf(ficlog,"%.3e ",hess[i][j]);
              }
         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));      printf("\n");
         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);      fprintf(ficlog,"\n");
         gp=vector(1,(nlstate)*(nlstate+ndeath));    }
         gm=vector(1,(nlstate)*(nlstate+ndeath));  
        /* Recompute Inverse */
         for(theta=1; theta <=npar; theta++){    for (i=1;i<=npar;i++)
           for(i=1; i<=npar; i++)      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
             xp[i] = x[i] + (i==theta ?delti[theta]:0);    ludcmp(a,npar,indx,&pd);
            
           pmij(pmmij,cov,ncovmodel,xp,nlstate);    /*  printf("\n#Hessian matrix recomputed#\n");
            
           k=0;    for (j=1;j<=npar;j++) {
           for(i=1; i<= (nlstate); i++){      for (i=1;i<=npar;i++) x[i]=0;
             for(j=1; j<=(nlstate+ndeath);j++){      x[j]=1;
               k=k+1;      lubksb(a,npar,indx,x);
               gp[k]=pmmij[i][j];      for (i=1;i<=npar;i++){ 
             }        y[i][j]=x[i];
           }        printf("%.3e ",y[i][j]);
                  fprintf(ficlog,"%.3e ",y[i][j]);
           for(i=1; i<=npar; i++)      }
             xp[i] = x[i] - (i==theta ?delti[theta]:0);      printf("\n");
          fprintf(ficlog,"\n");
           pmij(pmmij,cov,ncovmodel,xp,nlstate);    }
           k=0;    */
           for(i=1; i<=(nlstate); i++){  
             for(j=1; j<=(nlstate+ndeath);j++){    free_matrix(a,1,npar,1,npar);
               k=k+1;    free_matrix(y,1,npar,1,npar);
               gm[k]=pmmij[i][j];    free_vector(x,1,npar);
             }    free_ivector(indx,1,npar);
           }    free_matrix(hess,1,npar,1,npar);
        
           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)  
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];    }
         }  
   /*************** hessian matrix ****************/
         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
           for(theta=1; theta <=npar; theta++)  {
             trgradg[j][theta]=gradg[theta][j];    int i;
            int l=1, lmax=20;
         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);    double k1,k2;
         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);    double p2[MAXPARM+1]; /* identical to x */
            double res;
         pmij(pmmij,cov,ncovmodel,x,nlstate);    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
            double fx;
         k=0;    int k=0,kmax=10;
         for(i=1; i<=(nlstate); i++){    double l1;
           for(j=1; j<=(nlstate+ndeath);j++){  
             k=k+1;    fx=func(x);
             mu[k][(int) age]=pmmij[i][j];    for (i=1;i<=npar;i++) p2[i]=x[i];
           }    for(l=0 ; l <=lmax; l++){  /* Enlarging the zone around the Maximum */
         }      l1=pow(10,l);
         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)      delts=delt;
           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)      for(k=1 ; k <kmax; k=k+1){
             varpij[i][j][(int)age] = doldm[i][j];        delt = delta*(l1*k);
         p2[theta]=x[theta] +delt;
         /*printf("\n%d ",(int)age);        k1=func(p2)-fx;   /* Might be negative if too close to the theoretical maximum */
      for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){        p2[theta]=x[theta]-delt;
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));        k2=func(p2)-fx;
        fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));        /*res= (k1-2.0*fx+k2)/delt/delt; */
      }*/        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
         
         fprintf(ficresprob,"\n%d ",(int)age);  #ifdef DEBUGHESS
         fprintf(ficresprobcov,"\n%d ",(int)age);        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
         fprintf(ficresprobcor,"\n%d ",(int)age);        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
   #endif
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){          k=kmax;
           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);        }
           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
         }          k=kmax; l=lmax*10.;
         i=0;        }
         for (k=1; k<=(nlstate);k++){        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
           for (l=1; l<=(nlstate+ndeath);l++){          delts=delt;
             i=i++;        }
             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);      }
             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);    }
             for (j=1; j<=i;j++){    delti[theta]=delts;
               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);    return res; 
               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 */  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
       } /* end of loop for age */  {
     int i;
       /* Confidence intervalle of pij  */    int l=1, l1, lmax=20;
       /*    double k1,k2,k3,k4,res,fx;
       fprintf(ficgp,"\nset noparametric;unset label");    double p2[MAXPARM+1];
       fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");    int k;
       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);    fx=func(x);
       fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);    for (k=1; k<=2; k++) {
       fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);      for (i=1;i<=npar;i++) p2[i]=x[i];
       fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);      p2[thetai]=x[thetai]+delti[thetai]/k;
       */      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       k1=func(p2)-fx;
       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/    
       first1=1;      p2[thetai]=x[thetai]+delti[thetai]/k;
       for (k1=1; k1<=(nlstate);k1++){      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
         for (l1=1; l1<=(nlstate+ndeath);l1++){      k2=func(p2)-fx;
           if(l1==k1) continue;    
           i=(k1-1)*(nlstate+ndeath)+l1;      p2[thetai]=x[thetai]-delti[thetai]/k;
           for (k2=1; k2<=(nlstate);k2++){      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
             for (l2=1; l2<=(nlstate+ndeath);l2++){      k3=func(p2)-fx;
               if(l2==k2) continue;    
               j=(k2-1)*(nlstate+ndeath)+l2;      p2[thetai]=x[thetai]-delti[thetai]/k;
               if(j<=i) continue;      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
               for (age=bage; age<=fage; age ++){      k4=func(p2)-fx;
                 if ((int)age %5==0){      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;  #ifdef DEBUG
                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;      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);
                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;      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);
                   mu1=mu[i][(int) age]/stepm*YEARM ;  #endif
                   mu2=mu[j][(int) age]/stepm*YEARM;    }
                   /* Computing eigen value of matrix of covariance */    return res;
                   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));  
                   if(first1==1){  /************** Inverse of matrix **************/
                     first1=0;  void ludcmp(double **a, int n, int *indx, double *d) 
                     printf("Var %.4e %.4e cov %.4e Eigen %.3e %.3e\nOthers in log...\n",v1,v2,cv12,lc1,lc2);  { 
                   }    int i,imax,j,k; 
                   fprintf(ficlog,"Var %.4e %.4e cov %.4e Eigen %.3e %.3e\n",v1,v2,cv12,lc1,lc2);    double big,dum,sum,temp; 
                   /* Eigen vectors */    double *vv; 
                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));   
                   v21=sqrt(1.-v11*v11);    vv=vector(1,n); 
                   v12=-v21;    *d=1.0; 
                   v22=v11;    for (i=1;i<=n;i++) { 
                   /*printf(fignu*/      big=0.0; 
                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */      for (j=1;j<=n;j++) 
                   /* mu2+ v21*lc1*cost + v21*lc2*sin(t) */        if ((temp=fabs(a[i][j])) > big) big=temp; 
                   if(first==1){      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
                     first=0;      vv[i]=1.0/big; 
                     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);    for (j=1;j<=n;j++) { 
                     fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");      for (i=1;i<j;i++) { 
                     fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%d%1d%1d-%1d%1d.png\">varpijgr%s%d%1d%1d-%1d%1d.png</A>, ",k2,l2,k1,l1,optionfilefiname, j1,k2,l2,k1,l1,optionfilefiname, j1,k2,l2,k1,l1);        sum=a[i][j]; 
                     fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k2,l2,k1,l1);        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
                     fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k2,l2,k1,l1);        a[i][j]=sum; 
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);      } 
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);      big=0.0; 
                     /*              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\"",\      for (i=j;i<=n;i++) { 
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \        sum=a[i][j]; 
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);        for (k=1;k<j;k++) 
                     */          sum -= a[i][k]*a[k][j]; 
                     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",\        a[i][j]=sum; 
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \        if ( (dum=vv[i]*fabs(sum)) >= big) { 
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2));          big=dum; 
                   }else{          imax=i; 
                     first=0;        } 
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);      } 
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);      if (j != imax) { 
                     /*        for (k=1;k<=n;k++) { 
                     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\"",\          dum=a[imax][k]; 
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \          a[imax][k]=a[j][k]; 
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);          a[j][k]=dum; 
                     */        } 
                     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",\        *d = -(*d); 
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \        vv[imax]=vv[j]; 
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2));      } 
                   }/* if first */      indx[j]=imax; 
                 } /* age mod 5 */      if (a[j][j] == 0.0) a[j][j]=TINY; 
               } /* end loop age */      if (j != n) { 
               fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k2,l2,k1,l1);        dum=1.0/(a[j][j]); 
               first=1;        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
             } /*l12 */      } 
           } /* k12 */    } 
         } /*l1 */    free_vector(vv,1,n);  /* Doesn't work */
       }/* k1 */  ;
     } /* loop covariates */  } 
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);  
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));  void lubksb(double **a, int n, int *indx, double b[]) 
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));  { 
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);    int i,ii=0,ip,j; 
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    double sum; 
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);   
   }    for (i=1;i<=n;i++) { 
   free_vector(xp,1,npar);      ip=indx[i]; 
   fclose(ficresprob);      sum=b[ip]; 
   fclose(ficresprobcov);      b[ip]=b[i]; 
   fclose(ficresprobcor);      if (ii) 
   fclose(ficgp);        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
   fclose(fichtm);      else if (sum) ii=i; 
 }      b[i]=sum; 
     } 
     for (i=n;i>=1;i--) { 
 /******************* Printing html file ***********/      sum=b[i]; 
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
                   int lastpass, int stepm, int weightopt, char model[],\      b[i]=sum/a[i][i]; 
                   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){  void pstamp(FILE *fichier)
   int jj1, k1, i1, cpt;  {
   /*char optionfilehtm[FILENAMELENGTH];*/    fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {  }
     printf("Problem with %s \n",optionfilehtm), exit(0);  
     fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);  /************ Frequencies ********************/
   }  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[])
   {  /* Some frequencies */
    fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\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    int i, m, jk, k1,i1, j1, bool, z1,j;
  - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n    int first;
  - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n    double ***freq; /* Frequencies */
  - Life expectancies by age and initial health status (estepm=%2d months):    double *pp, **prop;
    <a href=\"e%s\">e%s</a> <br>\n</li>", \    double pos,posprop, k2, dateintsum=0,k2cpt=0;
   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);    char fileresp[FILENAMELENGTH];
     
 fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");    pp=vector(1,nlstate);
     prop=matrix(1,nlstate,iagemin,iagemax+3);
  m=cptcoveff;    strcpy(fileresp,"p");
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}    strcat(fileresp,fileres);
     if((ficresp=fopen(fileresp,"w"))==NULL) {
  jj1=0;      printf("Problem with prevalence resultfile: %s\n", fileresp);
  for(k1=1; k1<=m;k1++){      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
    for(i1=1; i1<=ncodemax[k1];i1++){      exit(0);
      jj1++;    }
      if (cptcovn > 0) {    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");    j1=0;
        for (cpt=1; cpt<=cptcoveff;cpt++)    
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);    j=cptcoveff;
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");    if (cptcovn<1) {j=1;ncodemax[1]=1;}
      }  
      /* Pij */    first=1;
      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>  
 <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);        /* for(k1=1; k1<=j ; k1++){   /* Loop on covariates */
      /* Quasi-incidences */    /*  for(i1=1; i1<=ncodemax[k1];i1++){ /* Now it is 2 */
      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>    /*    j1++;
 <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);  */
        /* Stable prevalence in each health state */    for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
        for(cpt=1; cpt<nlstate;cpt++){        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
          fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>          scanf("%d", i);*/
 <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);        for (i=-5; i<=nlstate+ndeath; i++)  
        }          for (jk=-5; jk<=nlstate+ndeath; jk++)  
      for(cpt=1; cpt<=nlstate;cpt++) {            for(m=iagemin; m <= iagemax+3; m++)
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>              freq[i][jk][m]=0;
 <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);        
      }        for (i=1; i<=nlstate; i++)  
      fprintf(fichtm,"\n<br>- Total life expectancy by age and          for(m=iagemin; m <= iagemax+3; m++)
 health expectancies in states (1) and (2): e%s%d.png<br>            prop[i][m]=0;
 <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);        
    } /* end i1 */        dateintsum=0;
  }/* End k1 */        k2cpt=0;
  fprintf(fichtm,"</ul>");        for (i=1; i<=imx; i++) {
           bool=1;
           if  (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
  fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n            for (z1=1; z1<=cptcoveff; z1++)       
  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
  - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n                  /* Tests if the value of each of the covariates of i is equal to filter j1 */
  - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n                bool=0;
  - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n                /* 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", 
  - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n                  bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
  - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n                  j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
  - 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);                /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
               } 
  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          if (bool==1){
         <br>",fileres,fileres,fileres,fileres);            for(m=firstpass; m<=lastpass; m++){
  else              k2=anint[m][i]+(mint[m][i]/12.);
    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);              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
 fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");                if(agev[m][i]==0) agev[m][i]=iagemax+1;
                 if(agev[m][i]==1) agev[m][i]=iagemax+2;
  m=cptcoveff;                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}                if (m<lastpass) {
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
  jj1=0;                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
  for(k1=1; k1<=m;k1++){                }
    for(i1=1; i1<=ncodemax[k1];i1++){                
      jj1++;                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
      if (cptcovn > 0) {                  dateintsum=dateintsum+k2;
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");                  k2cpt++;
        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++) {        } /* end i */
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident         
 interval) in state (%d): v%s%d%d.png <br>        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
 <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);          pstamp(ficresp);
      }        if  (cptcovn>0) {
    } /* end i1 */          fprintf(ficresp, "\n#********** Variable "); 
  }/* End k1 */          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
  fprintf(fichtm,"</ul>");          fprintf(ficresp, "**********\n#");
 fclose(fichtm);          fprintf(ficlog, "\n#********** Variable "); 
 }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficlog, "**********\n#");
 /******************* Gnuplot file **************/        }
 void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){        for(i=1; i<=nlstate;i++) 
           fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;        fprintf(ficresp, "\n");
   int ng;        
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {        for(i=iagemin; i <= iagemax+3; i++){
     printf("Problem with file %s",optionfilegnuplot);          if(i==iagemax+3){
     fprintf(ficlog,"Problem with file %s",optionfilegnuplot);            fprintf(ficlog,"Total");
   }          }else{
             if(first==1){
 #ifdef windows              first=0;
     fprintf(ficgp,"cd \"%s\" \n",pathc);              printf("See log file for details...\n");
 #endif            }
 m=pow(2,cptcoveff);            fprintf(ficlog,"Age %d", i);
            }
  /* 1eme*/          for(jk=1; jk <=nlstate ; jk++){
   for (cpt=1; cpt<= nlstate ; cpt ++) {            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
    for (k1=1; k1<= m ; k1 ++) {              pp[jk] += freq[jk][m][i]; 
           }
 #ifdef windows          for(jk=1; jk <=nlstate ; jk++){
      fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);            for(m=-1, pos=0; m <=0 ; m++)
      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);              pos += freq[jk][m][i];
 #endif            if(pp[jk]>=1.e-10){
 #ifdef unix              if(first==1){
 fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);                printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);              }
 #endif              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
             }else{
 for (i=1; i<= nlstate ; i ++) {              if(first==1)
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   else fprintf(ficgp," \%%*lf (\%%*lf)");              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
 }            }
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);          }
     for (i=1; i<= nlstate ; i ++) {  
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          for(jk=1; jk <=nlstate ; jk++){
   else fprintf(ficgp," \%%*lf (\%%*lf)");            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
 }              pp[jk] += freq[jk][m][i];
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);          }       
      for (i=1; i<= nlstate ; i ++) {          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");            pos += pp[jk];
   else fprintf(ficgp," \%%*lf (\%%*lf)");            posprop += prop[jk][i];
 }            }
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));          for(jk=1; jk <=nlstate ; jk++){
 #ifdef unix            if(pos>=1.e-5){
 fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");              if(first==1)
 #endif                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
    }              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   }            }else{
   /*2 eme*/              if(first==1)
                 printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   for (k1=1; k1<= m ; k1 ++) {              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
     fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);            }
     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);            if( i <= iagemax){
                  if(pos>=1.e-5){
     for (i=1; i<= nlstate+1 ; i ++) {                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
       k=2*i;                /*probs[i][jk][j1]= pp[jk]/pos;*/
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
       for (j=1; j<= nlstate+1 ; j ++) {              }
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");              else
   else fprintf(ficgp," \%%*lf (\%%*lf)");                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
 }              }
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");          }
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);          
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);          for(jk=-1; jk <=nlstate+ndeath; jk++)
       for (j=1; j<= nlstate+1 ; j ++) {            for(m=-1; m <=nlstate+ndeath; m++)
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");              if(freq[jk][m][i] !=0 ) {
         else fprintf(ficgp," \%%*lf (\%%*lf)");              if(first==1)
 }                  printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
       fprintf(ficgp,"\" t\"\" w l 0,");                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);              }
       for (j=1; j<= nlstate+1 ; j ++) {          if(i <= iagemax)
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");            fprintf(ficresp,"\n");
   else fprintf(ficgp," \%%*lf (\%%*lf)");          if(first==1)
 }              printf("Others in log...\n");
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");          fprintf(ficlog,"\n");
       else fprintf(ficgp,"\" t\"\" w l 0,");        }
     }        /*}*/
   }    }
      dateintmean=dateintsum/k2cpt; 
   /*3eme*/   
     fclose(ficresp);
   for (k1=1; k1<= m ; k1 ++) {    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
     for (cpt=1; cpt<= nlstate ; cpt ++) {    free_vector(pp,1,nlstate);
       k=2+nlstate*(2*cpt-2);    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
       fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);    /* End of Freq */
       fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);  }
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);  
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");  /************ Prevalence ********************/
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);  void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);  {  
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);       in each health status at the date of interview (if between dateprev1 and dateprev2).
        We still use firstpass and lastpass as another selection.
 */    */
       for (i=1; i< nlstate ; i ++) {   
         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);    int i, m, jk, k1, i1, j1, bool, z1,j;
     double ***freq; /* Frequencies */
       }    double *pp, **prop;
     }    double pos,posprop; 
   }    double  y2; /* in fractional years */
      int iagemin, iagemax;
   /* CV preval stat */    int first; /** to stop verbosity which is redirected to log file */
     for (k1=1; k1<= m ; k1 ++) {  
     for (cpt=1; cpt<nlstate ; cpt ++) {    iagemin= (int) agemin;
       k=3;    iagemax= (int) agemax;
       fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);    /*pp=vector(1,nlstate);*/
       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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);    prop=matrix(1,nlstate,iagemin,iagemax+3); 
     /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
       for (i=1; i< nlstate ; i ++)    j1=0;
         fprintf(ficgp,"+$%d",k+i+1);    
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);    /*j=cptcoveff;*/
          if (cptcovn<1) {j=1;ncodemax[1]=1;}
       l=3+(nlstate+ndeath)*cpt;    
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);    first=1;
       for (i=1; i< nlstate ; i ++) {    for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
         l=3+(nlstate+ndeath)*cpt;      /*for(i1=1; i1<=ncodemax[k1];i1++){
         fprintf(ficgp,"+$%d",l+i+1);        j1++;*/
       }        
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);          for (i=1; i<=nlstate; i++)  
     }          for(m=iagemin; m <= iagemax+3; m++)
   }              prop[i][m]=0.0;
         
   /* proba elementaires */        for (i=1; i<=imx; i++) { /* Each individual */
    for(i=1,jk=1; i <=nlstate; i++){          bool=1;
     for(k=1; k <=(nlstate+ndeath); k++){          if  (cptcovn>0) {
       if (k != i) {            for (z1=1; z1<=cptcoveff; z1++) 
         for(j=1; j <=ncovmodel; j++){              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);                bool=0;
           jk++;          } 
           fprintf(ficgp,"\n");          if (bool==1) { 
         }            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
       }              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
     }              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
    }                if(agev[m][i]==0) agev[m][i]=iagemax+1;
                 if(agev[m][i]==1) agev[m][i]=iagemax+2;
    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/                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); 
      for(jk=1; jk <=m; jk++) {                if (s[m][i]>0 && s[m][i]<=nlstate) { 
        fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);                  /*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]]);*/
        if (ng==2)                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");                  prop[s[m][i]][iagemax+3] += weight[i]; 
        else                } 
          fprintf(ficgp,"\nset title \"Probability\"\n");              }
        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);            } /* end selection of waves */
        i=1;          }
        for(k2=1; k2<=nlstate; k2++) {        }
          k3=i;        for(i=iagemin; i <= iagemax+3; i++){  
          for(k=1; k<=(nlstate+ndeath); k++) {          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
            if (k != k2){            posprop += prop[jk][i]; 
              if(ng==2)          } 
                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);            if( i <=  iagemax){ 
              ij=1;              if(posprop>=1.e-5){ 
              for(j=3; j <=ncovmodel; j++) {                probs[i][jk][j1]= prop[jk][i]/posprop;
                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {              } else{
                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);                if(first==1){
                  ij++;                  first=0;
                }                  printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others on log file...\n",jk,i,j1,probs[i][jk][j1]);
                else                }
                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);              }
              }            } 
              fprintf(ficgp,")/(1");          }/* end jk */ 
                      }/* end i */ 
              for(k1=1; k1 <=nlstate; k1++){        /*} *//* end i1 */
                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);    } /* end j1 */
                ij=1;    
                for(j=3; j <=ncovmodel; j++){    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    /*free_vector(pp,1,nlstate);*/
                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
                    ij++;  }  /* End of prevalence */
                  }  
                  else  /************* Waves Concatenation ***************/
                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);  
                }  void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
                fprintf(ficgp,")");  {
              }    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
              fprintf(ficgp,") t \"p%d%d\" ", k2,k);       Death is a valid wave (if date is known).
              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
              i=i+ncovmodel;       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.
          } /* end k */       */
        } /* end k2 */  
      } /* end jk */    int i, mi, m;
    } /* end ng */    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
    fclose(ficgp);       double sum=0., jmean=0.;*/
 }  /* end gnuplot */    int first;
     int j, k=0,jk, ju, jl;
     double sum=0.;
 /*************** Moving average **************/    first=0;
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){    jmin=1e+5;
     jmax=-1;
   int i, cpt, cptcod;    jmean=0.;
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)    for(i=1; i<=imx; i++){
       for (i=1; i<=nlstate;i++)      mi=0;
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)      m=firstpass;
           mobaverage[(int)agedeb][i][cptcod]=0.;      while(s[m][i] <= nlstate){
            if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){          mw[++mi][i]=m;
       for (i=1; i<=nlstate;i++){        if(m >=lastpass)
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){          break;
           for (cpt=0;cpt<=4;cpt++){        else
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];          m++;
           }      }/* end while */
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;      if (s[m][i] > nlstate){
         }        mi++;     /* Death is another wave */
       }        /* if(mi==0)  never been interviewed correctly before death */
     }           /* Only death is a correct wave */
            mw[mi][i]=m;
 }      }
   
       wav[i]=mi;
 /************** Forecasting ******************/      if(mi==0){
 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){        nbwarn++;
          if(first==0){
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
   int *popage;          first=1;
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;        }
   double *popeffectif,*popcount;        if(first==1){
   double ***p3mat;          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
   char fileresf[FILENAMELENGTH];        }
       } /* end mi==0 */
  agelim=AGESUP;    } /* End individuals */
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;  
     for(i=1; i<=imx; i++){
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);      for(mi=1; mi<wav[i];mi++){
          if (stepm <=0)
            dh[mi][i]=1;
   strcpy(fileresf,"f");        else{
   strcat(fileresf,fileres);          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
   if((ficresf=fopen(fileresf,"w"))==NULL) {            if (agedc[i] < 2*AGESUP) {
     printf("Problem with forecast resultfile: %s\n", fileresf);              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);              if(j==0) j=1;  /* Survives at least one month after exam */
   }              else if(j<0){
   printf("Computing forecasting: result on file '%s' \n", fileresf);                nberr++;
   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);                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 */
   if (cptcoveff==0) ncodemax[cptcoveff]=1;                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);
                 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]);
   if (mobilav==1) {                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);
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);              }
     movingaverage(agedeb, fage, ageminpar, mobaverage);              k=k+1;
   }              if (j >= jmax){
                 jmax=j;
   stepsize=(int) (stepm+YEARM-1)/YEARM;                ijmax=i;
   if (stepm<=12) stepsize=1;              }
                if (j <= jmin){
   agelim=AGESUP;                jmin=j;
                  ijmin=i;
   hstepm=1;              }
   hstepm=hstepm/stepm;              sum=sum+j;
   yp1=modf(dateintmean,&yp);              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
   anprojmean=yp;              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
   yp2=modf((yp1*12),&yp);            }
   mprojmean=yp;          }
   yp1=modf((yp2*30.5),&yp);          else{
   jprojmean=yp;            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
   if(jprojmean==0) jprojmean=1;  /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
   if(mprojmean==0) jprojmean=1;  
              k=k+1;
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);            if (j >= jmax) {
                jmax=j;
   for(cptcov=1;cptcov<=i2;cptcov++){              ijmax=i;
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){            }
       k=k+1;            else if (j <= jmin){
       fprintf(ficresf,"\n#******");              jmin=j;
       for(j=1;j<=cptcoveff;j++) {              ijmin=i;
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            }
       }            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
       fprintf(ficresf,"******\n");            /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
       fprintf(ficresf,"# StartingAge FinalAge");            if(j<0){
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);              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]);
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {            }
         fprintf(ficresf,"\n");            sum=sum+j;
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);            }
           jk= j/stepm;
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){          jl= j -jk*stepm;
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);          ju= j -(jk+1)*stepm;
           nhstepm = nhstepm/hstepm;          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
                      if(jl==0){
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              dh[mi][i]=jk;
           oldm=oldms;savm=savms;              bh[mi][i]=0;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);              }else{ /* We want a negative bias in order to only have interpolation ie
                            * to avoid the price of an extra matrix product in likelihood */
           for (h=0; h<=nhstepm; h++){              dh[mi][i]=jk+1;
             if (h==(int) (calagedate+YEARM*cpt)) {              bh[mi][i]=ju;
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);            }
             }          }else{
             for(j=1; j<=nlstate+ndeath;j++) {            if(jl <= -ju){
               kk1=0.;kk2=0;              dh[mi][i]=jk;
               for(i=1; i<=nlstate;i++) {                            bh[mi][i]=jl;       /* bias is positive if real duration
                 if (mobilav==1)                                   * is higher than the multiple of stepm and negative otherwise.
                   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];            else{
                 }              dh[mi][i]=jk+1;
                              bh[mi][i]=ju;
               }            }
               if (h==(int)(calagedate+12*cpt)){            if(dh[mi][i]==0){
                 fprintf(ficresf," %.3f", kk1);              dh[mi][i]=1; /* At least one step */
                                      bh[mi][i]=ju; /* At least one step */
               }              /*  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);*/
             }            }
           }          } /* end if mle */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        }
         }      } /* end wave */
       }    }
     }    jmean=sum/k;
   }    printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
            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);
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);   }
   
   fclose(ficresf);  /*********** Tricode ****************************/
 }  void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
 /************** Forecasting ******************/  {
 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){    /**< Uses cptcovn+2*cptcovprod as the number of covariates */
      /*      Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;    /* Boring subroutine which should only output nbcode[Tvar[j]][k]
   int *popage;     * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;    /* nbcode[Tvar[j]][1]= 
   double *popeffectif,*popcount;    */
   double ***p3mat,***tabpop,***tabpopprev;  
   char filerespop[FILENAMELENGTH];    int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
     int modmaxcovj=0; /* Modality max of covariates j */
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    int cptcode=0; /* Modality max of covariates j */
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    int modmincovj=0; /* Modality min of covariates j */
   agelim=AGESUP;  
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;  
      cptcoveff=0; 
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);   
      for (k=-1; k < maxncov; k++) Ndum[k]=0;
      for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
   strcpy(filerespop,"pop");  
   strcat(filerespop,fileres);    /* Loop on covariates without age and products */
   if((ficrespop=fopen(filerespop,"w"))==NULL) {    for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */
     printf("Problem with forecast resultfile: %s\n", filerespop);      for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the 
     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);                                 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
   printf("Computing forecasting: result on file '%s' \n", filerespop);                                      * If product of Vn*Vm, still boolean *:
   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);                                      * 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   */
   if (cptcoveff==0) ncodemax[cptcoveff]=1;        /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
                                         modality of the nth covariate of individual i. */
   if (mobilav==1) {        if (ij > modmaxcovj)
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          modmaxcovj=ij; 
     movingaverage(agedeb, fage, ageminpar, mobaverage);        else if (ij < modmincovj) 
   }          modmincovj=ij; 
         if ((ij < -1) && (ij > NCOVMAX)){
   stepsize=(int) (stepm+YEARM-1)/YEARM;          printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
   if (stepm<=12) stepsize=1;          exit(1);
          }else
   agelim=AGESUP;        Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
          /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
   hstepm=1;        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
   hstepm=hstepm/stepm;        /* getting the maximum value of the modality of the covariate
             (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
   if (popforecast==1) {           female is 1, then modmaxcovj=1.*/
     if((ficpop=fopen(popfile,"r"))==NULL) {      }
       printf("Problem with population file : %s\n",popfile);exit(0);      printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);      cptcode=modmaxcovj;
     }      /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
     popage=ivector(0,AGESUP);     /*for (i=0; i<=cptcode; i++) {*/
     popeffectif=vector(0,AGESUP);      for (i=modmincovj;  i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
     popcount=vector(0,AGESUP);        printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
            if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
     i=1;            ncodemax[j]++;  /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;        }
            /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for
     imx=i;           historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];      } /* Ndum[-1] number of undefined modalities */
   }  
       /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
   for(cptcov=1;cptcov<=i2;cptcov++){      /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
       k=k+1;         modmincovj=3; modmaxcovj = 7;
       fprintf(ficrespop,"\n#******");         There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
       for(j=1;j<=cptcoveff;j++) {         which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy 
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);         variables V1_1 and V1_2.
       }         nbcode[Tvar[j]][ij]=k;
       fprintf(ficrespop,"******\n");         nbcode[Tvar[j]][1]=0;
       fprintf(ficrespop,"# Age");         nbcode[Tvar[j]][2]=1;
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);         nbcode[Tvar[j]][3]=2;
       if (popforecast==1)  fprintf(ficrespop," [Population]");      */
            ij=1; /* ij is similar to i but can jumps over null modalities */
       for (cpt=0; cpt<=0;cpt++) {      for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);          for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
                  /*recode from 0 */
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){          if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);            nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode. 
           nhstepm = nhstepm/hstepm;                                       k is a modality. If we have model=V1+V1*sex 
                                                 then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            ij++;
           oldm=oldms;savm=savms;          }
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            if (ij > ncodemax[j]) break; 
                }  /* end of loop on */
           for (h=0; h<=nhstepm; h++){      } /* end of loop on modality */ 
             if (h==(int) (calagedate+YEARM*cpt)) {    } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/  
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);    
             }   for (k=-1; k< maxncov; k++) Ndum[k]=0; 
             for(j=1; j<=nlstate+ndeath;j++) {    
               kk1=0.;kk2=0;    for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */ 
               for(i=1; i<=nlstate;i++) {                   /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/ 
                 if (mobilav==1)     ij=Tvar[i]; /* Tvar might be -1 if status was unknown */ 
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];     Ndum[ij]++; 
                 else {   } 
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];  
                 }   ij=1;
               }   for (i=0; i<=  maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
               if (h==(int)(calagedate+12*cpt)){     /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;     if((Ndum[i]!=0) && (i<=ncovcol)){
                   /*fprintf(ficrespop," %.3f", kk1);       /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/       Tvaraff[ij]=i; /*For printing (unclear) */
               }       ij++;
             }     }else
             for(i=1; i<=nlstate;i++){         Tvaraff[ij]=0;
               kk1=0.;   }
                 for(j=1; j<=nlstate;j++){   ij--;
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];   cptcoveff=ij; /*Number of total covariates*/
                 }  
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];  }
             }  
   
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)  /*********** Health Expectancies ****************/
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);  
           }  void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
         }  {
       }    /* Health expectancies, no variances */
      int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
   /******/    int nhstepma, nstepma; /* Decreasing with age */
     double age, agelim, hf;
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {    double ***p3mat;
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);      double eip;
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){  
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    pstamp(ficreseij);
           nhstepm = nhstepm/hstepm;    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");
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    for(i=1; i<=nlstate;i++){
           oldm=oldms;savm=savms;      for(j=1; j<=nlstate;j++){
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);          fprintf(ficreseij," e%1d%1d ",i,j);
           for (h=0; h<=nhstepm; h++){      }
             if (h==(int) (calagedate+YEARM*cpt)) {      fprintf(ficreseij," e%1d. ",i);
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);    }
             }    fprintf(ficreseij,"\n");
             for(j=1; j<=nlstate+ndeath;j++) {  
               kk1=0.;kk2=0;    
               for(i=1; i<=nlstate;i++) {                  if(estepm < stepm){
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];          printf ("Problem %d lower than %d\n",estepm, stepm);
               }    }
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);    else  hstepm=estepm;   
             }    /* We compute the life expectancy from trapezoids spaced every estepm months
           }     * This is mainly to measure the difference between two models: for example
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);     * if stepm=24 months pijx are given only every 2 years and by summing them
         }     * we are calculating an estimate of the Life Expectancy assuming a linear 
       }     * progression in between and thus overestimating or underestimating according
    }     * to the curvature of the survival function. If, for the same date, we 
   }     * 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 
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);     * hypothesis. A more precise result, taking into account a more precise
      * curvature will be obtained if estepm is as small as stepm. */
   if (popforecast==1) {  
     free_ivector(popage,0,AGESUP);    /* For example we decided to compute the life expectancy with the smallest unit */
     free_vector(popeffectif,0,AGESUP);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
     free_vector(popcount,0,AGESUP);       nhstepm is the number of hstepm from age to agelim 
   }       nstepm is the number of stepm from age to agelin. 
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);       Look at hpijx to understand the reason of that which relies in memory size
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);       and note for a fixed period like estepm months */
   fclose(ficrespop);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
 }       survival function given by stepm (the optimization length). Unfortunately it
        means that if the survival funtion is printed only each two years of age and if
 /***********************************************/       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
 /**************** Main Program *****************/       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 */ 
 int main(int argc, char *argv[])  
 {    agelim=AGESUP;
     /* If stepm=6 months */
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;      /* Computed by stepm unit matrices, product of hstepm matrices, stored
   double agedeb, agefin,hf;         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;      
   /* nhstepm age range expressed in number of stepm */
   double fret;    nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
   double **xi,tmp,delta;    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     /* if (stepm >= YEARM) hstepm=1;*/
   double dum; /* Dummy variable */    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   double ***p3mat;    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   int *indx;  
   char line[MAXLINE], linepar[MAXLINE];    for (age=bage; age<=fage; age ++){ 
   char path[80],pathc[80],pathcd[80],pathtot[80],model[80];      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
   int firstobs=1, lastobs=10;      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   int sdeb, sfin; /* Status at beginning and end */      /* if (stepm >= YEARM) hstepm=1;*/
   int c,  h , cpt,l;      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
   int ju,jl, mi;  
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;      /* If stepm=6 months */
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;      /* Computed by stepm unit matrices, product of hstepma matrices, stored
   int mobilav=0,popforecast=0;         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
   int hstepm, nhstepm;      
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;      hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
       
   double bage, fage, age, agelim, agebase;      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   double ftolpl=FTOL;      
   double **prlim;      printf("%d|",(int)age);fflush(stdout);
   double *severity;      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
   double ***param; /* Matrix of parameters */      
   double  *p;      /* Computing expectancies */
   double **matcov; /* Matrix of covariance */      for(i=1; i<=nlstate;i++)
   double ***delti3; /* Scale */        for(j=1; j<=nlstate;j++)
   double *delti; /* Scale */          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
   double ***eij, ***vareij;            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
   double **varpl; /* Variances of prevalence limits by age */            
   double *epj, vepp;            /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
   double kk1, kk2;  
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;          }
    
       fprintf(ficreseij,"%3.0f",age );
   char *alph[]={"a","a","b","c","d","e"}, str[4];      for(i=1; i<=nlstate;i++){
         eip=0;
         for(j=1; j<=nlstate;j++){
   char z[1]="c", occ;          eip +=eij[i][j][(int)age];
 #include <sys/time.h>          fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
 #include <time.h>        }
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];        fprintf(ficreseij,"%9.4f", eip );
        }
   /* long total_usecs;      fprintf(ficreseij,"\n");
   struct timeval start_time, end_time;      
      }
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */    free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   getcwd(pathcd, size);    printf("\n");
     fprintf(ficlog,"\n");
   printf("\n%s",version);    
   if(argc <=1){  }
     printf("\nEnter the parameter file name: ");  
     scanf("%s",pathtot);  void cvevsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[] )
   }  
   else{  {
     strcpy(pathtot,argv[1]);    /* Covariances of health expectancies eij and of total life expectancies according
   }     to initial status i, ei. .
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/    */
   /*cygwin_split_path(pathtot,path,optionfile);    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/    int nhstepma, nstepma; /* Decreasing with age */
   /* cutv(path,optionfile,pathtot,'\\');*/    double age, agelim, hf;
     double ***p3matp, ***p3matm, ***varhe;
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);    double **dnewm,**doldm;
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);    double *xp, *xm;
   chdir(path);    double **gp, **gm;
   replace(pathc,path);    double ***gradg, ***trgradg;
     int theta;
 /*-------- arguments in the command line --------*/  
     double eip, vip;
   /* Log file */  
   strcat(filelog, optionfilefiname);    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
   strcat(filelog,".log");    /* */    xp=vector(1,npar);
   if((ficlog=fopen(filelog,"w"))==NULL)    {    xm=vector(1,npar);
     printf("Problem with logfile %s\n",filelog);    dnewm=matrix(1,nlstate*nlstate,1,npar);
     goto end;    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
   }    
   fprintf(ficlog,"Log filename:%s\n",filelog);    pstamp(ficresstdeij);
   fprintf(ficlog,"\n%s",version);    fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
   fprintf(ficlog,"\nEnter the parameter file name: ");    fprintf(ficresstdeij,"# Age");
   fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);    for(i=1; i<=nlstate;i++){
   fflush(ficlog);      for(j=1; j<=nlstate;j++)
         fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
   /* */      fprintf(ficresstdeij," e%1d. ",i);
   strcpy(fileres,"r");    }
   strcat(fileres, optionfilefiname);    fprintf(ficresstdeij,"\n");
   strcat(fileres,".txt");    /* Other files have txt extension */  
     pstamp(ficrescveij);
   /*---------arguments file --------*/    fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
     fprintf(ficrescveij,"# Age");
   if((ficpar=fopen(optionfile,"r"))==NULL)    {    for(i=1; i<=nlstate;i++)
     printf("Problem with optionfile %s\n",optionfile);      for(j=1; j<=nlstate;j++){
     fprintf(ficlog,"Problem with optionfile %s\n",optionfile);        cptj= (j-1)*nlstate+i;
     goto end;        for(i2=1; i2<=nlstate;i2++)
   }          for(j2=1; j2<=nlstate;j2++){
             cptj2= (j2-1)*nlstate+i2;
   strcpy(filereso,"o");            if(cptj2 <= cptj)
   strcat(filereso,fileres);              fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
   if((ficparo=fopen(filereso,"w"))==NULL) {          }
     printf("Problem with Output resultfile: %s\n", filereso);      }
     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);    fprintf(ficrescveij,"\n");
     goto end;    
   }    if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
   /* Reads comments: lines beginning with '#' */    }
   while((c=getc(ficpar))=='#' && c!= EOF){    else  hstepm=estepm;   
     ungetc(c,ficpar);    /* We compute the life expectancy from trapezoids spaced every estepm months
     fgets(line, MAXLINE, ficpar);     * This is mainly to measure the difference between two models: for example
     puts(line);     * if stepm=24 months pijx are given only every 2 years and by summing them
     fputs(line,ficparo);     * we are calculating an estimate of the Life Expectancy assuming a linear 
   }     * progression in between and thus overestimating or underestimating according
   ungetc(c,ficpar);     * to the curvature of the survival function. If, for the same date, we 
      * estimate the model with stepm=1 month, we can keep estepm to 24 months
   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);     * to compare the new estimate of Life expectancy with the same linear 
   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);     * hypothesis. A more precise result, taking into account a more precise
   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);     * 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
           survival function given by stepm (the optimization length). Unfortunately it
   covar=matrix(0,NCOVMAX,1,n);       means that if the survival funtion is printed only each two years of age and if
   cptcovn=0;       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;       results. So we changed our mind and took the option of the best precision.
     */
   ncovmodel=2+cptcovn;    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */  
      /* If stepm=6 months */
   /* Read guess parameters */    /* nhstepm age range expressed in number of stepm */
   /* Reads comments: lines beginning with '#' */    agelim=AGESUP;
   while((c=getc(ficpar))=='#' && c!= EOF){    nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
     ungetc(c,ficpar);    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     fgets(line, MAXLINE, ficpar);    /* if (stepm >= YEARM) hstepm=1;*/
     puts(line);    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     fputs(line,ficparo);    
   }    p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   ungetc(c,ficpar);    p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
     for(i=1; i <=nlstate; i++)    gp=matrix(0,nhstepm,1,nlstate*nlstate);
     for(j=1; j <=nlstate+ndeath-1; j++){    gm=matrix(0,nhstepm,1,nlstate*nlstate);
       fscanf(ficpar,"%1d%1d",&i1,&j1);  
       fprintf(ficparo,"%1d%1d",i1,j1);    for (age=bage; age<=fage; age ++){ 
       if(mle==1)      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
         printf("%1d%1d",i,j);      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       fprintf(ficlog,"%1d%1d",i,j);      /* if (stepm >= YEARM) hstepm=1;*/
       for(k=1; k<=ncovmodel;k++){      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
         fscanf(ficpar," %lf",&param[i][j][k]);  
         if(mle==1){      /* If stepm=6 months */
           printf(" %lf",param[i][j][k]);      /* Computed by stepm unit matrices, product of hstepma matrices, stored
           fprintf(ficlog," %lf",param[i][j][k]);         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
         }      
         else      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
           fprintf(ficlog," %lf",param[i][j][k]);  
         fprintf(ficparo," %lf",param[i][j][k]);      /* Computing  Variances of health expectancies */
       }      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
       fscanf(ficpar,"\n");         decrease memory allocation */
       if(mle==1)      for(theta=1; theta <=npar; theta++){
         printf("\n");        for(i=1; i<=npar; i++){ 
       fprintf(ficlog,"\n");          xp[i] = x[i] + (i==theta ?delti[theta]:0);
       fprintf(ficparo,"\n");          xm[i] = x[i] - (i==theta ?delti[theta]:0);
     }        }
          hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;        hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
     
   p=param[1][1];        for(j=1; j<= nlstate; j++){
            for(i=1; i<=nlstate; i++){
   /* Reads comments: lines beginning with '#' */            for(h=0; h<=nhstepm-1; h++){
   while((c=getc(ficpar))=='#' && c!= EOF){              gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
     ungetc(c,ficpar);              gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
     fgets(line, MAXLINE, ficpar);            }
     puts(line);          }
     fputs(line,ficparo);        }
   }       
   ungetc(c,ficpar);        for(ij=1; ij<= nlstate*nlstate; ij++)
           for(h=0; h<=nhstepm-1; h++){
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);            gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */          }
   for(i=1; i <=nlstate; i++){      }/* End theta */
     for(j=1; j <=nlstate+ndeath-1; j++){      
       fscanf(ficpar,"%1d%1d",&i1,&j1);      
       printf("%1d%1d",i,j);      for(h=0; h<=nhstepm-1; h++)
       fprintf(ficparo,"%1d%1d",i1,j1);        for(j=1; j<=nlstate*nlstate;j++)
       for(k=1; k<=ncovmodel;k++){          for(theta=1; theta <=npar; theta++)
         fscanf(ficpar,"%le",&delti3[i][j][k]);            trgradg[h][j][theta]=gradg[h][theta][j];
         printf(" %le",delti3[i][j][k]);      
         fprintf(ficparo," %le",delti3[i][j][k]);  
       }       for(ij=1;ij<=nlstate*nlstate;ij++)
       fscanf(ficpar,"\n");        for(ji=1;ji<=nlstate*nlstate;ji++)
       printf("\n");          varhe[ij][ji][(int)age] =0.;
       fprintf(ficparo,"\n");  
     }       printf("%d|",(int)age);fflush(stdout);
   }       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
   delti=delti3[1][1];       for(h=0;h<=nhstepm-1;h++){
          for(k=0;k<=nhstepm-1;k++){
   /* Reads comments: lines beginning with '#' */          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
   while((c=getc(ficpar))=='#' && c!= EOF){          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
     ungetc(c,ficpar);          for(ij=1;ij<=nlstate*nlstate;ij++)
     fgets(line, MAXLINE, ficpar);            for(ji=1;ji<=nlstate*nlstate;ji++)
     puts(line);              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
     fputs(line,ficparo);        }
   }      }
   ungetc(c,ficpar);  
        /* Computing expectancies */
   matcov=matrix(1,npar,1,npar);      hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
   for(i=1; i <=npar; i++){      for(i=1; i<=nlstate;i++)
     fscanf(ficpar,"%s",&str);        for(j=1; j<=nlstate;j++)
     if(mle==1)          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
       printf("%s",str);            eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
     fprintf(ficlog,"%s",str);            
     fprintf(ficparo,"%s",str);            /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
     for(j=1; j <=i; j++){  
       fscanf(ficpar," %le",&matcov[i][j]);          }
       if(mle==1){  
         printf(" %.5le",matcov[i][j]);      fprintf(ficresstdeij,"%3.0f",age );
         fprintf(ficlog," %.5le",matcov[i][j]);      for(i=1; i<=nlstate;i++){
       }        eip=0.;
       else        vip=0.;
         fprintf(ficlog," %.5le",matcov[i][j]);        for(j=1; j<=nlstate;j++){
       fprintf(ficparo," %.5le",matcov[i][j]);          eip += eij[i][j][(int)age];
     }          for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
     fscanf(ficpar,"\n");            vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
     if(mle==1)          fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
       printf("\n");        }
     fprintf(ficlog,"\n");        fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
     fprintf(ficparo,"\n");      }
   }      fprintf(ficresstdeij,"\n");
   for(i=1; i <=npar; i++)  
     for(j=i+1;j<=npar;j++)      fprintf(ficrescveij,"%3.0f",age );
       matcov[i][j]=matcov[j][i];      for(i=1; i<=nlstate;i++)
            for(j=1; j<=nlstate;j++){
   if(mle==1)          cptj= (j-1)*nlstate+i;
     printf("\n");          for(i2=1; i2<=nlstate;i2++)
   fprintf(ficlog,"\n");            for(j2=1; j2<=nlstate;j2++){
               cptj2= (j2-1)*nlstate+i2;
               if(cptj2 <= cptj)
     /*-------- Rewriting paramater file ----------*/                fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
      strcpy(rfileres,"r");    /* "Rparameterfile */            }
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/        }
      strcat(rfileres,".");    /* */      fprintf(ficrescveij,"\n");
      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;    free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;    free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
     }    free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
     fprintf(ficres,"#%s\n",version);    free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
        free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     /*-------- data file ----------*/    free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     if((fic=fopen(datafile,"r"))==NULL)    {    printf("\n");
       printf("Problem with datafile: %s\n", datafile);goto end;    fprintf(ficlog,"\n");
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;  
     }    free_vector(xm,1,npar);
     free_vector(xp,1,npar);
     n= lastobs;    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
     severity = vector(1,maxwav);    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
     outcome=imatrix(1,maxwav+1,1,n);    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
     num=ivector(1,n);  }
     moisnais=vector(1,n);  
     annais=vector(1,n);  /************ Variance ******************/
     moisdc=vector(1,n);  void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
     andc=vector(1,n);  {
     agedc=vector(1,n);    /* Variance of health expectancies */
     cod=ivector(1,n);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
     weight=vector(1,n);    /* double **newm;*/
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */    double **dnewm,**doldm;
     mint=matrix(1,maxwav,1,n);    double **dnewmp,**doldmp;
     anint=matrix(1,maxwav,1,n);    int i, j, nhstepm, hstepm, h, nstepm ;
     s=imatrix(1,maxwav+1,1,n);    int k, cptcode;
     adl=imatrix(1,maxwav+1,1,n);        double *xp;
     tab=ivector(1,NCOVMAX);    double **gp, **gm;  /* for var eij */
     ncodemax=ivector(1,8);    double ***gradg, ***trgradg; /*for var eij */
     double **gradgp, **trgradgp; /* for var p point j */
     i=1;    double *gpp, *gmp; /* for var p point j */
     while (fgets(line, MAXLINE, fic) != NULL)    {    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
       if ((i >= firstobs) && (i <=lastobs)) {    double ***p3mat;
            double age,agelim, hf;
         for (j=maxwav;j>=1;j--){    double ***mobaverage;
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);    int theta;
           strcpy(line,stra);    char digit[4];
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    char digitp[25];
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);  
         }    char fileresprobmorprev[FILENAMELENGTH];
          
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);    if(popbased==1){
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);      if(mobilav!=0)
         strcpy(digitp,"-populbased-mobilav-");
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);      else strcpy(digitp,"-populbased-nomobil-");
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);    }
     else 
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);      strcpy(digitp,"-stablbased-");
         for (j=ncovcol;j>=1;j--){  
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);    if (mobilav!=0) {
         }      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         num[i]=atol(stra);      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
                fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){        printf(" Error in movingaverage mobilav=%d\n",mobilav);
           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;}*/      }
     }
         i=i+1;  
       }    strcpy(fileresprobmorprev,"prmorprev"); 
     }    sprintf(digit,"%-d",ij);
     /* printf("ii=%d", ij);    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
        scanf("%d",i);*/    strcat(fileresprobmorprev,digit); /* Tvar to be done */
   imx=i-1; /* Number of individuals */    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
     strcat(fileresprobmorprev,fileres);
   /* for (i=1; i<=imx; i++){    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;      printf("Problem with resultfile: %s\n", fileresprobmorprev);
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;    }
     }*/    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
    /*  for (i=1; i<=imx; i++){   
      if (s[4][i]==9)  s[4][i]=-1;    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
      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]));}*/    pstamp(ficresprobmorprev);
      fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
      fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
   /* Calculation of the number of parameter from char model*/    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
   Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */      fprintf(ficresprobmorprev," p.%-d SE",j);
   Tprod=ivector(1,15);      for(i=1; i<=nlstate;i++)
   Tvaraff=ivector(1,15);        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
   Tvard=imatrix(1,15,1,2);    }  
   Tage=ivector(1,15);          fprintf(ficresprobmorprev,"\n");
        fprintf(ficgp,"\n# Routine varevsij");
   if (strlen(model) >1){    /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
     j=0, j1=0, k1=1, k2=1;    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");
     j=nbocc(model,'+');    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
     j1=nbocc(model,'*');  /*   } */
     cptcovn=j+1;    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     cptcovprod=j1;    pstamp(ficresvij);
        fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
     strcpy(modelsav,model);    if(popbased==1)
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){      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);
       printf("Error. Non available option model=%s ",model);    else
       fprintf(ficlog,"Error. Non available option model=%s ",model);      fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
       goto end;    fprintf(ficresvij,"# Age");
     }    for(i=1; i<=nlstate;i++)
          for(j=1; j<=nlstate;j++)
     for(i=(j+1); i>=1;i--){        fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
       cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */    fprintf(ficresvij,"\n");
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyze it */  
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/    xp=vector(1,npar);
       /*scanf("%d",i);*/    dnewm=matrix(1,nlstate,1,npar);
       if (strchr(strb,'*')) {  /* Model includes a product */    doldm=matrix(1,nlstate,1,nlstate);
         cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
         if (strcmp(strc,"age")==0) { /* Vn*age */    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
           cptcovprod--;  
           cutv(strb,stre,strd,'V');    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
           Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/    gpp=vector(nlstate+1,nlstate+ndeath);
           cptcovage++;    gmp=vector(nlstate+1,nlstate+ndeath);
             Tage[cptcovage]=i;    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
             /*printf("stre=%s ", stre);*/    
         }    if(estepm < stepm){
         else if (strcmp(strd,"age")==0) { /* or age*Vn */      printf ("Problem %d lower than %d\n",estepm, stepm);
           cptcovprod--;    }
           cutv(strb,stre,strc,'V');    else  hstepm=estepm;   
           Tvar[i]=atoi(stre);    /* For example we decided to compute the life expectancy with the smallest unit */
           cptcovage++;    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
           Tage[cptcovage]=i;       nhstepm is the number of hstepm from age to agelim 
         }       nstepm is the number of stepm from age to agelin. 
         else {  /* Age is not in the model */       Look at function hpijx to understand why (it is linked to memory size questions) */
           cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
           Tvar[i]=ncovcol+k1;       survival function given by stepm (the optimization length). Unfortunately it
           cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */       means that if the survival funtion is printed every two years of age and if
           Tprod[k1]=i;       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
           Tvard[k1][1]=atoi(strc); /* m*/       results. So we changed our mind and took the option of the best precision.
           Tvard[k1][2]=atoi(stre); /* n */    */
           Tvar[cptcovn+k2]=Tvard[k1][1];    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
           Tvar[cptcovn+k2+1]=Tvard[k1][2];    agelim = AGESUP;
           for (k=1; k<=lastobs;k++)    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
           k1++;      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
           k2=k2+2;      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         }      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
       }      gp=matrix(0,nhstepm,1,nlstate);
       else { /* no more sum */      gm=matrix(0,nhstepm,1,nlstate);
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/  
        /*  scanf("%d",i);*/  
       cutv(strd,strc,strb,'V');      for(theta=1; theta <=npar; theta++){
       Tvar[i]=atoi(strc);        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
       }          xp[i] = x[i] + (i==theta ?delti[theta]:0);
       strcpy(modelsav,stra);          }
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         scanf("%d",i);*/        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     } /* end of loop + */  
   } /* end model */        if (popbased==1) {
            if(mobilav ==0){
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);            for(i=1; i<=nlstate;i++)
   printf("cptcovprod=%d ", cptcovprod);              prlim[i][i]=probs[(int)age][i][ij];
   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);          }else{ /* mobilav */ 
   scanf("%d ",i);*/            for(i=1; i<=nlstate;i++)
     fclose(fic);              prlim[i][i]=mobaverage[(int)age][i][ij];
           }
     /*  if(mle==1){*/        }
     if (weightopt != 1) { /* Maximisation without weights*/    
       for(i=1;i<=n;i++) weight[i]=1.0;        for(j=1; j<= nlstate; j++){
     }          for(h=0; h<=nhstepm; h++){
     /*-calculation of age at interview from date of interview and age at death -*/            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
     agev=matrix(1,maxwav,1,imx);              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
     for (i=1; i<=imx; i++) {        }
       for(m=2; (m<= maxwav); m++) {        /* This for computing probability of death (h=1 means
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){           computed over hstepm matrices product = hstepm*stepm months) 
          anint[m][i]=9999;           as a weighted average of prlim.
          s[m][i]=-1;        */
        }        for(j=nlstate+1;j<=nlstate+ndeath;j++){
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;          for(i=1,gpp[j]=0.; i<= nlstate; i++)
       }            gpp[j] += prlim[i][i]*p3mat[i][j][1];
     }        }    
         /* end probability of death */
     for (i=1; i<=imx; i++)  {  
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
       for(m=1; (m<= maxwav); m++){          xp[i] = x[i] - (i==theta ?delti[theta]:0);
         if(s[m][i] >0){        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
           if (s[m][i] >= nlstate+1) {        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
             if(agedc[i]>0)   
               if(moisdc[i]!=99 && andc[i]!=9999)        if (popbased==1) {
                 agev[m][i]=agedc[i];          if(mobilav ==0){
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/            for(i=1; i<=nlstate;i++)
            else {              prlim[i][i]=probs[(int)age][i][ij];
               if (andc[i]!=9999){          }else{ /* mobilav */ 
               printf("Warning negative age at death: %d line:%d\n",num[i],i);            for(i=1; i<=nlstate;i++)
               fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);              prlim[i][i]=mobaverage[(int)age][i][ij];
               agev[m][i]=-1;          }
               }        }
             }  
           }        for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
           else if(s[m][i] !=9){ /* Should no more exist */          for(h=0; h<=nhstepm; h++){
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
             if(mint[m][i]==99 || anint[m][i]==9999)              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
               agev[m][i]=1;          }
             else if(agev[m][i] <agemin){        }
               agemin=agev[m][i];        /* This for computing probability of death (h=1 means
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/           computed over hstepm matrices product = hstepm*stepm months) 
             }           as a weighted average of prlim.
             else if(agev[m][i] >agemax){        */
               agemax=agev[m][i];        for(j=nlstate+1;j<=nlstate+ndeath;j++){
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/          for(i=1,gmp[j]=0.; i<= nlstate; i++)
             }           gmp[j] += prlim[i][i]*p3mat[i][j][1];
             /*agev[m][i]=anint[m][i]-annais[i];*/        }    
             /*   agev[m][i] = age[i]+2*m;*/        /* end probability of death */
           }  
           else { /* =9 */        for(j=1; j<= nlstate; j++) /* vareij */
             agev[m][i]=1;          for(h=0; h<=nhstepm; h++){
             s[m][i]=-1;            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
           }          }
         }  
         else /*= 0 Unknown */        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
           agev[m][i]=1;          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
       }        }
      
     }      } /* End theta */
     for (i=1; i<=imx; i++)  {  
       for(m=1; (m<= maxwav); m++){      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
         if (s[m][i] > (nlstate+ndeath)) {  
           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);        for(h=0; h<=nhstepm; h++) /* veij */
           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);          for(j=1; j<=nlstate;j++)
           goto end;          for(theta=1; theta <=npar; theta++)
         }            trgradg[h][j][theta]=gradg[h][theta][j];
       }  
     }      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
         for(theta=1; theta <=npar; theta++)
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);          trgradgp[j][theta]=gradgp[theta][j];
  fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);    
   
     free_vector(severity,1,maxwav);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     free_imatrix(outcome,1,maxwav+1,1,n);      for(i=1;i<=nlstate;i++)
     free_vector(moisnais,1,n);        for(j=1;j<=nlstate;j++)
     free_vector(annais,1,n);          vareij[i][j][(int)age] =0.;
     /* free_matrix(mint,1,maxwav,1,n);  
        free_matrix(anint,1,maxwav,1,n);*/      for(h=0;h<=nhstepm;h++){
     free_vector(moisdc,1,n);        for(k=0;k<=nhstepm;k++){
     free_vector(andc,1,n);          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
           matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
              for(i=1;i<=nlstate;i++)
     wav=ivector(1,imx);            for(j=1;j<=nlstate;j++)
     dh=imatrix(1,lastpass-firstpass+1,1,imx);              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
     mw=imatrix(1,lastpass-firstpass+1,1,imx);        }
          }
     /* Concatenates waves */    
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);      /* pptj */
       matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
       matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
       Tcode=ivector(1,100);      for(j=nlstate+1;j<=nlstate+ndeath;j++)
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);        for(i=nlstate+1;i<=nlstate+ndeath;i++)
       ncodemax[1]=1;          varppt[j][i]=doldmp[j][i];
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);      /* end ppptj */
            /*  x centered again */
    codtab=imatrix(1,100,1,10);      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
    h=0;      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
    m=pow(2,cptcoveff);   
        if (popbased==1) {
    for(k=1;k<=cptcoveff; k++){        if(mobilav ==0){
      for(i=1; i <=(m/pow(2,k));i++){          for(i=1; i<=nlstate;i++)
        for(j=1; j <= ncodemax[k]; j++){            prlim[i][i]=probs[(int)age][i][ij];
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){        }else{ /* mobilav */ 
            h++;          for(i=1; i<=nlstate;i++)
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;            prlim[i][i]=mobaverage[(int)age][i][ij];
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/        }
          }      }
        }               
      }      /* This for computing probability of death (h=1 means
    }         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);         as a weighted average of prlim.
       codtab[1][2]=1;codtab[2][2]=2; */      */
    /* for(i=1; i <=m ;i++){      for(j=nlstate+1;j<=nlstate+ndeath;j++){
       for(k=1; k <=cptcovn; k++){        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
       }      }    
       printf("\n");      /* end probability of death */
       }  
       scanf("%d",i);*/      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
          for(j=nlstate+1; j<=(nlstate+ndeath);j++){
    /* Calculates basic frequencies. Computes observed prevalence at single age        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
        and prints on file fileres'p'. */        for(i=1; i<=nlstate;i++){
           fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
            }
          } 
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      fprintf(ficresprobmorprev,"\n");
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      fprintf(ficresvij,"%.0f ",age );
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      for(i=1; i<=nlstate;i++)
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */        for(j=1; j<=nlstate;j++){
                fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
     /* 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] */      fprintf(ficresvij,"\n");
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */      free_matrix(gp,0,nhstepm,1,nlstate);
       free_matrix(gm,0,nhstepm,1,nlstate);
     if(mle==1){      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
     }      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
        } /* End age */
     /*--------- results files --------------*/    free_vector(gpp,nlstate+1,nlstate+ndeath);
     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);    free_vector(gmp,nlstate+1,nlstate+ndeath);
      free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
     free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
    jk=1;    fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
    fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
    for(i=1,jk=1; i <=nlstate; i++){  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
      for(k=1; k <=(nlstate+ndeath); k++){  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
        if (k != i)    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
          {    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
            printf("%d%d ",i,k);    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
            fprintf(ficlog,"%d%d ",i,k);    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
            fprintf(ficres,"%1d%1d ",i,k);    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
            for(j=1; j <=ncovmodel; j++){    /*  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);
              printf("%f ",p[jk]);  */
              fprintf(ficlog,"%f ",p[jk]);  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
              fprintf(ficres,"%f ",p[jk]);    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
              jk++;  
            }    free_vector(xp,1,npar);
            printf("\n");    free_matrix(doldm,1,nlstate,1,nlstate);
            fprintf(ficlog,"\n");    free_matrix(dnewm,1,nlstate,1,npar);
            fprintf(ficres,"\n");    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
          }    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
      }    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
    }    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
    if(mle==1){    fclose(ficresprobmorprev);
      /* Computing hessian and covariance matrix */    fflush(ficgp);
      ftolhess=ftol; /* Usually correct */    fflush(fichtm); 
      hesscov(matcov, p, npar, delti, ftolhess, func);  }  /* end varevsij */
    }  
    fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");  /************ Variance of prevlim ******************/
    printf("# Scales (for hessian or gradient estimation)\n");  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(ficlog,"# Scales (for hessian or gradient estimation)\n");  {
    for(i=1,jk=1; i <=nlstate; i++){    /* Variance of prevalence limit */
      for(j=1; j <=nlstate+ndeath; j++){    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
        if (j!=i) {    double **newm;
          fprintf(ficres,"%1d%1d",i,j);    double **dnewm,**doldm;
          printf("%1d%1d",i,j);    int i, j, nhstepm, hstepm;
          fprintf(ficlog,"%1d%1d",i,j);    int k, cptcode;
          for(k=1; k<=ncovmodel;k++){    double *xp;
            printf(" %.5e",delti[jk]);    double *gp, *gm;
            fprintf(ficlog," %.5e",delti[jk]);    double **gradg, **trgradg;
            fprintf(ficres," %.5e",delti[jk]);    double age,agelim;
            jk++;    int theta;
          }    
          printf("\n");    pstamp(ficresvpl);
          fprintf(ficlog,"\n");    fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
          fprintf(ficres,"\n");    fprintf(ficresvpl,"# Age");
        }    for(i=1; i<=nlstate;i++)
      }        fprintf(ficresvpl," %1d-%1d",i,i);
    }    fprintf(ficresvpl,"\n");
      
    k=1;    xp=vector(1,npar);
    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");    dnewm=matrix(1,nlstate,1,npar);
    if(mle==1)    doldm=matrix(1,nlstate,1,nlstate);
      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");    hstepm=1*YEARM; /* Every year of age */
    for(i=1;i<=npar;i++){    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
      /*  if (k>nlstate) k=1;    agelim = AGESUP;
          i1=(i-1)/(ncovmodel*nlstate)+1;    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
          fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
          printf("%s%d%d",alph[k],i1,tab[i]);*/      if (stepm >= YEARM) hstepm=1;
      fprintf(ficres,"%3d",i);      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
      if(mle==1)      gradg=matrix(1,npar,1,nlstate);
        printf("%3d",i);      gp=vector(1,nlstate);
      fprintf(ficlog,"%3d",i);      gm=vector(1,nlstate);
      for(j=1; j<=i;j++){  
        fprintf(ficres," %.5e",matcov[i][j]);      for(theta=1; theta <=npar; theta++){
        if(mle==1)        for(i=1; i<=npar; i++){ /* Computes gradient */
          printf(" %.5e",matcov[i][j]);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
        fprintf(ficlog," %.5e",matcov[i][j]);        }
      }        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
      fprintf(ficres,"\n");        for(i=1;i<=nlstate;i++)
      if(mle==1)          gp[i] = prlim[i][i];
        printf("\n");      
      fprintf(ficlog,"\n");        for(i=1; i<=npar; i++) /* Computes gradient */
      k++;          xp[i] = x[i] - (i==theta ?delti[theta]:0);
    }        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
            for(i=1;i<=nlstate;i++)
    while((c=getc(ficpar))=='#' && c!= EOF){          gm[i] = prlim[i][i];
      ungetc(c,ficpar);  
      fgets(line, MAXLINE, ficpar);        for(i=1;i<=nlstate;i++)
      puts(line);          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
      fputs(line,ficparo);      } /* End theta */
    }  
    ungetc(c,ficpar);      trgradg =matrix(1,nlstate,1,npar);
    estepm=0;  
    fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);      for(j=1; j<=nlstate;j++)
    if (estepm==0 || estepm < stepm) estepm=stepm;        for(theta=1; theta <=npar; theta++)
    if (fage <= 2) {          trgradg[j][theta]=gradg[theta][j];
      bage = ageminpar;  
      fage = agemaxpar;      for(i=1;i<=nlstate;i++)
    }        varpl[i][(int)age] =0.;
          matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
    fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
    fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);      for(i=1;i<=nlstate;i++)
    fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
      
    while((c=getc(ficpar))=='#' && c!= EOF){      fprintf(ficresvpl,"%.0f ",age );
      ungetc(c,ficpar);      for(i=1; i<=nlstate;i++)
      fgets(line, MAXLINE, ficpar);        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
      puts(line);      fprintf(ficresvpl,"\n");
      fputs(line,ficparo);      free_vector(gp,1,nlstate);
    }      free_vector(gm,1,nlstate);
    ungetc(c,ficpar);      free_matrix(gradg,1,npar,1,nlstate);
        free_matrix(trgradg,1,nlstate,1,npar);
    fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);    } /* End age */
    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);    free_vector(xp,1,npar);
        free_matrix(doldm,1,nlstate,1,npar);
    while((c=getc(ficpar))=='#' && c!= EOF){    free_matrix(dnewm,1,nlstate,1,nlstate);
      ungetc(c,ficpar);  
      fgets(line, MAXLINE, ficpar);  }
      puts(line);  
      fputs(line,ficparo);  /************ 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[])
    ungetc(c,ficpar);  {
      int i, j=0,  i1, k1, l1, t, tj;
     int k2, l2, j1,  z1;
    dateprev1=anprev1+mprev1/12.+jprev1/365.;    int k=0,l, cptcode;
    dateprev2=anprev2+mprev2/12.+jprev2/365.;    int first=1, first1, first2;
     double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
   fscanf(ficpar,"pop_based=%d\n",&popbased);    double **dnewm,**doldm;
   fprintf(ficparo,"pop_based=%d\n",popbased);      double *xp;
   fprintf(ficres,"pop_based=%d\n",popbased);      double *gp, *gm;
      double **gradg, **trgradg;
   while((c=getc(ficpar))=='#' && c!= EOF){    double **mu;
     ungetc(c,ficpar);    double age,agelim, cov[NCOVMAX+1];
     fgets(line, MAXLINE, ficpar);    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
     puts(line);    int theta;
     fputs(line,ficparo);    char fileresprob[FILENAMELENGTH];
   }    char fileresprobcov[FILENAMELENGTH];
   ungetc(c,ficpar);    char fileresprobcor[FILENAMELENGTH];
     double ***varpij;
   fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mov_average=%d\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);  
 fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);    strcpy(fileresprob,"prob"); 
 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);    strcat(fileresprob,fileres);
     if((ficresprob=fopen(fileresprob,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprob);
 while((c=getc(ficpar))=='#' && c!= EOF){      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
     ungetc(c,ficpar);    }
     fgets(line, MAXLINE, ficpar);    strcpy(fileresprobcov,"probcov"); 
     puts(line);    strcat(fileresprobcov,fileres);
     fputs(line,ficparo);    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
   }      printf("Problem with resultfile: %s\n", fileresprobcov);
   ungetc(c,ficpar);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
     }
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);    strcpy(fileresprobcor,"probcor"); 
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);    strcat(fileresprobcor,fileres);
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcor);
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
     }
 /*------------ gnuplot -------------*/    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
   strcpy(optionfilegnuplot,optionfilefiname);    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
   strcat(optionfilegnuplot,".gp");    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     printf("Problem with file %s",optionfilegnuplot);    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   }    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   fclose(ficgp);    pstamp(ficresprob);
  printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
 /*--------- index.htm --------*/    fprintf(ficresprob,"# Age");
     pstamp(ficresprobcov);
   strcpy(optionfilehtm,optionfile);    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
   strcat(optionfilehtm,".htm");    fprintf(ficresprobcov,"# Age");
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {    pstamp(ficresprobcor);
     printf("Problem with %s \n",optionfilehtm), exit(0);    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
   }    fprintf(ficresprobcor,"# Age");
   
   fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n  
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n    for(i=1; i<=nlstate;i++)
 \n      for(j=1; j<=(nlstate+ndeath);j++){
 Total number of observations=%d <br>\n        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n        fprintf(ficresprobcov," p%1d-%1d ",i,j);
 <hr  size=\"2\" color=\"#EC5E5E\">        fprintf(ficresprobcor," p%1d-%1d ",i,j);
  <ul><li><h4>Parameter files</h4>\n      }  
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n   /* fprintf(ficresprob,"\n");
  - Log file of the run: <a href=\"%s\">%s</a><br>\n    fprintf(ficresprobcov,"\n");
  - Gnuplot file name: <a href=\"%s\">%s</a></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,filelog,filelog,optionfilegnuplot,optionfilegnuplot);    fprintf(ficresprobcor,"\n");
   fclose(fichtm);   */
     xp=vector(1,npar);
  printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
      doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
 /*------------ free_vector  -------------*/    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
  chdir(path);    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
      first=1;
  free_ivector(wav,1,imx);    fprintf(ficgp,"\n# Routine varprob");
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);      fprintf(fichtm,"\n");
  free_ivector(num,1,n);  
  free_vector(agedc,1,n);    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
  /*free_matrix(covar,1,NCOVMAX,1,n);*/    fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
  fclose(ficparo);    file %s<br>\n",optionfilehtmcov);
  fclose(ficres);    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");
   /*--------------- Prevalence limit --------------*/    fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
    It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
   strcpy(filerespl,"pl");  would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
   strcat(filerespl,fileres);  standard deviations wide on each axis. <br>\
   if((ficrespl=fopen(filerespl,"w"))==NULL) {   Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;   and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
     fprintf(ficlog,"Problem with Prev limit resultfile: %s\n", filerespl);goto end;  To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
   }  
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);    cov[1]=1;
   fprintf(ficlog,"Computing prevalence limit: result on file '%s' \n", filerespl);    /* tj=cptcoveff; */
   fprintf(ficrespl,"#Prevalence limit\n");    tj = (int) pow(2,cptcoveff);
   fprintf(ficrespl,"#Age ");    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);    j1=0;
   fprintf(ficrespl,"\n");    for(j1=1; j1<=tj;j1++){
        /*for(i1=1; i1<=ncodemax[t];i1++){ */
   prlim=matrix(1,nlstate,1,nlstate);      /*j1++;*/
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        if  (cptcovn>0) {
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          fprintf(ficresprob, "\n#********** Variable "); 
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          fprintf(ficresprob, "**********\n#\n");
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */          fprintf(ficresprobcov, "\n#********** Variable "); 
   k=0;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   agebase=ageminpar;          fprintf(ficresprobcov, "**********\n#\n");
   agelim=agemaxpar;          
   ftolpl=1.e-10;          fprintf(ficgp, "\n#********** Variable "); 
   i1=cptcoveff;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   if (cptcovn < 1){i1=1;}          fprintf(ficgp, "**********\n#\n");
           
   for(cptcov=1;cptcov<=i1;cptcov++){          
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
         k=k+1;          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/          fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
         fprintf(ficrespl,"\n#******");          
         printf("\n#******");          fprintf(ficresprobcor, "\n#********** Variable ");    
         fprintf(ficlog,"\n#******");          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         for(j=1;j<=cptcoveff;j++) {          fprintf(ficresprobcor, "**********\n#");    
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        }
           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        
           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
         }        trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
         fprintf(ficrespl,"******\n");        gp=vector(1,(nlstate)*(nlstate+ndeath));
         printf("******\n");        gm=vector(1,(nlstate)*(nlstate+ndeath));
         fprintf(ficlog,"******\n");        for (age=bage; age<=fage; age ++){ 
                  cov[2]=age;
         for (age=agebase; age<=agelim; age++){          for (k=1; k<=cptcovn;k++) {
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
           fprintf(ficrespl,"%.0f",age );                                                           * 1  1 1 1 1
           for(i=1; i<=nlstate;i++)                                                           * 2  2 1 1 1
           fprintf(ficrespl," %.5f", prlim[i][i]);                                                           * 3  1 2 1 1
           fprintf(ficrespl,"\n");                                                           */
         }            /* nbcode[1][1]=0 nbcode[1][2]=1;*/
       }          }
     }          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   fclose(ficrespl);          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]]];
   /*------------- h Pij x at various ages ------------*/          
        
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);          for(theta=1; theta <=npar; theta++){
   if((ficrespij=fopen(filerespij,"w"))==NULL) {            for(i=1; i<=npar; i++)
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
     fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;            
   }            pmij(pmmij,cov,ncovmodel,xp,nlstate);
   printf("Computing pij: result on file '%s' \n", filerespij);            
   fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);            k=0;
              for(i=1; i<= (nlstate); i++){
   stepsize=(int) (stepm+YEARM-1)/YEARM;              for(j=1; j<=(nlstate+ndeath);j++){
   /*if (stepm<=24) stepsize=2;*/                k=k+1;
                 gp[k]=pmmij[i][j];
   agelim=AGESUP;              }
   hstepm=stepsize*YEARM; /* Every year of age */            }
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */            
             for(i=1; i<=npar; i++)
   /* hstepm=1;   aff par mois*/              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
       
   k=0;            pmij(pmmij,cov,ncovmodel,xp,nlstate);
   for(cptcov=1;cptcov<=i1;cptcov++){            k=0;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){            for(i=1; i<=(nlstate); i++){
       k=k+1;              for(j=1; j<=(nlstate+ndeath);j++){
         fprintf(ficrespij,"\n#****** ");                k=k+1;
         for(j=1;j<=cptcoveff;j++)                gm[k]=pmmij[i][j];
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);              }
         fprintf(ficrespij,"******\n");            }
               
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */          }
   
           /*      nhstepm=nhstepm*YEARM; aff par mois*/          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
             for(theta=1; theta <=npar; theta++)
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              trgradg[j][theta]=gradg[theta][j];
           oldm=oldms;savm=savms;          
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
           fprintf(ficrespij,"# Age");          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
           for(i=1; i<=nlstate;i++)  
             for(j=1; j<=nlstate+ndeath;j++)          pmij(pmmij,cov,ncovmodel,x,nlstate);
               fprintf(ficrespij," %1d-%1d",i,j);          
           fprintf(ficrespij,"\n");          k=0;
            for (h=0; h<=nhstepm; h++){          for(i=1; i<=(nlstate); i++){
             fprintf(ficrespij,"%d %f %f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );            for(j=1; j<=(nlstate+ndeath);j++){
             for(i=1; i<=nlstate;i++)              k=k+1;
               for(j=1; j<=nlstate+ndeath;j++)              mu[k][(int) age]=pmmij[i][j];
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);            }
             fprintf(ficrespij,"\n");          }
              }          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
           fprintf(ficrespij,"\n");              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]));
   varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             }*/
   fclose(ficrespij);  
           fprintf(ficresprob,"\n%d ",(int)age);
           fprintf(ficresprobcov,"\n%d ",(int)age);
   /*---------- Forecasting ------------------*/          fprintf(ficresprobcor,"\n%d ",(int)age);
   if((stepm == 1) && (strcmp(model,".")==0)){  
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
   }          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
   else{            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
     erreur=108;            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
     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);          i=0;
   }          for (k=1; k<=(nlstate);k++){
              for (l=1; l<=(nlstate+ndeath);l++){ 
               i++;
   /*---------- Health expectancies and variances ------------*/              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
               fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
   strcpy(filerest,"t");              for (j=1; j<=i;j++){
   strcat(filerest,fileres);                /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
   if((ficrest=fopen(filerest,"w"))==NULL) {                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
     fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;              }
   }            }
   printf("Computing Total LEs with variances: file '%s' \n", filerest);          }/* end of loop for state */
   fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);        } /* end of loop for age */
         free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
         free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
   strcpy(filerese,"e");        free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   strcat(filerese,fileres);        free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   if((ficreseij=fopen(filerese,"w"))==NULL) {        
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);        /* Confidence intervalle of pij  */
     fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);        /*
   }          fprintf(ficgp,"\nunset parametric;unset label");
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
   fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);          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);
   strcpy(fileresv,"v");          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
   strcat(fileresv,fileres);          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
   if((ficresvij=fopen(fileresv,"w"))==NULL) {          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);        */
     fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);  
   }        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);        first1=1;first2=2;
   fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);        for (k2=1; k2<=(nlstate);k2++){
   calagedate=-1;          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);            if(l2==k2) continue;
             j=(k2-1)*(nlstate+ndeath)+l2;
   k=0;            for (k1=1; k1<=(nlstate);k1++){
   for(cptcov=1;cptcov<=i1;cptcov++){              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){                if(l1==k1) continue;
       k=k+1;                i=(k1-1)*(nlstate+ndeath)+l1;
       fprintf(ficrest,"\n#****** ");                if(i<=j) continue;
       for(j=1;j<=cptcoveff;j++)                for (age=bage; age<=fage; age ++){ 
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                  if ((int)age %5==0){
       fprintf(ficrest,"******\n");                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                     v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
       fprintf(ficreseij,"\n#****** ");                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
       for(j=1;j<=cptcoveff;j++)                    mu1=mu[i][(int) age]/stepm*YEARM ;
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                    mu2=mu[j][(int) age]/stepm*YEARM;
       fprintf(ficreseij,"******\n");                    c12=cv12/sqrt(v1*v2);
                     /* Computing eigen value of matrix of covariance */
       fprintf(ficresvij,"\n#****** ");                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
       for(j=1;j<=cptcoveff;j++)                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                    if ((lc2 <0) || (lc1 <0) ){
       fprintf(ficresvij,"******\n");                      if(first2==1){
                         first1=0;
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);                      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);
       oldm=oldms;savm=savms;                      }
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);                        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 */
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);                      /* lc2=fabs(lc2); */
       oldm=oldms;savm=savms;                    }
       varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0);  
       if(popbased==1){                    /* Eigen vectors */
         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased);                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
        }                    /*v21=sqrt(1.-v11*v11); *//* error */
                     v21=(lc1-v1)/cv12*v11;
                      v12=-v21;
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");                    v22=v11;
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);                    tnalp=v21/v11;
       fprintf(ficrest,"\n");                    if(first1==1){
                       first1=0;
       epj=vector(1,nlstate+1);                      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);
       for(age=bage; age <=fage ;age++){                    }
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);                    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);
         if (popbased==1) {                    /*printf(fignu*/
           for(i=1; i<=nlstate;i++)                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
             prlim[i][i]=probs[(int)age][i][k];                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
         }                    if(first==1){
                              first=0;
         fprintf(ficrest," %4.0f",age);                      fprintf(ficgp,"\nset parametric;unset label");
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){                      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);
           for(i=1, epj[j]=0.;i <=nlstate;i++) {                      fprintf(ficgp,"\nset ter png small size 320, 240");
             epj[j] += prlim[i][i]*eij[i][j][(int)age];                      fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/   :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
           }  %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
           epj[nlstate+1] +=epj[j];                              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);
         for(i=1, vepp=0.;i <=nlstate;i++)                      fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
           for(j=1;j <=nlstate;j++)                      fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
             vepp += vareij[i][j][(int)age];                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
         for(j=1;j <=nlstate;j++){                      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",\
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
         }                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
         fprintf(ficrest,"\n");                    }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);
 free_matrix(mint,1,maxwav,1,n);                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);                      fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
     free_vector(weight,1,n);                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
   fclose(ficreseij);                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
   fclose(ficresvij);                    }/* if first */
   fclose(ficrest);                  } /* age mod 5 */
   fclose(ficpar);                } /* end loop age */
   free_vector(epj,1,nlstate+1);                fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                  first=1;
   /*------- Variance limit prevalence------*/                } /*l12 */
             } /* k12 */
   strcpy(fileresvpl,"vpl");          } /*l1 */
   strcat(fileresvpl,fileres);        }/* k1 */
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {        /* } /* loop covariates */
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);    }
     exit(0);    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
   }    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);    free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
   k=0;    free_vector(xp,1,npar);
   for(cptcov=1;cptcov<=i1;cptcov++){    fclose(ficresprob);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    fclose(ficresprobcov);
       k=k+1;    fclose(ficresprobcor);
       fprintf(ficresvpl,"\n#****** ");    fflush(ficgp);
       for(j=1;j<=cptcoveff;j++)    fflush(fichtmcov);
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  }
       fprintf(ficresvpl,"******\n");  
        
       varpl=matrix(1,nlstate,(int) bage, (int) fage);  /******************* Printing html file ***********/
       oldm=oldms;savm=savms;  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);                    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, \
   fclose(ficresvpl);                    double jprev2, double mprev2,double anprev2){
     int jj1, k1, i1, cpt;
   /*---------- End : free ----------------*/  
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);     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 \
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);  </ul>");
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);     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"));
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);     fprintf(fichtm,"\
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);   - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);             stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);     fprintf(fichtm,"\
     - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
   free_matrix(matcov,1,npar,1,npar);             subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
   free_vector(delti,1,npar);     fprintf(fichtm,"\
   free_matrix(agev,1,maxwav,1,imx);   - (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): \
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);     <a href=\"%s\">%s</a> <br>\n",
              estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
   fprintf(fichtm,"\n</body>");     fprintf(fichtm,"\
   fclose(fichtm);   - Population projections by age and states: \
   fclose(ficgp);     <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
    
   fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   if(erreur >0){  
     printf("End of Imach with error or warning %d\n",erreur);   m=pow(2,cptcoveff);
     fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   }else{  
    printf("End of Imach\n");   jj1=0;
    fprintf(ficlog,"End of Imach\n");   for(k1=1; k1<=m;k1++){
   }     for(i1=1; i1<=ncodemax[k1];i1++){
   printf("See log file on %s\n",filelog);       jj1++;
   fclose(ficlog);       if (cptcovn > 0) {
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
           for (cpt=1; cpt<=cptcoveff;cpt++) 
   /* 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);*/           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
   /*printf("Total time was %d uSec.\n", total_usecs);*/         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
   /*------ End -----------*/       }
        /* 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> \
  end:  <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
 #ifdef windows       /* Quasi-incidences */
   /* chdir(pathcd);*/       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
 #endif   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> \
  /*system("wgnuplot graph.plt");*/  <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
  /*system("../gp37mgw/wgnuplot graph.plt");*/         /* Period (stable) prevalence in each health state */
  /*system("cd ../gp37mgw");*/         for(cpt=1; cpt<=nlstate;cpt++){
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/           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> \
  strcpy(plotcmd,GNUPLOTPROGRAM);  <img src=\"%s%d_%d.png\">",nlstate, cpt, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
  strcat(plotcmd," ");         }
  strcat(plotcmd,optionfilegnuplot);       for(cpt=1; cpt<=nlstate;cpt++) {
  system(plotcmd);          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);
 #ifdef windows       }
   while (z[0] != 'q') {     } /* end i1 */
     /* chdir(path); */   }/* End k1 */
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");   fprintf(fichtm,"</ul>");
     scanf("%s",z);  
     if (z[0] == 'c') system("./imach");  
     else if (z[0] == 'e') system(optionfilehtm);   fprintf(fichtm,"\
     else if (z[0] == 'g') system(plotcmd);  \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
     else if (z[0] == 'q') exit(0);   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
   }  
 #endif   fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
 }           subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
    fprintf(fichtm,"\
    - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
   
    fprintf(fichtm,"\
    - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
    fprintf(fichtm,"\
    - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
            estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
    fprintf(fichtm,"\
    - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",
            estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
    fprintf(fichtm,"\
    - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
            subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   
   /*  if(popforecast==1) fprintf(fichtm,"\n */
   /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
   /*      <br>",fileres,fileres,fileres,fileres); */
   /*  else  */
   /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
    fflush(fichtm);
    fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   
    m=pow(2,cptcoveff);
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        for(cpt=1; cpt<=nlstate;cpt++) {
          fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
   prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
   <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
        }
        fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
   true period expectancies (those weighted with period prevalences are also\
    drawn in addition to the population based expectancies computed using\
    observed and cahotic prevalences: %s%d.png<br>\
   <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
    fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m0,cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
     int ng=0;
   /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   /*     printf("Problem with file %s",optionfilegnuplot); */
   /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   /*   } */
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
     m=pow(2,cptcoveff);
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
    /* 1eme*/
     fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
     for (cpt=1; cpt<= nlstate ; cpt ++) {
       for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
        fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
        fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
        fprintf(ficgp,"set xlabel \"Age\" \n\
   set ylabel \"Probability\" \n\
   set ter png small size 320, 240\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else        fprintf(ficgp," \%%*lf (\%%*lf)");
        }
        fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        } 
        fprintf(ficgp,"\" t\"95\%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }  
        fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
      }
     }
     /*2 eme*/
     fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
     for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
       fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
       
       for (i=1; i<= nlstate+1 ; i ++) {
         k=2*i;
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         fprintf(ficgp,"\" t\"\" w l lt 0,");
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
         else fprintf(ficgp,"\" t\"\" w l lt 0,");
       }
     }
     
     /*3eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<= nlstate ; cpt ++) {
         /*       k=2+nlstate*(2*cpt-2); */
         k=2+(nlstate+1)*(cpt-1);
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
         fprintf(ficgp,"set ter png small size 320, 240\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           
         */
         for (i=1; i< nlstate ; i ++) {
           fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1);
           /*      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
           
         } 
         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
       }
     }
     
     /* CV preval stable (period) */
     for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
         k=3;
         fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
         fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   set ter png small size 320, 240\n\
   unset log y\n\
   plot [%.f:%.f]  ", ageminpar, agemaxpar);
         for (i=1; i<= nlstate ; i ++){
           if(i==1)
             fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
           else
             fprintf(ficgp,", '' ");
           l=(nlstate+ndeath)*(i-1)+1;
           fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
           for (j=1; j<= (nlstate-1) ; j ++)
             fprintf(ficgp,"+$%d",k+l+j);
           fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
         } /* nlstate */
         fprintf(ficgp,"\n");
       } /* end cpt state*/ 
     } /* end covariate */  
     
     /* proba elementaires */
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             jk++; 
             fprintf(ficgp,"\n");
           }
         }
       }
      }
     /*goto avoid;*/
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        for(jk=1; jk <=m; jk++) {
          fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
          if (ng==2)
            fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
          else
            fprintf(ficgp,"\nset title \"Probability\"\n");
          fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
          for(k2=1; k2<=nlstate; k2++) {
            k3=i;
            for(k=1; k<=(nlstate+ndeath); k++) {
              if (k != k2){
                if(ng==2)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                else
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;/* To be checked else nbcode[0][0] wrong */
                for(j=3; j <=ncovmodel; j++) {
                  /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /\* Bug valgrind *\/ */
                  /*        /\*fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);*\/ */
                  /*        ij++; */
                  /* } */
                  /* else */
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
                fprintf(ficgp,")/(1");
                
                for(k1=1; k1 <=nlstate; k1++){   
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
                  for(j=3; j <=ncovmodel; j++){
                    /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { */
                    /*   fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); */
                    /*   ij++; */
                    /* } */
                    /* else */
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                  }
                  fprintf(ficgp,")");
                }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
              }
            } /* end k */
          } /* end k2 */
        } /* end jk */
      } /* end ng */
    avoid:
      fflush(ficgp); 
   }  /* end gnuplot */
   
   
   /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
     int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
     double age;
   
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          we use a 5 terms etc. until the borders are no more concerned. 
       */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
           }
         }/* end age */
       }/* end mob */
     }else return -1;
     return 0;
   }/* End movingaverage */
   
   
   /************** Forecasting ******************/
   prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
     int *popage;
     double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   
   
   /**************** function prwizard **********************/
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     /* Wizard to print covariance matrix template */
   
     char ca[32], cb[32], cc[32];
     int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
   } /* end of prwizard */
   /******************* Gompertz Likelihood ******************************/
   double gompertz(double x[])
   { 
     double A,B,L=0.0,sump=0.,num=0.;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
   
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
                +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           L=L+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
    
     return -2*L*num/sump;
   }
   
   #ifdef GSL
   /******************* Gompertz_f Likelihood ******************************/
   double gompertz_f(const gsl_vector *v, void *params)
   { 
     double A,B,LL=0.0,sump=0.,num=0.;
     double *x= (double *) v->data;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
     printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
                +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           LL=LL+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
     printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
    
     return -2*LL*num/sump;
   }
   #endif
   
   /******************* Printing html file ***********/
   void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,  double p[],double **matcov,double agemortsup){
     int i,k;
   
     fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
     fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
     for (i=1;i<=2;i++) 
       fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
     fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
     fprintf(fichtm,"</ul>");
   
   fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
   
    fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
   
    for (k=agegomp;k<(agemortsup-2);k++) 
      fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
   
    
     fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
     fprintf(ficgp,"set out \"graphmort.png\"\n "); 
     fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
     fprintf(ficgp, "set ter png small size 320, 240\n set log y\n"); 
     /* fprintf(ficgp, "set size 0.65,0.65\n"); */
     fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
   
   } 
   
   int readdata(char datafile[], int firstobs, int lastobs, int *imax)
   {
   
     /*-------- data file ----------*/
     FILE *fic;
     char dummy[]="                         ";
     int i, j, n;
     int linei, month, year,iout;
     char line[MAXLINE], linetmp[MAXLINE];
     char stra[80], strb[80];
     char *stratrunc;
     int lstra;
   
   
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem while opening datafile: %s\n", datafile);return 1;
       fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
     }
   
     i=1;
     linei=0;
     while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
       linei=linei+1;
       for(j=strlen(line); j>=0;j--){  /* Untabifies line */
         if(line[j] == '\t')
           line[j] = ' ';
       }
       for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
         ;
       };
       line[j+1]=0;  /* Trims blanks at end of line */
       if(line[0]=='#'){
         fprintf(ficlog,"Comment line\n%s\n",line);
         printf("Comment line\n%s\n",line);
         continue;
       }
       trimbb(linetmp,line); /* Trims multiple blanks in line */
       for (j=0; line[j]!='\0';j++){
         line[j]=linetmp[j];
       }
     
   
       for (j=maxwav;j>=1;j--){
         cutv(stra, strb, line, ' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
         /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
             fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);
             return 1;
           }
         }
         s[j][i]=lval;
         
         strcpy(line,stra);
         cutv(stra, strb,line,' ');
         if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
         }
         else  if(iout=sscanf(strb,"%s.",dummy) != 0){
           month=99;
           year=9999;
         }else{
           printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);fflush(ficlog);
           return 1;
         }
         anint[j][i]= (double) year; 
         mint[j][i]= (double)month; 
         strcpy(line,stra);
       } /* ENd Waves */
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.",dummy) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
       }
       andc[i]=(double) year; 
       moisdc[i]=(double) month; 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.", dummy) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
       }
       if (year==9999) {
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given.  Exiting.\n",strb, linei,i,line);
         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
   
       }
       annais[i]=(double)(year);
       moisnais[i]=(double)(month); 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       errno=0;
       dval=strtod(strb,&endptr); 
       if( strb[0]=='\0' || (*endptr != '\0')){
         printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fprintf(ficlog,"Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fflush(ficlog);
         return 1;
       }
       weight[i]=dval; 
       strcpy(line,stra);
       
       for (j=ncovcol;j>=1;j--){
         cutv(stra, strb,line,' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);
             fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);fflush(ficlog);
             return 1;
           }
         }
         if(lval <-1 || lval >1){
           printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);
           fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
           return 1;
         }
         covar[j][i]=(double)(lval);
         strcpy(line,stra);
       }  
       lstra=strlen(stra);
        
       if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
         stratrunc = &(stra[lstra-9]);
         num[i]=atol(stratrunc);
       }
       else
         num[i]=atol(stra);
       /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
         printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
       
       i=i+1;
     } /* End loop reading  data */
   
     *imax=i-1; /* Number of individuals */
     fclose(fic);
    
     return (0);
     endread:
       printf("Exiting readdata: ");
       fclose(fic);
       return (1);
   
   
   
   }
   void removespace(char *str) {
     char *p1 = str, *p2 = str;
     do
       while (*p2 == ' ')
         p2++;
     while (*p1++ = *p2++);
   }
   
   int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
      * Model  V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age
      * - cptcovt total number of covariates of the model nbocc(+)+1 = 8
      * - cptcovn or number of covariates k of the models excluding age*products =6
      * - cptcovage number of covariates with age*products =2
      * - cptcovs number of simple covariates
      * - Tvar[k] is the id of the kth covariate Tvar[1]@12 {1, 2, 3, 8, 10, 11, 8, 3, 7, 8, 5, 6}, thus Tvar[5=V7*V8]=10
      *     which is a new column after the 9 (ncovcol) variables. 
      * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
      * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
      *    Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
      * - Tvard[k]  p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
    */
   {
     int i, j, k, ks;
     int i1, j1, k1, k2;
     char modelsav[80];
     char stra[80], strb[80], strc[80], strd[80],stre[80];
   
     /*removespace(model);*/
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
       j=nbocc(model,'+'); /**< j=Number of '+' */
       j1=nbocc(model,'*'); /**< j1=Number of '*' */
       cptcovs=j+1-j1; /**<  Number of simple covariates V1+V2*age+V3 +V3*V4=> V1 + V3 =2  */
       cptcovt= j+1; /* Number of total covariates in the model V1 + V2*age+ V3 + V3*V4=> 4*/
                     /* including age products which are counted in cptcovage.
                     /* but the covariates which are products must be treated separately: ncovn=4- 2=2 (V1+V3). */
       cptcovprod=j1; /**< Number of products  V1*V2 +v3*age = 2 */
       cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1  */
       strcpy(modelsav,model); 
       if (strstr(model,"AGE") !=0){
         printf("Error. AGE must be in lower case 'age' model=%s ",model);
         fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
         return 1;
       }
       if (strstr(model,"v") !=0){
         printf("Error. 'v' must be in upper case 'V' model=%s ",model);
         fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
         return 1;
       }
       
       /*   Design
        *  V1   V2   V3   V4  V5  V6  V7  V8  V9 Weight
        *  <          ncovcol=8                >
        * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
        *   k=  1    2      3       4     5       6      7        8
        *  cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
        *  covar[k,i], value of kth covariate if not including age for individual i:
        *       covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
        *  Tvar[k] # of the kth covariate:  Tvar[1]=2  Tvar[4]=3 Tvar[8]=8
        *       if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and 
        *  Tage[++cptcovage]=k
        *       if products, new covar are created after ncovcol with k1
        *  Tvar[k]=ncovcol+k1; # of the kth covariate product:  Tvar[5]=ncovcol+1=10  Tvar[6]=ncovcol+1=11
        *  Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
        *  Tvard[k1][1]=m Tvard[k1][2]=m; Tvard[1][1]=5 (V5) Tvard[1][2]=6 Tvard[2][1]=7 (V7) Tvard[2][2]=8
        *  Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
        *  Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
        *  V1   V2   V3   V4  V5  V6  V7  V8  V9  V10  V11
        *  <          ncovcol=8                >
        *       Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8    d1   d1   d2  d2
        *          k=  1    2      3       4     5       6      7        8    9   10   11  12
        *     Tvar[k]= 2    1      3       3    10      11      8        8    5    6    7   8
        * p Tvar[1]@12={2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
        * p Tprod[1]@2={                         6, 5}
        *p Tvard[1][1]@4= {7, 8, 5, 6}
        * covar[k][i]= V2   V1      ?      V3    V5*V6?   V7*V8?  ?       V8   
        *  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
        *How to reorganize?
        * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
        * Tvars {2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
        *       {2,   1,     4,      8,    5,      6,     3,       7}
        * Struct []
        */
   
       /* This loop fills the array Tvar from the string 'model'.*/
       /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
       /*   modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4  */
       /*  k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
       /*  k=3 V4 Tvar[k=3]= 4 (from V4) */
       /*  k=2 V1 Tvar[k=2]= 1 (from V1) */
       /*  k=1 Tvar[1]=2 (from V2) */
       /*  k=5 Tvar[5] */
       /* for (k=1; k<=cptcovn;k++) { */
       /*  cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
       /*  } */
       /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
       /*
        * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
       for(k=cptcovt; k>=1;k--) /**< Number of covariates */
           Tvar[k]=0;
       cptcovage=0;
       for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
         cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' 
                                        modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
           cutl(strc,strd,strb,'*'); /**< strd*strc  Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
           if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
             /* covar is not filled and then is empty */
             cptcovprod--;
             cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
             Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2 */
             cptcovage++; /* Sums the number of covariates which include age as a product */
             Tage[cptcovage]=k;  /* Tage[1] = 4 */
             /*printf("stre=%s ", stre);*/
           } else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutl(stre,strb,strc,'V');
             Tvar[k]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=k;
           } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/
             /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
             cptcovn++;
             cptcovprodnoage++;k1++;
             cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
             Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
                                     because this model-covariate is a construction we invent a new column
                                     ncovcol + k1
                                     If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
                                     Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
             cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */
             Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
             Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
             k2=k2+2;
             Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
             Tvar[cptcovt+k2+1]=Tvard[k1][2];  /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
             for (i=1; i<=lastobs;i++){
               /* Computes the new covariate which is a product of
                  covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
               covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
             }
           } /* End age is not in the model */
         } /* End if model includes a product */
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
           cutl(strd,strc,strb,'V');
           ks++; /**< Number of simple covariates */
           cptcovn++;
           Tvar[k]=atoi(strd);
         }
         strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+V1+V4 */ 
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);*/
   
   
     return (0); /* with covar[new additional covariate if product] and Tage if age */ 
     endread:
       printf("Exiting decodemodel: ");
       return (1);
   }
   
   calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
   {
     int i, m;
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           *nberr++;
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           *nberr++;
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if ((int)andc[i]!=9999){
                   nbwarn++;
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] < *agemin){ 
               *agemin=agev[m][i];
               printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
             }
             else if(agev[m][i] >*agemax){
               *agemax=agev[m][i];
               /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           *nberr++;
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           return 1;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax); 
   
     return (0);
     endread:
       printf("Exiting calandcheckages: ");
       return (1);
   }
   
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
   #ifdef GSL
     const gsl_multimin_fminimizer_type *T;
     size_t iteri = 0, it;
     int rval = GSL_CONTINUE;
     int status = GSL_SUCCESS;
     double ssval;
   #endif
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
     int linei, month, year,iout;
     int jj, ll, li, lj, lk, imk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int itimes;
     int NDIM=2;
     int vpopbased=0;
   
     char ca[32], cb[32], cc[32];
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     struct stat info;
     double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE], pathimach[MAXLINE]; 
     char **bp, *tok, *val; /* pathtot */
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,*tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     int agemortsup;
     float  sumlpop=0.;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
     double **ximort;
     char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
     int *dcwave;
   
     char z[1]="c", occ;
   
     /*char  *strt;*/
     char strtend[80];
   
     long total_usecs;
    
   /*   setlocale (LC_ALL, ""); */
   /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   /*   textdomain (PACKAGE); */
   /*   setlocale (LC_CTYPE, ""); */
   /*   setlocale (LC_MESSAGES, ""); */
   
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     rstart_time = time(NULL);  
     /*  (void) gettimeofday(&start_time,&tzp);*/
     start_time = *localtime(&rstart_time);
     curr_time=start_time;
     /*tml = *localtime(&start_time.tm_sec);*/
     /* strcpy(strstart,asctime(&tml)); */
     strcpy(strstart,asctime(&start_time));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tm_sec = tp.tm_sec +86400; */
   /*  tm = *localtime(&start_time.tm_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tm_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     nberr=0; /* Number of errors and warnings */
     nbwarn=0;
     getcwd(pathcd, size);
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       fgets(pathr,FILENAMELENGTH,stdin);
       i=strlen(pathr);
       if(pathr[i-1]=='\n')
         pathr[i-1]='\0';
       i=strlen(pathr);
       if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
         pathr[i-1]='\0';
      for (tok = pathr; tok != NULL; ){
         printf("Pathr |%s|\n",pathr);
         while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
         printf("val= |%s| pathr=%s\n",val,pathr);
         strcpy (pathtot, val);
         if(pathr[0] == '\0') break; /* Dirty */
       }
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     /* Split argv[0], imach program to get pathimach */
     printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
     split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
     printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
    /*   strcpy(pathimach,argv[0]); */
     /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path); /* Can be a relative path */
     if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
       printf("Current directory %s!\n",pathcd);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s\n%s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: \n");
     fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     printf("Local time (at start):%s",strstart);
     fprintf(ficlog,"Local time (at start): %s",strstart);
     fflush(ficlog);
   /*   (void) gettimeofday(&curr_time,&tzp); */
   /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
       fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
       fflush(ficlog);
       /* goto end; */
       exit(70); 
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       fputs(line,stdout);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       fputs(line, stdout);
       //puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n);  /**< used in readdata */
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
     /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
        v1+v2*age+v2*v3 makes cptcovn = 3
     */
     if (strlen(model)>1) 
       ncovmodel=2+nbocc(model,'+')+1; /*Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7*/
     else
       ncovmodel=2;
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
     npar= nforce*ncovmodel; /* Number of parameters like aij*/
     if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
       printf("Too complex model for current IMaCh: npar=(nlstate+ndeath-1)*nlstate*ncovmodel=%d >= %d(MAXPARM) or nlstate=%d >= %d(NLSTATEMAX) or ndeath=%d >= %d(NDEATHMAX) or ncovmodel=(k+age+#of+signs)=%d(NCOVMAX) >= %d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fprintf(ficlog,"Too complex model for current IMaCh: %d >=%d(MAXPARM) or %d >=%d(NLSTATEMAX) or %d >=%d(NDEATHMAX) or %d(NCOVMAX) >=%d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fflush(stdout);
       fclose (ficlog);
       goto end;
     }
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     delti=delti3[1][1];
     /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
     if(mle==-1){ /* Print a wizard for help writing covariance matrix */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       fclose (ficparo);
       fclose (ficlog);
       goto end;
       exit(0);
     }
     else if(mle==-3) {
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       matcov=matrix(1,npar,1,npar);
     }
     else{
       /* Read guessed parameters */
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
       
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       for(i=1; i <=nlstate; i++){
         j=0;
         for(jj=1; jj <=nlstate+ndeath; jj++){
           if(jj==i) continue;
           j++;
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1 != i) && (j1 != j)){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
   It might be a problem of design; if ncovcol and the model are correct\n \
   run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           fprintf(ficparo,"%1d%1d",i1,j1);
           if(mle==1)
             printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar," %lf",&param[i][j][k]);
             if(mle==1){
               printf(" %lf",param[i][j][k]);
               fprintf(ficlog," %lf",param[i][j][k]);
             }
             else
               fprintf(ficlog," %lf",param[i][j][k]);
             fprintf(ficparo," %lf",param[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           if(mle==1)
             printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficparo,"\n");
         }
       }  
       fflush(ficlog);
   
       /* Reads scales values */
       p=param[1][1];
       
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
   
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath-1; j++){
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1-i)*(j1-j)!=0){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           printf("%1d%1d",i,j);
           fprintf(ficparo,"%1d%1d",i1,j1);
           fprintf(ficlog,"%1d%1d",i1,j1);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar,"%le",&delti3[i][j][k]);
             printf(" %le",delti3[i][j][k]);
             fprintf(ficparo," %le",delti3[i][j][k]);
             fprintf(ficlog," %le",delti3[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           printf("\n");
           fprintf(ficparo,"\n");
           fprintf(ficlog,"\n");
         }
       }
       fflush(ficlog);
   
       /* Reads covariance matrix */
       delti=delti3[1][1];
   
   
       /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
     
       matcov=matrix(1,npar,1,npar);
       for(i=1; i <=npar; i++)
         for(j=1; j <=npar; j++) matcov[i][j]=0.;
         
       for(i=1; i <=npar; i++){
         fscanf(ficpar,"%s",str);
         if(mle==1)
           printf("%s",str);
         fprintf(ficlog,"%s",str);
         fprintf(ficparo,"%s",str);
         for(j=1; j <=i; j++){
           fscanf(ficpar," %le",&matcov[i][j]);
           if(mle==1){
             printf(" %.5le",matcov[i][j]);
           }
           fprintf(ficlog," %.5le",matcov[i][j]);
           fprintf(ficparo," %.5le",matcov[i][j]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
       for(i=1; i <=npar; i++)
         for(j=i+1;j<=npar;j++)
           matcov[i][j]=matcov[j][i];
       
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       
       fflush(ficlog);
       
       /*-------- Rewriting parameter file ----------*/
       strcpy(rfileres,"r");    /* "Rparameterfile */
       strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
       strcat(rfileres,".");    /* */
       strcat(rfileres,optionfilext);    /* Other files have txt extension */
       if((ficres =fopen(rfileres,"w"))==NULL) {
         printf("Problem writing new parameter file: %s\n", fileres);goto end;
         fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
       }
       fprintf(ficres,"#%s\n",version);
     }    /* End of mle != -3 */
   
   
     n= lastobs;
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */ 
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
   
     /* Reads data from file datafile */
     if (readdata(datafile, firstobs, lastobs, &imx)==1)
       goto end;
   
     /* Calculation of the number of parameters from char model */
       /*    modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 
           k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
           k=3 V4 Tvar[k=3]= 4 (from V4)
           k=2 V1 Tvar[k=2]= 1 (from V1)
           k=1 Tvar[1]=2 (from V2)
       */
     Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
     /*  V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs). 
         For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4, 
         Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
     */
     /* For model-covariate k tells which data-covariate to use but
       because this model-covariate is a construction we invent a new column
       ncovcol + k1
       If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
       Tvar[3=V1*V4]=4+1 etc */
     Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
     /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
        if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2)
     */
     Tvaraff=ivector(1,NCOVMAX); /* Unclear */
     Tvard=imatrix(1,NCOVMAX,1,2); /* n=Tvard[k1][1]  and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm
                               * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd. 
                               * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
     Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
                            4 covariates (3 plus signs)
                            Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
                         */  
   
     if(decodemodel(model, lastobs) == 1)
       goto end;
   
     if((double)(lastobs-imx)/(double)imx > 1.10){
       nbwarn++;
       printf("Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
       fprintf(ficlog,"Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
     }
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
       for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
     }
   
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
       goto end;
   
   
     agegomp=(int)agemin;
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
     /* */
     
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
     /* */
    
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     Ndum =ivector(-1,NCOVMAX);  
     if (ncovmodel > 2)
       tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
   
     codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
     /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
     h=0;
   
   
     /*if (cptcovn > 0) */
         
    
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
       for(i=1; i <=pow(2,cptcoveff-k);i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */ 
         for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
           for(cpt=1; cpt <=pow(2,k-1); cpt++){  /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */ 
             h++;
             if (h>m) 
               h=1;
             /**< codtab(h,k)  k   = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
              *     h     1     2     3     4
              *______________________________  
              *     1 i=1 1 i=1 1 i=1 1 i=1 1
              *     2     2     1     1     1
              *     3 i=2 1     2     1     1
              *     4     2     2     1     1
              *     5 i=3 1 i=2 1     2     1
              *     6     2     1     2     1
              *     7 i=4 1     2     2     1
              *     8     2     2     2     1
              *     9 i=5 1 i=3 1 i=2 1     1
              *    10     2     1     1     1
              *    11 i=6 1     2     1     1
              *    12     2     2     1     1
              *    13 i=7 1 i=4 1     2     1    
              *    14     2     1     2     1
              *    15 i=8 1     2     2     1
              *    16     2     2     2     1
              */
             codtab[h][k]=j;
             /*codtab[h][Tvar[k]]=j;*/
             printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]);
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
          printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
   
    free_ivector(Ndum,-1,NCOVMAX);
   
   
       
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     if(mle==-3)
       strcat(optionfilegnuplot,"-mort");
     strcat(optionfilegnuplot,".gp");
   
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       //fprintf(ficgp,"set missing 'NaNq'\n");
       fprintf(ficgp,"set datafile missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname); /* Main html file */
     if(mle==-3)
       strcat(optionfilehtm,"-mort");
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm);
       exit(0);
     }
   
     strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
     strcat(optionfilehtmcov,"-cov.htm");
     if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtmcov), exit(0);
     }
     else{
     fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
             optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
    - Log file of the run: <a href=\"%s\">%s</a><br>\n\
    - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
    - Date and time at start: %s</ul>\n",\
             optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
             optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
             fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
     chdir(optionfilefiname); /* Move to directory named optionfile */
     
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
   
     fprintf(fichtm,"\n");
     fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
             imx,agemin,agemax,jmin,jmax,jmean);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
   
     if (mle==-3){
       ximort=matrix(1,NDIM,1,NDIM); 
   /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
       cens=ivector(1,n);
       ageexmed=vector(1,n);
       agecens=vector(1,n);
       dcwave=ivector(1,n);
    
       for (i=1; i<=imx; i++){
         dcwave[i]=-1;
         for (m=firstpass; m<=lastpass; m++)
           if (s[m][i]>nlstate) {
             dcwave[i]=m;
             /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
             break;
           }
       }
   
       for (i=1; i<=imx; i++) {
         if (wav[i]>0){
           ageexmed[i]=agev[mw[1][i]][i];
           j=wav[i];
           agecens[i]=1.; 
   
           if (ageexmed[i]> 1 && wav[i] > 0){
             agecens[i]=agev[mw[j][i]][i];
             cens[i]= 1;
           }else if (ageexmed[i]< 1) 
             cens[i]= -1;
           if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
             cens[i]=0 ;
         }
         else cens[i]=-1;
       }
       
       for (i=1;i<=NDIM;i++) {
         for (j=1;j<=NDIM;j++)
           ximort[i][j]=(i == j ? 1.0 : 0.0);
       }
       
       /*p[1]=0.0268; p[NDIM]=0.083;*/
       /*printf("%lf %lf", p[1], p[2]);*/
       
       
   #ifdef GSL
       printf("GSL optimization\n");  fprintf(ficlog,"Powell\n");
   #else
       printf("Powell\n");  fprintf(ficlog,"Powell\n");
   #endif
       strcpy(filerespow,"pow-mort"); 
       strcat(filerespow,fileres);
       if((ficrespow=fopen(filerespow,"w"))==NULL) {
         printf("Problem with resultfile: %s\n", filerespow);
         fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
       }
   #ifdef GSL
       fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
   #else
       fprintf(ficrespow,"# Powell\n# iter -2*LL");
   #endif
       /*  for (i=1;i<=nlstate;i++)
           for(j=1;j<=nlstate+ndeath;j++)
           if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       */
       fprintf(ficrespow,"\n");
   #ifdef GSL
       /* gsl starts here */ 
       T = gsl_multimin_fminimizer_nmsimplex;
       gsl_multimin_fminimizer *sfm = NULL;
       gsl_vector *ss, *x;
       gsl_multimin_function minex_func;
   
       /* Initial vertex size vector */
       ss = gsl_vector_alloc (NDIM);
       
       if (ss == NULL){
         GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
       }
       /* Set all step sizes to 1 */
       gsl_vector_set_all (ss, 0.001);
   
       /* Starting point */
       
       x = gsl_vector_alloc (NDIM);
       
       if (x == NULL){
         gsl_vector_free(ss);
         GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
       }
     
       /* Initialize method and iterate */
       /*     p[1]=0.0268; p[NDIM]=0.083; */
   /*     gsl_vector_set(x, 0, 0.0268); */
   /*     gsl_vector_set(x, 1, 0.083); */
       gsl_vector_set(x, 0, p[1]);
       gsl_vector_set(x, 1, p[2]);
   
       minex_func.f = &gompertz_f;
       minex_func.n = NDIM;
       minex_func.params = (void *)&p; /* ??? */
       
       sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
       gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
       
       printf("Iterations beginning .....\n\n");
       printf("Iter. #    Intercept       Slope     -Log Likelihood     Simplex size\n");
   
       iteri=0;
       while (rval == GSL_CONTINUE){
         iteri++;
         status = gsl_multimin_fminimizer_iterate(sfm);
         
         if (status) printf("error: %s\n", gsl_strerror (status));
         fflush(0);
         
         if (status) 
           break;
         
         rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
         ssval = gsl_multimin_fminimizer_size (sfm);
         
         if (rval == GSL_SUCCESS)
           printf ("converged to a local maximum at\n");
         
         printf("%5d ", iteri);
         for (it = 0; it < NDIM; it++){
           printf ("%10.5f ", gsl_vector_get (sfm->x, it));
         }
         printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
       }
       
       printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
       
       gsl_vector_free(x); /* initial values */
       gsl_vector_free(ss); /* inital step size */
       for (it=0; it<NDIM; it++){
         p[it+1]=gsl_vector_get(sfm->x,it);
         fprintf(ficrespow," %.12lf", p[it]);
       }
       gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1)  */
   #endif
   #ifdef POWELL
        powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
   #endif  
       fclose(ficrespow);
       
       hesscov(matcov, p, NDIM, delti, 1e-4, gompertz); 
   
       for(i=1; i <=NDIM; i++)
         for(j=i+1;j<=NDIM;j++)
           matcov[i][j]=matcov[j][i];
       
       printf("\nCovariance matrix\n ");
       for(i=1; i <=NDIM; i++) {
         for(j=1;j<=NDIM;j++){ 
           printf("%f ",matcov[i][j]);
         }
         printf("\n ");
       }
       
       printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
       for (i=1;i<=NDIM;i++) 
         printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
   
       lsurv=vector(1,AGESUP);
       lpop=vector(1,AGESUP);
       tpop=vector(1,AGESUP);
       lsurv[agegomp]=100000;
       
       for (k=agegomp;k<=AGESUP;k++) {
         agemortsup=k;
         if (p[1]*exp(p[2]*(k-agegomp))>1) break;
       }
       
       for (k=agegomp;k<agemortsup;k++)
         lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
       
       for (k=agegomp;k<agemortsup;k++){
         lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
         sumlpop=sumlpop+lpop[k];
       }
       
       tpop[agegomp]=sumlpop;
       for (k=agegomp;k<(agemortsup-3);k++){
         /*  tpop[k+1]=2;*/
         tpop[k+1]=tpop[k]-lpop[k];
       }
       
       
       printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
       for (k=agegomp;k<(agemortsup-2);k++) 
         printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
       
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
                        stepm, weightopt,\
                        model,imx,p,matcov,agemortsup);
       
       free_vector(lsurv,1,AGESUP);
       free_vector(lpop,1,AGESUP);
       free_vector(tpop,1,AGESUP);
   #ifdef GSL
       free_ivector(cens,1,n);
       free_vector(agecens,1,n);
       free_ivector(dcwave,1,n);
       free_matrix(ximort,1,NDIM,1,NDIM);
   #endif
     } /* Endof if mle==-3 */
     
     else{ /* For mle >=1 */
       globpr=0;/* debug */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       globpr=1; /* to print the contributions */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       if(mle>=1){ /* Could be 1 or 2 */
         mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
       }
       
       /*--------- results files --------------*/
       fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
       
       
       fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(k=1; k <=(nlstate+ndeath); k++){
           if (k != i) {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%lf ",p[jk]);
               fprintf(ficlog,"%lf ",p[jk]);
               fprintf(ficres,"%lf ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       if(mle!=0){
         /* Computing hessian and covariance matrix */
         ftolhess=ftol; /* Usually correct */
         hesscov(matcov, p, npar, delti, ftolhess, func);
       }
       fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
       printf("# Scales (for hessian or gradient estimation)\n");
       fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if (j!=i) {
             fprintf(ficres,"%1d%1d",i,j);
             printf("%1d%1d",i,j);
             fprintf(ficlog,"%1d%1d",i,j);
             for(k=1; k<=ncovmodel;k++){
               printf(" %.5e",delti[jk]);
               fprintf(ficlog," %.5e",delti[jk]);
               fprintf(ficres," %.5e",delti[jk]);
               jk++;
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       
       fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       if(mle>=1)
         printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       /* # 121 Var(a12)\n\ */
       /* # 122 Cov(b12,a12) Var(b12)\n\ */
       /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
       /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
       /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
       /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
       /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
       /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
       
       
       /* Just to have a covariance matrix which will be more understandable
          even is we still don't want to manage dictionary of variables
       */
       for(itimes=1;itimes<=2;itimes++){
         jj=0;
         for(i=1; i <=nlstate; i++){
           for(j=1; j <=nlstate+ndeath; j++){
             if(j==i) continue;
             for(k=1; k<=ncovmodel;k++){
               jj++;
               ca[0]= k+'a'-1;ca[1]='\0';
               if(itimes==1){
                 if(mle>=1)
                   printf("#%1d%1d%d",i,j,k);
                 fprintf(ficlog,"#%1d%1d%d",i,j,k);
                 fprintf(ficres,"#%1d%1d%d",i,j,k);
               }else{
                 if(mle>=1)
                   printf("%1d%1d%d",i,j,k);
                 fprintf(ficlog,"%1d%1d%d",i,j,k);
                 fprintf(ficres,"%1d%1d%d",i,j,k);
               }
               ll=0;
               for(li=1;li <=nlstate; li++){
                 for(lj=1;lj <=nlstate+ndeath; lj++){
                   if(lj==li) continue;
                   for(lk=1;lk<=ncovmodel;lk++){
                     ll++;
                     if(ll<=jj){
                       cb[0]= lk +'a'-1;cb[1]='\0';
                       if(ll<jj){
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }else{
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }
                     }
                   } /* end lk */
                 } /* end lj */
               } /* end li */
               if(mle>=1)
                 printf("\n");
               fprintf(ficlog,"\n");
               fprintf(ficres,"\n");
               numlinepar++;
             } /* end k*/
           } /*end j */
         } /* end i */
       } /* end itimes */
       
       fflush(ficlog);
       fflush(ficres);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       estepm=0;
       fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
       if (estepm==0 || estepm < stepm) estepm=stepm;
       if (fage <= 2) {
         bage = ageminpar;
         fage = agemaxpar;
       }
       
       fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
       fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
       fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       
       dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
       dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
       
       fscanf(ficpar,"pop_based=%d\n",&popbased);
       fprintf(ficparo,"pop_based=%d\n",popbased);   
       fprintf(ficres,"pop_based=%d\n",popbased);   
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
       fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       /* day and month of proj2 are not used but only year anproj2.*/
       
       
       
        /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
       /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                    model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                    jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
         
      /*------------ free_vector  -------------*/
      /*  chdir(path); */
    
       free_ivector(wav,1,imx);
       free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
       free_lvector(num,1,n);
       free_vector(agedc,1,n);
       /*free_matrix(covar,0,NCOVMAX,1,n);*/
       /*free_matrix(covar,1,NCOVMAX,1,n);*/
       fclose(ficparo);
       fclose(ficres);
   
   
       /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
   #include "prevlim.h"  /* Use ficrespl, ficlog */
       fclose(ficrespl);
   
   #ifdef FREEEXIT2
   #include "freeexit2.h"
   #endif
   
       /*------------- h Pij x at various ages ------------*/
   #include "hpijx.h"
       fclose(ficrespij);
   
     /*-------------- Variance of one-step probabilities---*/
       k=1;
       varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
   
   
       probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for(i=1;i<=AGESUP;i++)
         for(j=1;j<=NCOVMAX;j++)
           for(k=1;k<=NCOVMAX;k++)
             probs[i][j][k]=0.;
   
       /*---------- Forecasting ------------------*/
       /*if((stepm == 1) && (strcmp(model,".")==0)){*/
       if(prevfcast==1){
         /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
         /*      }  */
         /*      else{ */
         /*        erreur=108; */
         /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*      } */
       }
     
   
       /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
   
       prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
       /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
           ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
       */
   
       if (mobilav!=0) {
         mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
           fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
           printf(" Error in movingaverage mobilav=%d\n",mobilav);
         }
       }
   
   
       /*---------- Health expectancies, no variances ------------*/
   
       strcpy(filerese,"e");
       strcat(filerese,fileres);
       if((ficreseij=fopen(filerese,"w"))==NULL) {
         printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
         fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       }
       printf("Computing Health Expectancies: result on file '%s' \n", filerese);
       fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficreseij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficreseij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);  
         
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         /*}*/
       }
       fclose(ficreseij);
   
   
       /*---------- Health expectancies and variances ------------*/
   
   
       strcpy(filerest,"t");
       strcat(filerest,fileres);
       if((ficrest=fopen(filerest,"w"))==NULL) {
         printf("Problem with total LE resultfile: %s\n", filerest);goto end;
         fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
       }
       printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
       fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
   
   
       strcpy(fileresstde,"stde");
       strcat(fileresstde,fileres);
       if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
         printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
         fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
       }
       printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
       fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
   
       strcpy(filerescve,"cve");
       strcat(filerescve,fileres);
       if((ficrescveij=fopen(filerescve,"w"))==NULL) {
         printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
         fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
       }
       printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
       fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
   
       strcpy(fileresv,"v");
       strcat(fileresv,fileres);
       if((ficresvij=fopen(fileresv,"w"))==NULL) {
         printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
         fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
       }
       printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
       fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficrest,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrest,"******\n");
   
           fprintf(ficresstdeij,"\n#****** ");
           fprintf(ficrescveij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficresstdeij,"******\n");
           fprintf(ficrescveij,"******\n");
   
           fprintf(ficresvij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);  
           /*
            */
           /* goto endfree; */
    
           vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           pstamp(ficrest);
   
   
           for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
             oldm=oldms;savm=savms; /* Segmentation fault */
             cptcod= 0; /* To be deleted */
             varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */
             fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");
             if(vpopbased==1)
               fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
             else
               fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
             fprintf(ficrest,"# Age e.. (std) ");
             for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
             fprintf(ficrest,"\n");
   
             epj=vector(1,nlstate+1);
             for(age=bage; age <=fage ;age++){
               prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
               if (vpopbased==1) {
                 if(mobilav ==0){
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=probs[(int)age][i][k];
                 }else{ /* mobilav */ 
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=mobaverage[(int)age][i][k];
                 }
               }
           
               fprintf(ficrest," %4.0f",age);
               for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
                 for(i=1, epj[j]=0.;i <=nlstate;i++) {
                   epj[j] += prlim[i][i]*eij[i][j][(int)age];
                   /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
                 }
                 epj[nlstate+1] +=epj[j];
               }
   
               for(i=1, vepp=0.;i <=nlstate;i++)
                 for(j=1;j <=nlstate;j++)
                   vepp += vareij[i][j][(int)age];
               fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
               for(j=1;j <=nlstate;j++){
                 fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
               }
               fprintf(ficrest,"\n");
             }
           }
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_vector(epj,1,nlstate+1);
         /*}*/
       }
       free_vector(weight,1,n);
       free_imatrix(Tvard,1,NCOVMAX,1,2);
       free_imatrix(s,1,maxwav+1,1,n);
       free_matrix(anint,1,maxwav,1,n); 
       free_matrix(mint,1,maxwav,1,n);
       free_ivector(cod,1,n);
       free_ivector(tab,1,NCOVMAX);
       fclose(ficresstdeij);
       fclose(ficrescveij);
       fclose(ficresvij);
       fclose(ficrest);
       fclose(ficpar);
     
       /*------- Variance of period (stable) prevalence------*/   
   
       strcpy(fileresvpl,"vpl");
       strcat(fileresvpl,fileres);
       if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
         printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
         exit(0);
       }
       printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
   
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficresvpl,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvpl,"******\n");
         
           varpl=matrix(1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
           free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
         /*}*/
       }
   
       fclose(ficresvpl);
   
       /*---------- End : free ----------------*/
       if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
     }  /* mle==-3 arrives here for freeing */
    endfree:
       free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
       free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(covar,0,NCOVMAX,1,n);
       free_matrix(matcov,1,npar,1,npar);
       /*free_vector(delti,1,npar);*/
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       free_matrix(agev,1,maxwav,1,imx);
       free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   
       free_ivector(ncodemax,1,NCOVMAX);
       free_ivector(Tvar,1,NCOVMAX);
       free_ivector(Tprod,1,NCOVMAX);
       free_ivector(Tvaraff,1,NCOVMAX);
       free_ivector(Tage,1,NCOVMAX);
   
       free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
       free_imatrix(codtab,1,100,1,10);
     fflush(fichtm);
     fflush(ficgp);
     
   
     if((nberr >0) || (nbwarn>0)){
       printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
       fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
     }else{
       printf("End of Imach\n");
       fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     /*(void) gettimeofday(&end_time,&tzp);*/
     rend_time = time(NULL);  
     end_time = *localtime(&rend_time);
     /* tml = *localtime(&end_time.tm_sec); */
     strcpy(strtend,asctime(&end_time));
     printf("Local time at start %s\nLocal time at end   %s",strstart, strtend); 
     fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
     printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
   
     printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
     fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
     fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
     /*  printf("Total time was %d uSec.\n", total_usecs);*/
   /*   if(fileappend(fichtm,optionfilehtm)){ */
     fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtm);
     fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtmcov);
     fclose(ficgp);
     fclose(ficlog);
     /*------ End -----------*/
   
   
      printf("Before Current directory %s!\n",pathcd);
      if(chdir(pathcd) != 0)
       printf("Can't move to directory %s!\n",path);
     if(getcwd(pathcd,MAXLINE) > 0)
       printf("Current directory %s!\n",pathcd);
     /*strcat(plotcmd,CHARSEPARATOR);*/
     sprintf(plotcmd,"gnuplot");
   #ifdef _WIN32
     sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
   #endif
     if(!stat(plotcmd,&info)){
       printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
       if(!stat(getenv("GNUPLOTBIN"),&info)){
         printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #ifdef __unix
       strcpy(plotcmd,GNUPLOTPROGRAM);
       if(!stat(plotcmd,&info)){
         printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #endif
     }else
       strcpy(pplotcmd,plotcmd);
     
     sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
     printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
   
     if((outcmd=system(plotcmd)) != 0){
       printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
       printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
       sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
       if((outcmd=system(plotcmd)) != 0)
         printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
     }
     printf(" Successful, please wait...");
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
       scanf("%s",z);
   /*     if (z[0] == 'c') system("./imach"); */
       if (z[0] == 'e') {
   #ifdef __APPLE__
         sprintf(pplotcmd, "open %s", optionfilehtm);
   #elif __linux
         sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
   #else
         sprintf(pplotcmd, "%s", optionfilehtm);
   #endif
         printf("Starting browser with: %s",pplotcmd);fflush(stdout);
         system(pplotcmd);
       }
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     end:
     while (z[0] != 'q') {
       printf("\nType  q for exiting: ");
       scanf("%s",z);
     }
   }

Removed from v.1.50  
changed lines
  Added in v.1.163


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