Diff for /imach/src/imach.c between versions 1.49 and 1.163

version 1.49, 2002/06/20 14:03:39 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.
 #else  
 #define DIRSEPARATOR '/'    Revision 1.145  2014/06/10 21:23:15  brouard
 #endif    Summary: Debugging with valgrind
     Author: Nicolas Brouard
 char version[80]="Imach version 0.8h, May 2002, INED-EUROREVES ";  
 int erreur; /* Error number */    Lot of changes in order to output the results with some covariates
 int nvar;    After the Edimburgh REVES conference 2014, it seems mandatory to
 int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;    improve the code.
 int npar=NPARMAX;    No more memory valgrind error but a lot has to be done in order to
 int nlstate=2; /* Number of live states */    continue the work of splitting the code into subroutines.
 int ndeath=1; /* Number of dead states */    Also, decodemodel has been improved. Tricode is still not
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    optimal. nbcode should be improved. Documentation has been added in
 int popbased=0;    the source code.
   
 int *wav; /* Number of waves for this individuual 0 is possible */    Revision 1.143  2014/01/26 09:45:38  brouard
 int maxwav; /* Maxim number of waves */    Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
 int jmin, jmax; /* min, max spacing between 2 waves */  
 int mle, weightopt;    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */  
 double jmean; /* Mean space between 2 waves */    Revision 1.142  2014/01/26 03:57:36  brouard
 double **oldm, **newm, **savm; /* Working pointers to matrices */    Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
 FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;  
 FILE *fichtm; /* Html File */    Revision 1.141  2014/01/26 02:42:01  brouard
 FILE *ficreseij;    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
 char filerese[FILENAMELENGTH];  
 FILE  *ficresvij;    Revision 1.140  2011/09/02 10:37:54  brouard
 char fileresv[FILENAMELENGTH];    Summary: times.h is ok with mingw32 now.
 FILE  *ficresvpl;  
 char fileresvpl[FILENAMELENGTH];    Revision 1.139  2010/06/14 07:50:17  brouard
 char title[MAXLINE];    After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
 char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];    I remember having already fixed agemin agemax which are pointers now but not cvs saved.
 char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];  
     Revision 1.138  2010/04/30 18:19:40  brouard
 char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];    *** empty log message ***
   
 char filerest[FILENAMELENGTH];    Revision 1.137  2010/04/29 18:11:38  brouard
 char fileregp[FILENAMELENGTH];    (Module): Checking covariates for more complex models
 char popfile[FILENAMELENGTH];    than V1+V2. A lot of change to be done. Unstable.
   
 char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];    Revision 1.136  2010/04/26 20:30:53  brouard
     (Module): merging some libgsl code. Fixing computation
 #define NR_END 1    of likelione (using inter/intrapolation if mle = 0) in order to
 #define FREE_ARG char*    get same likelihood as if mle=1.
 #define FTOL 1.0e-10    Some cleaning of code and comments added.
   
 #define NRANSI    Revision 1.135  2009/10/29 15:33:14  brouard
 #define ITMAX 200    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
   
 #define TOL 2.0e-4    Revision 1.134  2009/10/29 13:18:53  brouard
     (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
 #define CGOLD 0.3819660  
 #define ZEPS 1.0e-10    Revision 1.133  2009/07/06 10:21:25  brouard
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    just nforces
   
 #define GOLD 1.618034    Revision 1.132  2009/07/06 08:22:05  brouard
 #define GLIMIT 100.0    Many tings
 #define TINY 1.0e-20  
     Revision 1.131  2009/06/20 16:22:47  brouard
 static double maxarg1,maxarg2;    Some dimensions resccaled
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    Revision 1.130  2009/05/26 06:44:34  brouard
      (Module): Max Covariate is now set to 20 instead of 8. A
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    lot of cleaning with variables initialized to 0. Trying to make
 #define rint(a) floor(a+0.5)    V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
   
 static double sqrarg;    Revision 1.129  2007/08/31 13:49:27  lievre
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    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 SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  
     Revision 1.128  2006/06/30 13:02:05  brouard
 int imx;    (Module): Clarifications on computing e.j
 int stepm;  
 /* Stepm, step in month: minimum step interpolation*/    Revision 1.127  2006/04/28 18:11:50  brouard
     (Module): Yes the sum of survivors was wrong since
 int estepm;    imach-114 because nhstepm was no more computed in the age
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/    loop. Now we define nhstepma in the age loop.
     (Module): In order to speed up (in case of numerous covariates) we
 int m,nb;    compute health expectancies (without variances) in a first step
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    and then all the health expectancies with variances or standard
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    deviation (needs data from the Hessian matrices) which slows the
 double **pmmij, ***probs, ***mobaverage;    computation.
 double dateintmean=0;    In the future we should be able to stop the program is only health
     expectancies and graph are needed without standard deviations.
 double *weight;  
 int **s; /* Status */    Revision 1.126  2006/04/28 17:23:28  brouard
 double *agedc, **covar, idx;    (Module): Yes the sum of survivors was wrong since
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    imach-114 because nhstepm was no more computed in the age
     loop. Now we define nhstepma in the age loop.
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    Version 0.98h
 double ftolhess; /* Tolerance for computing hessian */  
     Revision 1.125  2006/04/04 15:20:31  lievre
 /**************** split *************************/    Errors in calculation of health expectancies. Age was not initialized.
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    Forecasting file added.
 {  
    char *s;                             /* pointer */    Revision 1.124  2006/03/22 17:13:53  lievre
    int  l1, l2;                         /* length counters */    Parameters are printed with %lf instead of %f (more numbers after the comma).
     The log-likelihood is printed in the log file
    l1 = strlen( path );                 /* length of path */  
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    Revision 1.123  2006/03/20 10:52:43  brouard
    s = strrchr( path,  DIRSEPARATOR );          /* find last / */    * imach.c (Module): <title> changed, corresponds to .htm file
    if ( s == NULL ) {                   /* no directory, so use current */    name. <head> headers where missing.
 #if     defined(__bsd__)                /* get current working directory */  
       extern char       *getwd( );    * imach.c (Module): Weights can have a decimal point as for
     English (a comma might work with a correct LC_NUMERIC environment,
       if ( getwd( dirc ) == NULL ) {    otherwise the weight is truncated).
 #else    Modification of warning when the covariates values are not 0 or
       extern char       *getcwd( );    1.
     Version 0.98g
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  
 #endif    Revision 1.122  2006/03/20 09:45:41  brouard
          return( GLOCK_ERROR_GETCWD );    (Module): Weights can have a decimal point as for
       }    English (a comma might work with a correct LC_NUMERIC environment,
       strcpy( name, path );             /* we've got it */    otherwise the weight is truncated).
    } else {                             /* strip direcotry from path */    Modification of warning when the covariates values are not 0 or
       s++;                              /* after this, the filename */    1.
       l2 = strlen( s );                 /* length of filename */    Version 0.98g
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  
       strcpy( name, s );                /* save file name */    Revision 1.121  2006/03/16 17:45:01  lievre
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    * imach.c (Module): Comments concerning covariates added
       dirc[l1-l2] = 0;                  /* add zero */  
    }    * imach.c (Module): refinements in the computation of lli if
    l1 = strlen( dirc );                 /* length of directory */    status=-2 in order to have more reliable computation if stepm is
 #ifdef windows    not 1 month. Version 0.98f
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  
 #else    Revision 1.120  2006/03/16 15:10:38  lievre
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }    (Module): refinements in the computation of lli if
 #endif    status=-2 in order to have more reliable computation if stepm is
    s = strrchr( name, '.' );            /* find last / */    not 1 month. Version 0.98f
    s++;  
    strcpy(ext,s);                       /* save extension */    Revision 1.119  2006/03/15 17:42:26  brouard
    l1= strlen( name);    (Module): Bug if status = -2, the loglikelihood was
    l2= strlen( s)+1;    computed as likelihood omitting the logarithm. Version O.98e
    strncpy( finame, name, l1-l2);  
    finame[l1-l2]= 0;    Revision 1.118  2006/03/14 18:20:07  brouard
    return( 0 );                         /* we're done */    (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 1.117  2006/03/14 17:16:22  brouard
 {    (Module): varevsij Comments added explaining the second
   int i;    table of variances if popbased=1 .
   int lg=20;    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
   i=0;    (Module): Function pstamp added
   lg=strlen(t);    (Module): Version 0.98d
   for(i=0; i<= lg; i++) {  
     (s[i] = t[i]);    Revision 1.116  2006/03/06 10:29:27  brouard
     if (t[i]== '\\') s[i]='/';    (Module): Variance-covariance wrong links and
   }    varian-covariance of ej. is needed (Saito).
 }  
     Revision 1.115  2006/02/27 12:17:45  brouard
 int nbocc(char *s, char occ)    (Module): One freematrix added in mlikeli! 0.98c
 {  
   int i,j=0;    Revision 1.114  2006/02/26 12:57:58  brouard
   int lg=20;    (Module): Some improvements in processing parameter
   i=0;    filename with strsep.
   lg=strlen(s);  
   for(i=0; i<= lg; i++) {    Revision 1.113  2006/02/24 14:20:24  brouard
   if  (s[i] == occ ) j++;    (Module): Memory leaks checks with valgrind and:
   }    datafile was not closed, some imatrix were not freed and on matrix
   return j;    allocation too.
 }  
     Revision 1.112  2006/01/30 09:55:26  brouard
 void cutv(char *u,char *v, char*t, char occ)    (Module): Back to gnuplot.exe instead of wgnuplot.exe
 {  
   int i,lg,j,p=0;    Revision 1.111  2006/01/25 20:38:18  brouard
   i=0;    (Module): Lots of cleaning and bugs added (Gompertz)
   for(j=0; j<=strlen(t)-1; j++) {    (Module): Comments can be added in data file. Missing date values
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    can be a simple dot '.'.
   }  
     Revision 1.110  2006/01/25 00:51:50  brouard
   lg=strlen(t);    (Module): Lots of cleaning and bugs added (Gompertz)
   for(j=0; j<p; j++) {  
     (u[j] = t[j]);    Revision 1.109  2006/01/24 19:37:15  brouard
   }    (Module): Comments (lines starting with a #) are allowed in data.
      u[p]='\0';  
     Revision 1.108  2006/01/19 18:05:42  lievre
    for(j=0; j<= lg; j++) {    Gnuplot problem appeared...
     if (j>=(p+1))(v[j-p-1] = t[j]);    To be fixed
   }  
 }    Revision 1.107  2006/01/19 16:20:37  brouard
     Test existence of gnuplot in imach path
 /********************** nrerror ********************/  
     Revision 1.106  2006/01/19 13:24:36  brouard
 void nrerror(char error_text[])    Some cleaning and links added in html output
 {  
   fprintf(stderr,"ERREUR ...\n");    Revision 1.105  2006/01/05 20:23:19  lievre
   fprintf(stderr,"%s\n",error_text);    *** empty log message ***
   exit(1);  
 }    Revision 1.104  2005/09/30 16:11:43  lievre
 /*********************** vector *******************/    (Module): sump fixed, loop imx fixed, and simplifications.
 double *vector(int nl, int nh)    (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
   double *v;    (instead of missing=-1 in earlier versions) and his/her
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    contributions to the likelihood is 1 - Prob of dying from last
   if (!v) nrerror("allocation failure in vector");    health status (= 1-p13= p11+p12 in the easiest case of somebody in
   return v-nl+NR_END;    the healthy state at last known wave). Version is 0.98
 }  
     Revision 1.103  2005/09/30 15:54:49  lievre
 /************************ free vector ******************/    (Module): sump fixed, loop imx fixed, and simplifications.
 void free_vector(double*v, int nl, int nh)  
 {    Revision 1.102  2004/09/15 17:31:30  brouard
   free((FREE_ARG)(v+nl-NR_END));    Add the possibility to read data file including tab characters.
 }  
     Revision 1.101  2004/09/15 10:38:38  brouard
 /************************ivector *******************************/    Fix on curr_time
 int *ivector(long nl,long nh)  
 {    Revision 1.100  2004/07/12 18:29:06  brouard
   int *v;    Add version for Mac OS X. Just define UNIX in Makefile
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  
   if (!v) nrerror("allocation failure in ivector");    Revision 1.99  2004/06/05 08:57:40  brouard
   return v-nl+NR_END;    *** empty log message ***
 }  
     Revision 1.98  2004/05/16 15:05:56  brouard
 /******************free ivector **************************/    New version 0.97 . First attempt to estimate force of mortality
 void free_ivector(int *v, 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 .
   free((FREE_ARG)(v+nl-NR_END));    This is the basic analysis of mortality and should be done before any
 }    other analysis, in order to test if the mortality estimated from the
     cross-longitudinal survey is different from the mortality estimated
 /******************* imatrix *******************************/    from other sources like vital statistic data.
 int **imatrix(long nrl, long nrh, long ncl, long nch)  
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    The same imach parameter file can be used but the option for mle should be -3.
 {  
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    Agnès, who wrote this part of the code, tried to keep most of the
   int **m;    former routines in order to include the new code within the former code.
    
   /* allocate pointers to rows */    The output is very simple: only an estimate of the intercept and of
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    the slope with 95% confident intervals.
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;    Current limitations:
   m -= nrl;    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.
      B) There is no computation of Life Expectancy nor Life Table.
   /* allocate rows and set pointers to them */  
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    Revision 1.97  2004/02/20 13:25:42  lievre
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    Version 0.96d. Population forecasting command line is (temporarily)
   m[nrl] += NR_END;    suppressed.
   m[nrl] -= ncl;  
      Revision 1.96  2003/07/15 15:38:55  brouard
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
      rewritten within the same printf. Workaround: many printfs.
   /* return pointer to array of pointers to rows */  
   return m;    Revision 1.95  2003/07/08 07:54:34  brouard
 }    * imach.c (Repository):
     (Repository): Using imachwizard code to output a more meaningful covariance
 /****************** free_imatrix *************************/    matrix (cov(a12,c31) instead of numbers.
 void free_imatrix(m,nrl,nrh,ncl,nch)  
       int **m;    Revision 1.94  2003/06/27 13:00:02  brouard
       long nch,ncl,nrh,nrl;    Just cleaning
      /* free an int matrix allocated by imatrix() */  
 {    Revision 1.93  2003/06/25 16:33:55  brouard
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    (Module): On windows (cygwin) function asctime_r doesn't
   free((FREE_ARG) (m+nrl-NR_END));    exist so I changed back to asctime which exists.
 }    (Module): Version 0.96b
   
 /******************* matrix *******************************/    Revision 1.92  2003/06/25 16:30:45  brouard
 double **matrix(long nrl, long nrh, long ncl, long nch)    (Module): On windows (cygwin) function asctime_r doesn't
 {    exist so I changed back to asctime which exists.
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  
   double **m;    Revision 1.91  2003/06/25 15:30:29  brouard
     * imach.c (Repository): Duplicated warning errors corrected.
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    (Repository): Elapsed time after each iteration is now output. It
   if (!m) nrerror("allocation failure 1 in matrix()");    helps to forecast when convergence will be reached. Elapsed time
   m += NR_END;    is stamped in powell.  We created a new html file for the graphs
   m -= nrl;    concerning matrix of covariance. It has extension -cov.htm.
   
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    Revision 1.90  2003/06/24 12:34:15  brouard
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    (Module): Some bugs corrected for windows. Also, when
   m[nrl] += NR_END;    mle=-1 a template is output in file "or"mypar.txt with the design
   m[nrl] -= ncl;    of the covariance matrix to be input.
   
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    Revision 1.89  2003/06/24 12:30:52  brouard
   return m;    (Module): Some bugs corrected for windows. Also, when
 }    mle=-1 a template is output in file "or"mypar.txt with the design
     of the covariance matrix to be input.
 /*************************free matrix ************************/  
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    Revision 1.88  2003/06/23 17:54:56  brouard
 {    * imach.c (Repository): Create a sub-directory where all the secondary files are. Only imach, htm, gp and r(imach) are on the main directory. Correct time and other things.
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  
   free((FREE_ARG)(m+nrl-NR_END));    Revision 1.87  2003/06/18 12:26:01  brouard
 }    Version 0.96
   
 /******************* ma3x *******************************/    Revision 1.86  2003/06/17 20:04:08  brouard
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    (Module): Change position of html and gnuplot routines and added
 {    routine fileappend.
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  
   double ***m;    Revision 1.85  2003/06/17 13:12:43  brouard
     * imach.c (Repository): Check when date of death was earlier that
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    current date of interview. It may happen when the death was just
   if (!m) nrerror("allocation failure 1 in matrix()");    prior to the death. In this case, dh was negative and likelihood
   m += NR_END;    was wrong (infinity). We still send an "Error" but patch by
   m -= nrl;    assuming that the date of death was just one stepm after the
     interview.
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    (Repository): Because some people have very long ID (first column)
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    we changed int to long in num[] and we added a new lvector for
   m[nrl] += NR_END;    memory allocation. But we also truncated to 8 characters (left
   m[nrl] -= ncl;    truncation)
     (Repository): No more line truncation errors.
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  
     Revision 1.84  2003/06/13 21:44:43  brouard
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    * imach.c (Repository): Replace "freqsummary" at a correct
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    place. It differs from routine "prevalence" which may be called
   m[nrl][ncl] += NR_END;    many times. Probs is memory consuming and must be used with
   m[nrl][ncl] -= nll;    parcimony.
   for (j=ncl+1; j<=nch; j++)    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
     m[nrl][j]=m[nrl][j-1]+nlay;  
      Revision 1.83  2003/06/10 13:39:11  lievre
   for (i=nrl+1; i<=nrh; i++) {    *** empty log message ***
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  
     for (j=ncl+1; j<=nch; j++)    Revision 1.82  2003/06/05 15:57:20  brouard
       m[i][j]=m[i][j-1]+nlay;    Add log in  imach.c and  fullversion number is now printed.
   }  
   return m;  */
 }  /*
      Interpolated Markov Chain
 /*************************free ma3x ************************/  
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    Short summary of the programme:
 {    
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    This program computes Healthy Life Expectancies from
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
   free((FREE_ARG)(m+nrl-NR_END));    first survey ("cross") where individuals from different ages are
 }    interviewed on their health status or degree of disability (in the
     case of a health survey which is our main interest) -2- at least a
 /***************** f1dim *************************/    second wave of interviews ("longitudinal") which measure each change
 extern int ncom;    (if any) in individual health status.  Health expectancies are
 extern double *pcom,*xicom;    computed from the time spent in each health state according to a
 extern double (*nrfunc)(double []);    model. More health states you consider, more time is necessary to reach the
      Maximum Likelihood of the parameters involved in the model.  The
 double f1dim(double x)    simplest model is the multinomial logistic model where pij is the
 {    probability to be observed in state j at the second wave
   int j;    conditional to be observed in state i at the first wave. Therefore
   double f;    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
   double *xt;    '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
   xt=vector(1,ncom);    where the markup *Covariates have to be included here again* invites
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    you to do it.  More covariates you add, slower the
   f=(*nrfunc)(xt);    convergence.
   free_vector(xt,1,ncom);  
   return f;    The advantage of this computer programme, compared to a simple
 }    multinomial logistic model, is clear when the delay between waves is not
     identical for each individual. Also, if a individual missed an
 /*****************brent *************************/    intermediate interview, the information is lost, but taken into
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    account using an interpolation or extrapolation.  
 {  
   int iter;    hPijx is the probability to be observed in state i at age x+h
   double a,b,d,etemp;    conditional to the observed state i at age x. The delay 'h' can be
   double fu,fv,fw,fx;    split into an exact number (nh*stepm) of unobserved intermediate
   double ftemp;    states. This elementary transition (by month, quarter,
   double p,q,r,tol1,tol2,u,v,w,x,xm;    semester or year) is modelled as a multinomial logistic.  The hPx
   double e=0.0;    matrix is simply the matrix product of nh*stepm elementary matrices
      and the contribution of each individual to the likelihood is simply
   a=(ax < cx ? ax : cx);    hPijx.
   b=(ax > cx ? ax : cx);  
   x=w=v=bx;    Also this programme outputs the covariance matrix of the parameters but also
   fw=fv=fx=(*f)(x);    of the life expectancies. It also computes the period (stable) prevalence. 
   for (iter=1;iter<=ITMAX;iter++) {    
     xm=0.5*(a+b);    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);             Institut national d'études démographiques, Paris.
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    This software have been partly granted by Euro-REVES, a concerted action
     printf(".");fflush(stdout);    from the European Union.
 #ifdef DEBUG    It is copyrighted identically to a GNU software product, ie programme and
     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);    software can be distributed freely for non commercial use. Latest version
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    can be accessed at http://euroreves.ined.fr/imach .
 #endif  
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
       *xmin=x;    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
       return fx;    
     }    **********************************************************************/
     ftemp=fu;  /*
     if (fabs(e) > tol1) {    main
       r=(x-w)*(fx-fv);    read parameterfile
       q=(x-v)*(fx-fw);    read datafile
       p=(x-v)*q-(x-w)*r;    concatwav
       q=2.0*(q-r);    freqsummary
       if (q > 0.0) p = -p;    if (mle >= 1)
       q=fabs(q);      mlikeli
       etemp=e;    print results files
       e=d;    if mle==1 
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))       computes hessian
         d=CGOLD*(e=(x >= xm ? a-x : b-x));    read end of parameter file: agemin, agemax, bage, fage, estepm
       else {        begin-prev-date,...
         d=p/q;    open gnuplot file
         u=x+d;    open html file
         if (u-a < tol2 || b-u < tol2)    period (stable) prevalence      | pl_nom    1-1 2-2 etc by covariate
           d=SIGN(tol1,xm-x);     for age prevalim()             | #****** V1=0  V2=1  V3=1  V4=0 ******
       }                                    | 65 1 0 2 1 3 1 4 0  0.96326 0.03674
     } else {      freexexit2 possible for memory heap.
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  
     }    h Pij x                         | pij_nom  ficrestpij
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));     # Cov Agex agex+h hpijx with i,j= 1-1 1-2     1-3     2-1     2-2     2-3
     fu=(*f)(u);         1  85   85    1.00000             0.00000 0.00000 0.00000 1.00000 0.00000
     if (fu <= fx) {         1  85   86    0.68299             0.22291 0.09410 0.71093 0.00000 0.28907
       if (u >= x) a=x; else b=x;  
       SHFT(v,w,x,u)         1  65   99    0.00364             0.00322 0.99314 0.00350 0.00310 0.99340
         SHFT(fv,fw,fx,fu)         1  65  100    0.00214             0.00204 0.99581 0.00206 0.00196 0.99597
         } else {    variance of p one-step probabilities varprob  | prob_nom   ficresprob #One-step probabilities and stand. devi in ()
           if (u < x) a=u; else b=u;     Standard deviation of one-step probabilities | probcor_nom   ficresprobcor #One-step probabilities and correlation matrix
           if (fu <= fw || w == x) {     Matrix of variance covariance of one-step probabilities |  probcov_nom ficresprobcov #One-step probabilities and covariance matrix
             v=w;  
             w=u;    forecasting if prevfcast==1 prevforecast call prevalence()
             fv=fw;    health expectancies
             fw=fu;    Variance-covariance of DFLE
           } else if (fu <= fv || v == x || v == w) {    prevalence()
             v=u;     movingaverage()
             fv=fu;    varevsij() 
           }    if popbased==1 varevsij(,popbased)
         }    total life expectancies
   }    Variance of period (stable) prevalence
   nrerror("Too many iterations in brent");   end
   *xmin=x;  */
   return fx;  
 }  
   
 /****************** mnbrak ***********************/   
   #include <math.h>
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  #include <stdio.h>
             double (*func)(double))  #include <stdlib.h>
 {  #include <string.h>
   double ulim,u,r,q, dum;  
   double fu;  #ifdef _WIN32
    #include <io.h>
   *fa=(*func)(*ax);  #else
   *fb=(*func)(*bx);  #include <unistd.h>
   if (*fb > *fa) {  #endif
     SHFT(dum,*ax,*bx,dum)  
       SHFT(dum,*fb,*fa,dum)  #include <limits.h>
       }  #include <sys/types.h>
   *cx=(*bx)+GOLD*(*bx-*ax);  #include <sys/stat.h>
   *fc=(*func)(*cx);  #include <errno.h>
   while (*fb > *fc) {  /* extern int errno; */
     r=(*bx-*ax)*(*fb-*fc);  
     q=(*bx-*cx)*(*fb-*fa);  /* #ifdef LINUX */
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  /* #include <time.h> */
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  /* #include "timeval.h" */
     ulim=(*bx)+GLIMIT*(*cx-*bx);  /* #else */
     if ((*bx-u)*(u-*cx) > 0.0) {  /* #include <sys/time.h> */
       fu=(*func)(u);  /* #endif */
     } else if ((*cx-u)*(u-ulim) > 0.0) {  
       fu=(*func)(u);  #include <time.h>
       if (fu < *fc) {  
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  #ifdef GSL
           SHFT(*fb,*fc,fu,(*func)(u))  #include <gsl/gsl_errno.h>
           }  #include <gsl/gsl_multimin.h>
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  #endif
       u=ulim;  
       fu=(*func)(u);  #ifdef NLOPT
     } else {  #include <nlopt.h>
       u=(*cx)+GOLD*(*cx-*bx);  typedef struct {
       fu=(*func)(u);    double (* function)(double [] );
     }  } myfunc_data ;
     SHFT(*ax,*bx,*cx,u)  #endif
       SHFT(*fa,*fb,*fc,fu)  
       }  /* #include <libintl.h> */
 }  /* #define _(String) gettext (String) */
   
 /*************** linmin ************************/  #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
   
 int ncom;  #define GNUPLOTPROGRAM "gnuplot"
 double *pcom,*xicom;  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 double (*nrfunc)(double []);  #define FILENAMELENGTH 132
    
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 {  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   double brent(double ax, double bx, double cx,  
                double (*f)(double), double tol, double *xmin);  #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
   double f1dim(double x);  #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  
               double *fc, double (*func)(double));  #define NINTERVMAX 8
   int j;  #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
   double xx,xmin,bx,ax;  #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
   double fx,fb,fa;  #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
    #define codtabm(h,k)  1 & (h-1) >> (k-1) ;
   ncom=n;  #define MAXN 20000
   pcom=vector(1,n);  #define YEARM 12. /**< Number of months per year */
   xicom=vector(1,n);  #define AGESUP 130
   nrfunc=func;  #define AGEBASE 40
   for (j=1;j<=n;j++) {  #define AGEGOMP 10. /**< Minimal age for Gompertz adjustment */
     pcom[j]=p[j];  #ifdef _WIN32
     xicom[j]=xi[j];  #define DIRSEPARATOR '\\'
   }  #define CHARSEPARATOR "\\"
   ax=0.0;  #define ODIRSEPARATOR '/'
   xx=1.0;  #else
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  #define DIRSEPARATOR '/'
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  #define CHARSEPARATOR "/"
 #ifdef DEBUG  #define ODIRSEPARATOR '\\'
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  #endif
 #endif  
   for (j=1;j<=n;j++) {  /* $Id$ */
     xi[j] *= xmin;  /* $State$ */
     p[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)";
   free_vector(xicom,1,n);  char fullversion[]="$Revision$ $Date$"; 
   free_vector(pcom,1,n);  char strstart[80];
 }  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
   int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
 /*************** powell ************************/  int nvar=0, nforce=0; /* Number of variables, number of forces */
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
             double (*func)(double []))  int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
 {  int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
   void linmin(double p[], double xi[], int n, double *fret,  int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
               double (*func)(double []));  int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
   int i,ibig,j;  int cptcovprodnoage=0; /**< Number of covariate products without age */   
   double del,t,*pt,*ptt,*xit;  int cptcoveff=0; /* Total number of covariates to vary for printing results */
   double fp,fptt;  int cptcov=0; /* Working variable */
   double *xits;  int npar=NPARMAX;
   pt=vector(1,n);  int nlstate=2; /* Number of live states */
   ptt=vector(1,n);  int ndeath=1; /* Number of dead states */
   xit=vector(1,n);  int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   xits=vector(1,n);  int popbased=0;
   *fret=(*func)(p);  
   for (j=1;j<=n;j++) pt[j]=p[j];  int *wav; /* Number of waves for this individuual 0 is possible */
   for (*iter=1;;++(*iter)) {  int maxwav=0; /* Maxim number of waves */
     fp=(*fret);  int jmin=0, jmax=0; /* min, max spacing between 2 waves */
     ibig=0;  int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
     del=0.0;  int gipmx=0, gsw=0; /* Global variables on the number of contributions 
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);                     to the likelihood and the sum of weights (done by funcone)*/
     for (i=1;i<=n;i++)  int mle=1, weightopt=0;
       printf(" %d %.12f",i, p[i]);  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
     printf("\n");  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
     for (i=1;i<=n;i++) {  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
       for (j=1;j<=n;j++) xit[j]=xi[j][i];             * wave mi and wave mi+1 is not an exact multiple of stepm. */
       fptt=(*fret);  int countcallfunc=0;  /* Count the number of calls to func */
 #ifdef DEBUG  double jmean=1; /* Mean space between 2 waves */
       printf("fret=%lf \n",*fret);  double **matprod2(); /* test */
 #endif  double **oldm, **newm, **savm; /* Working pointers to matrices */
       printf("%d",i);fflush(stdout);  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
       linmin(p,xit,n,fret,func);  /*FILE *fic ; */ /* Used in readdata only */
       if (fabs(fptt-(*fret)) > del) {  FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
         del=fabs(fptt-(*fret));  FILE *ficlog, *ficrespow;
         ibig=i;  int globpr=0; /* Global variable for printing or not */
       }  double fretone; /* Only one call to likelihood */
 #ifdef DEBUG  long ipmx=0; /* Number of contributions */
       printf("%d %.12e",i,(*fret));  double sw; /* Sum of weights */
       for (j=1;j<=n;j++) {  char filerespow[FILENAMELENGTH];
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
         printf(" x(%d)=%.12e",j,xit[j]);  FILE *ficresilk;
       }  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
       for(j=1;j<=n;j++)  FILE *ficresprobmorprev;
         printf(" p=%.12e",p[j]);  FILE *fichtm, *fichtmcov; /* Html File */
       printf("\n");  FILE *ficreseij;
 #endif  char filerese[FILENAMELENGTH];
     }  FILE *ficresstdeij;
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  char fileresstde[FILENAMELENGTH];
 #ifdef DEBUG  FILE *ficrescveij;
       int k[2],l;  char filerescve[FILENAMELENGTH];
       k[0]=1;  FILE  *ficresvij;
       k[1]=-1;  char fileresv[FILENAMELENGTH];
       printf("Max: %.12e",(*func)(p));  FILE  *ficresvpl;
       for (j=1;j<=n;j++)  char fileresvpl[FILENAMELENGTH];
         printf(" %.12e",p[j]);  char title[MAXLINE];
       printf("\n");  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
       for(l=0;l<=1;l++) {  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
         for (j=1;j<=n;j++) {  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  char command[FILENAMELENGTH];
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  int  outcmd=0;
         }  
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
       }  
 #endif  char filelog[FILENAMELENGTH]; /* Log file */
   char filerest[FILENAMELENGTH];
   char fileregp[FILENAMELENGTH];
       free_vector(xit,1,n);  char popfile[FILENAMELENGTH];
       free_vector(xits,1,n);  
       free_vector(ptt,1,n);  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
       free_vector(pt,1,n);  
       return;  /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
     }  /* struct timezone tzp; */
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  /* extern int gettimeofday(); */
     for (j=1;j<=n;j++) {  struct tm tml, *gmtime(), *localtime();
       ptt[j]=2.0*p[j]-pt[j];  
       xit[j]=p[j]-pt[j];  extern time_t time();
       pt[j]=p[j];  
     }  struct tm start_time, end_time, curr_time, last_time, forecast_time;
     fptt=(*func)(ptt);  time_t  rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
     if (fptt < fp) {  struct tm tm;
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  
       if (t < 0.0) {  char strcurr[80], strfor[80];
         linmin(p,xit,n,fret,func);  
         for (j=1;j<=n;j++) {  char *endptr;
           xi[j][ibig]=xi[j][n];  long lval;
           xi[j][n]=xit[j];  double dval;
         }  
 #ifdef DEBUG  #define NR_END 1
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  #define FREE_ARG char*
         for(j=1;j<=n;j++)  #define FTOL 1.0e-10
           printf(" %.12e",xit[j]);  
         printf("\n");  #define NRANSI 
 #endif  #define ITMAX 200 
       }  
     }  #define TOL 2.0e-4 
   }  
 }  #define CGOLD 0.3819660 
   #define ZEPS 1.0e-10 
 /**** Prevalence limit ****************/  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
   
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  #define GOLD 1.618034 
 {  #define GLIMIT 100.0 
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit  #define TINY 1.0e-20 
      matrix by transitions matrix until convergence is reached */  
   static double maxarg1,maxarg2;
   int i, ii,j,k;  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
   double min, max, maxmin, maxmax,sumnew=0.;  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
   double **matprod2();    
   double **out, cov[NCOVMAX], **pmij();  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   double **newm;  #define rint(a) floor(a+0.5)
   double agefin, delaymax=50 ; /* Max number of years to converge */  
   static double sqrarg;
   for (ii=1;ii<=nlstate+ndeath;ii++)  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
     for (j=1;j<=nlstate+ndeath;j++){  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);  int agegomp= AGEGOMP;
     }  
   int imx; 
    cov[1]=1.;  int stepm=1;
    /* Stepm, step in month: minimum step interpolation*/
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */  
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){  int estepm;
     newm=savm;  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
     /* Covariates have to be included here again */  
      cov[2]=agefin;  int m,nb;
    long *num;
       for (k=1; k<=cptcovn;k++) {  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
         /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/  double **pmmij, ***probs;
       }  double *ageexmed,*agecens;
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  double dateintmean=0;
       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]]];  double *weight;
   int **s; /* Status */
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/  double *agedc;
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/  double  **covar; /**< covar[j,i], value of jth covariate for individual i,
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/                    * covar=matrix(0,NCOVMAX,1,n); 
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);                    * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
   double  idx; 
     savm=oldm;  int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
     oldm=newm;  int *Ndum; /** Freq of modality (tricode */
     maxmax=0.;  int **codtab; /**< codtab=imatrix(1,100,1,10); */
     for(j=1;j<=nlstate;j++){  int **Tvard, *Tprod, cptcovprod, *Tvaraff;
       min=1.;  double *lsurv, *lpop, *tpop;
       max=0.;  
       for(i=1; i<=nlstate; i++) {  double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
         sumnew=0;  double ftolhess; /**< Tolerance for computing hessian */
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  
         prlim[i][j]= newm[i][j]/(1-sumnew);  /**************** split *************************/
         max=FMAX(max,prlim[i][j]);  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
         min=FMIN(min,prlim[i][j]);  {
       }    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
       maxmin=max-min;       the name of the file (name), its extension only (ext) and its first part of the name (finame)
       maxmax=FMAX(maxmax,maxmin);    */ 
     }    char  *ss;                            /* pointer */
     if(maxmax < ftolpl){    int   l1, l2;                         /* length counters */
       return prlim;  
     }    l1 = strlen(path );                   /* length of path */
   }    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
 }    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
     if ( ss == NULL ) {                   /* no directory, so determine current directory */
 /*************** transition probabilities ***************/      strcpy( name, path );               /* we got the fullname name because no directory */
       /*if(strrchr(path, ODIRSEPARATOR )==NULL)
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
 {      /* get current working directory */
   double s1, s2;      /*    extern  char* getcwd ( char *buf , int len);*/
   /*double t34;*/      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
   int i,j,j1, nc, ii, jj;        return( GLOCK_ERROR_GETCWD );
       }
     for(i=1; i<= nlstate; i++){      /* got dirc from getcwd*/
     for(j=1; j<i;j++){      printf(" DIRC = %s \n",dirc);
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    } else {                              /* strip direcotry from path */
         /*s2 += param[i][j][nc]*cov[nc];*/      ss++;                               /* after this, the filename */
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];      l2 = strlen( ss );                  /* length of filename */
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
       }      strcpy( name, ss );         /* save file name */
       ps[i][j]=s2;      strncpy( dirc, path, l1 - l2 );     /* now the directory */
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/      dirc[l1-l2] = 0;                    /* add zero */
     }      printf(" DIRC2 = %s \n",dirc);
     for(j=i+1; j<=nlstate+ndeath;j++){    }
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    /* We add a separator at the end of dirc if not exists */
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    l1 = strlen( dirc );                  /* length of directory */
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/    if( dirc[l1-1] != DIRSEPARATOR ){
       }      dirc[l1] =  DIRSEPARATOR;
       ps[i][j]=s2;      dirc[l1+1] = 0; 
     }      printf(" DIRC3 = %s \n",dirc);
   }    }
     /*ps[3][2]=1;*/    ss = strrchr( name, '.' );            /* find last / */
     if (ss >0){
   for(i=1; i<= nlstate; i++){      ss++;
      s1=0;      strcpy(ext,ss);                     /* save extension */
     for(j=1; j<i; j++)      l1= strlen( name);
       s1+=exp(ps[i][j]);      l2= strlen(ss)+1;
     for(j=i+1; j<=nlstate+ndeath; j++)      strncpy( finame, name, l1-l2);
       s1+=exp(ps[i][j]);      finame[l1-l2]= 0;
     ps[i][i]=1./(s1+1.);    }
     for(j=1; j<i; j++)  
       ps[i][j]= exp(ps[i][j])*ps[i][i];    return( 0 );                          /* we're done */
     for(j=i+1; j<=nlstate+ndeath; j++)  }
       ps[i][j]= exp(ps[i][j])*ps[i][i];  
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */  
   } /* end i */  /******************************************/
   
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){  void replace_back_to_slash(char *s, char*t)
     for(jj=1; jj<= nlstate+ndeath; jj++){  {
       ps[ii][jj]=0;    int i;
       ps[ii][ii]=1;    int lg=0;
     }    i=0;
   }    lg=strlen(t);
     for(i=0; i<= lg; i++) {
       (s[i] = t[i]);
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){      if (t[i]== '\\') s[i]='/';
     for(jj=1; jj<= nlstate+ndeath; jj++){    }
      printf("%lf ",ps[ii][jj]);  }
    }  
     printf("\n ");  char *trimbb(char *out, char *in)
     }  { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
     printf("\n ");printf("%lf ",cov[2]);*/    char *s;
 /*    s=out;
   for(i=1; i<= npar; i++) printf("%f ",x[i]);    while (*in != '\0'){
   goto end;*/      while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
     return ps;        in++;
 }      }
       *out++ = *in++;
 /**************** Product of 2 matrices ******************/    }
     *out='\0';
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)    return s;
 {  }
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times  
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */  char *cutl(char *blocc, char *alocc, char *in, char occ)
   /* in, b, out are matrice of pointers which should have been initialized  {
      before: only the contents of out is modified. The function returns    /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ' 
      a pointer to pointers identical to out */       and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
   long i, j, k;       gives blocc="abcdef2ghi" and alocc="j".
   for(i=nrl; i<= nrh; i++)       If occ is not found blocc is null and alocc is equal to in. Returns blocc
     for(k=ncolol; k<=ncoloh; k++)    */
       for(j=ncl,out[i][k]=0.; j<=nch; j++)    char *s, *t;
         out[i][k] +=in[i][j]*b[j][k];    t=in;s=in;
     while ((*in != occ) && (*in != '\0')){
   return out;      *alocc++ = *in++;
 }    }
     if( *in == occ){
       *(alocc)='\0';
 /************* Higher Matrix Product ***************/      s=++in;
     }
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )   
 {    if (s == t) {/* occ not found */
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month      *(alocc-(in-s))='\0';
      duration (i.e. until      in=s;
      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    while ( *in != '\0'){
      (typically every 2 years instead of every month which is too big).      *blocc++ = *in++;
      Model is determined by parameters x and covariates have to be    }
      included manually here.  
     *blocc='\0';
      */    return t;
   }
   int i, j, d, h, k;  char *cutv(char *blocc, char *alocc, char *in, char occ)
   double **out, cov[NCOVMAX];  {
   double **newm;    /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ' 
        and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
   /* Hstepm could be zero and should return the unit matrix */       gives blocc="abcdef2ghi" and alocc="j".
   for (i=1;i<=nlstate+ndeath;i++)       If occ is not found blocc is null and alocc is equal to in. Returns alocc
     for (j=1;j<=nlstate+ndeath;j++){    */
       oldm[i][j]=(i==j ? 1.0 : 0.0);    char *s, *t;
       po[i][j][0]=(i==j ? 1.0 : 0.0);    t=in;s=in;
     }    while (*in != '\0'){
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */      while( *in == occ){
   for(h=1; h <=nhstepm; h++){        *blocc++ = *in++;
     for(d=1; d <=hstepm; d++){        s=in;
       newm=savm;      }
       /* Covariates have to be included here again */      *blocc++ = *in++;
       cov[1]=1.;    }
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;    if (s == t) /* occ not found */
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];      *(blocc-(in-s))='\0';
       for (k=1; k<=cptcovage;k++)    else
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];      *(blocc-(in-s)-1)='\0';
       for (k=1; k<=cptcovprod;k++)    in=s;
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    while ( *in != '\0'){
       *alocc++ = *in++;
     }
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/  
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/    *alocc='\0';
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,    return s;
                    pmij(pmmij,cov,ncovmodel,x,nlstate));  }
       savm=oldm;  
       oldm=newm;  int nbocc(char *s, char occ)
     }  {
     for(i=1; i<=nlstate+ndeath; i++)    int i,j=0;
       for(j=1;j<=nlstate+ndeath;j++) {    int lg=20;
         po[i][j][h]=newm[i][j];    i=0;
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);    lg=strlen(s);
          */    for(i=0; i<= lg; i++) {
       }    if  (s[i] == occ ) j++;
   } /* end h */    }
   return po;    return j;
 }  }
   
   /* void cutv(char *u,char *v, char*t, char occ) */
 /*************** log-likelihood *************/  /* { */
 double func( double *x)  /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
 {  /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
   int i, ii, j, k, mi, d, kk;  /*      gives u="abcdef2ghi" and v="j" *\/ */
   double l, ll[NLSTATEMAX], cov[NCOVMAX];  /*   int i,lg,j,p=0; */
   double **out;  /*   i=0; */
   double sw; /* Sum of weights */  /*   lg=strlen(t); */
   double lli; /* Individual log likelihood */  /*   for(j=0; j<=lg-1; j++) { */
   long ipmx;  /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
   /*extern weight */  /*   } */
   /* We are differentiating ll according to initial status */  
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/  /*   for(j=0; j<p; j++) { */
   /*for(i=1;i<imx;i++)  /*     (u[j] = t[j]); */
     printf(" %d\n",s[4][i]);  /*   } */
   */  /*      u[p]='\0'; */
   cov[1]=1.;  
   /*    for(j=0; j<= lg; j++) { */
   for(k=1; k<=nlstate; k++) ll[k]=0.;  /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){  /*   } */
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];  /* } */
     for(mi=1; mi<= wav[i]-1; mi++){  
       for (ii=1;ii<=nlstate+ndeath;ii++)  #ifdef _WIN32
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);  char * strsep(char **pp, const char *delim)
       for(d=0; d<dh[mi][i]; d++){  {
         newm=savm;    char *p, *q;
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;           
         for (kk=1; kk<=cptcovage;kk++) {    if ((p = *pp) == NULL)
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];      return 0;
         }    if ((q = strpbrk (p, delim)) != NULL)
            {
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,      *pp = q + 1;
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));      *q = '\0';
         savm=oldm;    }
         oldm=newm;    else
              *pp = 0;
            return p;
       } /* end mult */  }
        #endif
       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]]);*/  /********************** nrerror ********************/
       ipmx +=1;  
       sw += weight[i];  void nrerror(char error_text[])
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;  {
     } /* end of wave */    fprintf(stderr,"ERREUR ...\n");
   } /* end of individual */    fprintf(stderr,"%s\n",error_text);
     exit(EXIT_FAILURE);
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];  }
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */  /*********************** vector *******************/
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */  double *vector(int nl, int nh)
   return -l;  {
 }    double *v;
     v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
     if (!v) nrerror("allocation failure in vector");
 /*********** Maximum Likelihood Estimation ***************/    return v-nl+NR_END;
   }
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))  
 {  /************************ free vector ******************/
   int i,j, iter;  void free_vector(double*v, int nl, int nh)
   double **xi,*delti;  {
   double fret;    free((FREE_ARG)(v+nl-NR_END));
   xi=matrix(1,npar,1,npar);  }
   for (i=1;i<=npar;i++)  
     for (j=1;j<=npar;j++)  /************************ivector *******************************/
       xi[i][j]=(i==j ? 1.0 : 0.0);  int *ivector(long nl,long nh)
   printf("Powell\n");  {
   powell(p,xi,npar,ftol,&iter,&fret,func);    int *v;
     v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));    if (!v) nrerror("allocation failure in ivector");
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));    return v-nl+NR_END;
   }
 }  
   /******************free ivector **************************/
 /**** Computes Hessian and covariance matrix ***/  void free_ivector(int *v, long nl, long nh)
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))  {
 {    free((FREE_ARG)(v+nl-NR_END));
   double  **a,**y,*x,pd;  }
   double **hess;  
   int i, j,jk;  /************************lvector *******************************/
   int *indx;  long *lvector(long nl,long nh)
   {
   double hessii(double p[], double delta, int theta, double delti[]);    long *v;
   double hessij(double p[], double delti[], int i, int j);    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
   void lubksb(double **a, int npar, int *indx, double b[]) ;    if (!v) nrerror("allocation failure in ivector");
   void ludcmp(double **a, int npar, int *indx, double *d) ;    return v-nl+NR_END;
   }
   hess=matrix(1,npar,1,npar);  
   /******************free lvector **************************/
   printf("\nCalculation of the hessian matrix. Wait...\n");  void free_lvector(long *v, long nl, long nh)
   for (i=1;i<=npar;i++){  {
     printf("%d",i);fflush(stdout);    free((FREE_ARG)(v+nl-NR_END));
     hess[i][i]=hessii(p,ftolhess,i,delti);  }
     /*printf(" %f ",p[i]);*/  
     /*printf(" %lf ",hess[i][i]);*/  /******************* imatrix *******************************/
   }  int **imatrix(long nrl, long nrh, long ncl, long nch) 
         /* allocate a int matrix with subscript range m[nrl..nrh][ncl..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) {    int **m; 
         printf(".%d%d",i,j);fflush(stdout);    
         hess[i][j]=hessij(p,delti,i,j);    /* allocate pointers to rows */ 
         hess[j][i]=hess[i][j];        m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
         /*printf(" %lf ",hess[i][j]);*/    if (!m) nrerror("allocation failure 1 in matrix()"); 
       }    m += NR_END; 
     }    m -= nrl; 
   }    
   printf("\n");    
     /* allocate rows and set pointers to them */ 
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
      if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
   a=matrix(1,npar,1,npar);    m[nrl] += NR_END; 
   y=matrix(1,npar,1,npar);    m[nrl] -= ncl; 
   x=vector(1,npar);    
   indx=ivector(1,npar);    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]=hess[i][j];    /* return pointer to array of pointers to rows */ 
   ludcmp(a,npar,indx,&pd);    return m; 
   } 
   for (j=1;j<=npar;j++) {  
     for (i=1;i<=npar;i++) x[i]=0;  /****************** free_imatrix *************************/
     x[j]=1;  void free_imatrix(m,nrl,nrh,ncl,nch)
     lubksb(a,npar,indx,x);        int **m;
     for (i=1;i<=npar;i++){        long nch,ncl,nrh,nrl; 
       matcov[i][j]=x[i];       /* free an int matrix allocated by imatrix() */ 
     }  { 
   }    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
     free((FREE_ARG) (m+nrl-NR_END)); 
   printf("\n#Hessian matrix#\n");  } 
   for (i=1;i<=npar;i++) {  
     for (j=1;j<=npar;j++) {  /******************* matrix *******************************/
       printf("%.3e ",hess[i][j]);  double **matrix(long nrl, long nrh, long ncl, long nch)
     }  {
     printf("\n");    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
   }    double **m;
   
   /* Recompute Inverse */    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++) a[i][j]=matcov[i][j];    m += NR_END;
   ludcmp(a,npar,indx,&pd);    m -= nrl;
   
   /*  printf("\n#Hessian matrix recomputed#\n");    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   for (j=1;j<=npar;j++) {    m[nrl] += NR_END;
     for (i=1;i<=npar;i++) x[i]=0;    m[nrl] -= ncl;
     x[j]=1;  
     lubksb(a,npar,indx,x);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     for (i=1;i<=npar;i++){    return m;
       y[i][j]=x[i];    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
       printf("%.3e ",y[i][j]);  m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
     }  that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
     printf("\n");     */
   }  }
   */  
   /*************************free matrix ************************/
   free_matrix(a,1,npar,1,npar);  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   free_matrix(y,1,npar,1,npar);  {
   free_vector(x,1,npar);    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   free_ivector(indx,1,npar);    free((FREE_ARG)(m+nrl-NR_END));
   free_matrix(hess,1,npar,1,npar);  }
   
   /******************* ma3x *******************************/
 }  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
   {
 /*************** hessian matrix ****************/    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
 double hessii( double x[], double delta, int theta, double delti[])    double ***m;
 {  
   int i;    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   int l=1, lmax=20;    if (!m) nrerror("allocation failure 1 in matrix()");
   double k1,k2;    m += NR_END;
   double p2[NPARMAX+1];    m -= nrl;
   double res;  
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   double fx;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   int k=0,kmax=10;    m[nrl] += NR_END;
   double l1;    m[nrl] -= ncl;
   
   fx=func(x);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   for (i=1;i<=npar;i++) p2[i]=x[i];  
   for(l=0 ; l <=lmax; l++){    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
     l1=pow(10,l);    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
     delts=delt;    m[nrl][ncl] += NR_END;
     for(k=1 ; k <kmax; k=k+1){    m[nrl][ncl] -= nll;
       delt = delta*(l1*k);    for (j=ncl+1; j<=nch; j++) 
       p2[theta]=x[theta] +delt;      m[nrl][j]=m[nrl][j-1]+nlay;
       k1=func(p2)-fx;    
       p2[theta]=x[theta]-delt;    for (i=nrl+1; i<=nrh; i++) {
       k2=func(p2)-fx;      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
       /*res= (k1-2.0*fx+k2)/delt/delt; */      for (j=ncl+1; j<=nch; j++) 
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */        m[i][j]=m[i][j-1]+nlay;
          }
 #ifdef DEBUG    return m; 
       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);    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
 #endif             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */    */
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){  }
         k=kmax;  
       }  /*************************free ma3x ************************/
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
         k=kmax; l=lmax*10.;  {
       }    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){    free((FREE_ARG)(m[nrl]+ncl-NR_END));
         delts=delt;    free((FREE_ARG)(m+nrl-NR_END));
       }  }
     }  
   }  /*************** function subdirf ***********/
   delti[theta]=delts;  char *subdirf(char fileres[])
   return res;  {
      /* Caution optionfilefiname is hidden */
 }    strcpy(tmpout,optionfilefiname);
     strcat(tmpout,"/"); /* Add to the right */
 double hessij( double x[], double delti[], int thetai,int thetaj)    strcat(tmpout,fileres);
 {    return tmpout;
   int i;  }
   int l=1, l1, lmax=20;  
   double k1,k2,k3,k4,res,fx;  /*************** function subdirf2 ***********/
   double p2[NPARMAX+1];  char *subdirf2(char fileres[], char *preop)
   int k;  {
     
   fx=func(x);    /* Caution optionfilefiname is hidden */
   for (k=1; k<=2; k++) {    strcpy(tmpout,optionfilefiname);
     for (i=1;i<=npar;i++) p2[i]=x[i];    strcat(tmpout,"/");
     p2[thetai]=x[thetai]+delti[thetai]/k;    strcat(tmpout,preop);
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    strcat(tmpout,fileres);
     k1=func(p2)-fx;    return tmpout;
    }
     p2[thetai]=x[thetai]+delti[thetai]/k;  
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;  /*************** function subdirf3 ***********/
     k2=func(p2)-fx;  char *subdirf3(char fileres[], char *preop, char *preop2)
    {
     p2[thetai]=x[thetai]-delti[thetai]/k;    
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    /* Caution optionfilefiname is hidden */
     k3=func(p2)-fx;    strcpy(tmpout,optionfilefiname);
      strcat(tmpout,"/");
     p2[thetai]=x[thetai]-delti[thetai]/k;    strcat(tmpout,preop);
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    strcat(tmpout,preop2);
     k4=func(p2)-fx;    strcat(tmpout,fileres);
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */    return tmpout;
 #ifdef DEBUG  }
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);  
 #endif  char *asc_diff_time(long time_sec, char ascdiff[])
   }  {
   return res;    long sec_left, days, hours, minutes;
 }    days = (time_sec) / (60*60*24);
     sec_left = (time_sec) % (60*60*24);
 /************** Inverse of matrix **************/    hours = (sec_left) / (60*60) ;
 void ludcmp(double **a, int n, int *indx, double *d)    sec_left = (sec_left) %(60*60);
 {    minutes = (sec_left) /60;
   int i,imax,j,k;    sec_left = (sec_left) % (60);
   double big,dum,sum,temp;    sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);  
   double *vv;    return ascdiff;
    }
   vv=vector(1,n);  
   *d=1.0;  /***************** f1dim *************************/
   for (i=1;i<=n;i++) {  extern int ncom; 
     big=0.0;  extern double *pcom,*xicom;
     for (j=1;j<=n;j++)  extern double (*nrfunc)(double []); 
       if ((temp=fabs(a[i][j])) > big) big=temp;   
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");  double f1dim(double x) 
     vv[i]=1.0/big;  { 
   }    int j; 
   for (j=1;j<=n;j++) {    double f;
     for (i=1;i<j;i++) {    double *xt; 
       sum=a[i][j];   
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];    xt=vector(1,ncom); 
       a[i][j]=sum;    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
     }    f=(*nrfunc)(xt); 
     big=0.0;    free_vector(xt,1,ncom); 
     for (i=j;i<=n;i++) {    return f; 
       sum=a[i][j];  } 
       for (k=1;k<j;k++)  
         sum -= a[i][k]*a[k][j];  /*****************brent *************************/
       a[i][j]=sum;  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
       if ( (dum=vv[i]*fabs(sum)) >= big) {  { 
         big=dum;    int iter; 
         imax=i;    double a,b,d,etemp;
       }    double fu=0,fv,fw,fx;
     }    double ftemp;
     if (j != imax) {    double p,q,r,tol1,tol2,u,v,w,x,xm; 
       for (k=1;k<=n;k++) {    double e=0.0; 
         dum=a[imax][k];   
         a[imax][k]=a[j][k];    a=(ax < cx ? ax : cx); 
         a[j][k]=dum;    b=(ax > cx ? ax : cx); 
       }    x=w=v=bx; 
       *d = -(*d);    fw=fv=fx=(*f)(x); 
       vv[imax]=vv[j];    for (iter=1;iter<=ITMAX;iter++) { 
     }      xm=0.5*(a+b); 
     indx[j]=imax;      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
     if (a[j][j] == 0.0) a[j][j]=TINY;      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
     if (j != n) {      printf(".");fflush(stdout);
       dum=1.0/(a[j][j]);      fprintf(ficlog,".");fflush(ficlog);
       for (i=j+1;i<=n;i++) a[i][j] *= dum;  #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);
   }      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);
   free_vector(vv,1,n);  /* Doesn't work */      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
 ;  #endif
 }      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
         *xmin=x; 
 void lubksb(double **a, int n, int *indx, double b[])        return fx; 
 {      } 
   int i,ii=0,ip,j;      ftemp=fu;
   double sum;      if (fabs(e) > tol1) { 
          r=(x-w)*(fx-fv); 
   for (i=1;i<=n;i++) {        q=(x-v)*(fx-fw); 
     ip=indx[i];        p=(x-v)*q-(x-w)*r; 
     sum=b[ip];        q=2.0*(q-r); 
     b[ip]=b[i];        if (q > 0.0) p = -p; 
     if (ii)        q=fabs(q); 
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];        etemp=e; 
     else if (sum) ii=i;        e=d; 
     b[i]=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)); 
   for (i=n;i>=1;i--) {        else { 
     sum=b[i];          d=p/q; 
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];          u=x+d; 
     b[i]=sum/a[i][i];          if (u-a < tol2 || b-u < tol2) 
   }            d=SIGN(tol1,xm-x); 
 }        } 
       } else { 
 /************ Frequencies ********************/        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
 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)      } 
 {  /* Some frequencies */      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
        fu=(*f)(u); 
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;      if (fu <= fx) { 
   double ***freq; /* Frequencies */        if (u >= x) a=x; else b=x; 
   double *pp;        SHFT(v,w,x,u) 
   double pos, k2, dateintsum=0,k2cpt=0;          SHFT(fv,fw,fx,fu) 
   FILE *ficresp;          } else { 
   char fileresp[FILENAMELENGTH];            if (u < x) a=u; else b=u; 
              if (fu <= fw || w == x) { 
   pp=vector(1,nlstate);              v=w; 
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);              w=u; 
   strcpy(fileresp,"p");              fv=fw; 
   strcat(fileresp,fileres);              fw=fu; 
   if((ficresp=fopen(fileresp,"w"))==NULL) {            } else if (fu <= fv || v == x || v == w) { 
     printf("Problem with prevalence resultfile: %s\n", fileresp);              v=u; 
     exit(0);              fv=fu; 
   }            } 
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);          } 
   j1=0;    } 
      nrerror("Too many iterations in brent"); 
   j=cptcoveff;    *xmin=x; 
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    return fx; 
    } 
   for(k1=1; k1<=j;k1++){  
     for(i1=1; i1<=ncodemax[k1];i1++){  /****************** mnbrak ***********************/
       j1++;  
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
         scanf("%d", i);*/              double (*func)(double)) 
       for (i=-1; i<=nlstate+ndeath; i++)    { 
         for (jk=-1; jk<=nlstate+ndeath; jk++)      double ulim,u,r,q, dum;
           for(m=agemin; m <= agemax+3; m++)    double fu; 
             freq[i][jk][m]=0;   
          *fa=(*func)(*ax); 
       dateintsum=0;    *fb=(*func)(*bx); 
       k2cpt=0;    if (*fb > *fa) { 
       for (i=1; i<=imx; i++) {      SHFT(dum,*ax,*bx,dum) 
         bool=1;        SHFT(dum,*fb,*fa,dum) 
         if  (cptcovn>0) {        } 
           for (z1=1; z1<=cptcoveff; z1++)    *cx=(*bx)+GOLD*(*bx-*ax); 
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])    *fc=(*func)(*cx); 
               bool=0;    while (*fb > *fc) { /* Declining fa, fb, fc */
         }      r=(*bx-*ax)*(*fb-*fc); 
         if (bool==1) {      q=(*bx-*cx)*(*fb-*fa); 
           for(m=firstpass; m<=lastpass; m++){      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
             k2=anint[m][i]+(mint[m][i]/12.);        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscisse of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
             if ((k2>=dateprev1) && (k2<=dateprev2)) {      ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscisse where function can be evaluated */
               if(agev[m][i]==0) agev[m][i]=agemax+1;      if ((*bx-u)*(u-*cx) > 0.0) { /* if u between b and c */
               if(agev[m][i]==1) agev[m][i]=agemax+2;        fu=(*func)(u); 
               if (m<lastpass) {  #ifdef DEBUG
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];        /* f(x)=A(x-u)**2+f(u) */
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];        double A, fparabu; 
               }        A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
                      fparabu= *fa - A*(*ax-u)*(*ax-u);
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {        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);
                 dateintsum=dateintsum+k2;        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);
                 k2cpt++;  #endif 
               }      } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
             }        fu=(*func)(u); 
           }        if (fu < *fc) { 
         }          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
       }            SHFT(*fb,*fc,fu,(*func)(u)) 
                    } 
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
         u=ulim; 
       if  (cptcovn>0) {        fu=(*func)(u); 
         fprintf(ficresp, "\n#********** Variable ");      } else { 
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);        u=(*cx)+GOLD*(*cx-*bx); 
         fprintf(ficresp, "**********\n#");        fu=(*func)(u); 
       }      } 
       for(i=1; i<=nlstate;i++)      SHFT(*ax,*bx,*cx,u) 
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);        SHFT(*fa,*fb,*fc,fu) 
       fprintf(ficresp, "\n");        } 
        } 
       for(i=(int)agemin; i <= (int)agemax+3; i++){  
         if(i==(int)agemax+3)  /*************** linmin ************************/
           printf("Total");  /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
         else  resets p to where the function func(p) takes on a minimum along the direction xi from p ,
           printf("Age %d", i);  and replaces xi by the actual vector displacement that p was moved. Also returns as fret
         for(jk=1; jk <=nlstate ; jk++){  the value of func at the returned location p . This is actually all accomplished by calling the
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)  routines mnbrak and brent .*/
             pp[jk] += freq[jk][m][i];  int ncom; 
         }  double *pcom,*xicom;
         for(jk=1; jk <=nlstate ; jk++){  double (*nrfunc)(double []); 
           for(m=-1, pos=0; m <=0 ; m++)   
             pos += freq[jk][m][i];  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
           if(pp[jk]>=1.e-10)  { 
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);    double brent(double ax, double bx, double cx, 
           else                 double (*f)(double), double tol, double *xmin); 
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);    double f1dim(double x); 
         }    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
                 double *fc, double (*func)(double)); 
         for(jk=1; jk <=nlstate ; jk++){    int j; 
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)    double xx,xmin,bx,ax; 
             pp[jk] += freq[jk][m][i];    double fx,fb,fa;
         }   
     ncom=n; 
         for(jk=1,pos=0; jk <=nlstate ; jk++)    pcom=vector(1,n); 
           pos += pp[jk];    xicom=vector(1,n); 
         for(jk=1; jk <=nlstate ; jk++){    nrfunc=func; 
           if(pos>=1.e-5)    for (j=1;j<=n;j++) { 
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);      pcom[j]=p[j]; 
           else      xicom[j]=xi[j]; 
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);    } 
           if( i <= (int) agemax){    ax=0.0; 
             if(pos>=1.e-5){    xx=1.0; 
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Find a bracket a,x,b in direction n=xi ie xicom */
               probs[i][jk][j1]= pp[jk]/pos;    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Find a minimum P+lambda n in that direction (lambdamin), with TOL between abscisses */
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/  #ifdef DEBUG
             }    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
             else    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);  #endif
           }    for (j=1;j<=n;j++) { 
         }      xi[j] *= xmin; 
              p[j] += xi[j]; 
         for(jk=-1; jk <=nlstate+ndeath; jk++)    } 
           for(m=-1; m <=nlstate+ndeath; m++)    free_vector(xicom,1,n); 
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);    free_vector(pcom,1,n); 
         if(i <= (int) agemax)  } 
           fprintf(ficresp,"\n");  
         printf("\n");  
       }  /*************** powell ************************/
     }  /*
   }  Minimization of a function func of n variables. Input consists of an initial starting point
   dateintmean=dateintsum/k2cpt;  p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
    rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
   fclose(ficresp);  such that failure to decrease by more than this amount on one iteration signals doneness. On
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);  output, p is set to the best point found, xi is the then-current direction set, fret is the returned
   free_vector(pp,1,nlstate);  function value at p , and iter is the number of iterations taken. The routine linmin is used.
     */
   /* End of Freq */  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
 }              double (*func)(double [])) 
   { 
 /************ Prevalence ********************/    void linmin(double p[], double xi[], int n, double *fret, 
 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)                double (*func)(double [])); 
 {  /* Some frequencies */    int i,ibig,j; 
      double del,t,*pt,*ptt,*xit;
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;    double fp,fptt;
   double ***freq; /* Frequencies */    double *xits;
   double *pp;    int niterf, itmp;
   double pos, k2;  
     pt=vector(1,n); 
   pp=vector(1,nlstate);    ptt=vector(1,n); 
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    xit=vector(1,n); 
      xits=vector(1,n); 
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    *fret=(*func)(p); 
   j1=0;    for (j=1;j<=n;j++) pt[j]=p[j]; 
        rcurr_time = time(NULL);  
   j=cptcoveff;    for (*iter=1;;++(*iter)) { 
   if (cptcovn<1) {j=1;ncodemax[1]=1;}      fp=(*fret); 
        ibig=0; 
   for(k1=1; k1<=j;k1++){      del=0.0; 
     for(i1=1; i1<=ncodemax[k1];i1++){      rlast_time=rcurr_time;
       j1++;      /* (void) gettimeofday(&curr_time,&tzp); */
            rcurr_time = time(NULL);  
       for (i=-1; i<=nlstate+ndeath; i++)        curr_time = *localtime(&rcurr_time);
         for (jk=-1; jk<=nlstate+ndeath; jk++)        printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
           for(m=agemin; m <= agemax+3; m++)      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
             freq[i][jk][m]=0;  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
           for (i=1;i<=n;i++) {
       for (i=1; i<=imx; i++) {        printf(" %d %.12f",i, p[i]);
         bool=1;        fprintf(ficlog," %d %.12lf",i, p[i]);
         if  (cptcovn>0) {        fprintf(ficrespow," %.12lf", p[i]);
           for (z1=1; z1<=cptcoveff; z1++)      }
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])      printf("\n");
               bool=0;      fprintf(ficlog,"\n");
         }      fprintf(ficrespow,"\n");fflush(ficrespow);
         if (bool==1) {      if(*iter <=3){
           for(m=firstpass; m<=lastpass; m++){        tml = *localtime(&rcurr_time);
             k2=anint[m][i]+(mint[m][i]/12.);        strcpy(strcurr,asctime(&tml));
             if ((k2>=dateprev1) && (k2<=dateprev2)) {        rforecast_time=rcurr_time; 
               if(agev[m][i]==0) agev[m][i]=agemax+1;        itmp = strlen(strcurr);
               if(agev[m][i]==1) agev[m][i]=agemax+2;        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
               if (m<lastpass) {          strcurr[itmp-1]='\0';
                 if (calagedate>0)        printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
                   freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
                 else        for(niterf=10;niterf<=30;niterf+=10){
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];          rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
                 freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];          forecast_time = *localtime(&rforecast_time);
               }          strcpy(strfor,asctime(&forecast_time));
             }          itmp = strlen(strfor);
           }          if(strfor[itmp-1]=='\n')
         }          strfor[itmp-1]='\0';
       }          printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
       for(i=(int)agemin; i <= (int)agemax+3; 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);
         for(jk=1; jk <=nlstate ; jk++){        }
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)      }
             pp[jk] += freq[jk][m][i];      for (i=1;i<=n;i++) { 
         }        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
         for(jk=1; jk <=nlstate ; jk++){        fptt=(*fret); 
           for(m=-1, pos=0; m <=0 ; m++)  #ifdef DEBUG
             pos += freq[jk][m][i];        printf("fret=%lf \n",*fret);
         }        fprintf(ficlog,"fret=%lf \n",*fret);
          #endif
         for(jk=1; jk <=nlstate ; jk++){        printf("%d",i);fflush(stdout);
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)        fprintf(ficlog,"%d",i);fflush(ficlog);
             pp[jk] += freq[jk][m][i];        linmin(p,xit,n,fret,func); 
         }        if (fabs(fptt-(*fret)) > del) { 
                  del=fabs(fptt-(*fret)); 
         for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];          ibig=i; 
                } 
         for(jk=1; jk <=nlstate ; jk++){      #ifdef DEBUG
           if( i <= (int) agemax){        printf("%d %.12e",i,(*fret));
             if(pos>=1.e-5){        fprintf(ficlog,"%d %.12e",i,(*fret));
               probs[i][jk][j1]= pp[jk]/pos;        for (j=1;j<=n;j++) {
             }          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
           }          printf(" x(%d)=%.12e",j,xit[j]);
         }          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
                }
       }        for(j=1;j<=n;j++) {
     }          printf(" p(%d)=%.12e",j,p[j]);
   }          fprintf(ficlog," p(%d)=%.12e",j,p[j]);
         }
          printf("\n");
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);        fprintf(ficlog,"\n");
   free_vector(pp,1,nlstate);  #endif
        } /* end i */
 }  /* End of Freq */      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
   #ifdef DEBUG
 /************* Waves Concatenation ***************/        int k[2],l;
         k[0]=1;
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)        k[1]=-1;
 {        printf("Max: %.12e",(*func)(p));
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.        fprintf(ficlog,"Max: %.12e",(*func)(p));
      Death is a valid wave (if date is known).        for (j=1;j<=n;j++) {
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i          printf(" %.12e",p[j]);
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]          fprintf(ficlog," %.12e",p[j]);
      and mw[mi+1][i]. dh depends on stepm.        }
      */        printf("\n");
         fprintf(ficlog,"\n");
   int i, mi, m;        for(l=0;l<=1;l++) {
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;          for (j=1;j<=n;j++) {
      double sum=0., jmean=0.;*/            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
             printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   int j, k=0,jk, ju, jl;            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   double sum=0.;          }
   jmin=1e+5;          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   jmax=-1;          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   jmean=0.;        }
   for(i=1; i<=imx; i++){  #endif
     mi=0;  
     m=firstpass;  
     while(s[m][i] <= nlstate){        free_vector(xit,1,n); 
       if(s[m][i]>=1)        free_vector(xits,1,n); 
         mw[++mi][i]=m;        free_vector(ptt,1,n); 
       if(m >=lastpass)        free_vector(pt,1,n); 
         break;        return; 
       else      } 
         m++;      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
     }/* end while */      for (j=1;j<=n;j++) { /* Computes an extrapolated point */
     if (s[m][i] > nlstate){        ptt[j]=2.0*p[j]-pt[j]; 
       mi++;     /* Death is another wave */        xit[j]=p[j]-pt[j]; 
       /* if(mi==0)  never been interviewed correctly before death */        pt[j]=p[j]; 
          /* Only death is a correct wave */      } 
       mw[mi][i]=m;      fptt=(*func)(ptt); 
     }      if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
         /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
     wav[i]=mi;        /* From x1 (P0) distance of x2 is at h and x3 is 2h */
     if(mi==0)        /* Let f"(x2) be the 2nd derivative equal everywhere.  */
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);        /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
   }        /* will reach at f3 = fm + h^2/2 f"m  ; f" = (f1 -2f2 +f3 ) / h**2 */
         /* f1-f3 = delta(2h) = 2 h**2 f'' = 2(f1- 2f2 +f3) */
   for(i=1; i<=imx; i++){        /* Thus we compare delta(2h) with observed f1-f3 */
     for(mi=1; mi<wav[i];mi++){        /* or best gain on one ancient line 'del' with total  */
       if (stepm <=0)        /* gain f1-f2 = f1 - f2 - 'del' with del  */
         dh[mi][i]=1;        /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
       else{  
         if (s[mw[mi+1][i]][i] > nlstate) {        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del);
           if (agedc[i] < 2*AGESUP) {        t= t- del*SQR(fp-fptt);
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);        printf("t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t);
           if(j==0) j=1;  /* Survives at least one month after exam */        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);
           k=k+1;  #ifdef DEBUG
           if (j >= jmax) jmax=j;        printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
           if (j <= jmin) jmin=j;               (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
           sum=sum+j;        fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
           /*if (j<0) printf("j=%d num=%d \n",j,i); */               (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);
         else{  #endif
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));        if (t < 0.0) { /* Then we use it for last direction */
           k=k+1;          linmin(p,xit,n,fret,func); /* computes mean on the extrapolated direction.*/
           if (j >= jmax) jmax=j;          for (j=1;j<=n;j++) { 
           else if (j <= jmin)jmin=j;            xi[j][ibig]=xi[j][n]; /* Replace the direction with biggest decrease by n */
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */            xi[j][n]=xit[j];      /* and nth direction by the extrapolated */
           sum=sum+j;          }
         }          printf("Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
         jk= j/stepm;          fprintf(ficlog,"Gaining to use average direction of P0 P%d instead of biggest increase direction :\n",n,ibig);
         jl= j -jk*stepm;  
         ju= j -(jk+1)*stepm;  #ifdef DEBUG
         if(jl <= -ju)          for(j=1;j<=n;j++){
           dh[mi][i]=jk;            printf(" %.12e",xit[j]);
         else            fprintf(ficlog," %.12e",xit[j]);
           dh[mi][i]=jk+1;          }
         if(dh[mi][i]==0)          printf("\n");
           dh[mi][i]=1; /* At least one step */          fprintf(ficlog,"\n");
       }  #endif
     }        } /* end of t negative */
   }      } /* end if (fptt < fp)  */
   jmean=sum/k;    } 
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);  } 
  }  
 /*********** Tricode ****************************/  /**** Prevalence limit (stable or period prevalence)  ****************/
 void tricode(int *Tvar, int **nbcode, int imx)  
 {  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
   int Ndum[20],ij=1, k, j, i;  {
   int cptcode=0;    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
   cptcoveff=0;       matrix by transitions matrix until convergence is reached */
    
   for (k=0; k<19; k++) Ndum[k]=0;    int i, ii,j,k;
   for (k=1; k<=7; k++) ncodemax[k]=0;    double min, max, maxmin, maxmax,sumnew=0.;
     /* double **matprod2(); */ /* test */
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {    double **out, cov[NCOVMAX+1], **pmij();
     for (i=1; i<=imx; i++) {    double **newm;
       ij=(int)(covar[Tvar[j]][i]);    double agefin, delaymax=50 ; /* Max number of years to converge */
       Ndum[ij]++;  
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/    for (ii=1;ii<=nlstate+ndeath;ii++)
       if (ij > cptcode) cptcode=ij;      for (j=1;j<=nlstate+ndeath;j++){
     }        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       }
     for (i=0; i<=cptcode; i++) {  
       if(Ndum[i]!=0) ncodemax[j]++;     cov[1]=1.;
     }   
     ij=1;   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
       newm=savm;
     for (i=1; i<=ncodemax[j]; i++) {      /* Covariates have to be included here again */
       for (k=0; k<=19; k++) {      cov[2]=agefin;
         if (Ndum[k] != 0) {      
           nbcode[Tvar[j]][ij]=k;      for (k=1; k<=cptcovn;k++) {
                  cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
           ij++;        /*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]]);*/
         }      }
         if (ij > ncodemax[j]) break;      /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
       }        /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
     }      /*   cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */
   }        
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
  for (k=0; k<19; k++) Ndum[k]=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]);*/
  for (i=1; i<=ncovmodel-2; i++) {      /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
       ij=Tvar[i];      /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
       Ndum[ij]++;      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
     }      
       savm=oldm;
  ij=1;      oldm=newm;
  for (i=1; i<=10; i++) {      maxmax=0.;
    if((Ndum[i]!=0) && (i<=ncovcol)){      for(j=1;j<=nlstate;j++){
      Tvaraff[ij]=i;        min=1.;
      ij++;        max=0.;
    }        for(i=1; i<=nlstate; i++) {
  }          sumnew=0;
            for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
     cptcoveff=ij-1;          prlim[i][j]= newm[i][j]/(1-sumnew);
 }          /*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]);
 /*********** Health Expectancies ****************/          min=FMIN(min,prlim[i][j]);
         }
 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 )        maxmin=max-min;
         maxmax=FMAX(maxmax,maxmin);
 {      }
   /* Health expectancies */      if(maxmax < ftolpl){
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;        return prlim;
   double age, agelim, hf;      }
   double ***p3mat,***varhe;    }
   double **dnewm,**doldm;  }
   double *xp;  
   double **gp, **gm;  /*************** transition probabilities ***************/ 
   double ***gradg, ***trgradg;  
   int theta;  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
   {
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);    /* According to parameters values stored in x and the covariate's values stored in cov,
   xp=vector(1,npar);       computes the probability to be observed in state j being in state i by appying the
   dnewm=matrix(1,nlstate*2,1,npar);       model to the ncovmodel covariates (including constant and age).
   doldm=matrix(1,nlstate*2,1,nlstate*2);       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
   fprintf(ficreseij,"# Health expectancies\n");       ncth covariate in the global vector x is given by the formula:
   fprintf(ficreseij,"# Age");       j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
   for(i=1; i<=nlstate;i++)       j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
     for(j=1; j<=nlstate;j++)       Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
       fprintf(ficreseij," %1d-%1d (SE)",i,j);       sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
   fprintf(ficreseij,"\n");       Outputs ps[i][j] the probability to be observed in j being in j according to
        the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
   if(estepm < stepm){    */
     printf ("Problem %d lower than %d\n",estepm, stepm);    double s1, lnpijopii;
   }    /*double t34;*/
   else  hstepm=estepm;      int i,j,j1, nc, ii, jj;
   /* We compute the life expectancy from trapezoids spaced every estepm months  
    * This is mainly to measure the difference between two models: for example      for(i=1; i<= nlstate; i++){
    * if stepm=24 months pijx are given only every 2 years and by summing them        for(j=1; j<i;j++){
    * we are calculating an estimate of the Life Expectancy assuming a linear          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
    * progression inbetween and thus overestimating or underestimating according            /*lnpijopii += param[i][j][nc]*cov[nc];*/
    * to the curvature of the survival function. If, for the same date, we            lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
    * estimate the model with stepm=1 month, we can keep estepm to 24 months  /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
    * to compare the new estimate of Life expectancy with the same linear          }
    * hypothesis. A more precise result, taking into account a more precise          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
    * curvature will be obtained if estepm is as small as stepm. */  /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
         }
   /* For example we decided to compute the life expectancy with the smallest unit */        for(j=i+1; j<=nlstate+ndeath;j++){
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
      nhstepm is the number of hstepm from age to agelim            /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
      nstepm is the number of stepm from age to agelin.            lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
      Look at hpijx to understand the reason of that which relies in memory size  /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
      and note for a fixed period like estepm months */          }
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
      survival function given by stepm (the optimization length). Unfortunately it        }
      means that if the survival funtion is printed only each two years of age and if      }
      you sum them up and add 1 year (area under the trapezoids) you won't get the same      
      results. So we changed our mind and took the option of the best precision.      for(i=1; i<= nlstate; i++){
   */        s1=0;
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */        for(j=1; j<i; j++){
           s1+=exp(ps[i][j]); /* In fact sums pij/pii */
   agelim=AGESUP;          /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        }
     /* nhstepm age range expressed in number of stepm */        for(j=i+1; j<=nlstate+ndeath; j++){
     nstepm=(int) rint((agelim-age)*YEARM/stepm);          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */          /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
     /* if (stepm >= YEARM) hstepm=1;*/        }
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */        /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        ps[i][i]=1./(s1+1.);
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);        /* Computing other pijs */
     gp=matrix(0,nhstepm,1,nlstate*2);        for(j=1; j<i; j++)
     gm=matrix(0,nhstepm,1,nlstate*2);          ps[i][j]= exp(ps[i][j])*ps[i][i];
         for(j=i+1; j<=nlstate+ndeath; j++)
     /* Computed by stepm unit matrices, product of hstepm matrices, stored          ps[i][j]= exp(ps[i][j])*ps[i][i];
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);        } /* end i */
        
       for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */        for(jj=1; jj<= nlstate+ndeath; jj++){
           ps[ii][jj]=0;
     /* Computing Variances of health expectancies */          ps[ii][ii]=1;
         }
      for(theta=1; theta <=npar; theta++){      }
       for(i=1; i<=npar; i++){      
         xp[i] = x[i] + (i==theta ?delti[theta]:0);      
       }      /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
        /*  printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
       cptj=0;      /*   } */
       for(j=1; j<= nlstate; j++){      /*   printf("\n "); */
         for(i=1; i<=nlstate; i++){      /* } */
           cptj=cptj+1;      /* printf("\n ");printf("%lf ",cov[2]);*/
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){      /*
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;        for(i=1; i<= npar; i++) printf("%f ",x[i]);
           }        goto end;*/
         }      return ps;
       }  }
        
        /**************** Product of 2 matrices ******************/
       for(i=1; i<=npar; i++)  
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);    {
          /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
       cptj=0;       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
       for(j=1; j<= nlstate; j++){    /* in, b, out are matrice of pointers which should have been initialized 
         for(i=1;i<=nlstate;i++){       before: only the contents of out is modified. The function returns
           cptj=cptj+1;       a pointer to pointers identical to out */
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){    int i, j, k;
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;    for(i=nrl; i<= nrh; i++)
           }      for(k=ncolol; k<=ncoloh; k++){
         }        out[i][k]=0.;
       }        for(j=ncl; j<=nch; j++)
       for(j=1; j<= nlstate*2; j++)          out[i][k] +=in[i][j]*b[j][k];
         for(h=0; h<=nhstepm-1; h++){      }
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    return out;
         }  }
      }  
      
 /* End theta */  /************* Higher Matrix Product ***************/
   
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
   {
      for(h=0; h<=nhstepm-1; h++)    /* Computes the transition matrix starting at age 'age' over 
       for(j=1; j<=nlstate*2;j++)       'nhstepm*hstepm*stepm' months (i.e. until
         for(theta=1; theta <=npar; theta++)       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
           trgradg[h][j][theta]=gradg[h][theta][j];       nhstepm*hstepm matrices. 
             Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
        (typically every 2 years instead of every month which is too big 
      for(i=1;i<=nlstate*2;i++)       for the memory).
       for(j=1;j<=nlstate*2;j++)       Model is determined by parameters x and covariates have to be 
         varhe[i][j][(int)age] =0.;       included manually here. 
   
      printf("%d|",(int)age);fflush(stdout);       */
      for(h=0;h<=nhstepm-1;h++){  
       for(k=0;k<=nhstepm-1;k++){    int i, j, d, h, k;
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);    double **out, cov[NCOVMAX+1];
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);    double **newm;
         for(i=1;i<=nlstate*2;i++)  
           for(j=1;j<=nlstate*2;j++)    /* Hstepm could be zero and should return the unit matrix */
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;    for (i=1;i<=nlstate+ndeath;i++)
       }      for (j=1;j<=nlstate+ndeath;j++){
     }        oldm[i][j]=(i==j ? 1.0 : 0.0);
     /* Computing expectancies */        po[i][j][0]=(i==j ? 1.0 : 0.0);
     for(i=1; i<=nlstate;i++)      }
       for(j=1; j<=nlstate;j++)    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){    for(h=1; h <=nhstepm; h++){
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;      for(d=1; d <=hstepm; d++){
                  newm=savm;
 /* 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]);*/        /* Covariates have to be included here again */
         cov[1]=1.;
         }        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
         for (k=1; k<=cptcovn;k++) 
     fprintf(ficreseij,"%3.0f",age );          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
     cptj=0;        for (k=1; k<=cptcovage;k++)
     for(i=1; i<=nlstate;i++)          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
       for(j=1; j<=nlstate;j++){        for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
         cptj++;          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );  
       }  
     fprintf(ficreseij,"\n");        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
            /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
     free_matrix(gm,0,nhstepm,1,nlstate*2);        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
     free_matrix(gp,0,nhstepm,1,nlstate*2);                     pmij(pmmij,cov,ncovmodel,x,nlstate));
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);        savm=oldm;
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);        oldm=newm;
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      }
   }      for(i=1; i<=nlstate+ndeath; i++)
   printf("\n");        for(j=1;j<=nlstate+ndeath;j++) {
           po[i][j][h]=newm[i][j];
   free_vector(xp,1,npar);          /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
   free_matrix(dnewm,1,nlstate*2,1,npar);        }
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);      /*printf("h=%d ",h);*/
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);    } /* end h */
 }  /*     printf("\n H=%d \n",h); */
     return po;
 /************ Variance ******************/  }
 void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm)  
 {  #ifdef NLOPT
   /* Variance of health expectancies */    double  myfunc(unsigned n, const double *p1, double *grad, void *pd){
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    double fret;
   double **newm;    double *xt;
   double **dnewm,**doldm;    int j;
   int i, j, nhstepm, hstepm, h, nstepm ;    myfunc_data *d2 = (myfunc_data *) pd;
   int k, cptcode;  /* xt = (p1-1); */
   double *xp;    xt=vector(1,n); 
   double **gp, **gm;    for (j=1;j<=n;j++)   xt[j]=p1[j-1]; /* xt[1]=p1[0] */
   double ***gradg, ***trgradg;  
   double ***p3mat;    fret=(d2->function)(xt); /*  p xt[1]@8 is fine */
   double age,agelim, hf;    /* fret=(*func)(xt); /\*  p xt[1]@8 is fine *\/ */
   int theta;    printf("Function = %.12lf ",fret);
     for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]); 
   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("\n");
   fprintf(ficresvij,"# Age");   free_vector(xt,1,n);
   for(i=1; i<=nlstate;i++)    return fret;
     for(j=1; j<=nlstate;j++)  }
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);  #endif
   fprintf(ficresvij,"\n");  
   /*************** log-likelihood *************/
   xp=vector(1,npar);  double func( double *x)
   dnewm=matrix(1,nlstate,1,npar);  {
   doldm=matrix(1,nlstate,1,nlstate);    int i, ii, j, k, mi, d, kk;
      double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
   if(estepm < stepm){    double **out;
     printf ("Problem %d lower than %d\n",estepm, stepm);    double sw; /* Sum of weights */
   }    double lli; /* Individual log likelihood */
   else  hstepm=estepm;      int s1, s2;
   /* For example we decided to compute the life expectancy with the smallest unit */    double bbh, survp;
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.    long ipmx;
      nhstepm is the number of hstepm from age to agelim    /*extern weight */
      nstepm is the number of stepm from age to agelin.    /* We are differentiating ll according to initial status */
      Look at hpijx to understand the reason of that which relies in memory size    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
      and note for a fixed period like k years */    /*for(i=1;i<imx;i++) 
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the      printf(" %d\n",s[4][i]);
      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    ++countcallfunc;
      results. So we changed our mind and took the option of the best precision.  
   */    cov[1]=1.;
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */  
   agelim = AGESUP;    for(k=1; k<=nlstate; k++) ll[k]=0.;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */  
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    if(mle==1){
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        /* Computes the values of the ncovmodel covariates of the model
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);           depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
     gp=matrix(0,nhstepm,1,nlstate);           Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
     gm=matrix(0,nhstepm,1,nlstate);           to be observed in j being in i according to the model.
          */
     for(theta=1; theta <=npar; theta++){        for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
       for(i=1; i<=npar; i++){ /* Computes gradient */          cov[2+k]=covar[Tvar[k]][i];
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        }
       }        /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);             is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);           has been calculated etc */
         for(mi=1; mi<= wav[i]-1; mi++){
       if (popbased==1) {          for (ii=1;ii<=nlstate+ndeath;ii++)
         for(i=1; i<=nlstate;i++)            for (j=1;j<=nlstate+ndeath;j++){
           prlim[i][i]=probs[(int)age][i][ij];              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
              }
       for(j=1; j<= nlstate; j++){          for(d=0; d<dh[mi][i]; d++){
         for(h=0; h<=nhstepm; h++){            newm=savm;
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];            for (kk=1; kk<=cptcovage;kk++) {
         }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
       }            }
                out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       for(i=1; i<=npar; i++) /* Computes gradient */                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         xp[i] = x[i] - (i==theta ?delti[theta]:0);            savm=oldm;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);              oldm=newm;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          } /* end mult */
          
       if (popbased==1) {          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
         for(i=1; i<=nlstate;i++)          /* But now since version 0.9 we anticipate for bias at large stepm.
           prlim[i][i]=probs[(int)age][i][ij];           * 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
       for(j=1; j<= nlstate; j++){           * we keep into memory the bias bh[mi][i] and also the previous matrix product
         for(h=0; h<=nhstepm; h++){           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)           * probability in order to take into account the bias as a fraction of the way
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
         }           * -stepm/2 to stepm/2 .
       }           * For stepm=1 the results are the same as for previous versions of Imach.
            * For stepm > 1 the results are less biased than in previous versions. 
       for(j=1; j<= nlstate; j++)           */
         for(h=0; h<=nhstepm; h++){          s1=s[mw[mi][i]][i];
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];          s2=s[mw[mi+1][i]][i];
         }          bbh=(double)bh[mi][i]/(double)stepm; 
     } /* End theta */          /* bias bh is positive if real duration
            * is higher than the multiple of stepm and negative otherwise.
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);           */
           /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
     for(h=0; h<=nhstepm; h++)          if( s2 > nlstate){ 
       for(j=1; j<=nlstate;j++)            /* i.e. if s2 is a death state and if the date of death is known 
         for(theta=1; theta <=npar; theta++)               then the contribution to the likelihood is the probability to 
           trgradg[h][j][theta]=gradg[h][theta][j];               die between last step unit time and current  step unit time, 
                which is also equal to probability to die before dh 
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */               minus probability to die before dh-stepm . 
     for(i=1;i<=nlstate;i++)               In version up to 0.92 likelihood was computed
       for(j=1;j<=nlstate;j++)          as if date of death was unknown. Death was treated as any other
         vareij[i][j][(int)age] =0.;          health state: the date of the interview describes the actual state
           and not the date of a change in health state. The former idea was
     for(h=0;h<=nhstepm;h++){          to consider that at each interview the state was recorded
       for(k=0;k<=nhstepm;k++){          (healthy, disable or death) and IMaCh was corrected; but when we
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);          introduced the exact date of death then we should have modified
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);          the contribution of an exact death to the likelihood. This new
         for(i=1;i<=nlstate;i++)          contribution is smaller and very dependent of the step unit
           for(j=1;j<=nlstate;j++)          stepm. It is no more the probability to die between last interview
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;          and month of death but the probability to survive from last
       }          interview up to one month before death multiplied by the
     }          probability to die within a month. Thanks to Chris
           Jackson for correcting this bug.  Former versions increased
     fprintf(ficresvij,"%.0f ",age );          mortality artificially. The bad side is that we add another loop
     for(i=1; i<=nlstate;i++)          which slows down the processing. The difference can be up to 10%
       for(j=1; j<=nlstate;j++){          lower mortality.
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);            */
       }            lli=log(out[s1][s2] - savm[s1][s2]);
     fprintf(ficresvij,"\n");  
     free_matrix(gp,0,nhstepm,1,nlstate);  
     free_matrix(gm,0,nhstepm,1,nlstate);          } else if  (s2==-2) {
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);            for (j=1,survp=0. ; j<=nlstate; j++) 
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            /*survp += out[s1][j]; */
   } /* End age */            lli= log(survp);
            }
   free_vector(xp,1,npar);          
   free_matrix(doldm,1,nlstate,1,npar);          else if  (s2==-4) { 
   free_matrix(dnewm,1,nlstate,1,nlstate);            for (j=3,survp=0. ; j<=nlstate; j++)  
               survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
 }            lli= log(survp); 
           } 
 /************ Variance of prevlim ******************/  
 void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)          else if  (s2==-5) { 
 {            for (j=1,survp=0. ; j<=2; j++)  
   /* Variance of prevalence limit */              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/            lli= log(survp); 
   double **newm;          } 
   double **dnewm,**doldm;          
   int i, j, nhstepm, hstepm;          else{
   int k, cptcode;            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   double *xp;            /*  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 */
   double *gp, *gm;          } 
   double **gradg, **trgradg;          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   double age,agelim;          /*if(lli ==000.0)*/
   int theta;          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
              ipmx +=1;
   fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n");          sw += weight[i];
   fprintf(ficresvpl,"# Age");          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   for(i=1; i<=nlstate;i++)        } /* end of wave */
       fprintf(ficresvpl," %1d-%1d",i,i);      } /* end of individual */
   fprintf(ficresvpl,"\n");    }  else if(mle==2){
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   xp=vector(1,npar);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   dnewm=matrix(1,nlstate,1,npar);        for(mi=1; mi<= wav[i]-1; mi++){
   doldm=matrix(1,nlstate,1,nlstate);          for (ii=1;ii<=nlstate+ndeath;ii++)
              for (j=1;j<=nlstate+ndeath;j++){
   hstepm=1*YEARM; /* Every year of age */              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   agelim = AGESUP;            }
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          for(d=0; d<=dh[mi][i]; d++){
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */            newm=savm;
     if (stepm >= YEARM) hstepm=1;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */            for (kk=1; kk<=cptcovage;kk++) {
     gradg=matrix(1,npar,1,nlstate);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     gp=vector(1,nlstate);            }
     gm=vector(1,nlstate);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     for(theta=1; theta <=npar; theta++){            savm=oldm;
       for(i=1; i<=npar; i++){ /* Computes gradient */            oldm=newm;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          } /* end mult */
       }        
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          s1=s[mw[mi][i]][i];
       for(i=1;i<=nlstate;i++)          s2=s[mw[mi+1][i]][i];
         gp[i] = prlim[i][i];          bbh=(double)bh[mi][i]/(double)stepm; 
              lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
       for(i=1; i<=npar; i++) /* Computes gradient */          ipmx +=1;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          sw += weight[i];
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       for(i=1;i<=nlstate;i++)        } /* end of wave */
         gm[i] = prlim[i][i];      } /* end of individual */
     }  else if(mle==3){  /* exponential inter-extrapolation */
       for(i=1;i<=nlstate;i++)      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     } /* End theta */        for(mi=1; mi<= wav[i]-1; mi++){
           for (ii=1;ii<=nlstate+ndeath;ii++)
     trgradg =matrix(1,nlstate,1,npar);            for (j=1;j<=nlstate+ndeath;j++){
               oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     for(j=1; j<=nlstate;j++)              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       for(theta=1; theta <=npar; theta++)            }
         trgradg[j][theta]=gradg[theta][j];          for(d=0; d<dh[mi][i]; d++){
             newm=savm;
     for(i=1;i<=nlstate;i++)            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       varpl[i][(int)age] =0.;            for (kk=1; kk<=cptcovage;kk++) {
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);            }
     for(i=1;i<=nlstate;i++)            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
     fprintf(ficresvpl,"%.0f ",age );            oldm=newm;
     for(i=1; i<=nlstate;i++)          } /* end mult */
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));        
     fprintf(ficresvpl,"\n");          s1=s[mw[mi][i]][i];
     free_vector(gp,1,nlstate);          s2=s[mw[mi+1][i]][i];
     free_vector(gm,1,nlstate);          bbh=(double)bh[mi][i]/(double)stepm; 
     free_matrix(gradg,1,npar,1,nlstate);          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 */
     free_matrix(trgradg,1,nlstate,1,npar);          ipmx +=1;
   } /* End age */          sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   free_vector(xp,1,npar);        } /* end of wave */
   free_matrix(doldm,1,nlstate,1,npar);      } /* end of individual */
   free_matrix(dnewm,1,nlstate,1,nlstate);    }else if (mle==4){  /* ml=4 no inter-extrapolation */
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
 }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for(mi=1; mi<= wav[i]-1; mi++){
 /************ Variance of one-step probabilities  ******************/          for (ii=1;ii<=nlstate+ndeath;ii++)
 void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)            for (j=1;j<=nlstate+ndeath;j++){
 {              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   int i, j=0,  i1, k1, l1, t, tj;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   int k2, l2, j1,  z1;            }
   int k=0,l, cptcode;          for(d=0; d<dh[mi][i]; d++){
   int first=1;            newm=savm;
   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   double **dnewm,**doldm;            for (kk=1; kk<=cptcovage;kk++) {
   double *xp;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   double *gp, *gm;            }
   double **gradg, **trgradg;          
   double **mu;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   double age,agelim, cov[NCOVMAX];                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */            savm=oldm;
   int theta;            oldm=newm;
   char fileresprob[FILENAMELENGTH];          } /* end mult */
   char fileresprobcov[FILENAMELENGTH];        
   char fileresprobcor[FILENAMELENGTH];          s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
   double ***varpij;          if( s2 > nlstate){ 
             lli=log(out[s1][s2] - savm[s1][s2]);
   strcpy(fileresprob,"prob");          }else{
   strcat(fileresprob,fileres);            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {          }
     printf("Problem with resultfile: %s\n", fileresprob);          ipmx +=1;
   }          sw += weight[i];
   strcpy(fileresprobcov,"probcov");          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   strcat(fileresprobcov,fileres);  /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {        } /* end of wave */
     printf("Problem with resultfile: %s\n", fileresprobcov);      } /* end of individual */
   }    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
   strcpy(fileresprobcor,"probcor");      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   strcat(fileresprobcor,fileres);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {        for(mi=1; mi<= wav[i]-1; mi++){
     printf("Problem with resultfile: %s\n", fileresprobcor);          for (ii=1;ii<=nlstate+ndeath;ii++)
   }            for (j=1;j<=nlstate+ndeath;j++){
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);            }
            for(d=0; d<dh[mi][i]; d++){
   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");            newm=savm;
   fprintf(ficresprob,"# Age");            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");            for (kk=1; kk<=cptcovage;kk++) {
   fprintf(ficresprobcov,"# Age");              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");            }
   fprintf(ficresprobcov,"# Age");          
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   for(i=1; i<=nlstate;i++)            savm=oldm;
     for(j=1; j<=(nlstate+ndeath);j++){            oldm=newm;
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);          } /* end mult */
       fprintf(ficresprobcov," p%1d-%1d ",i,j);        
       fprintf(ficresprobcor," p%1d-%1d ",i,j);          s1=s[mw[mi][i]][i];
     }            s2=s[mw[mi+1][i]][i];
   fprintf(ficresprob,"\n");          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   fprintf(ficresprobcov,"\n");          ipmx +=1;
   fprintf(ficresprobcor,"\n");          sw += weight[i];
   xp=vector(1,npar);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);          /*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]);*/
   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));        } /* end of wave */
   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);      } /* end of individual */
   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);    } /* End of if */
   first=1;    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     exit(0);    return -l;
   }  }
   else{  
     fprintf(ficgp,"\n# Routine varprob");  /*************** log-likelihood *************/
   }  double funcone( double *x)
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {  {
     printf("Problem with html file: %s\n", optionfilehtm);    /* Same as likeli but slower because of a lot of printf and if */
     exit(0);    int i, ii, j, k, mi, d, kk;
   }    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
   else{    double **out;
     fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");    double lli; /* Individual log likelihood */
     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");    double llt;
     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");    int s1, s2;
     double bbh, survp;
   }    /*extern weight */
     /* We are differentiating ll according to initial status */
      /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   cov[1]=1;    /*for(i=1;i<imx;i++) 
   tj=cptcoveff;      printf(" %d\n",s[4][i]);
   if (cptcovn<1) {tj=1;ncodemax[1]=1;}    */
   j1=0;    cov[1]=1.;
   for(t=1; t<=tj;t++){  
     for(i1=1; i1<=ncodemax[t];i1++){    for(k=1; k<=nlstate; k++) ll[k]=0.;
       j1++;  
          for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       if  (cptcovn>0) {      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         fprintf(ficresprob, "\n#********** Variable ");      for(mi=1; mi<= wav[i]-1; mi++){
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);        for (ii=1;ii<=nlstate+ndeath;ii++)
         fprintf(ficresprob, "**********\n#");          for (j=1;j<=nlstate+ndeath;j++){
         fprintf(ficresprobcov, "\n#********** Variable ");            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);            savm[ii][j]=(ii==j ? 1.0 : 0.0);
         fprintf(ficresprobcov, "**********\n#");          }
                for(d=0; d<dh[mi][i]; d++){
         fprintf(ficgp, "\n#********** Variable ");          newm=savm;
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         fprintf(ficgp, "**********\n#");          for (kk=1; kk<=cptcovage;kk++) {
                    cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
                  }
         fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");          /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
                  /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
         fprintf(ficresprobcor, "\n#********** Variable ");              /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          savm=oldm;
         fprintf(ficgp, "**********\n#");              oldm=newm;
       }        } /* end mult */
              
       for (age=bage; age<=fage; age ++){        s1=s[mw[mi][i]][i];
         cov[2]=age;        s2=s[mw[mi+1][i]][i];
         for (k=1; k<=cptcovn;k++) {        bbh=(double)bh[mi][i]/(double)stepm; 
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];        /* bias is positive if real duration
         }         * is higher than the multiple of stepm and negative otherwise.
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];         */
         for (k=1; k<=cptcovprod;k++)        if( s2 > nlstate && (mle <5) ){  /* Jackson */
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];          lli=log(out[s1][s2] - savm[s1][s2]);
                } else if  (s2==-2) {
         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));          for (j=1,survp=0. ; j<=nlstate; j++) 
         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
         gp=vector(1,(nlstate)*(nlstate+ndeath));          lli= log(survp);
         gm=vector(1,(nlstate)*(nlstate+ndeath));        }else if (mle==1){
              lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
         for(theta=1; theta <=npar; theta++){        } else if(mle==2){
           for(i=1; i<=npar; i++)          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
             xp[i] = x[i] + (i==theta ?delti[theta]:0);        } 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 */
           pmij(pmmij,cov,ncovmodel,xp,nlstate);        } else if (mle==4){  /* mle=4 no inter-extrapolation */
                    lli=log(out[s1][s2]); /* Original formula */
           k=0;        } else{  /* mle=0 back to 1 */
           for(i=1; i<= (nlstate); i++){          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
             for(j=1; j<=(nlstate+ndeath);j++){          /*lli=log(out[s1][s2]); */ /* Original formula */
               k=k+1;        } /* End of if */
               gp[k]=pmmij[i][j];        ipmx +=1;
             }        sw += weight[i];
           }        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
                  /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
           for(i=1; i<=npar; i++)        if(globpr){
             xp[i] = x[i] - (i==theta ?delti[theta]:0);          fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
       %11.6f %11.6f %11.6f ", \
           pmij(pmmij,cov,ncovmodel,xp,nlstate);                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
           k=0;                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
           for(i=1; i<=(nlstate); i++){          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
             for(j=1; j<=(nlstate+ndeath);j++){            llt +=ll[k]*gipmx/gsw;
               k=k+1;            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
               gm[k]=pmmij[i][j];          }
             }          fprintf(ficresilk," %10.6f\n", -llt);
           }        }
            } /* end of wave */
           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)    } /* end of individual */
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];      for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
         }    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)    if(globpr==0){ /* First time we count the contributions and weights */
           for(theta=1; theta <=npar; theta++)      gipmx=ipmx;
             trgradg[j][theta]=gradg[theta][j];      gsw=sw;
            }
         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);    return -l;
         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);  }
          
         pmij(pmmij,cov,ncovmodel,x,nlstate);  
          /*************** function likelione ***********/
         k=0;  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
         for(i=1; i<=(nlstate); i++){  {
           for(j=1; j<=(nlstate+ndeath);j++){    /* This routine should help understanding what is done with 
             k=k+1;       the selection of individuals/waves and
             mu[k][(int) age]=pmmij[i][j];       to check the exact contribution to the likelihood.
           }       Plotting could be done.
         }     */
         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)    int k;
           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)  
             varpij[i][j][(int)age] = doldm[i][j];    if(*globpri !=0){ /* Just counts and sums, no printings */
       strcpy(fileresilk,"ilk"); 
         /*printf("\n%d ",(int)age);      strcat(fileresilk,fileres);
      for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));        printf("Problem with resultfile: %s\n", fileresilk);
      }*/        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
       }
         fprintf(ficresprob,"\n%d ",(int)age);      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(ficresprobcov,"\n%d ",(int)age);      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
         fprintf(ficresprobcor,"\n%d ",(int)age);      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
       for(k=1; k<=nlstate; k++) 
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){    }
           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);  
           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);    *fretone=(*funcone)(p);
         }    if(*globpri !=0){
         i=0;      fclose(ficresilk);
         for (k=1; k<=(nlstate);k++){      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
           for (l=1; l<=(nlstate+ndeath);l++){      fflush(fichtm); 
             i=i++;    } 
             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);    return;
             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);  }
             for (j=1; j<=i;j++){  
               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);  
               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));  /*********** Maximum Likelihood Estimation ***************/
             }  
           }  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
         }/* end of loop for state */  {
       } /* end of loop for age */    int i,j, iter;
         /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/    double **xi;
       for (k1=1; k1<=(nlstate);k1++){    double fret;
         for (l1=1; l1<=(nlstate+ndeath);l1++){    double fretone; /* Only one call to likelihood */
           if(l1==k1) continue;    /*  char filerespow[FILENAMELENGTH];*/
           i=(k1-1)*(nlstate+ndeath)+l1;  
           for (k2=1; k2<=(nlstate);k2++){  #ifdef NLOPT
             for (l2=1; l2<=(nlstate+ndeath);l2++){    int creturn;
               if(l2==k2) continue;    nlopt_opt opt;
               j=(k2-1)*(nlstate+ndeath)+l2;    /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
               if(j<=i) continue;    double *lb;
               for (age=bage; age<=fage; age ++){    double minf; /* the minimum objective value, upon return */
                 if ((int)age %5==0){    double * p1; /* Shifted parameters from 0 instead of 1 */
                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;    myfunc_data dinst, *d = &dinst;
                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;  #endif
                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;  
                   mu1=mu[i][(int) age]/stepm*YEARM ;  
                   mu2=mu[j][(int) age]/stepm*YEARM;    xi=matrix(1,npar,1,npar);
                   /* Computing eigen value of matrix of covariance */    for (i=1;i<=npar;i++)
                   lc1=(v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12));      for (j=1;j<=npar;j++)
                   lc2=(v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12));        xi[i][j]=(i==j ? 1.0 : 0.0);
                   printf("Var %.4e %.4e cov %.4e Eigen %.3e %.3e\n",v1,v2,cv12,lc1,lc2);    printf("Powell\n");  fprintf(ficlog,"Powell\n");
                   /* Eigen vectors */    strcpy(filerespow,"pow"); 
                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));    strcat(filerespow,fileres);
                   v21=sqrt(1.-v11*v11);    if((ficrespow=fopen(filerespow,"w"))==NULL) {
                   v12=-v21;      printf("Problem with resultfile: %s\n", filerespow);
                   v22=v11;      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
                   /*printf(fignu*/    }
                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */    fprintf(ficrespow,"# Powell\n# iter -2*LL");
                   /* mu2+ v21*lc1*cost + v21*lc2*sin(t) */    for (i=1;i<=nlstate;i++)
                   if(first==1){      for(j=1;j<=nlstate+ndeath;j++)
                     first=0;        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
                     fprintf(ficgp,"\nset parametric;set nolabel");    fprintf(ficrespow,"\n");
                     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);  #ifdef POWELL
                     fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");    powell(p,xi,npar,ftol,&iter,&fret,func);
                     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);  #endif
                     fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k2,l2,k1,l1);  
                     fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k2,l2,k1,l1);  #ifdef NLOPT
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);  #ifdef NEWUOA
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);    opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
                     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\"",\  #else
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \    opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);  #endif
                   }else{    lb=vector(0,npar-1);
                     first=0;    for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);    nlopt_set_lower_bounds(opt, lb);
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);    nlopt_set_initial_step1(opt, 0.1);
                     fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(-%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) t \"%d\"",\    
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \    p1= (p+1); /*  p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);    d->function = func;
                   }/* if first */    printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
                 } /* age mod 5 */    nlopt_set_min_objective(opt, myfunc, d);
               } /* end loop age */    nlopt_set_xtol_rel(opt, ftol);
               fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k2,l2,k1,l1);    if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
               first=1;      printf("nlopt failed! %d\n",creturn); 
             } /*l12 */    }
           } /* k12 */    else {
         } /*l1 */      printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
       }/* k1 */      printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
     } /* loop covariates */      iter=1; /* not equal */
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);    }
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));    nlopt_destroy(opt);
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));  #endif
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);    free_matrix(xi,1,npar,1,npar);
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    fclose(ficrespow);
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
   }    fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
   free_vector(xp,1,npar);    fprintf(ficres,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
   fclose(ficresprob);  
   fclose(ficresprobcov);  }
   fclose(ficresprobcor);  
   fclose(ficgp);  /**** Computes Hessian and covariance matrix ***/
   fclose(fichtm);  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
 }  {
     double  **a,**y,*x,pd;
     double **hess;
 /******************* Printing html file ***********/    int i, j,jk;
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \    int *indx;
                   int lastpass, int stepm, int weightopt, char model[],\  
                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
                   int popforecast, int estepm ,\    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
                   double jprev1, double mprev1,double anprev1, \    void lubksb(double **a, int npar, int *indx, double b[]) ;
                   double jprev2, double mprev2,double anprev2){    void ludcmp(double **a, int npar, int *indx, double *d) ;
   int jj1, k1, i1, cpt;    double gompertz(double p[]);
   /*char optionfilehtm[FILENAMELENGTH];*/    hess=matrix(1,npar,1,npar);
   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {  
     printf("Problem with %s \n",optionfilehtm), exit(0);    printf("\nCalculation of the hessian matrix. Wait...\n");
   }    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
     for (i=1;i<=npar;i++){
    fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n      printf("%d",i);fflush(stdout);
  - 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      fprintf(ficlog,"%d",i);fflush(ficlog);
  - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n     
  - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
  - Life expectancies by age and initial health status (estepm=%2d months):      
    <a href=\"e%s\">e%s</a> <br>\n</li>", \      /*  printf(" %f ",p[i]);
   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
     }
  fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n    
  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n    for (i=1;i<=npar;i++) {
  - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n      for (j=1;j<=npar;j++)  {
  - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n        if (j>i) { 
  - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n          printf(".%d%d",i,j);fflush(stdout);
  - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
  - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n          hess[i][j]=hessij(p,delti,i,j,func,npar);
  - 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);          
           hess[j][i]=hess[i][j];    
  if(popforecast==1) fprintf(fichtm,"\n          /*printf(" %lf ",hess[i][j]);*/
  - 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    printf("\n");
    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model);    fprintf(ficlog,"\n");
 fprintf(fichtm," <li><b>Graphs</b></li><p>");  
     printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
  m=cptcoveff;    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}    
     a=matrix(1,npar,1,npar);
  jj1=0;    y=matrix(1,npar,1,npar);
  for(k1=1; k1<=m;k1++){    x=vector(1,npar);
    for(i1=1; i1<=ncodemax[k1];i1++){    indx=ivector(1,npar);
      jj1++;    for (i=1;i<=npar;i++)
      if (cptcovn > 0) {      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");    ludcmp(a,npar,indx,&pd);
        for (cpt=1; cpt<=cptcoveff;cpt++)  
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);    for (j=1;j<=npar;j++) {
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");      for (i=1;i<=npar;i++) x[i]=0;
      }      x[j]=1;
      /* Pij */      lubksb(a,npar,indx,x);
      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before: pe%s%d1.png<br>      for (i=1;i<=npar;i++){ 
 <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);            matcov[i][j]=x[i];
      /* Quasi-incidences */      }
      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br>    }
 <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);  
        /* Stable prevalence in each health state */    printf("\n#Hessian matrix#\n");
        for(cpt=1; cpt<nlstate;cpt++){    fprintf(ficlog,"\n#Hessian matrix#\n");
          fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>    for (i=1;i<=npar;i++) { 
 <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);      for (j=1;j<=npar;j++) { 
        }        printf("%.3e ",hess[i][j]);
     for(cpt=1; cpt<=nlstate;cpt++) {        fprintf(ficlog,"%.3e ",hess[i][j]);
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident      }
 interval) in state (%d): v%s%d%d.png <br>      printf("\n");
 <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);        fprintf(ficlog,"\n");
      }    }
      for(cpt=1; cpt<=nlstate;cpt++) {  
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>    /* Recompute Inverse */
 <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    for (i=1;i<=npar;i++)
      }      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
      fprintf(fichtm,"\n<br>- Total life expectancy by age and    ludcmp(a,npar,indx,&pd);
 health expectancies in states (1) and (2): e%s%d.png<br>  
 <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);    /*  printf("\n#Hessian matrix recomputed#\n");
    }  
  }    for (j=1;j<=npar;j++) {
 fclose(fichtm);      for (i=1;i<=npar;i++) x[i]=0;
 }      x[j]=1;
       lubksb(a,npar,indx,x);
 /******************* Gnuplot file **************/      for (i=1;i<=npar;i++){ 
 void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){        y[i][j]=x[i];
         printf("%.3e ",y[i][j]);
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;        fprintf(ficlog,"%.3e ",y[i][j]);
   int ng;      }
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {      printf("\n");
     printf("Problem with file %s",optionfilegnuplot);      fprintf(ficlog,"\n");
   }    }
     */
 #ifdef windows  
     fprintf(ficgp,"cd \"%s\" \n",pathc);    free_matrix(a,1,npar,1,npar);
 #endif    free_matrix(y,1,npar,1,npar);
 m=pow(2,cptcoveff);    free_vector(x,1,npar);
      free_ivector(indx,1,npar);
  /* 1eme*/    free_matrix(hess,1,npar,1,npar);
   for (cpt=1; cpt<= nlstate ; cpt ++) {  
    for (k1=1; k1<= m ; k1 ++) {  
   }
 #ifdef windows  
      fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);  /*************** hessian matrix ****************/
      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);  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
 #endif  {
 #ifdef unix    int i;
 fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);    int l=1, lmax=20;
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);    double k1,k2;
 #endif    double p2[MAXPARM+1]; /* identical to x */
     double res;
 for (i=1; i<= nlstate ; i ++) {    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    double fx;
   else fprintf(ficgp," \%%*lf (\%%*lf)");    int k=0,kmax=10;
 }    double l1;
     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 ++) {    fx=func(x);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    for (i=1;i<=npar;i++) p2[i]=x[i];
   else fprintf(ficgp," \%%*lf (\%%*lf)");    for(l=0 ; l <=lmax; l++){  /* Enlarging the zone around the Maximum */
 }      l1=pow(10,l);
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);      delts=delt;
      for (i=1; i<= nlstate ; i ++) {      for(k=1 ; k <kmax; k=k+1){
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        delt = delta*(l1*k);
   else fprintf(ficgp," \%%*lf (\%%*lf)");        p2[theta]=x[theta] +delt;
 }          k1=func(p2)-fx;   /* Might be negative if too close to the theoretical maximum */
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));        p2[theta]=x[theta]-delt;
 #ifdef unix        k2=func(p2)-fx;
 fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");        /*res= (k1-2.0*fx+k2)/delt/delt; */
 #endif        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
    }        
   }  #ifdef DEBUGHESS
   /*2 eme*/        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
         fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
   for (k1=1; k1<= m ; k1 ++) {  #endif
     fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
              k=kmax;
     for (i=1; i<= nlstate+1 ; i ++) {        }
       k=2*i;        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);          k=kmax; l=lmax*10.;
       for (j=1; j<= nlstate+1 ; j ++) {        }
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
   else fprintf(ficgp," \%%*lf (\%%*lf)");          delts=delt;
 }          }
       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);    delti[theta]=delts;
       for (j=1; j<= nlstate+1 ; j ++) {    return res; 
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    
         else fprintf(ficgp," \%%*lf (\%%*lf)");  }
 }    
       fprintf(ficgp,"\" t\"\" w l 0,");  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);  {
       for (j=1; j<= nlstate+1 ; j ++) {    int i;
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    int l=1, l1, lmax=20;
   else fprintf(ficgp," \%%*lf (\%%*lf)");    double k1,k2,k3,k4,res,fx;
 }      double p2[MAXPARM+1];
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");    int k;
       else fprintf(ficgp,"\" t\"\" w l 0,");  
     }    fx=func(x);
   }    for (k=1; k<=2; k++) {
        for (i=1;i<=npar;i++) p2[i]=x[i];
   /*3eme*/      p2[thetai]=x[thetai]+delti[thetai]/k;
       p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   for (k1=1; k1<= m ; k1 ++) {      k1=func(p2)-fx;
     for (cpt=1; cpt<= nlstate ; cpt ++) {    
       k=2+nlstate*(2*cpt-2);      p2[thetai]=x[thetai]+delti[thetai]/k;
       fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);      k2=func(p2)-fx;
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);    
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");      p2[thetai]=x[thetai]-delti[thetai]/k;
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);      k3=func(p2)-fx;
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");    
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);      p2[thetai]=x[thetai]-delti[thetai]/k;
       p2[thetaj]=x[thetaj]-delti[thetaj]/k;
 */      k4=func(p2)-fx;
       for (i=1; i< nlstate ; i ++) {      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
         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);  #ifdef DEBUG
       printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
       }      fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
     }  #endif
   }    }
      return res;
   /* CV preval stat */  }
     for (k1=1; k1<= m ; k1 ++) {  
     for (cpt=1; cpt<nlstate ; cpt ++) {  /************** Inverse of matrix **************/
       k=3;  void ludcmp(double **a, int n, int *indx, double *d) 
       fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);  { 
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);    int i,imax,j,k; 
     double big,dum,sum,temp; 
       for (i=1; i< nlstate ; i ++)    double *vv; 
         fprintf(ficgp,"+$%d",k+i+1);   
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);    vv=vector(1,n); 
          *d=1.0; 
       l=3+(nlstate+ndeath)*cpt;    for (i=1;i<=n;i++) { 
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);      big=0.0; 
       for (i=1; i< nlstate ; i ++) {      for (j=1;j<=n;j++) 
         l=3+(nlstate+ndeath)*cpt;        if ((temp=fabs(a[i][j])) > big) big=temp; 
         fprintf(ficgp,"+$%d",l+i+1);      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
       }      vv[i]=1.0/big; 
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);      } 
     }    for (j=1;j<=n;j++) { 
   }        for (i=1;i<j;i++) { 
          sum=a[i][j]; 
   /* proba elementaires */        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
    for(i=1,jk=1; i <=nlstate; i++){        a[i][j]=sum; 
     for(k=1; k <=(nlstate+ndeath); k++){      } 
       if (k != i) {      big=0.0; 
         for(j=1; j <=ncovmodel; j++){      for (i=j;i<=n;i++) { 
                sum=a[i][j]; 
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);        for (k=1;k<j;k++) 
           jk++;          sum -= a[i][k]*a[k][j]; 
           fprintf(ficgp,"\n");        a[i][j]=sum; 
         }        if ( (dum=vv[i]*fabs(sum)) >= big) { 
       }          big=dum; 
     }          imax=i; 
    }        } 
       } 
    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/      if (j != imax) { 
      for(jk=1; jk <=m; jk++) {        for (k=1;k<=n;k++) { 
        fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);          dum=a[imax][k]; 
        if (ng==2)          a[imax][k]=a[j][k]; 
          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");          a[j][k]=dum; 
        else        } 
          fprintf(ficgp,"\nset title \"Probability\"\n");        *d = -(*d); 
        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);        vv[imax]=vv[j]; 
        i=1;      } 
        for(k2=1; k2<=nlstate; k2++) {      indx[j]=imax; 
          k3=i;      if (a[j][j] == 0.0) a[j][j]=TINY; 
          for(k=1; k<=(nlstate+ndeath); k++) {      if (j != n) { 
            if (k != k2){        dum=1.0/(a[j][j]); 
              if(ng==2)        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
                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);    free_vector(vv,1,n);  /* Doesn't work */
              ij=1;  ;
              for(j=3; j <=ncovmodel; j++) {  } 
                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {  
                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);  void lubksb(double **a, int n, int *indx, double b[]) 
                  ij++;  { 
                }    int i,ii=0,ip,j; 
                else    double sum; 
                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);   
              }    for (i=1;i<=n;i++) { 
              fprintf(ficgp,")/(1");      ip=indx[i]; 
                    sum=b[ip]; 
              for(k1=1; k1 <=nlstate; k1++){        b[ip]=b[i]; 
                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);      if (ii) 
                ij=1;        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
                for(j=3; j <=ncovmodel; j++){      else if (sum) ii=i; 
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {      b[i]=sum; 
                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    } 
                    ij++;    for (i=n;i>=1;i--) { 
                  }      sum=b[i]; 
                  else      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);      b[i]=sum/a[i][i]; 
                }    } 
                fprintf(ficgp,")");  } 
              }  
              fprintf(ficgp,") t \"p%d%d\" ", k2,k);  void pstamp(FILE *fichier)
              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");  {
              i=i+ncovmodel;    fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
            }  }
          }  
        }  /************ 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 */
    fclose(ficgp);    
 }  /* end gnuplot */    int i, m, jk, k1,i1, j1, bool, z1,j;
     int first;
     double ***freq; /* Frequencies */
 /*************** Moving average **************/    double *pp, **prop;
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){    double pos,posprop, k2, dateintsum=0,k2cpt=0;
     char fileresp[FILENAMELENGTH];
   int i, cpt, cptcod;    
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)    pp=vector(1,nlstate);
       for (i=1; i<=nlstate;i++)    prop=matrix(1,nlstate,iagemin,iagemax+3);
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)    strcpy(fileresp,"p");
           mobaverage[(int)agedeb][i][cptcod]=0.;    strcat(fileresp,fileres);
        if((ficresp=fopen(fileresp,"w"))==NULL) {
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){      printf("Problem with prevalence resultfile: %s\n", fileresp);
       for (i=1; i<=nlstate;i++){      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      exit(0);
           for (cpt=0;cpt<=4;cpt++){    }
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
           }    j1=0;
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;    
         }    j=cptcoveff;
       }    if (cptcovn<1) {j=1;ncodemax[1]=1;}
     }  
        first=1;
 }  
     /* for(k1=1; k1<=j ; k1++){   /* Loop on covariates */
     /*  for(i1=1; i1<=ncodemax[k1];i1++){ /* Now it is 2 */
 /************** Forecasting ******************/    /*    j1++;
 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){  */
      for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
   int *popage;          scanf("%d", i);*/
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;        for (i=-5; i<=nlstate+ndeath; i++)  
   double *popeffectif,*popcount;          for (jk=-5; jk<=nlstate+ndeath; jk++)  
   double ***p3mat;            for(m=iagemin; m <= iagemax+3; m++)
   char fileresf[FILENAMELENGTH];              freq[i][jk][m]=0;
         
  agelim=AGESUP;        for (i=1; i<=nlstate; i++)  
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;          for(m=iagemin; m <= iagemax+3; m++)
             prop[i][m]=0;
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);        
          dateintsum=0;
          k2cpt=0;
   strcpy(fileresf,"f");        for (i=1; i<=imx; i++) {
   strcat(fileresf,fileres);          bool=1;
   if((ficresf=fopen(fileresf,"w"))==NULL) {          if  (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
     printf("Problem with forecast resultfile: %s\n", fileresf);            for (z1=1; z1<=cptcoveff; z1++)       
   }              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
   printf("Computing forecasting: result on file '%s' \n", fileresf);                  /* Tests if the value of each of the covariates of i is equal to filter j1 */
                 bool=0;
   if (cptcoveff==0) ncodemax[cptcoveff]=1;                /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtab[%d][%d]=%d, nbcode[Tvaraff][codtab[%d][%d]=%d, j1=%d\n", 
                   bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
   if (mobilav==1) {                  j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);                /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
     movingaverage(agedeb, fage, ageminpar, mobaverage);              } 
   }          }
    
   stepsize=(int) (stepm+YEARM-1)/YEARM;          if (bool==1){
   if (stepm<=12) stepsize=1;            for(m=firstpass; m<=lastpass; m++){
                k2=anint[m][i]+(mint[m][i]/12.);
   agelim=AGESUP;              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
                  if(agev[m][i]==0) agev[m][i]=iagemax+1;
   hstepm=1;                if(agev[m][i]==1) agev[m][i]=iagemax+2;
   hstepm=hstepm/stepm;                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
   yp1=modf(dateintmean,&yp);                if (m<lastpass) {
   anprojmean=yp;                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
   yp2=modf((yp1*12),&yp);                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
   mprojmean=yp;                }
   yp1=modf((yp2*30.5),&yp);                
   jprojmean=yp;                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
   if(jprojmean==0) jprojmean=1;                  dateintsum=dateintsum+k2;
   if(mprojmean==0) jprojmean=1;                  k2cpt++;
                  }
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);                /*}*/
              }
   for(cptcov=1;cptcov<=i2;cptcov++){          }
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){        } /* end i */
       k=k+1;         
       fprintf(ficresf,"\n#******");        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
       for(j=1;j<=cptcoveff;j++) {        pstamp(ficresp);
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        if  (cptcovn>0) {
       }          fprintf(ficresp, "\n#********** Variable "); 
       fprintf(ficresf,"******\n");          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       fprintf(ficresf,"# StartingAge FinalAge");          fprintf(ficresp, "**********\n#");
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);          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#");
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {        }
         fprintf(ficresf,"\n");        for(i=1; i<=nlstate;i++) 
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);            fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
         fprintf(ficresp, "\n");
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){        
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);        for(i=iagemin; i <= iagemax+3; i++){
           nhstepm = nhstepm/hstepm;          if(i==iagemax+3){
                      fprintf(ficlog,"Total");
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          }else{
           oldm=oldms;savm=savms;            if(first==1){
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);                first=0;
                      printf("See log file for details...\n");
           for (h=0; h<=nhstepm; h++){            }
             if (h==(int) (calagedate+YEARM*cpt)) {            fprintf(ficlog,"Age %d", i);
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);          }
             }          for(jk=1; jk <=nlstate ; jk++){
             for(j=1; j<=nlstate+ndeath;j++) {            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
               kk1=0.;kk2=0;              pp[jk] += freq[jk][m][i]; 
               for(i=1; i<=nlstate;i++) {                        }
                 if (mobilav==1)          for(jk=1; jk <=nlstate ; jk++){
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];            for(m=-1, pos=0; m <=0 ; m++)
                 else {              pos += freq[jk][m][i];
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];            if(pp[jk]>=1.e-10){
                 }              if(first==1){
                                printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
               }              }
               if (h==(int)(calagedate+12*cpt)){              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
                 fprintf(ficresf," %.3f", kk1);            }else{
                                      if(first==1)
               }                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
             }              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
           }            }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          }
         }  
       }          for(jk=1; jk <=nlstate ; jk++){
     }            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
   }              pp[jk] += freq[jk][m][i];
                  }       
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
             pos += pp[jk];
   fclose(ficresf);            posprop += prop[jk][i];
 }          }
 /************** Forecasting ******************/          for(jk=1; jk <=nlstate ; jk++){
 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){            if(pos>=1.e-5){
                if(first==1)
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   int *popage;              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;            }else{
   double *popeffectif,*popcount;              if(first==1)
   double ***p3mat,***tabpop,***tabpopprev;                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   char filerespop[FILENAMELENGTH];              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
             }
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            if( i <= iagemax){
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);              if(pos>=1.e-5){
   agelim=AGESUP;                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;                /*probs[i][jk][j1]= pp[jk]/pos;*/
                  /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);              }
                else
                  fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
   strcpy(filerespop,"pop");            }
   strcat(filerespop,fileres);          }
   if((ficrespop=fopen(filerespop,"w"))==NULL) {          
     printf("Problem with forecast resultfile: %s\n", filerespop);          for(jk=-1; jk <=nlstate+ndeath; jk++)
   }            for(m=-1; m <=nlstate+ndeath; m++)
   printf("Computing forecasting: result on file '%s' \n", filerespop);              if(freq[jk][m][i] !=0 ) {
               if(first==1)
   if (cptcoveff==0) ncodemax[cptcoveff]=1;                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
                 fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
   if (mobilav==1) {              }
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          if(i <= iagemax)
     movingaverage(agedeb, fage, ageminpar, mobaverage);            fprintf(ficresp,"\n");
   }          if(first==1)
             printf("Others in log...\n");
   stepsize=(int) (stepm+YEARM-1)/YEARM;          fprintf(ficlog,"\n");
   if (stepm<=12) stepsize=1;        }
          /*}*/
   agelim=AGESUP;    }
      dateintmean=dateintsum/k2cpt; 
   hstepm=1;   
   hstepm=hstepm/stepm;    fclose(ficresp);
      free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
   if (popforecast==1) {    free_vector(pp,1,nlstate);
     if((ficpop=fopen(popfile,"r"))==NULL) {    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
       printf("Problem with population file : %s\n",popfile);exit(0);    /* End of Freq */
     }  }
     popage=ivector(0,AGESUP);  
     popeffectif=vector(0,AGESUP);  /************ Prevalence ********************/
     popcount=vector(0,AGESUP);  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)
      {  
     i=1;      /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;       in each health status at the date of interview (if between dateprev1 and dateprev2).
           We still use firstpass and lastpass as another selection.
     imx=i;    */
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];   
   }    int i, m, jk, k1, i1, j1, bool, z1,j;
     double ***freq; /* Frequencies */
   for(cptcov=1;cptcov<=i2;cptcov++){    double *pp, **prop;
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    double pos,posprop; 
       k=k+1;    double  y2; /* in fractional years */
       fprintf(ficrespop,"\n#******");    int iagemin, iagemax;
       for(j=1;j<=cptcoveff;j++) {    int first; /** to stop verbosity which is redirected to log file */
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
       }    iagemin= (int) agemin;
       fprintf(ficrespop,"******\n");    iagemax= (int) agemax;
       fprintf(ficrespop,"# Age");    /*pp=vector(1,nlstate);*/
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);    prop=matrix(1,nlstate,iagemin,iagemax+3); 
       if (popforecast==1)  fprintf(ficrespop," [Population]");    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
          j1=0;
       for (cpt=0; cpt<=0;cpt++) {    
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);      /*j=cptcoveff;*/
            if (cptcovn<1) {j=1;ncodemax[1]=1;}
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    first=1;
           nhstepm = nhstepm/hstepm;    for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
                /*for(i1=1; i1<=ncodemax[k1];i1++){
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        j1++;*/
           oldm=oldms;savm=savms;        
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);          for (i=1; i<=nlstate; i++)  
                  for(m=iagemin; m <= iagemax+3; m++)
           for (h=0; h<=nhstepm; h++){            prop[i][m]=0.0;
             if (h==(int) (calagedate+YEARM*cpt)) {       
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);        for (i=1; i<=imx; i++) { /* Each individual */
             }          bool=1;
             for(j=1; j<=nlstate+ndeath;j++) {          if  (cptcovn>0) {
               kk1=0.;kk2=0;            for (z1=1; z1<=cptcoveff; z1++) 
               for(i=1; i<=nlstate;i++) {                            if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
                 if (mobilav==1)                bool=0;
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];          } 
                 else {          if (bool==1) { 
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];            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 (h==(int)(calagedate+12*cpt)){                if(agev[m][i]==0) agev[m][i]=iagemax+1;
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;                if(agev[m][i]==1) agev[m][i]=iagemax+2;
                   /*fprintf(ficrespop," %.3f", kk1);                if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/                if (s[m][i]>0 && s[m][i]<=nlstate) { 
               }                  /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
             }                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
             for(i=1; i<=nlstate;i++){                  prop[s[m][i]][iagemax+3] += weight[i]; 
               kk1=0.;                } 
                 for(j=1; j<=nlstate;j++){              }
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];            } /* end selection of waves */
                 }          }
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];        }
             }        for(i=iagemin; i <= iagemax+3; i++){  
           for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)            posprop += prop[jk][i]; 
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);          } 
           }          
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          for(jk=1; jk <=nlstate ; jk++){     
         }            if( i <=  iagemax){ 
       }              if(posprop>=1.e-5){ 
                  probs[i][jk][j1]= prop[jk][i]/posprop;
   /******/              } else{
                 if(first==1){
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {                  first=0;
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);                    printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others on log file...\n",jk,i,j1,probs[i][jk][j1]);
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){                }
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);              }
           nhstepm = nhstepm/hstepm;            } 
                    }/* end jk */ 
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        }/* end i */ 
           oldm=oldms;savm=savms;      /*} *//* end i1 */
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      } /* end j1 */
           for (h=0; h<=nhstepm; h++){    
             if (h==(int) (calagedate+YEARM*cpt)) {    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);    /*free_vector(pp,1,nlstate);*/
             }    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
             for(j=1; j<=nlstate+ndeath;j++) {  }  /* End of prevalence */
               kk1=0.;kk2=0;  
               for(i=1; i<=nlstate;i++) {                /************* Waves Concatenation ***************/
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];      
               }  void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);  {
             }    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
           }       Death is a valid wave (if date is known).
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
         }       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.
    }       */
   }  
      int i, mi, m;
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
        double sum=0., jmean=0.;*/
   if (popforecast==1) {    int first;
     free_ivector(popage,0,AGESUP);    int j, k=0,jk, ju, jl;
     free_vector(popeffectif,0,AGESUP);    double sum=0.;
     free_vector(popcount,0,AGESUP);    first=0;
   }    jmin=1e+5;
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    jmax=-1;
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    jmean=0.;
   fclose(ficrespop);    for(i=1; i<=imx; i++){
 }      mi=0;
       m=firstpass;
 /***********************************************/      while(s[m][i] <= nlstate){
 /**************** Main Program *****************/        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
 /***********************************************/          mw[++mi][i]=m;
         if(m >=lastpass)
 int main(int argc, char *argv[])          break;
 {        else
           m++;
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;      }/* end while */
   double agedeb, agefin,hf;      if (s[m][i] > nlstate){
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;        mi++;     /* Death is another wave */
         /* if(mi==0)  never been interviewed correctly before death */
   double fret;           /* Only death is a correct wave */
   double **xi,tmp,delta;        mw[mi][i]=m;
       }
   double dum; /* Dummy variable */  
   double ***p3mat;      wav[i]=mi;
   int *indx;      if(mi==0){
   char line[MAXLINE], linepar[MAXLINE];        nbwarn++;
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];        if(first==0){
   int firstobs=1, lastobs=10;          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
   int sdeb, sfin; /* Status at beginning and end */          first=1;
   int c,  h , cpt,l;        }
   int ju,jl, mi;        if(first==1){
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;        }
   int mobilav=0,popforecast=0;      } /* end mi==0 */
   int hstepm, nhstepm;    } /* End individuals */
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;  
     for(i=1; i<=imx; i++){
   double bage, fage, age, agelim, agebase;      for(mi=1; mi<wav[i];mi++){
   double ftolpl=FTOL;        if (stepm <=0)
   double **prlim;          dh[mi][i]=1;
   double *severity;        else{
   double ***param; /* Matrix of parameters */          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
   double  *p;            if (agedc[i] < 2*AGESUP) {
   double **matcov; /* Matrix of covariance */              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
   double ***delti3; /* Scale */              if(j==0) j=1;  /* Survives at least one month after exam */
   double *delti; /* Scale */              else if(j<0){
   double ***eij, ***vareij;                nberr++;
   double **varpl; /* Variances of prevalence limits by age */                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]);
   double *epj, vepp;                j=1; /* Temporary Dangerous patch */
   double kk1, kk2;                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);
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;                fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
                  fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
               }
   char *alph[]={"a","a","b","c","d","e"}, str[4];              k=k+1;
               if (j >= jmax){
                 jmax=j;
   char z[1]="c", occ;                ijmax=i;
 #include <sys/time.h>              }
 #include <time.h>              if (j <= jmin){
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];                jmin=j;
                  ijmin=i;
   /* long total_usecs;              }
   struct timeval start_time, end_time;              sum=sum+j;
                /*if (j<0) printf("j=%d num=%d \n",j,i);*/
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
   getcwd(pathcd, size);            }
           }
   printf("\n%s",version);          else{
   if(argc <=1){            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
     printf("\nEnter the parameter file name: ");  /*        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]); */
     scanf("%s",pathtot);  
   }            k=k+1;
   else{            if (j >= jmax) {
     strcpy(pathtot,argv[1]);              jmax=j;
   }              ijmax=i;
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/            }
   /*cygwin_split_path(pathtot,path,optionfile);            else if (j <= jmin){
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/              jmin=j;
   /* cutv(path,optionfile,pathtot,'\\');*/              ijmin=i;
             }
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);            /*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]);*/
   chdir(path);            if(j<0){
   replace(pathc,path);              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]);
 /*-------- arguments in the command line --------*/              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]);
             }
   strcpy(fileres,"r");            sum=sum+j;
   strcat(fileres, optionfilefiname);          }
   strcat(fileres,".txt");    /* Other files have txt extension */          jk= j/stepm;
           jl= j -jk*stepm;
   /*---------arguments file --------*/          ju= j -(jk+1)*stepm;
           if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
   if((ficpar=fopen(optionfile,"r"))==NULL)    {            if(jl==0){
     printf("Problem with optionfile %s\n",optionfile);              dh[mi][i]=jk;
     goto end;              bh[mi][i]=0;
   }            }else{ /* We want a negative bias in order to only have interpolation ie
                     * to avoid the price of an extra matrix product in likelihood */
   strcpy(filereso,"o");              dh[mi][i]=jk+1;
   strcat(filereso,fileres);              bh[mi][i]=ju;
   if((ficparo=fopen(filereso,"w"))==NULL) {            }
     printf("Problem with Output resultfile: %s\n", filereso);goto end;          }else{
   }            if(jl <= -ju){
               dh[mi][i]=jk;
   /* Reads comments: lines beginning with '#' */              bh[mi][i]=jl;       /* bias is positive if real duration
   while((c=getc(ficpar))=='#' && c!= EOF){                                   * is higher than the multiple of stepm and negative otherwise.
     ungetc(c,ficpar);                                   */
     fgets(line, MAXLINE, ficpar);            }
     puts(line);            else{
     fputs(line,ficparo);              dh[mi][i]=jk+1;
   }              bh[mi][i]=ju;
   ungetc(c,ficpar);            }
             if(dh[mi][i]==0){
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);              dh[mi][i]=1; /* At least one step */
   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);              bh[mi][i]=ju; /* At least one step */
   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);              /*  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);*/
 while((c=getc(ficpar))=='#' && c!= EOF){            }
     ungetc(c,ficpar);          } /* end if mle */
     fgets(line, MAXLINE, ficpar);        }
     puts(line);      } /* end wave */
     fputs(line,ficparo);    }
   }    jmean=sum/k;
   ungetc(c,ficpar);    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);
       }
   covar=matrix(0,NCOVMAX,1,n);  
   cptcovn=0;  /*********** Tricode ****************************/
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;  void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
   {
   ncovmodel=2+cptcovn;    /**< Uses cptcovn+2*cptcovprod as the number of covariates */
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */    /*      Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 
      /* Boring subroutine which should only output nbcode[Tvar[j]][k]
   /* Read guess parameters */     * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
   /* Reads comments: lines beginning with '#' */    /* nbcode[Tvar[j]][1]= 
   while((c=getc(ficpar))=='#' && c!= EOF){    */
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);    int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
     puts(line);    int modmaxcovj=0; /* Modality max of covariates j */
     fputs(line,ficparo);    int cptcode=0; /* Modality max of covariates j */
   }    int modmincovj=0; /* Modality min of covariates j */
   ungetc(c,ficpar);  
    
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    cptcoveff=0; 
     for(i=1; i <=nlstate; i++)   
     for(j=1; j <=nlstate+ndeath-1; j++){    for (k=-1; k < maxncov; k++) Ndum[k]=0;
       fscanf(ficpar,"%1d%1d",&i1,&j1);    for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
       fprintf(ficparo,"%1d%1d",i1,j1);  
       printf("%1d%1d",i,j);    /* Loop on covariates without age and products */
       for(k=1; k<=ncovmodel;k++){    for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */
         fscanf(ficpar," %lf",&param[i][j][k]);      for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the 
         printf(" %lf",param[i][j][k]);                                 modality of this covariate Vj*/ 
         fprintf(ficparo," %lf",param[i][j][k]);        ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
       }                                      * If product of Vn*Vm, still boolean *:
       fscanf(ficpar,"\n");                                      * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
       printf("\n");                                      * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
       fprintf(ficparo,"\n");        /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
     }                                        modality of the nth covariate of individual i. */
          if (ij > modmaxcovj)
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;          modmaxcovj=ij; 
         else if (ij < modmincovj) 
   p=param[1][1];          modmincovj=ij; 
          if ((ij < -1) && (ij > NCOVMAX)){
   /* Reads comments: lines beginning with '#' */          printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
   while((c=getc(ficpar))=='#' && c!= EOF){          exit(1);
     ungetc(c,ficpar);        }else
     fgets(line, MAXLINE, ficpar);        Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
     puts(line);        /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
     fputs(line,ficparo);        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
   }        /* getting the maximum value of the modality of the covariate
   ungetc(c,ficpar);           (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
            female is 1, then modmaxcovj=1.*/
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);      }
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */      printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
   for(i=1; i <=nlstate; i++){      cptcode=modmaxcovj;
     for(j=1; j <=nlstate+ndeath-1; j++){      /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
       fscanf(ficpar,"%1d%1d",&i1,&j1);     /*for (i=0; i<=cptcode; i++) {*/
       printf("%1d%1d",i,j);      for (i=modmincovj;  i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
       fprintf(ficparo,"%1d%1d",i1,j1);        printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
       for(k=1; k<=ncovmodel;k++){        if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
         fscanf(ficpar,"%le",&delti3[i][j][k]);          ncodemax[j]++;  /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
         printf(" %le",delti3[i][j][k]);        }
         fprintf(ficparo," %le",delti3[i][j][k]);        /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for
       }           historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
       fscanf(ficpar,"\n");      } /* Ndum[-1] number of undefined modalities */
       printf("\n");  
       fprintf(ficparo,"\n");      /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
     }      /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
   }      /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
   delti=delti3[1][1];         modmincovj=3; modmaxcovj = 7;
           There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
   /* Reads comments: lines beginning with '#' */         which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy 
   while((c=getc(ficpar))=='#' && c!= EOF){         variables V1_1 and V1_2.
     ungetc(c,ficpar);         nbcode[Tvar[j]][ij]=k;
     fgets(line, MAXLINE, ficpar);         nbcode[Tvar[j]][1]=0;
     puts(line);         nbcode[Tvar[j]][2]=1;
     fputs(line,ficparo);         nbcode[Tvar[j]][3]=2;
   }      */
   ungetc(c,ficpar);      ij=1; /* ij is similar to i but can jumps over null modalities */
        for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
   matcov=matrix(1,npar,1,npar);        for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
   for(i=1; i <=npar; i++){          /*recode from 0 */
     fscanf(ficpar,"%s",&str);          if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
     printf("%s",str);            nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode. 
     fprintf(ficparo,"%s",str);                                       k is a modality. If we have model=V1+V1*sex 
     for(j=1; j <=i; j++){                                       then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
       fscanf(ficpar," %le",&matcov[i][j]);            ij++;
       printf(" %.5le",matcov[i][j]);          }
       fprintf(ficparo," %.5le",matcov[i][j]);          if (ij > ncodemax[j]) break; 
     }        }  /* end of loop on */
     fscanf(ficpar,"\n");      } /* end of loop on modality */ 
     printf("\n");    } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/  
     fprintf(ficparo,"\n");    
   }   for (k=-1; k< maxncov; k++) Ndum[k]=0; 
   for(i=1; i <=npar; i++)    
     for(j=i+1;j<=npar;j++)    for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */ 
       matcov[i][j]=matcov[j][i];     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/ 
         ij=Tvar[i]; /* Tvar might be -1 if status was unknown */ 
   printf("\n");     Ndum[ij]++; 
    } 
   
     /*-------- Rewriting paramater file ----------*/   ij=1;
      strcpy(rfileres,"r");    /* "Rparameterfile */   for (i=0; i<=  maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/     /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
      strcat(rfileres,".");    /* */     if((Ndum[i]!=0) && (i<=ncovcol)){
      strcat(rfileres,optionfilext);    /* Other files have txt extension */       /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
     if((ficres =fopen(rfileres,"w"))==NULL) {       Tvaraff[ij]=i; /*For printing (unclear) */
       printf("Problem writing new parameter file: %s\n", fileres);goto end;       ij++;
     }     }else
     fprintf(ficres,"#%s\n",version);         Tvaraff[ij]=0;
       }
     /*-------- data file ----------*/   ij--;
     if((fic=fopen(datafile,"r"))==NULL)    {   cptcoveff=ij; /*Number of total covariates*/
       printf("Problem with datafile: %s\n", datafile);goto end;  
     }  }
   
     n= lastobs;  
     severity = vector(1,maxwav);  /*********** Health Expectancies ****************/
     outcome=imatrix(1,maxwav+1,1,n);  
     num=ivector(1,n);  void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
     moisnais=vector(1,n);  
     annais=vector(1,n);  {
     moisdc=vector(1,n);    /* Health expectancies, no variances */
     andc=vector(1,n);    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
     agedc=vector(1,n);    int nhstepma, nstepma; /* Decreasing with age */
     cod=ivector(1,n);    double age, agelim, hf;
     weight=vector(1,n);    double ***p3mat;
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */    double eip;
     mint=matrix(1,maxwav,1,n);  
     anint=matrix(1,maxwav,1,n);    pstamp(ficreseij);
     s=imatrix(1,maxwav+1,1,n);    fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
     adl=imatrix(1,maxwav+1,1,n);        fprintf(ficreseij,"# Age");
     tab=ivector(1,NCOVMAX);    for(i=1; i<=nlstate;i++){
     ncodemax=ivector(1,8);      for(j=1; j<=nlstate;j++){
         fprintf(ficreseij," e%1d%1d ",i,j);
     i=1;      }
     while (fgets(line, MAXLINE, fic) != NULL)    {      fprintf(ficreseij," e%1d. ",i);
       if ((i >= firstobs) && (i <=lastobs)) {    }
            fprintf(ficreseij,"\n");
         for (j=maxwav;j>=1;j--){  
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);    
           strcpy(line,stra);    if(estepm < stepm){
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);      printf ("Problem %d lower than %d\n",estepm, stepm);
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    }
         }    else  hstepm=estepm;   
            /* We compute the life expectancy from trapezoids spaced every estepm months
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);     * This is mainly to measure the difference between two models: for example
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);     * 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 
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);     * progression in between and thus overestimating or underestimating according
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);     * 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
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);     * to compare the new estimate of Life expectancy with the same linear 
         for (j=ncovcol;j>=1;j--){     * hypothesis. A more precise result, taking into account a more precise
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);     * curvature will be obtained if estepm is as small as stepm. */
         }  
         num[i]=atol(stra);    /* For example we decided to compute the life expectancy with the smallest unit */
            /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){       nhstepm is the number of hstepm from age to agelim 
           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;}*/       nstepm is the number of stepm from age to agelin. 
        Look at hpijx to understand the reason of that which relies in memory size
         i=i+1;       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
     /* printf("ii=%d", ij);       means that if the survival funtion is printed only each two years of age and if
        scanf("%d",i);*/       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   imx=i-1; /* Number of individuals */       results. So we changed our mind and took the option of the best precision.
     */
   /* for (i=1; i<=imx; i++){    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;  
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;    agelim=AGESUP;
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;    /* If stepm=6 months */
     }*/      /* Computed by stepm unit matrices, product of hstepm matrices, stored
    /*  for (i=1; i<=imx; i++){         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
      if (s[4][i]==9)  s[4][i]=-1;      
      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]));}*/  /* nhstepm age range expressed in number of stepm */
      nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   /* Calculation of the number of parameter from char model*/    /* if (stepm >= YEARM) hstepm=1;*/
   Tvar=ivector(1,15);    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   Tprod=ivector(1,15);    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   Tvaraff=ivector(1,15);  
   Tvard=imatrix(1,15,1,2);    for (age=bage; age<=fage; age ++){ 
   Tage=ivector(1,15);            nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
          /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   if (strlen(model) >1){      /* if (stepm >= YEARM) hstepm=1;*/
     j=0, j1=0, k1=1, k2=1;      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
     j=nbocc(model,'+');  
     j1=nbocc(model,'*');      /* If stepm=6 months */
     cptcovn=j+1;      /* Computed by stepm unit matrices, product of hstepma matrices, stored
     cptcovprod=j1;         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
          
     strcpy(modelsav,model);      hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){      
       printf("Error. Non available option model=%s ",model);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       goto end;      
     }      printf("%d|",(int)age);fflush(stdout);
          fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
     for(i=(j+1); i>=1;i--){      
       cutv(stra,strb,modelsav,'+');      /* Computing expectancies */
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);      for(i=1; i<=nlstate;i++)
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/        for(j=1; j<=nlstate;j++)
       /*scanf("%d",i);*/          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
       if (strchr(strb,'*')) {            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
         cutv(strd,strc,strb,'*');            
         if (strcmp(strc,"age")==0) {            /* 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]);*/
           cptcovprod--;  
           cutv(strb,stre,strd,'V');          }
           Tvar[i]=atoi(stre);  
           cptcovage++;      fprintf(ficreseij,"%3.0f",age );
             Tage[cptcovage]=i;      for(i=1; i<=nlstate;i++){
             /*printf("stre=%s ", stre);*/        eip=0;
         }        for(j=1; j<=nlstate;j++){
         else if (strcmp(strd,"age")==0) {          eip +=eij[i][j][(int)age];
           cptcovprod--;          fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
           cutv(strb,stre,strc,'V');        }
           Tvar[i]=atoi(stre);        fprintf(ficreseij,"%9.4f", eip );
           cptcovage++;      }
           Tage[cptcovage]=i;      fprintf(ficreseij,"\n");
         }      
         else {    }
           cutv(strb,stre,strc,'V');    free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           Tvar[i]=ncovcol+k1;    printf("\n");
           cutv(strb,strc,strd,'V');    fprintf(ficlog,"\n");
           Tprod[k1]=i;    
           Tvard[k1][1]=atoi(strc);  }
           Tvard[k1][2]=atoi(stre);  
           Tvar[cptcovn+k2]=Tvard[k1][1];  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[] )
           Tvar[cptcovn+k2+1]=Tvard[k1][2];  
           for (k=1; k<=lastobs;k++)  {
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];    /* Covariances of health expectancies eij and of total life expectancies according
           k1++;     to initial status i, ei. .
           k2=k2+2;    */
         }    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
       }    int nhstepma, nstepma; /* Decreasing with age */
       else {    double age, agelim, hf;
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/    double ***p3matp, ***p3matm, ***varhe;
        /*  scanf("%d",i);*/    double **dnewm,**doldm;
       cutv(strd,strc,strb,'V');    double *xp, *xm;
       Tvar[i]=atoi(strc);    double **gp, **gm;
       }    double ***gradg, ***trgradg;
       strcpy(modelsav,stra);      int theta;
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);  
         scanf("%d",i);*/    double eip, vip;
     }  
 }    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
      xp=vector(1,npar);
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);    xm=vector(1,npar);
   printf("cptcovprod=%d ", cptcovprod);    dnewm=matrix(1,nlstate*nlstate,1,npar);
   scanf("%d ",i);*/    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
     fclose(fic);    
     pstamp(ficresstdeij);
     /*  if(mle==1){*/    fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
     if (weightopt != 1) { /* Maximisation without weights*/    fprintf(ficresstdeij,"# Age");
       for(i=1;i<=n;i++) weight[i]=1.0;    for(i=1; i<=nlstate;i++){
     }      for(j=1; j<=nlstate;j++)
     /*-calculation of age at interview from date of interview and age at death -*/        fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
     agev=matrix(1,maxwav,1,imx);      fprintf(ficresstdeij," e%1d. ",i);
     }
     for (i=1; i<=imx; i++) {    fprintf(ficresstdeij,"\n");
       for(m=2; (m<= maxwav); m++) {  
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){    pstamp(ficrescveij);
          anint[m][i]=9999;    fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
          s[m][i]=-1;    fprintf(ficrescveij,"# Age");
        }    for(i=1; i<=nlstate;i++)
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;      for(j=1; j<=nlstate;j++){
       }        cptj= (j-1)*nlstate+i;
     }        for(i2=1; i2<=nlstate;i2++)
           for(j2=1; j2<=nlstate;j2++){
     for (i=1; i<=imx; i++)  {            cptj2= (j2-1)*nlstate+i2;
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);            if(cptj2 <= cptj)
       for(m=1; (m<= maxwav); m++){              fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
         if(s[m][i] >0){          }
           if (s[m][i] >= nlstate+1) {      }
             if(agedc[i]>0)    fprintf(ficrescveij,"\n");
               if(moisdc[i]!=99 && andc[i]!=9999)    
                 agev[m][i]=agedc[i];    if(estepm < stepm){
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/      printf ("Problem %d lower than %d\n",estepm, stepm);
            else {    }
               if (andc[i]!=9999){    else  hstepm=estepm;   
               printf("Warning negative age at death: %d line:%d\n",num[i],i);    /* We compute the life expectancy from trapezoids spaced every estepm months
               agev[m][i]=-1;     * This is mainly to measure the difference between two models: for example
               }     * if stepm=24 months pijx are given only every 2 years and by summing them
             }     * we are calculating an estimate of the Life Expectancy assuming a linear 
           }     * progression in between and thus overestimating or underestimating according
           else if(s[m][i] !=9){ /* Should no more exist */     * to the curvature of the survival function. If, for the same date, we 
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);     * estimate the model with stepm=1 month, we can keep estepm to 24 months
             if(mint[m][i]==99 || anint[m][i]==9999)     * to compare the new estimate of Life expectancy with the same linear 
               agev[m][i]=1;     * hypothesis. A more precise result, taking into account a more precise
             else if(agev[m][i] <agemin){     * curvature will be obtained if estepm is as small as stepm. */
               agemin=agev[m][i];  
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/    /* For example we decided to compute the life expectancy with the smallest unit */
             }    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
             else if(agev[m][i] >agemax){       nhstepm is the number of hstepm from age to agelim 
               agemax=agev[m][i];       nstepm is the number of stepm from age to agelin. 
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/       Look at hpijx to understand the reason of that which relies in memory size
             }       and note for a fixed period like estepm months */
             /*agev[m][i]=anint[m][i]-annais[i];*/    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
             /*   agev[m][i] = age[i]+2*m;*/       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
           else { /* =9 */       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
             agev[m][i]=1;       results. So we changed our mind and took the option of the best precision.
             s[m][i]=-1;    */
           }    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
         }  
         else /*= 0 Unknown */    /* If stepm=6 months */
           agev[m][i]=1;    /* nhstepm age range expressed in number of stepm */
       }    agelim=AGESUP;
        nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
     }    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     for (i=1; i<=imx; i++)  {    /* if (stepm >= YEARM) hstepm=1;*/
       for(m=1; (m<= maxwav); m++){    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
         if (s[m][i] > (nlstate+ndeath)) {    
           printf("Error: Wrong value in nlstate or ndeath\n");      p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           goto end;    p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         }    gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
       }    trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
     }    gp=matrix(0,nhstepm,1,nlstate*nlstate);
     gm=matrix(0,nhstepm,1,nlstate*nlstate);
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);  
     for (age=bage; age<=fage; age ++){ 
     free_vector(severity,1,maxwav);      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
     free_imatrix(outcome,1,maxwav+1,1,n);      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     free_vector(moisnais,1,n);      /* if (stepm >= YEARM) hstepm=1;*/
     free_vector(annais,1,n);      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
     /* free_matrix(mint,1,maxwav,1,n);  
        free_matrix(anint,1,maxwav,1,n);*/      /* If stepm=6 months */
     free_vector(moisdc,1,n);      /* Computed by stepm unit matrices, product of hstepma matrices, stored
     free_vector(andc,1,n);         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
       
          hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     wav=ivector(1,imx);  
     dh=imatrix(1,lastpass-firstpass+1,1,imx);      /* Computing  Variances of health expectancies */
     mw=imatrix(1,lastpass-firstpass+1,1,imx);      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
             decrease memory allocation */
     /* Concatenates waves */      for(theta=1; theta <=npar; theta++){
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);        for(i=1; i<=npar; i++){ 
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
           xm[i] = x[i] - (i==theta ?delti[theta]:0);
       Tcode=ivector(1,100);        }
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);        hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
       ncodemax[1]=1;        hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);    
              for(j=1; j<= nlstate; j++){
    codtab=imatrix(1,100,1,10);          for(i=1; i<=nlstate; i++){
    h=0;            for(h=0; h<=nhstepm-1; h++){
    m=pow(2,cptcoveff);              gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
                gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
    for(k=1;k<=cptcoveff; k++){            }
      for(i=1; i <=(m/pow(2,k));i++){          }
        for(j=1; j <= ncodemax[k]; j++){        }
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){       
            h++;        for(ij=1; ij<= nlstate*nlstate; ij++)
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;          for(h=0; h<=nhstepm-1; h++){
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/            gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
          }          }
        }      }/* End theta */
      }      
    }      
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);      for(h=0; h<=nhstepm-1; h++)
       codtab[1][2]=1;codtab[2][2]=2; */        for(j=1; j<=nlstate*nlstate;j++)
    /* for(i=1; i <=m ;i++){          for(theta=1; theta <=npar; theta++)
       for(k=1; k <=cptcovn; k++){            trgradg[h][j][theta]=gradg[h][theta][j];
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);      
       }  
       printf("\n");       for(ij=1;ij<=nlstate*nlstate;ij++)
       }        for(ji=1;ji<=nlstate*nlstate;ji++)
       scanf("%d",i);*/          varhe[ij][ji][(int)age] =0.;
      
    /* Calculates basic frequencies. Computes observed prevalence at single age       printf("%d|",(int)age);fflush(stdout);
        and prints on file fileres'p'. */       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
        for(h=0;h<=nhstepm-1;h++){
            for(k=0;k<=nhstepm-1;k++){
              matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          for(ij=1;ij<=nlstate*nlstate;ij++)
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            for(ji=1;ji<=nlstate*nlstate;ji++)
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
     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] */      /* Computing expectancies */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */      hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
       for(i=1; i<=nlstate;i++)
     if(mle==1){        for(j=1; j<=nlstate;j++)
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
     }            eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
                
     /*--------- results files --------------*/            /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
     fprintf(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);  
            }
   
    jk=1;      fprintf(ficresstdeij,"%3.0f",age );
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");      for(i=1; i<=nlstate;i++){
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");        eip=0.;
    for(i=1,jk=1; i <=nlstate; i++){        vip=0.;
      for(k=1; k <=(nlstate+ndeath); k++){        for(j=1; j<=nlstate;j++){
        if (k != i)          eip += eij[i][j][(int)age];
          {          for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
            printf("%d%d ",i,k);            vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
            fprintf(ficres,"%1d%1d ",i,k);          fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
            for(j=1; j <=ncovmodel; j++){        }
              printf("%f ",p[jk]);        fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
              fprintf(ficres,"%f ",p[jk]);      }
              jk++;      fprintf(ficresstdeij,"\n");
            }  
            printf("\n");      fprintf(ficrescveij,"%3.0f",age );
            fprintf(ficres,"\n");      for(i=1; i<=nlstate;i++)
          }        for(j=1; j<=nlstate;j++){
      }          cptj= (j-1)*nlstate+i;
    }          for(i2=1; i2<=nlstate;i2++)
  if(mle==1){            for(j2=1; j2<=nlstate;j2++){
     /* Computing hessian and covariance matrix */              cptj2= (j2-1)*nlstate+i2;
     ftolhess=ftol; /* Usually correct */              if(cptj2 <= cptj)
     hesscov(matcov, p, npar, delti, ftolhess, func);                fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
  }            }
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");        }
     printf("# Scales (for hessian or gradient estimation)\n");      fprintf(ficrescveij,"\n");
      for(i=1,jk=1; i <=nlstate; i++){     
       for(j=1; j <=nlstate+ndeath; j++){    }
         if (j!=i) {    free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
           fprintf(ficres,"%1d%1d",i,j);    free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
           printf("%1d%1d",i,j);    free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
           for(k=1; k<=ncovmodel;k++){    free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
             printf(" %.5e",delti[jk]);    free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             fprintf(ficres," %.5e",delti[jk]);    free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             jk++;    printf("\n");
           }    fprintf(ficlog,"\n");
           printf("\n");  
           fprintf(ficres,"\n");    free_vector(xm,1,npar);
         }    free_vector(xp,1,npar);
       }    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
      }    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
        free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
     k=1;  }
     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");  
     printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");  /************ Variance ******************/
     for(i=1;i<=npar;i++){  void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
       /*  if (k>nlstate) k=1;  {
       i1=(i-1)/(ncovmodel*nlstate)+1;    /* Variance of health expectancies */
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
       printf("%s%d%d",alph[k],i1,tab[i]);*/    /* double **newm;*/
       fprintf(ficres,"%3d",i);    double **dnewm,**doldm;
       printf("%3d",i);    double **dnewmp,**doldmp;
       for(j=1; j<=i;j++){    int i, j, nhstepm, hstepm, h, nstepm ;
         fprintf(ficres," %.5e",matcov[i][j]);    int k, cptcode;
         printf(" %.5e",matcov[i][j]);    double *xp;
       }    double **gp, **gm;  /* for var eij */
       fprintf(ficres,"\n");    double ***gradg, ***trgradg; /*for var eij */
       printf("\n");    double **gradgp, **trgradgp; /* for var p point j */
       k++;    double *gpp, *gmp; /* for var p point j */
     }    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
        double ***p3mat;
     while((c=getc(ficpar))=='#' && c!= EOF){    double age,agelim, hf;
       ungetc(c,ficpar);    double ***mobaverage;
       fgets(line, MAXLINE, ficpar);    int theta;
       puts(line);    char digit[4];
       fputs(line,ficparo);    char digitp[25];
     }  
     ungetc(c,ficpar);    char fileresprobmorprev[FILENAMELENGTH];
     estepm=0;  
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);    if(popbased==1){
     if (estepm==0 || estepm < stepm) estepm=stepm;      if(mobilav!=0)
     if (fage <= 2) {        strcpy(digitp,"-populbased-mobilav-");
       bage = ageminpar;      else strcpy(digitp,"-populbased-nomobil-");
       fage = agemaxpar;    }
     }    else 
          strcpy(digitp,"-stablbased-");
     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);    if (mobilav!=0) {
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
        if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
     while((c=getc(ficpar))=='#' && c!= EOF){        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
     ungetc(c,ficpar);        printf(" Error in movingaverage mobilav=%d\n",mobilav);
     fgets(line, MAXLINE, ficpar);      }
     puts(line);    }
     fputs(line,ficparo);  
   }    strcpy(fileresprobmorprev,"prmorprev"); 
   ungetc(c,ficpar);    sprintf(digit,"%-d",ij);
      /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);    strcat(fileresprobmorprev,digit); /* Tvar to be done */
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    strcat(fileresprobmorprev,fileres);
          if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
   while((c=getc(ficpar))=='#' && c!= EOF){      printf("Problem with resultfile: %s\n", fileresprobmorprev);
     ungetc(c,ficpar);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
     fgets(line, MAXLINE, ficpar);    }
     puts(line);    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     fputs(line,ficparo);   
   }    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   ungetc(c,ficpar);    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);
    dateprev1=anprev1+mprev1/12.+jprev1/365.;    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
    dateprev2=anprev2+mprev2/12.+jprev2/365.;      fprintf(ficresprobmorprev," p.%-d SE",j);
       for(i=1; i<=nlstate;i++)
   fscanf(ficpar,"pop_based=%d\n",&popbased);        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
   fprintf(ficparo,"pop_based=%d\n",popbased);      }  
   fprintf(ficres,"pop_based=%d\n",popbased);      fprintf(ficresprobmorprev,"\n");
      fprintf(ficgp,"\n# Routine varevsij");
   while((c=getc(ficpar))=='#' && c!= EOF){    /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
     ungetc(c,ficpar);    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");
     fgets(line, MAXLINE, ficpar);    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
     puts(line);  /*   } */
     fputs(line,ficparo);    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   }    pstamp(ficresvij);
   ungetc(c,ficpar);    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
     if(popbased==1)
   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(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);
 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);    else
 fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);      fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
     fprintf(ficresvij,"# Age");
     for(i=1; i<=nlstate;i++)
 while((c=getc(ficpar))=='#' && c!= EOF){      for(j=1; j<=nlstate;j++)
     ungetc(c,ficpar);        fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
     fgets(line, MAXLINE, ficpar);    fprintf(ficresvij,"\n");
     puts(line);  
     fputs(line,ficparo);    xp=vector(1,npar);
   }    dnewm=matrix(1,nlstate,1,npar);
   ungetc(c,ficpar);    doldm=matrix(1,nlstate,1,nlstate);
     dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);  
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
     gpp=vector(nlstate+1,nlstate+ndeath);
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    gmp=vector(nlstate+1,nlstate+ndeath);
     trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
 /*------------ gnuplot -------------*/    
   strcpy(optionfilegnuplot,optionfilefiname);    if(estepm < stepm){
   strcat(optionfilegnuplot,".gp");      printf ("Problem %d lower than %d\n",estepm, stepm);
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {    }
     printf("Problem with file %s",optionfilegnuplot);    else  hstepm=estepm;   
   }    /* For example we decided to compute the life expectancy with the smallest unit */
   fclose(ficgp);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
  printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);       nhstepm is the number of hstepm from age to agelim 
 /*--------- index.htm --------*/       nstepm is the number of stepm from age to agelin. 
        Look at function hpijx to understand why (it is linked to memory size questions) */
   strcpy(optionfilehtm,optionfile);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   strcat(optionfilehtm,".htm");       survival function given by stepm (the optimization length). Unfortunately it
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {       means that if the survival funtion is printed every two years of age and if
     printf("Problem with %s \n",optionfilehtm), exit(0);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   }       results. So we changed our mind and took the option of the best precision.
     */
   fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n    agelim = AGESUP;
 \n    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
 Total number of observations=%d <br>\n      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
 <hr  size=\"2\" color=\"#EC5E5E\">      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
  <ul><li><h4>Parameter files</h4>\n      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n      gp=matrix(0,nhstepm,1,nlstate);
  - Gnuplot file name: <a href=\"%s\">%s</a></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot);      gm=matrix(0,nhstepm,1,nlstate);
   fclose(fichtm);  
   
  printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);      for(theta=1; theta <=npar; theta++){
          for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
 /*------------ free_vector  -------------*/          xp[i] = x[i] + (i==theta ?delti[theta]:0);
  chdir(path);        }
          hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
  free_ivector(wav,1,imx);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);  
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);          if (popbased==1) {
  free_ivector(num,1,n);          if(mobilav ==0){
  free_vector(agedc,1,n);            for(i=1; i<=nlstate;i++)
  /*free_matrix(covar,1,NCOVMAX,1,n);*/              prlim[i][i]=probs[(int)age][i][ij];
  fclose(ficparo);          }else{ /* mobilav */ 
  fclose(ficres);            for(i=1; i<=nlstate;i++)
               prlim[i][i]=mobaverage[(int)age][i][ij];
           }
   /*--------------- Prevalence limit --------------*/        }
      
   strcpy(filerespl,"pl");        for(j=1; j<= nlstate; j++){
   strcat(filerespl,fileres);          for(h=0; h<=nhstepm; h++){
   if((ficrespl=fopen(filerespl,"w"))==NULL) {            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
   }          }
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);        }
   fprintf(ficrespl,"#Prevalence limit\n");        /* This for computing probability of death (h=1 means
   fprintf(ficrespl,"#Age ");           computed over hstepm matrices product = hstepm*stepm months) 
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);           as a weighted average of prlim.
   fprintf(ficrespl,"\n");        */
          for(j=nlstate+1;j<=nlstate+ndeath;j++){
   prlim=matrix(1,nlstate,1,nlstate);          for(i=1,gpp[j]=0.; i<= nlstate; i++)
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            gpp[j] += prlim[i][i]*p3mat[i][j][1];
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        }    
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        /* end probability of death */
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
   k=0;          xp[i] = x[i] - (i==theta ?delti[theta]:0);
   agebase=ageminpar;        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   agelim=agemaxpar;        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   ftolpl=1.e-10;   
   i1=cptcoveff;        if (popbased==1) {
   if (cptcovn < 1){i1=1;}          if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
   for(cptcov=1;cptcov<=i1;cptcov++){              prlim[i][i]=probs[(int)age][i][ij];
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          }else{ /* mobilav */ 
         k=k+1;            for(i=1; i<=nlstate;i++)
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/              prlim[i][i]=mobaverage[(int)age][i][ij];
         fprintf(ficrespl,"\n#******");          }
         for(j=1;j<=cptcoveff;j++)        }
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
         fprintf(ficrespl,"******\n");        for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
                  for(h=0; h<=nhstepm; h++){
         for (age=agebase; age<=agelim; age++){            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
           fprintf(ficrespl,"%.0f",age );          }
           for(i=1; i<=nlstate;i++)        }
           fprintf(ficrespl," %.5f", prlim[i][i]);        /* This for computing probability of death (h=1 means
           fprintf(ficrespl,"\n");           computed over hstepm matrices product = hstepm*stepm months) 
         }           as a weighted average of prlim.
       }        */
     }        for(j=nlstate+1;j<=nlstate+ndeath;j++){
   fclose(ficrespl);          for(i=1,gmp[j]=0.; i<= nlstate; i++)
            gmp[j] += prlim[i][i]*p3mat[i][j][1];
   /*------------- h Pij x at various ages ------------*/        }    
          /* end probability of death */
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);  
   if((ficrespij=fopen(filerespij,"w"))==NULL) {        for(j=1; j<= nlstate; j++) /* vareij */
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;          for(h=0; h<=nhstepm; h++){
   }            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
   printf("Computing pij: result on file '%s' \n", filerespij);          }
    
   stepsize=(int) (stepm+YEARM-1)/YEARM;        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
   /*if (stepm<=24) stepsize=2;*/          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
         }
   agelim=AGESUP;  
   hstepm=stepsize*YEARM; /* Every year of age */      } /* End theta */
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */  
       trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   /* hstepm=1;   aff par mois*/  
       for(h=0; h<=nhstepm; h++) /* veij */
   k=0;        for(j=1; j<=nlstate;j++)
   for(cptcov=1;cptcov<=i1;cptcov++){          for(theta=1; theta <=npar; theta++)
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){            trgradg[h][j][theta]=gradg[h][theta][j];
       k=k+1;  
         fprintf(ficrespij,"\n#****** ");      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
         for(j=1;j<=cptcoveff;j++)        for(theta=1; theta <=npar; theta++)
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          trgradgp[j][theta]=gradgp[theta][j];
         fprintf(ficrespij,"******\n");    
          
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      for(i=1;i<=nlstate;i++)
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */        for(j=1;j<=nlstate;j++)
           vareij[i][j][(int)age] =0.;
           /*      nhstepm=nhstepm*YEARM; aff par mois*/  
       for(h=0;h<=nhstepm;h++){
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        for(k=0;k<=nhstepm;k++){
           oldm=oldms;savm=savms;          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
           fprintf(ficrespij,"# Age");          for(i=1;i<=nlstate;i++)
           for(i=1; i<=nlstate;i++)            for(j=1;j<=nlstate;j++)
             for(j=1; j<=nlstate+ndeath;j++)              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
               fprintf(ficrespij," %1d-%1d",i,j);        }
           fprintf(ficrespij,"\n");      }
            for (h=0; h<=nhstepm; h++){    
             fprintf(ficrespij,"%d %f %f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );      /* pptj */
             for(i=1; i<=nlstate;i++)      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
               for(j=1; j<=nlstate+ndeath;j++)      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);      for(j=nlstate+1;j<=nlstate+ndeath;j++)
             fprintf(ficrespij,"\n");        for(i=nlstate+1;i<=nlstate+ndeath;i++)
              }          varppt[j][i]=doldmp[j][i];
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      /* end ppptj */
           fprintf(ficrespij,"\n");      /*  x centered again */
         }      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
     }      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
   }   
       if (popbased==1) {
   varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);        if(mobilav ==0){
           for(i=1; i<=nlstate;i++)
   fclose(ficrespij);            prlim[i][i]=probs[(int)age][i][ij];
         }else{ /* mobilav */ 
           for(i=1; i<=nlstate;i++)
   /*---------- Forecasting ------------------*/            prlim[i][i]=mobaverage[(int)age][i][ij];
   if((stepm == 1) && (strcmp(model,".")==0)){        }
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);      }
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);               
   }      /* This for computing probability of death (h=1 means
   else{         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
     erreur=108;         as a weighted average of prlim.
     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);      */
   }      for(j=nlstate+1;j<=nlstate+ndeath;j++){
          for(i=1,gmp[j]=0.;i<= nlstate; i++) 
           gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
   /*---------- Health expectancies and variances ------------*/      }    
       /* end probability of death */
   strcpy(filerest,"t");  
   strcat(filerest,fileres);      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
   if((ficrest=fopen(filerest,"w"))==NULL) {      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
   }        for(i=1; i<=nlstate;i++){
   printf("Computing Total LEs with variances: file '%s' \n", filerest);          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
         }
       } 
   strcpy(filerese,"e");      fprintf(ficresprobmorprev,"\n");
   strcat(filerese,fileres);  
   if((ficreseij=fopen(filerese,"w"))==NULL) {      fprintf(ficresvij,"%.0f ",age );
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);      for(i=1; i<=nlstate;i++)
   }        for(j=1; j<=nlstate;j++){
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
         }
  strcpy(fileresv,"v");      fprintf(ficresvij,"\n");
   strcat(fileresv,fileres);      free_matrix(gp,0,nhstepm,1,nlstate);
   if((ficresvij=fopen(fileresv,"w"))==NULL) {      free_matrix(gm,0,nhstepm,1,nlstate);
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
   }      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   calagedate=-1;    } /* End age */
 prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    free_vector(gpp,nlstate+1,nlstate+ndeath);
     free_vector(gmp,nlstate+1,nlstate+ndeath);
   k=0;    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
   for(cptcov=1;cptcov<=i1;cptcov++){    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
       k=k+1;    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
       fprintf(ficrest,"\n#****** ");    fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
       for(j=1;j<=cptcoveff;j++)  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
       fprintf(ficrest,"******\n");  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
     fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
       fprintf(ficreseij,"\n#****** ");    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
       for(j=1;j<=cptcoveff;j++)    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
       fprintf(ficreseij,"******\n");    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
     /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
       fprintf(ficresvij,"\n#****** ");  */
       for(j=1;j<=cptcoveff;j++)  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
       fprintf(ficresvij,"******\n");  
     free_vector(xp,1,npar);
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    free_matrix(doldm,1,nlstate,1,nlstate);
       oldm=oldms;savm=savms;    free_matrix(dnewm,1,nlstate,1,npar);
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);      free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
      free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
       oldm=oldms;savm=savms;    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);    fclose(ficresprobmorprev);
        fflush(ficgp);
     fflush(fichtm); 
    }  /* end varevsij */
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");  
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);  /************ Variance of prevlim ******************/
       fprintf(ficrest,"\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[])
   {
       epj=vector(1,nlstate+1);    /* Variance of prevalence limit */
       for(age=bage; age <=fage ;age++){    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    double **newm;
         if (popbased==1) {    double **dnewm,**doldm;
           for(i=1; i<=nlstate;i++)    int i, j, nhstepm, hstepm;
             prlim[i][i]=probs[(int)age][i][k];    int k, cptcode;
         }    double *xp;
            double *gp, *gm;
         fprintf(ficrest," %4.0f",age);    double **gradg, **trgradg;
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){    double age,agelim;
           for(i=1, epj[j]=0.;i <=nlstate;i++) {    int theta;
             epj[j] += prlim[i][i]*eij[i][j][(int)age];    
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/    pstamp(ficresvpl);
           }    fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
           epj[nlstate+1] +=epj[j];    fprintf(ficresvpl,"# Age");
         }    for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %1d-%1d",i,i);
         for(i=1, vepp=0.;i <=nlstate;i++)    fprintf(ficresvpl,"\n");
           for(j=1;j <=nlstate;j++)  
             vepp += vareij[i][j][(int)age];    xp=vector(1,npar);
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));    dnewm=matrix(1,nlstate,1,npar);
         for(j=1;j <=nlstate;j++){    doldm=matrix(1,nlstate,1,nlstate);
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));    
         }    hstepm=1*YEARM; /* Every year of age */
         fprintf(ficrest,"\n");    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
       }    agelim = AGESUP;
     }    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   }      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
 free_matrix(mint,1,maxwav,1,n);      if (stepm >= YEARM) hstepm=1;
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
     free_vector(weight,1,n);      gradg=matrix(1,npar,1,nlstate);
   fclose(ficreseij);      gp=vector(1,nlstate);
   fclose(ficresvij);      gm=vector(1,nlstate);
   fclose(ficrest);  
   fclose(ficpar);      for(theta=1; theta <=npar; theta++){
   free_vector(epj,1,nlstate+1);        for(i=1; i<=npar; i++){ /* Computes gradient */
            xp[i] = x[i] + (i==theta ?delti[theta]:0);
   /*------- Variance limit prevalence------*/          }
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   strcpy(fileresvpl,"vpl");        for(i=1;i<=nlstate;i++)
   strcat(fileresvpl,fileres);          gp[i] = prlim[i][i];
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {      
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);        for(i=1; i<=npar; i++) /* Computes gradient */
     exit(0);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
   }        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);        for(i=1;i<=nlstate;i++)
           gm[i] = prlim[i][i];
   k=0;  
   for(cptcov=1;cptcov<=i1;cptcov++){        for(i=1;i<=nlstate;i++)
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
       k=k+1;      } /* End theta */
       fprintf(ficresvpl,"\n#****** ");  
       for(j=1;j<=cptcoveff;j++)      trgradg =matrix(1,nlstate,1,npar);
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
       fprintf(ficresvpl,"******\n");      for(j=1; j<=nlstate;j++)
              for(theta=1; theta <=npar; theta++)
       varpl=matrix(1,nlstate,(int) bage, (int) fage);          trgradg[j][theta]=gradg[theta][j];
       oldm=oldms;savm=savms;  
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);      for(i=1;i<=nlstate;i++)
     }        varpl[i][(int)age] =0.;
  }      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
       matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
   fclose(ficresvpl);      for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   /*---------- End : free ----------------*/  
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);      fprintf(ficresvpl,"%.0f ",age );
        for(i=1; i<=nlstate;i++)
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);      fprintf(ficresvpl,"\n");
        free_vector(gp,1,nlstate);
        free_vector(gm,1,nlstate);
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);      free_matrix(gradg,1,npar,1,nlstate);
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);      free_matrix(trgradg,1,nlstate,1,npar);
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);    } /* End age */
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);  
      free_vector(xp,1,npar);
   free_matrix(matcov,1,npar,1,npar);    free_matrix(doldm,1,nlstate,1,npar);
   free_vector(delti,1,npar);    free_matrix(dnewm,1,nlstate,1,nlstate);
   free_matrix(agev,1,maxwav,1,imx);  
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);  }
   
   fprintf(fichtm,"\n</body>");  /************ Variance of one-step probabilities  ******************/
   fclose(fichtm);  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[])
   fclose(ficgp);  {
      int i, j=0,  i1, k1, l1, t, tj;
     int k2, l2, j1,  z1;
   if(erreur >0)    int k=0,l, cptcode;
     printf("End of Imach with error or warning %d\n",erreur);    int first=1, first1, first2;
   else   printf("End of Imach\n");    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */    double **dnewm,**doldm;
      double *xp;
   /* 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);*/    double *gp, *gm;
   /*printf("Total time was %d uSec.\n", total_usecs);*/    double **gradg, **trgradg;
   /*------ End -----------*/    double **mu;
     double age,agelim, cov[NCOVMAX+1];
     double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
  end:    int theta;
 #ifdef windows    char fileresprob[FILENAMELENGTH];
   /* chdir(pathcd);*/    char fileresprobcov[FILENAMELENGTH];
 #endif    char fileresprobcor[FILENAMELENGTH];
  /*system("wgnuplot graph.plt");*/    double ***varpij;
  /*system("../gp37mgw/wgnuplot graph.plt");*/  
  /*system("cd ../gp37mgw");*/    strcpy(fileresprob,"prob"); 
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/    strcat(fileresprob,fileres);
  strcpy(plotcmd,GNUPLOTPROGRAM);    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
  strcat(plotcmd," ");      printf("Problem with resultfile: %s\n", fileresprob);
  strcat(plotcmd,optionfilegnuplot);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
  system(plotcmd);    }
     strcpy(fileresprobcov,"probcov"); 
 #ifdef windows    strcat(fileresprobcov,fileres);
   while (z[0] != 'q') {    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
     /* chdir(path); */      printf("Problem with resultfile: %s\n", fileresprobcov);
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
     scanf("%s",z);    }
     if (z[0] == 'c') system("./imach");    strcpy(fileresprobcor,"probcor"); 
     else if (z[0] == 'e') system(optionfilehtm);    strcat(fileresprobcor,fileres);
     else if (z[0] == 'g') system(plotcmd);    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
     else if (z[0] == 'q') exit(0);      printf("Problem with resultfile: %s\n", fileresprobcor);
   }      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
 #endif    }
 }    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     pstamp(ficresprob);
     fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
     fprintf(ficresprob,"# Age");
     pstamp(ficresprobcov);
     fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
     fprintf(ficresprobcov,"# Age");
     pstamp(ficresprobcor);
     fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
     fprintf(ficresprobcor,"# Age");
   
   
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprob," p%1d-%1d (SE)",i,j);
         fprintf(ficresprobcov," p%1d-%1d ",i,j);
         fprintf(ficresprobcor," p%1d-%1d ",i,j);
       }  
    /* fprintf(ficresprob,"\n");
     fprintf(ficresprobcov,"\n");
     fprintf(ficresprobcor,"\n");
    */
     xp=vector(1,npar);
     dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
     varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
     first=1;
     fprintf(ficgp,"\n# Routine varprob");
     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
     fprintf(fichtm,"\n");
   
     fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
     fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
     file %s<br>\n",optionfilehtmcov);
     fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
   and drawn. It helps understanding how is the covariance between two incidences.\
    They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
     fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
   It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
   would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
   standard deviations wide on each axis. <br>\
    Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
    and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
   To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
   
     cov[1]=1;
     /* tj=cptcoveff; */
     tj = (int) pow(2,cptcoveff);
     if (cptcovn<1) {tj=1;ncodemax[1]=1;}
     j1=0;
     for(j1=1; j1<=tj;j1++){
       /*for(i1=1; i1<=ncodemax[t];i1++){ */
       /*j1++;*/
         if  (cptcovn>0) {
           fprintf(ficresprob, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprob, "**********\n#\n");
           fprintf(ficresprobcov, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcov, "**********\n#\n");
           
           fprintf(ficgp, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficgp, "**********\n#\n");
           
           
           fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
           
           fprintf(ficresprobcor, "\n#********** Variable ");    
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcor, "**********\n#");    
         }
         
         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
         gp=vector(1,(nlstate)*(nlstate+ndeath));
         gm=vector(1,(nlstate)*(nlstate+ndeath));
         for (age=bage; age<=fage; age ++){ 
           cov[2]=age;
           for (k=1; k<=cptcovn;k++) {
             cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
                                                            * 1  1 1 1 1
                                                            * 2  2 1 1 1
                                                            * 3  1 2 1 1
                                                            */
             /* nbcode[1][1]=0 nbcode[1][2]=1;*/
           }
           for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
           for (k=1; k<=cptcovprod;k++)
             cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
           
       
           for(theta=1; theta <=npar; theta++){
             for(i=1; i<=npar; i++)
               xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
             
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             
             k=0;
             for(i=1; i<= (nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gp[k]=pmmij[i][j];
               }
             }
             
             for(i=1; i<=npar; i++)
               xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
       
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             k=0;
             for(i=1; i<=(nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gm[k]=pmmij[i][j];
               }
             }
        
             for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
               gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
           }
   
           for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
             for(theta=1; theta <=npar; theta++)
               trgradg[j][theta]=gradg[theta][j];
           
           matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
           matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
   
           pmij(pmmij,cov,ncovmodel,x,nlstate);
           
           k=0;
           for(i=1; i<=(nlstate); i++){
             for(j=1; j<=(nlstate+ndeath);j++){
               k=k+1;
               mu[k][(int) age]=pmmij[i][j];
             }
           }
           for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
             for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
               varpij[i][j][(int)age] = doldm[i][j];
   
           /*printf("\n%d ",(int)age);
             for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             }*/
   
           fprintf(ficresprob,"\n%d ",(int)age);
           fprintf(ficresprobcov,"\n%d ",(int)age);
           fprintf(ficresprobcor,"\n%d ",(int)age);
   
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
             fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
             fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
           }
           i=0;
           for (k=1; k<=(nlstate);k++){
             for (l=1; l<=(nlstate+ndeath);l++){ 
               i++;
               fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
               fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
               for (j=1; j<=i;j++){
                 /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
                 fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
                 fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
               }
             }
           }/* end of loop for state */
         } /* end of loop for age */
         free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
         free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
         free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
         free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
         
         /* Confidence intervalle of pij  */
         /*
           fprintf(ficgp,"\nunset parametric;unset label");
           fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
           fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
           fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
           fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
           fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
           fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
         */
   
         /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
         first1=1;first2=2;
         for (k2=1; k2<=(nlstate);k2++){
           for (l2=1; l2<=(nlstate+ndeath);l2++){ 
             if(l2==k2) continue;
             j=(k2-1)*(nlstate+ndeath)+l2;
             for (k1=1; k1<=(nlstate);k1++){
               for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                 if(l1==k1) continue;
                 i=(k1-1)*(nlstate+ndeath)+l1;
                 if(i<=j) continue;
                 for (age=bage; age<=fage; age ++){ 
                   if ((int)age %5==0){
                     v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                     v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     mu1=mu[i][(int) age]/stepm*YEARM ;
                     mu2=mu[j][(int) age]/stepm*YEARM;
                     c12=cv12/sqrt(v1*v2);
                     /* Computing eigen value of matrix of covariance */
                     lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     if ((lc2 <0) || (lc1 <0) ){
                       if(first2==1){
                         first1=0;
                       printf("Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS. See log file for details...\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);
                       }
                       fprintf(ficlog,"Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS.\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);fflush(ficlog);
                       /* lc1=fabs(lc1); */ /* If we want to have them positive */
                       /* lc2=fabs(lc2); */
                     }
   
                     /* Eigen vectors */
                     v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                     /*v21=sqrt(1.-v11*v11); *//* error */
                     v21=(lc1-v1)/cv12*v11;
                     v12=-v21;
                     v22=v11;
                     tnalp=v21/v11;
                     if(first1==1){
                       first1=0;
                       printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     }
                     fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     /*printf(fignu*/
                     /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                     /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                     if(first==1){
                       first=0;
                       fprintf(ficgp,"\nset parametric;unset label");
                       fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
                       fprintf(ficgp,"\nset ter png small size 320, 240");
                       fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
    :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
   %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }else{
                       first=0;
                       fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }/* if first */
                   } /* age mod 5 */
                 } /* end loop age */
                 fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                 first=1;
               } /*l12 */
             } /* k12 */
           } /*l1 */
         }/* k1 */
         /* } /* loop covariates */
     }
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
     free_vector(xp,1,npar);
     fclose(ficresprob);
     fclose(ficresprobcov);
     fclose(ficresprobcor);
     fflush(ficgp);
     fflush(fichtmcov);
   }
   
   
   /******************* Printing html file ***********/
   void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                     int popforecast, int estepm ,\
                     double jprev1, double mprev1,double anprev1, \
                     double jprev2, double mprev2,double anprev2){
     int jj1, k1, i1, cpt;
   
      fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
      <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
   </ul>");
      fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
    - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
              jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
      fprintf(fichtm,"\
    - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
              stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
      fprintf(fichtm,"\
    - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
              subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
      fprintf(fichtm,"\
    - (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n",
              estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
      fprintf(fichtm,"\
    - Population projections by age and states: \
      <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
   
   fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
    m=pow(2,cptcoveff);
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        /* Pij */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d_1.png\">%s%d_1.png</a><br> \
   <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
        /* Quasi-incidences */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
    before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d_2.png\">%s%d_2.png</a><br> \
   <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
          /* Period (stable) prevalence in each health state */
          for(cpt=1; cpt<=nlstate;cpt++){
            fprintf(fichtm,"<br>- Convergence from each state (1 to %d) to period (stable) prevalence in state %d <a href=\"%s%d_%d.png\">%s%d_%d.png</a><br> \
   <img src=\"%s%d_%d.png\">",nlstate, cpt, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
          }
        for(cpt=1; cpt<=nlstate;cpt++) {
           fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
   <img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
        }
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
   
   
    fprintf(fichtm,"\
   \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
    - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
   
    fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
    fprintf(fichtm,"\
    - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
   
    fprintf(fichtm,"\
    - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
    fprintf(fichtm,"\
    - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
            estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
    fprintf(fichtm,"\
    - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",
            estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
    fprintf(fichtm,"\
    - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
            subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   
   /*  if(popforecast==1) fprintf(fichtm,"\n */
   /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
   /*      <br>",fileres,fileres,fileres,fileres); */
   /*  else  */
   /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
    fflush(fichtm);
    fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   
    m=pow(2,cptcoveff);
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        for(cpt=1; cpt<=nlstate;cpt++) {
          fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
   prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
   <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
        }
        fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
   true period expectancies (those weighted with period prevalences are also\
    drawn in addition to the population based expectancies computed using\
    observed and cahotic prevalences: %s%d.png<br>\
   <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
    fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m0,cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
     int ng=0;
   /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   /*     printf("Problem with file %s",optionfilegnuplot); */
   /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   /*   } */
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
     m=pow(2,cptcoveff);
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
    /* 1eme*/
     fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
     for (cpt=1; cpt<= nlstate ; cpt ++) {
       for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
        fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
        fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
        fprintf(ficgp,"set xlabel \"Age\" \n\
   set ylabel \"Probability\" \n\
   set ter png small size 320, 240\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else        fprintf(ficgp," \%%*lf (\%%*lf)");
        }
        fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        } 
        fprintf(ficgp,"\" t\"95\%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }  
        fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
      }
     }
     /*2 eme*/
     fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
     for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
       fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
       
       for (i=1; i<= nlstate+1 ; i ++) {
         k=2*i;
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         fprintf(ficgp,"\" t\"\" w l lt 0,");
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
         else fprintf(ficgp,"\" t\"\" w l lt 0,");
       }
     }
     
     /*3eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<= nlstate ; cpt ++) {
         /*       k=2+nlstate*(2*cpt-2); */
         k=2+(nlstate+1)*(cpt-1);
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
         fprintf(ficgp,"set ter png small size 320, 240\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           
         */
         for (i=1; i< nlstate ; i ++) {
           fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1);
           /*      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
           
         } 
         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
       }
     }
     
     /* CV preval stable (period) */
     for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
         k=3;
         fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
         fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   set ter png small size 320, 240\n\
   unset log y\n\
   plot [%.f:%.f]  ", ageminpar, agemaxpar);
         for (i=1; i<= nlstate ; i ++){
           if(i==1)
             fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
           else
             fprintf(ficgp,", '' ");
           l=(nlstate+ndeath)*(i-1)+1;
           fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
           for (j=1; j<= (nlstate-1) ; j ++)
             fprintf(ficgp,"+$%d",k+l+j);
           fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
         } /* nlstate */
         fprintf(ficgp,"\n");
       } /* end cpt state*/ 
     } /* end covariate */  
     
     /* proba elementaires */
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             jk++; 
             fprintf(ficgp,"\n");
           }
         }
       }
      }
     /*goto avoid;*/
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        for(jk=1; jk <=m; jk++) {
          fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
          if (ng==2)
            fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
          else
            fprintf(ficgp,"\nset title \"Probability\"\n");
          fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
          for(k2=1; k2<=nlstate; k2++) {
            k3=i;
            for(k=1; k<=(nlstate+ndeath); k++) {
              if (k != k2){
                if(ng==2)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                else
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;/* To be checked else nbcode[0][0] wrong */
                for(j=3; j <=ncovmodel; j++) {
                  /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /\* Bug valgrind *\/ */
                  /*        /\*fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);*\/ */
                  /*        ij++; */
                  /* } */
                  /* else */
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
                fprintf(ficgp,")/(1");
                
                for(k1=1; k1 <=nlstate; k1++){   
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
                  for(j=3; j <=ncovmodel; j++){
                    /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { */
                    /*   fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); */
                    /*   ij++; */
                    /* } */
                    /* else */
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                  }
                  fprintf(ficgp,")");
                }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
              }
            } /* end k */
          } /* end k2 */
        } /* end jk */
      } /* end ng */
    avoid:
      fflush(ficgp); 
   }  /* end gnuplot */
   
   
   /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
     int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
     double age;
   
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          we use a 5 terms etc. until the borders are no more concerned. 
       */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
           }
         }/* end age */
       }/* end mob */
     }else return -1;
     return 0;
   }/* End movingaverage */
   
   
   /************** Forecasting ******************/
   prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
     int *popage;
     double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   
   
   /**************** function prwizard **********************/
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     /* Wizard to print covariance matrix template */
   
     char ca[32], cb[32], cc[32];
     int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
   } /* end of prwizard */
   /******************* Gompertz Likelihood ******************************/
   double gompertz(double x[])
   { 
     double A,B,L=0.0,sump=0.,num=0.;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
   
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
                +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           L=L+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
    
     return -2*L*num/sump;
   }
   
   #ifdef GSL
   /******************* Gompertz_f Likelihood ******************************/
   double gompertz_f(const gsl_vector *v, void *params)
   { 
     double A,B,LL=0.0,sump=0.,num=0.;
     double *x= (double *) v->data;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
     printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
                +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           LL=LL+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
     printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
    
     return -2*LL*num/sump;
   }
   #endif
   
   /******************* Printing html file ***********/
   void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,  double p[],double **matcov,double agemortsup){
     int i,k;
   
     fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
     fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
     for (i=1;i<=2;i++) 
       fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
     fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
     fprintf(fichtm,"</ul>");
   
   fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
   
    fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
   
    for (k=agegomp;k<(agemortsup-2);k++) 
      fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
   
    
     fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
     fprintf(ficgp,"set out \"graphmort.png\"\n "); 
     fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
     fprintf(ficgp, "set ter png small size 320, 240\n set log y\n"); 
     /* fprintf(ficgp, "set size 0.65,0.65\n"); */
     fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
   
   } 
   
   int readdata(char datafile[], int firstobs, int lastobs, int *imax)
   {
   
     /*-------- data file ----------*/
     FILE *fic;
     char dummy[]="                         ";
     int i, j, n;
     int linei, month, year,iout;
     char line[MAXLINE], linetmp[MAXLINE];
     char stra[80], strb[80];
     char *stratrunc;
     int lstra;
   
   
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem while opening datafile: %s\n", datafile);return 1;
       fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
     }
   
     i=1;
     linei=0;
     while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
       linei=linei+1;
       for(j=strlen(line); j>=0;j--){  /* Untabifies line */
         if(line[j] == '\t')
           line[j] = ' ';
       }
       for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
         ;
       };
       line[j+1]=0;  /* Trims blanks at end of line */
       if(line[0]=='#'){
         fprintf(ficlog,"Comment line\n%s\n",line);
         printf("Comment line\n%s\n",line);
         continue;
       }
       trimbb(linetmp,line); /* Trims multiple blanks in line */
       for (j=0; line[j]!='\0';j++){
         line[j]=linetmp[j];
       }
     
   
       for (j=maxwav;j>=1;j--){
         cutv(stra, strb, line, ' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
         /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
             fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);
             return 1;
           }
         }
         s[j][i]=lval;
         
         strcpy(line,stra);
         cutv(stra, strb,line,' ');
         if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
         }
         else  if(iout=sscanf(strb,"%s.",dummy) != 0){
           month=99;
           year=9999;
         }else{
           printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);fflush(ficlog);
           return 1;
         }
         anint[j][i]= (double) year; 
         mint[j][i]= (double)month; 
         strcpy(line,stra);
       } /* ENd Waves */
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.",dummy) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
       }
       andc[i]=(double) year; 
       moisdc[i]=(double) month; 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.", dummy) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
       }
       if (year==9999) {
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given.  Exiting.\n",strb, linei,i,line);
         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
   
       }
       annais[i]=(double)(year);
       moisnais[i]=(double)(month); 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       errno=0;
       dval=strtod(strb,&endptr); 
       if( strb[0]=='\0' || (*endptr != '\0')){
         printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fprintf(ficlog,"Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fflush(ficlog);
         return 1;
       }
       weight[i]=dval; 
       strcpy(line,stra);
       
       for (j=ncovcol;j>=1;j--){
         cutv(stra, strb,line,' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);
             fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);fflush(ficlog);
             return 1;
           }
         }
         if(lval <-1 || lval >1){
           printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);
           fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
           return 1;
         }
         covar[j][i]=(double)(lval);
         strcpy(line,stra);
       }  
       lstra=strlen(stra);
        
       if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
         stratrunc = &(stra[lstra-9]);
         num[i]=atol(stratrunc);
       }
       else
         num[i]=atol(stra);
       /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
         printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
       
       i=i+1;
     } /* End loop reading  data */
   
     *imax=i-1; /* Number of individuals */
     fclose(fic);
    
     return (0);
     endread:
       printf("Exiting readdata: ");
       fclose(fic);
       return (1);
   
   
   
   }
   void removespace(char *str) {
     char *p1 = str, *p2 = str;
     do
       while (*p2 == ' ')
         p2++;
     while (*p1++ = *p2++);
   }
   
   int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
      * Model  V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age
      * - cptcovt total number of covariates of the model nbocc(+)+1 = 8
      * - cptcovn or number of covariates k of the models excluding age*products =6
      * - cptcovage number of covariates with age*products =2
      * - cptcovs number of simple covariates
      * - Tvar[k] is the id of the kth covariate Tvar[1]@12 {1, 2, 3, 8, 10, 11, 8, 3, 7, 8, 5, 6}, thus Tvar[5=V7*V8]=10
      *     which is a new column after the 9 (ncovcol) variables. 
      * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
      * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
      *    Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
      * - Tvard[k]  p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
    */
   {
     int i, j, k, ks;
     int i1, j1, k1, k2;
     char modelsav[80];
     char stra[80], strb[80], strc[80], strd[80],stre[80];
   
     /*removespace(model);*/
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
       j=nbocc(model,'+'); /**< j=Number of '+' */
       j1=nbocc(model,'*'); /**< j1=Number of '*' */
       cptcovs=j+1-j1; /**<  Number of simple covariates V1+V2*age+V3 +V3*V4=> V1 + V3 =2  */
       cptcovt= j+1; /* Number of total covariates in the model V1 + V2*age+ V3 + V3*V4=> 4*/
                     /* including age products which are counted in cptcovage.
                     /* but the covariates which are products must be treated separately: ncovn=4- 2=2 (V1+V3). */
       cptcovprod=j1; /**< Number of products  V1*V2 +v3*age = 2 */
       cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1  */
       strcpy(modelsav,model); 
       if (strstr(model,"AGE") !=0){
         printf("Error. AGE must be in lower case 'age' model=%s ",model);
         fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
         return 1;
       }
       if (strstr(model,"v") !=0){
         printf("Error. 'v' must be in upper case 'V' model=%s ",model);
         fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
         return 1;
       }
       
       /*   Design
        *  V1   V2   V3   V4  V5  V6  V7  V8  V9 Weight
        *  <          ncovcol=8                >
        * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
        *   k=  1    2      3       4     5       6      7        8
        *  cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
        *  covar[k,i], value of kth covariate if not including age for individual i:
        *       covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
        *  Tvar[k] # of the kth covariate:  Tvar[1]=2  Tvar[4]=3 Tvar[8]=8
        *       if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and 
        *  Tage[++cptcovage]=k
        *       if products, new covar are created after ncovcol with k1
        *  Tvar[k]=ncovcol+k1; # of the kth covariate product:  Tvar[5]=ncovcol+1=10  Tvar[6]=ncovcol+1=11
        *  Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
        *  Tvard[k1][1]=m Tvard[k1][2]=m; Tvard[1][1]=5 (V5) Tvard[1][2]=6 Tvard[2][1]=7 (V7) Tvard[2][2]=8
        *  Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
        *  Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
        *  V1   V2   V3   V4  V5  V6  V7  V8  V9  V10  V11
        *  <          ncovcol=8                >
        *       Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8    d1   d1   d2  d2
        *          k=  1    2      3       4     5       6      7        8    9   10   11  12
        *     Tvar[k]= 2    1      3       3    10      11      8        8    5    6    7   8
        * p Tvar[1]@12={2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
        * p Tprod[1]@2={                         6, 5}
        *p Tvard[1][1]@4= {7, 8, 5, 6}
        * covar[k][i]= V2   V1      ?      V3    V5*V6?   V7*V8?  ?       V8   
        *  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
        *How to reorganize?
        * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
        * Tvars {2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
        *       {2,   1,     4,      8,    5,      6,     3,       7}
        * Struct []
        */
   
       /* This loop fills the array Tvar from the string 'model'.*/
       /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
       /*   modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4  */
       /*  k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
       /*  k=3 V4 Tvar[k=3]= 4 (from V4) */
       /*  k=2 V1 Tvar[k=2]= 1 (from V1) */
       /*  k=1 Tvar[1]=2 (from V2) */
       /*  k=5 Tvar[5] */
       /* for (k=1; k<=cptcovn;k++) { */
       /*  cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
       /*  } */
       /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
       /*
        * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
       for(k=cptcovt; k>=1;k--) /**< Number of covariates */
           Tvar[k]=0;
       cptcovage=0;
       for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
         cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' 
                                        modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
           cutl(strc,strd,strb,'*'); /**< strd*strc  Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
           if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
             /* covar is not filled and then is empty */
             cptcovprod--;
             cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
             Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2 */
             cptcovage++; /* Sums the number of covariates which include age as a product */
             Tage[cptcovage]=k;  /* Tage[1] = 4 */
             /*printf("stre=%s ", stre);*/
           } else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutl(stre,strb,strc,'V');
             Tvar[k]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=k;
           } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/
             /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
             cptcovn++;
             cptcovprodnoage++;k1++;
             cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
             Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
                                     because this model-covariate is a construction we invent a new column
                                     ncovcol + k1
                                     If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
                                     Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
             cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */
             Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
             Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
             k2=k2+2;
             Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
             Tvar[cptcovt+k2+1]=Tvard[k1][2];  /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
             for (i=1; i<=lastobs;i++){
               /* Computes the new covariate which is a product of
                  covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
               covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
             }
           } /* End age is not in the model */
         } /* End if model includes a product */
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
           cutl(strd,strc,strb,'V');
           ks++; /**< Number of simple covariates */
           cptcovn++;
           Tvar[k]=atoi(strd);
         }
         strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+V1+V4 */ 
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);*/
   
   
     return (0); /* with covar[new additional covariate if product] and Tage if age */ 
     endread:
       printf("Exiting decodemodel: ");
       return (1);
   }
   
   calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
   {
     int i, m;
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           *nberr++;
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           *nberr++;
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if ((int)andc[i]!=9999){
                   nbwarn++;
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] < *agemin){ 
               *agemin=agev[m][i];
               printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
             }
             else if(agev[m][i] >*agemax){
               *agemax=agev[m][i];
               /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           *nberr++;
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           return 1;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax); 
   
     return (0);
     endread:
       printf("Exiting calandcheckages: ");
       return (1);
   }
   
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
   #ifdef GSL
     const gsl_multimin_fminimizer_type *T;
     size_t iteri = 0, it;
     int rval = GSL_CONTINUE;
     int status = GSL_SUCCESS;
     double ssval;
   #endif
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
     int linei, month, year,iout;
     int jj, ll, li, lj, lk, imk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int itimes;
     int NDIM=2;
     int vpopbased=0;
   
     char ca[32], cb[32], cc[32];
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     struct stat info;
     double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE], pathimach[MAXLINE]; 
     char **bp, *tok, *val; /* pathtot */
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,*tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     int agemortsup;
     float  sumlpop=0.;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
     double **ximort;
     char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
     int *dcwave;
   
     char z[1]="c", occ;
   
     /*char  *strt;*/
     char strtend[80];
   
     long total_usecs;
    
   /*   setlocale (LC_ALL, ""); */
   /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   /*   textdomain (PACKAGE); */
   /*   setlocale (LC_CTYPE, ""); */
   /*   setlocale (LC_MESSAGES, ""); */
   
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     rstart_time = time(NULL);  
     /*  (void) gettimeofday(&start_time,&tzp);*/
     start_time = *localtime(&rstart_time);
     curr_time=start_time;
     /*tml = *localtime(&start_time.tm_sec);*/
     /* strcpy(strstart,asctime(&tml)); */
     strcpy(strstart,asctime(&start_time));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tm_sec = tp.tm_sec +86400; */
   /*  tm = *localtime(&start_time.tm_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tm_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     nberr=0; /* Number of errors and warnings */
     nbwarn=0;
     getcwd(pathcd, size);
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       fgets(pathr,FILENAMELENGTH,stdin);
       i=strlen(pathr);
       if(pathr[i-1]=='\n')
         pathr[i-1]='\0';
       i=strlen(pathr);
       if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
         pathr[i-1]='\0';
      for (tok = pathr; tok != NULL; ){
         printf("Pathr |%s|\n",pathr);
         while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
         printf("val= |%s| pathr=%s\n",val,pathr);
         strcpy (pathtot, val);
         if(pathr[0] == '\0') break; /* Dirty */
       }
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     /* Split argv[0], imach program to get pathimach */
     printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
     split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
     printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
    /*   strcpy(pathimach,argv[0]); */
     /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path); /* Can be a relative path */
     if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
       printf("Current directory %s!\n",pathcd);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s\n%s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: \n");
     fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     printf("Local time (at start):%s",strstart);
     fprintf(ficlog,"Local time (at start): %s",strstart);
     fflush(ficlog);
   /*   (void) gettimeofday(&curr_time,&tzp); */
   /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
       fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
       fflush(ficlog);
       /* goto end; */
       exit(70); 
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       fputs(line,stdout);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       fputs(line, stdout);
       //puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n);  /**< used in readdata */
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
     /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
        v1+v2*age+v2*v3 makes cptcovn = 3
     */
     if (strlen(model)>1) 
       ncovmodel=2+nbocc(model,'+')+1; /*Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7*/
     else
       ncovmodel=2;
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
     npar= nforce*ncovmodel; /* Number of parameters like aij*/
     if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
       printf("Too complex model for current IMaCh: npar=(nlstate+ndeath-1)*nlstate*ncovmodel=%d >= %d(MAXPARM) or nlstate=%d >= %d(NLSTATEMAX) or ndeath=%d >= %d(NDEATHMAX) or ncovmodel=(k+age+#of+signs)=%d(NCOVMAX) >= %d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fprintf(ficlog,"Too complex model for current IMaCh: %d >=%d(MAXPARM) or %d >=%d(NLSTATEMAX) or %d >=%d(NDEATHMAX) or %d(NCOVMAX) >=%d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fflush(stdout);
       fclose (ficlog);
       goto end;
     }
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     delti=delti3[1][1];
     /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
     if(mle==-1){ /* Print a wizard for help writing covariance matrix */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       fclose (ficparo);
       fclose (ficlog);
       goto end;
       exit(0);
     }
     else if(mle==-3) {
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       matcov=matrix(1,npar,1,npar);
     }
     else{
       /* Read guessed parameters */
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
       
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       for(i=1; i <=nlstate; i++){
         j=0;
         for(jj=1; jj <=nlstate+ndeath; jj++){
           if(jj==i) continue;
           j++;
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1 != i) && (j1 != j)){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
   It might be a problem of design; if ncovcol and the model are correct\n \
   run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           fprintf(ficparo,"%1d%1d",i1,j1);
           if(mle==1)
             printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar," %lf",&param[i][j][k]);
             if(mle==1){
               printf(" %lf",param[i][j][k]);
               fprintf(ficlog," %lf",param[i][j][k]);
             }
             else
               fprintf(ficlog," %lf",param[i][j][k]);
             fprintf(ficparo," %lf",param[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           if(mle==1)
             printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficparo,"\n");
         }
       }  
       fflush(ficlog);
   
       /* Reads scales values */
       p=param[1][1];
       
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
   
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath-1; j++){
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1-i)*(j1-j)!=0){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           printf("%1d%1d",i,j);
           fprintf(ficparo,"%1d%1d",i1,j1);
           fprintf(ficlog,"%1d%1d",i1,j1);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar,"%le",&delti3[i][j][k]);
             printf(" %le",delti3[i][j][k]);
             fprintf(ficparo," %le",delti3[i][j][k]);
             fprintf(ficlog," %le",delti3[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           printf("\n");
           fprintf(ficparo,"\n");
           fprintf(ficlog,"\n");
         }
       }
       fflush(ficlog);
   
       /* Reads covariance matrix */
       delti=delti3[1][1];
   
   
       /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
     
       matcov=matrix(1,npar,1,npar);
       for(i=1; i <=npar; i++)
         for(j=1; j <=npar; j++) matcov[i][j]=0.;
         
       for(i=1; i <=npar; i++){
         fscanf(ficpar,"%s",str);
         if(mle==1)
           printf("%s",str);
         fprintf(ficlog,"%s",str);
         fprintf(ficparo,"%s",str);
         for(j=1; j <=i; j++){
           fscanf(ficpar," %le",&matcov[i][j]);
           if(mle==1){
             printf(" %.5le",matcov[i][j]);
           }
           fprintf(ficlog," %.5le",matcov[i][j]);
           fprintf(ficparo," %.5le",matcov[i][j]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
       for(i=1; i <=npar; i++)
         for(j=i+1;j<=npar;j++)
           matcov[i][j]=matcov[j][i];
       
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       
       fflush(ficlog);
       
       /*-------- Rewriting parameter file ----------*/
       strcpy(rfileres,"r");    /* "Rparameterfile */
       strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
       strcat(rfileres,".");    /* */
       strcat(rfileres,optionfilext);    /* Other files have txt extension */
       if((ficres =fopen(rfileres,"w"))==NULL) {
         printf("Problem writing new parameter file: %s\n", fileres);goto end;
         fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
       }
       fprintf(ficres,"#%s\n",version);
     }    /* End of mle != -3 */
   
   
     n= lastobs;
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */ 
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
   
     /* Reads data from file datafile */
     if (readdata(datafile, firstobs, lastobs, &imx)==1)
       goto end;
   
     /* Calculation of the number of parameters from char model */
       /*    modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 
           k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
           k=3 V4 Tvar[k=3]= 4 (from V4)
           k=2 V1 Tvar[k=2]= 1 (from V1)
           k=1 Tvar[1]=2 (from V2)
       */
     Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
     /*  V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs). 
         For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4, 
         Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
     */
     /* For model-covariate k tells which data-covariate to use but
       because this model-covariate is a construction we invent a new column
       ncovcol + k1
       If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
       Tvar[3=V1*V4]=4+1 etc */
     Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
     /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
        if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2)
     */
     Tvaraff=ivector(1,NCOVMAX); /* Unclear */
     Tvard=imatrix(1,NCOVMAX,1,2); /* n=Tvard[k1][1]  and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm
                               * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd. 
                               * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
     Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
                            4 covariates (3 plus signs)
                            Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
                         */  
   
     if(decodemodel(model, lastobs) == 1)
       goto end;
   
     if((double)(lastobs-imx)/(double)imx > 1.10){
       nbwarn++;
       printf("Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
       fprintf(ficlog,"Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
     }
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
       for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
     }
   
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
       goto end;
   
   
     agegomp=(int)agemin;
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
     /* */
     
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
     /* */
    
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     Ndum =ivector(-1,NCOVMAX);  
     if (ncovmodel > 2)
       tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
   
     codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
     /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
     h=0;
   
   
     /*if (cptcovn > 0) */
         
    
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
       for(i=1; i <=pow(2,cptcoveff-k);i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */ 
         for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
           for(cpt=1; cpt <=pow(2,k-1); cpt++){  /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */ 
             h++;
             if (h>m) 
               h=1;
             /**< codtab(h,k)  k   = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
              *     h     1     2     3     4
              *______________________________  
              *     1 i=1 1 i=1 1 i=1 1 i=1 1
              *     2     2     1     1     1
              *     3 i=2 1     2     1     1
              *     4     2     2     1     1
              *     5 i=3 1 i=2 1     2     1
              *     6     2     1     2     1
              *     7 i=4 1     2     2     1
              *     8     2     2     2     1
              *     9 i=5 1 i=3 1 i=2 1     1
              *    10     2     1     1     1
              *    11 i=6 1     2     1     1
              *    12     2     2     1     1
              *    13 i=7 1 i=4 1     2     1    
              *    14     2     1     2     1
              *    15 i=8 1     2     2     1
              *    16     2     2     2     1
              */
             codtab[h][k]=j;
             /*codtab[h][Tvar[k]]=j;*/
             printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]);
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
          printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
   
    free_ivector(Ndum,-1,NCOVMAX);
   
   
       
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     if(mle==-3)
       strcat(optionfilegnuplot,"-mort");
     strcat(optionfilegnuplot,".gp");
   
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       //fprintf(ficgp,"set missing 'NaNq'\n");
       fprintf(ficgp,"set datafile missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname); /* Main html file */
     if(mle==-3)
       strcat(optionfilehtm,"-mort");
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm);
       exit(0);
     }
   
     strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
     strcat(optionfilehtmcov,"-cov.htm");
     if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtmcov), exit(0);
     }
     else{
     fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
             optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
    - Log file of the run: <a href=\"%s\">%s</a><br>\n\
    - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
    - Date and time at start: %s</ul>\n",\
             optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
             optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
             fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
     chdir(optionfilefiname); /* Move to directory named optionfile */
     
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
   
     fprintf(fichtm,"\n");
     fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
             imx,agemin,agemax,jmin,jmax,jmean);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
   
     if (mle==-3){
       ximort=matrix(1,NDIM,1,NDIM); 
   /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
       cens=ivector(1,n);
       ageexmed=vector(1,n);
       agecens=vector(1,n);
       dcwave=ivector(1,n);
    
       for (i=1; i<=imx; i++){
         dcwave[i]=-1;
         for (m=firstpass; m<=lastpass; m++)
           if (s[m][i]>nlstate) {
             dcwave[i]=m;
             /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
             break;
           }
       }
   
       for (i=1; i<=imx; i++) {
         if (wav[i]>0){
           ageexmed[i]=agev[mw[1][i]][i];
           j=wav[i];
           agecens[i]=1.; 
   
           if (ageexmed[i]> 1 && wav[i] > 0){
             agecens[i]=agev[mw[j][i]][i];
             cens[i]= 1;
           }else if (ageexmed[i]< 1) 
             cens[i]= -1;
           if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
             cens[i]=0 ;
         }
         else cens[i]=-1;
       }
       
       for (i=1;i<=NDIM;i++) {
         for (j=1;j<=NDIM;j++)
           ximort[i][j]=(i == j ? 1.0 : 0.0);
       }
       
       /*p[1]=0.0268; p[NDIM]=0.083;*/
       /*printf("%lf %lf", p[1], p[2]);*/
       
       
   #ifdef GSL
       printf("GSL optimization\n");  fprintf(ficlog,"Powell\n");
   #else
       printf("Powell\n");  fprintf(ficlog,"Powell\n");
   #endif
       strcpy(filerespow,"pow-mort"); 
       strcat(filerespow,fileres);
       if((ficrespow=fopen(filerespow,"w"))==NULL) {
         printf("Problem with resultfile: %s\n", filerespow);
         fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
       }
   #ifdef GSL
       fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
   #else
       fprintf(ficrespow,"# Powell\n# iter -2*LL");
   #endif
       /*  for (i=1;i<=nlstate;i++)
           for(j=1;j<=nlstate+ndeath;j++)
           if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       */
       fprintf(ficrespow,"\n");
   #ifdef GSL
       /* gsl starts here */ 
       T = gsl_multimin_fminimizer_nmsimplex;
       gsl_multimin_fminimizer *sfm = NULL;
       gsl_vector *ss, *x;
       gsl_multimin_function minex_func;
   
       /* Initial vertex size vector */
       ss = gsl_vector_alloc (NDIM);
       
       if (ss == NULL){
         GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
       }
       /* Set all step sizes to 1 */
       gsl_vector_set_all (ss, 0.001);
   
       /* Starting point */
       
       x = gsl_vector_alloc (NDIM);
       
       if (x == NULL){
         gsl_vector_free(ss);
         GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
       }
     
       /* Initialize method and iterate */
       /*     p[1]=0.0268; p[NDIM]=0.083; */
   /*     gsl_vector_set(x, 0, 0.0268); */
   /*     gsl_vector_set(x, 1, 0.083); */
       gsl_vector_set(x, 0, p[1]);
       gsl_vector_set(x, 1, p[2]);
   
       minex_func.f = &gompertz_f;
       minex_func.n = NDIM;
       minex_func.params = (void *)&p; /* ??? */
       
       sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
       gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
       
       printf("Iterations beginning .....\n\n");
       printf("Iter. #    Intercept       Slope     -Log Likelihood     Simplex size\n");
   
       iteri=0;
       while (rval == GSL_CONTINUE){
         iteri++;
         status = gsl_multimin_fminimizer_iterate(sfm);
         
         if (status) printf("error: %s\n", gsl_strerror (status));
         fflush(0);
         
         if (status) 
           break;
         
         rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
         ssval = gsl_multimin_fminimizer_size (sfm);
         
         if (rval == GSL_SUCCESS)
           printf ("converged to a local maximum at\n");
         
         printf("%5d ", iteri);
         for (it = 0; it < NDIM; it++){
           printf ("%10.5f ", gsl_vector_get (sfm->x, it));
         }
         printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
       }
       
       printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
       
       gsl_vector_free(x); /* initial values */
       gsl_vector_free(ss); /* inital step size */
       for (it=0; it<NDIM; it++){
         p[it+1]=gsl_vector_get(sfm->x,it);
         fprintf(ficrespow," %.12lf", p[it]);
       }
       gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1)  */
   #endif
   #ifdef POWELL
        powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
   #endif  
       fclose(ficrespow);
       
       hesscov(matcov, p, NDIM, delti, 1e-4, gompertz); 
   
       for(i=1; i <=NDIM; i++)
         for(j=i+1;j<=NDIM;j++)
           matcov[i][j]=matcov[j][i];
       
       printf("\nCovariance matrix\n ");
       for(i=1; i <=NDIM; i++) {
         for(j=1;j<=NDIM;j++){ 
           printf("%f ",matcov[i][j]);
         }
         printf("\n ");
       }
       
       printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
       for (i=1;i<=NDIM;i++) 
         printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
   
       lsurv=vector(1,AGESUP);
       lpop=vector(1,AGESUP);
       tpop=vector(1,AGESUP);
       lsurv[agegomp]=100000;
       
       for (k=agegomp;k<=AGESUP;k++) {
         agemortsup=k;
         if (p[1]*exp(p[2]*(k-agegomp))>1) break;
       }
       
       for (k=agegomp;k<agemortsup;k++)
         lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
       
       for (k=agegomp;k<agemortsup;k++){
         lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
         sumlpop=sumlpop+lpop[k];
       }
       
       tpop[agegomp]=sumlpop;
       for (k=agegomp;k<(agemortsup-3);k++){
         /*  tpop[k+1]=2;*/
         tpop[k+1]=tpop[k]-lpop[k];
       }
       
       
       printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
       for (k=agegomp;k<(agemortsup-2);k++) 
         printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
       
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
                        stepm, weightopt,\
                        model,imx,p,matcov,agemortsup);
       
       free_vector(lsurv,1,AGESUP);
       free_vector(lpop,1,AGESUP);
       free_vector(tpop,1,AGESUP);
   #ifdef GSL
       free_ivector(cens,1,n);
       free_vector(agecens,1,n);
       free_ivector(dcwave,1,n);
       free_matrix(ximort,1,NDIM,1,NDIM);
   #endif
     } /* Endof if mle==-3 */
     
     else{ /* For mle >=1 */
       globpr=0;/* debug */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       globpr=1; /* to print the contributions */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       if(mle>=1){ /* Could be 1 or 2 */
         mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
       }
       
       /*--------- results files --------------*/
       fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
       
       
       fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(k=1; k <=(nlstate+ndeath); k++){
           if (k != i) {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%lf ",p[jk]);
               fprintf(ficlog,"%lf ",p[jk]);
               fprintf(ficres,"%lf ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       if(mle!=0){
         /* Computing hessian and covariance matrix */
         ftolhess=ftol; /* Usually correct */
         hesscov(matcov, p, npar, delti, ftolhess, func);
       }
       fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
       printf("# Scales (for hessian or gradient estimation)\n");
       fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if (j!=i) {
             fprintf(ficres,"%1d%1d",i,j);
             printf("%1d%1d",i,j);
             fprintf(ficlog,"%1d%1d",i,j);
             for(k=1; k<=ncovmodel;k++){
               printf(" %.5e",delti[jk]);
               fprintf(ficlog," %.5e",delti[jk]);
               fprintf(ficres," %.5e",delti[jk]);
               jk++;
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       
       fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       if(mle>=1)
         printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       /* # 121 Var(a12)\n\ */
       /* # 122 Cov(b12,a12) Var(b12)\n\ */
       /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
       /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
       /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
       /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
       /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
       /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
       
       
       /* Just to have a covariance matrix which will be more understandable
          even is we still don't want to manage dictionary of variables
       */
       for(itimes=1;itimes<=2;itimes++){
         jj=0;
         for(i=1; i <=nlstate; i++){
           for(j=1; j <=nlstate+ndeath; j++){
             if(j==i) continue;
             for(k=1; k<=ncovmodel;k++){
               jj++;
               ca[0]= k+'a'-1;ca[1]='\0';
               if(itimes==1){
                 if(mle>=1)
                   printf("#%1d%1d%d",i,j,k);
                 fprintf(ficlog,"#%1d%1d%d",i,j,k);
                 fprintf(ficres,"#%1d%1d%d",i,j,k);
               }else{
                 if(mle>=1)
                   printf("%1d%1d%d",i,j,k);
                 fprintf(ficlog,"%1d%1d%d",i,j,k);
                 fprintf(ficres,"%1d%1d%d",i,j,k);
               }
               ll=0;
               for(li=1;li <=nlstate; li++){
                 for(lj=1;lj <=nlstate+ndeath; lj++){
                   if(lj==li) continue;
                   for(lk=1;lk<=ncovmodel;lk++){
                     ll++;
                     if(ll<=jj){
                       cb[0]= lk +'a'-1;cb[1]='\0';
                       if(ll<jj){
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }else{
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }
                     }
                   } /* end lk */
                 } /* end lj */
               } /* end li */
               if(mle>=1)
                 printf("\n");
               fprintf(ficlog,"\n");
               fprintf(ficres,"\n");
               numlinepar++;
             } /* end k*/
           } /*end j */
         } /* end i */
       } /* end itimes */
       
       fflush(ficlog);
       fflush(ficres);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       estepm=0;
       fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
       if (estepm==0 || estepm < stepm) estepm=stepm;
       if (fage <= 2) {
         bage = ageminpar;
         fage = agemaxpar;
       }
       
       fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
       fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
       fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       
       dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
       dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
       
       fscanf(ficpar,"pop_based=%d\n",&popbased);
       fprintf(ficparo,"pop_based=%d\n",popbased);   
       fprintf(ficres,"pop_based=%d\n",popbased);   
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
       fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       /* day and month of proj2 are not used but only year anproj2.*/
       
       
       
        /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
       /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                    model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                    jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
         
      /*------------ free_vector  -------------*/
      /*  chdir(path); */
    
       free_ivector(wav,1,imx);
       free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
       free_lvector(num,1,n);
       free_vector(agedc,1,n);
       /*free_matrix(covar,0,NCOVMAX,1,n);*/
       /*free_matrix(covar,1,NCOVMAX,1,n);*/
       fclose(ficparo);
       fclose(ficres);
   
   
       /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
   #include "prevlim.h"  /* Use ficrespl, ficlog */
       fclose(ficrespl);
   
   #ifdef FREEEXIT2
   #include "freeexit2.h"
   #endif
   
       /*------------- h Pij x at various ages ------------*/
   #include "hpijx.h"
       fclose(ficrespij);
   
     /*-------------- Variance of one-step probabilities---*/
       k=1;
       varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
   
   
       probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for(i=1;i<=AGESUP;i++)
         for(j=1;j<=NCOVMAX;j++)
           for(k=1;k<=NCOVMAX;k++)
             probs[i][j][k]=0.;
   
       /*---------- Forecasting ------------------*/
       /*if((stepm == 1) && (strcmp(model,".")==0)){*/
       if(prevfcast==1){
         /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
         /*      }  */
         /*      else{ */
         /*        erreur=108; */
         /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*      } */
       }
     
   
       /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
   
       prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
       /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
           ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
       */
   
       if (mobilav!=0) {
         mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
           fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
           printf(" Error in movingaverage mobilav=%d\n",mobilav);
         }
       }
   
   
       /*---------- Health expectancies, no variances ------------*/
   
       strcpy(filerese,"e");
       strcat(filerese,fileres);
       if((ficreseij=fopen(filerese,"w"))==NULL) {
         printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
         fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       }
       printf("Computing Health Expectancies: result on file '%s' \n", filerese);
       fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficreseij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficreseij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);  
         
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         /*}*/
       }
       fclose(ficreseij);
   
   
       /*---------- Health expectancies and variances ------------*/
   
   
       strcpy(filerest,"t");
       strcat(filerest,fileres);
       if((ficrest=fopen(filerest,"w"))==NULL) {
         printf("Problem with total LE resultfile: %s\n", filerest);goto end;
         fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
       }
       printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
       fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
   
   
       strcpy(fileresstde,"stde");
       strcat(fileresstde,fileres);
       if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
         printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
         fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
       }
       printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
       fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
   
       strcpy(filerescve,"cve");
       strcat(filerescve,fileres);
       if((ficrescveij=fopen(filerescve,"w"))==NULL) {
         printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
         fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
       }
       printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
       fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
   
       strcpy(fileresv,"v");
       strcat(fileresv,fileres);
       if((ficresvij=fopen(fileresv,"w"))==NULL) {
         printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
         fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
       }
       printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
       fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficrest,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrest,"******\n");
   
           fprintf(ficresstdeij,"\n#****** ");
           fprintf(ficrescveij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficresstdeij,"******\n");
           fprintf(ficrescveij,"******\n");
   
           fprintf(ficresvij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);  
           /*
            */
           /* goto endfree; */
    
           vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           pstamp(ficrest);
   
   
           for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
             oldm=oldms;savm=savms; /* Segmentation fault */
             cptcod= 0; /* To be deleted */
             varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */
             fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");
             if(vpopbased==1)
               fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
             else
               fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
             fprintf(ficrest,"# Age e.. (std) ");
             for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
             fprintf(ficrest,"\n");
   
             epj=vector(1,nlstate+1);
             for(age=bage; age <=fage ;age++){
               prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
               if (vpopbased==1) {
                 if(mobilav ==0){
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=probs[(int)age][i][k];
                 }else{ /* mobilav */ 
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=mobaverage[(int)age][i][k];
                 }
               }
           
               fprintf(ficrest," %4.0f",age);
               for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
                 for(i=1, epj[j]=0.;i <=nlstate;i++) {
                   epj[j] += prlim[i][i]*eij[i][j][(int)age];
                   /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
                 }
                 epj[nlstate+1] +=epj[j];
               }
   
               for(i=1, vepp=0.;i <=nlstate;i++)
                 for(j=1;j <=nlstate;j++)
                   vepp += vareij[i][j][(int)age];
               fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
               for(j=1;j <=nlstate;j++){
                 fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
               }
               fprintf(ficrest,"\n");
             }
           }
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_vector(epj,1,nlstate+1);
         /*}*/
       }
       free_vector(weight,1,n);
       free_imatrix(Tvard,1,NCOVMAX,1,2);
       free_imatrix(s,1,maxwav+1,1,n);
       free_matrix(anint,1,maxwav,1,n); 
       free_matrix(mint,1,maxwav,1,n);
       free_ivector(cod,1,n);
       free_ivector(tab,1,NCOVMAX);
       fclose(ficresstdeij);
       fclose(ficrescveij);
       fclose(ficresvij);
       fclose(ficrest);
       fclose(ficpar);
     
       /*------- Variance of period (stable) prevalence------*/   
   
       strcpy(fileresvpl,"vpl");
       strcat(fileresvpl,fileres);
       if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
         printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
         exit(0);
       }
       printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
   
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficresvpl,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvpl,"******\n");
         
           varpl=matrix(1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
           free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
         /*}*/
       }
   
       fclose(ficresvpl);
   
       /*---------- End : free ----------------*/
       if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
     }  /* mle==-3 arrives here for freeing */
    endfree:
       free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
       free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(covar,0,NCOVMAX,1,n);
       free_matrix(matcov,1,npar,1,npar);
       /*free_vector(delti,1,npar);*/
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       free_matrix(agev,1,maxwav,1,imx);
       free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   
       free_ivector(ncodemax,1,NCOVMAX);
       free_ivector(Tvar,1,NCOVMAX);
       free_ivector(Tprod,1,NCOVMAX);
       free_ivector(Tvaraff,1,NCOVMAX);
       free_ivector(Tage,1,NCOVMAX);
   
       free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
       free_imatrix(codtab,1,100,1,10);
     fflush(fichtm);
     fflush(ficgp);
     
   
     if((nberr >0) || (nbwarn>0)){
       printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
       fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
     }else{
       printf("End of Imach\n");
       fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     /*(void) gettimeofday(&end_time,&tzp);*/
     rend_time = time(NULL);  
     end_time = *localtime(&rend_time);
     /* tml = *localtime(&end_time.tm_sec); */
     strcpy(strtend,asctime(&end_time));
     printf("Local time at start %s\nLocal time at end   %s",strstart, strtend); 
     fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
     printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
   
     printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
     fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
     fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
     /*  printf("Total time was %d uSec.\n", total_usecs);*/
   /*   if(fileappend(fichtm,optionfilehtm)){ */
     fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtm);
     fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtmcov);
     fclose(ficgp);
     fclose(ficlog);
     /*------ End -----------*/
   
   
      printf("Before Current directory %s!\n",pathcd);
      if(chdir(pathcd) != 0)
       printf("Can't move to directory %s!\n",path);
     if(getcwd(pathcd,MAXLINE) > 0)
       printf("Current directory %s!\n",pathcd);
     /*strcat(plotcmd,CHARSEPARATOR);*/
     sprintf(plotcmd,"gnuplot");
   #ifdef _WIN32
     sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
   #endif
     if(!stat(plotcmd,&info)){
       printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
       if(!stat(getenv("GNUPLOTBIN"),&info)){
         printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #ifdef __unix
       strcpy(plotcmd,GNUPLOTPROGRAM);
       if(!stat(plotcmd,&info)){
         printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #endif
     }else
       strcpy(pplotcmd,plotcmd);
     
     sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
     printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
   
     if((outcmd=system(plotcmd)) != 0){
       printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
       printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
       sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
       if((outcmd=system(plotcmd)) != 0)
         printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
     }
     printf(" Successful, please wait...");
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
       scanf("%s",z);
   /*     if (z[0] == 'c') system("./imach"); */
       if (z[0] == 'e') {
   #ifdef __APPLE__
         sprintf(pplotcmd, "open %s", optionfilehtm);
   #elif __linux
         sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
   #else
         sprintf(pplotcmd, "%s", optionfilehtm);
   #endif
         printf("Starting browser with: %s",pplotcmd);fflush(stdout);
         system(pplotcmd);
       }
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     end:
     while (z[0] != 'q') {
       printf("\nType  q for exiting: ");
       scanf("%s",z);
     }
   }

Removed from v.1.49  
changed lines
  Added in v.1.163


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