Diff for /imach/src/imach.c between versions 1.20 and 1.159

version 1.20, 2002/02/20 17:22:01 version 1.159, 2014/09/01 10:34:10
Line 1 Line 1
      /* $Id$
 /*********************** Imach **************************************            $State$
   This program computes Healthy Life Expectancies from cross-longitudinal    $Log$
   data. Cross-longitudinal consist in a first survey ("cross") where    Revision 1.159  2014/09/01 10:34:10  brouard
   individuals from different ages are interviewed on their health status    Summary: WIN32
   or degree of  disability. At least a second wave of interviews    Author: Brouard
   ("longitudinal") should  measure each new individual health status.  
   Health expectancies are computed from the transistions observed between    Revision 1.158  2014/08/27 17:11:51  brouard
   waves and are computed for each degree of severity of disability (number    *** empty log message ***
   of life states). More degrees you consider, more time is necessary to  
   reach the Maximum Likelihood of the parameters involved in the model.    Revision 1.157  2014/08/27 16:26:55  brouard
   The simplest model is the multinomial logistic model where pij is    Summary: Preparing windows Visual studio version
   the probabibility to be observed in state j at the second wave conditional    Author: Brouard
   to be observed in state i at the first wave. Therefore the model is:  
   log(pij/pii)= aij + bij*age+ cij*sex + etc , where 'age' is age and 'sex'    In order to compile on Visual studio, time.h is now correct and time_t
   is a covariate. If you want to have a more complex model than "constant and    and tm struct should be used. difftime should be used but sometimes I
   age", you should modify the program where the markup    just make the differences in raw time format (time(&now).
     *Covariates have to be included here again* invites you to do it.    Trying to suppress #ifdef LINUX
   More covariates you add, less is the speed of the convergence.    Add xdg-open for __linux in order to open default browser.
   
   The advantage that this computer programme claims, comes from that if the    Revision 1.156  2014/08/25 20:10:10  brouard
   delay between waves is not identical for each individual, or if some    *** empty log message ***
   individual missed an interview, the information is not rounded or lost, but  
   taken into account using an interpolation or extrapolation.    Revision 1.155  2014/08/25 18:32:34  brouard
   hPijx is the probability to be    Summary: New compile, minor changes
   observed in state i at age x+h conditional to the observed state i at age    Author: Brouard
   x. The delay 'h' can be split into an exact number (nh*stepm) of  
   unobserved intermediate  states. This elementary transition (by month or    Revision 1.154  2014/06/20 17:32:08  brouard
   quarter trimester, semester or year) is model as a multinomial logistic.    Summary: Outputs now all graphs of convergence to period prevalence
   The hPx matrix is simply the matrix product of nh*stepm elementary matrices  
   and the contribution of each individual to the likelihood is simply hPijx.    Revision 1.153  2014/06/20 16:45:46  brouard
     Summary: If 3 live state, convergence to period prevalence on same graph
   Also this programme outputs the covariance matrix of the parameters but also    Author: Brouard
   of the life expectancies. It also computes the prevalence limits.  
      Revision 1.152  2014/06/18 17:54:09  brouard
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    Summary: open browser, use gnuplot on same dir than imach if not found in the path
            Institut national d'études démographiques, Paris.  
   This software have been partly granted by Euro-REVES, a concerted action    Revision 1.151  2014/06/18 16:43:30  brouard
   from the European Union.    *** empty log message ***
   It is copyrighted identically to a GNU software product, ie programme and  
   software can be distributed freely for non commercial use. Latest version    Revision 1.150  2014/06/18 16:42:35  brouard
   can be accessed at http://euroreves.ined.fr/imach .    Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
   **********************************************************************/    Author: brouard
    
 #include <math.h>    Revision 1.149  2014/06/18 15:51:14  brouard
 #include <stdio.h>    Summary: Some fixes in parameter files errors
 #include <stdlib.h>    Author: Nicolas Brouard
 #include <unistd.h>  
     Revision 1.148  2014/06/17 17:38:48  brouard
 #define MAXLINE 256    Summary: Nothing new
 #define FILENAMELENGTH 80    Author: Brouard
 /*#define DEBUG*/  
 #define windows    Just a new packaging for OS/X version 0.98nS
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */  
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    Revision 1.147  2014/06/16 10:33:11  brouard
     *** empty log message ***
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */  
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    Revision 1.146  2014/06/16 10:20:28  brouard
     Summary: Merge
 #define NINTERVMAX 8    Author: Brouard
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */  
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    Merge, before building revised version.
 #define NCOVMAX 8 /* Maximum number of covariates */  
 #define MAXN 20000    Revision 1.145  2014/06/10 21:23:15  brouard
 #define YEARM 12. /* Number of months per year */    Summary: Debugging with valgrind
 #define AGESUP 130    Author: Nicolas Brouard
 #define AGEBASE 40  
     Lot of changes in order to output the results with some covariates
     After the Edimburgh REVES conference 2014, it seems mandatory to
 int nvar;    improve the code.
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    No more memory valgrind error but a lot has to be done in order to
 int npar=NPARMAX;    continue the work of splitting the code into subroutines.
 int nlstate=2; /* Number of live states */    Also, decodemodel has been improved. Tricode is still not
 int ndeath=1; /* Number of dead states */    optimal. nbcode should be improved. Documentation has been added in
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    the source code.
 int popbased=0;  
     Revision 1.143  2014/01/26 09:45:38  brouard
 int *wav; /* Number of waves for this individuual 0 is possible */    Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
 int maxwav; /* Maxim number of waves */  
 int jmin, jmax; /* min, max spacing between 2 waves */    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
 int mle, weightopt;    (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */  
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    Revision 1.142  2014/01/26 03:57:36  brouard
 double jmean; /* Mean space between 2 waves */    Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
 double **oldm, **newm, **savm; /* Working pointers to matrices */  
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf;  
 FILE *ficgp, *fichtm,*ficresprob,*ficpop;    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
     After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
 #define NR_END 1    I remember having already fixed agemin agemax which are pointers now but not cvs saved.
 #define FREE_ARG char*  
 #define FTOL 1.0e-10    Revision 1.138  2010/04/30 18:19:40  brouard
     *** empty log message ***
 #define NRANSI  
 #define ITMAX 200    Revision 1.137  2010/04/29 18:11:38  brouard
     (Module): Checking covariates for more complex models
 #define TOL 2.0e-4    than V1+V2. A lot of change to be done. Unstable.
   
 #define CGOLD 0.3819660    Revision 1.136  2010/04/26 20:30:53  brouard
 #define ZEPS 1.0e-10    (Module): merging some libgsl code. Fixing computation
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    of likelione (using inter/intrapolation if mle = 0) in order to
     get same likelihood as if mle=1.
 #define GOLD 1.618034    Some cleaning of code and comments added.
 #define GLIMIT 100.0  
 #define TINY 1.0e-20    Revision 1.135  2009/10/29 15:33:14  brouard
     (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
 static double maxarg1,maxarg2;  
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    Revision 1.134  2009/10/29 13:18:53  brouard
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
    
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    Revision 1.133  2009/07/06 10:21:25  brouard
 #define rint(a) floor(a+0.5)    just nforces
   
 static double sqrarg;    Revision 1.132  2009/07/06 08:22:05  brouard
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    Many tings
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  
     Revision 1.131  2009/06/20 16:22:47  brouard
 int imx;    Some dimensions resccaled
 int stepm;  
 /* Stepm, step in month: minimum step interpolation*/    Revision 1.130  2009/05/26 06:44:34  brouard
     (Module): Max Covariate is now set to 20 instead of 8. A
 int m,nb;    lot of cleaning with variables initialized to 0. Trying to make
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  
 double **pmmij, ***probs, ***mobaverage;    Revision 1.129  2007/08/31 13:49:27  lievre
 double dateintmean=0;    Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
   
 double *weight;    Revision 1.128  2006/06/30 13:02:05  brouard
 int **s; /* Status */    (Module): Clarifications on computing e.j
 double *agedc, **covar, idx;  
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    Revision 1.127  2006/04/28 18:11:50  brouard
     (Module): Yes the sum of survivors was wrong since
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    imach-114 because nhstepm was no more computed in the age
 double ftolhess; /* Tolerance for computing hessian */    loop. Now we define nhstepma in the age loop.
     (Module): In order to speed up (in case of numerous covariates) we
 /**************** split *************************/    compute health expectancies (without variances) in a first step
 static  int split( char *path, char *dirc, char *name )    and then all the health expectancies with variances or standard
 {    deviation (needs data from the Hessian matrices) which slows the
    char *s;                             /* pointer */    computation.
    int  l1, l2;                         /* length counters */    In the future we should be able to stop the program is only health
     expectancies and graph are needed without standard deviations.
    l1 = strlen( path );                 /* length of path */  
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    Revision 1.126  2006/04/28 17:23:28  brouard
    s = strrchr( path, '\\' );           /* find last / */    (Module): Yes the sum of survivors was wrong since
    if ( s == NULL ) {                   /* no directory, so use current */    imach-114 because nhstepm was no more computed in the age
 #if     defined(__bsd__)                /* get current working directory */    loop. Now we define nhstepma in the age loop.
       extern char       *getwd( );    Version 0.98h
   
       if ( getwd( dirc ) == NULL ) {    Revision 1.125  2006/04/04 15:20:31  lievre
 #else    Errors in calculation of health expectancies. Age was not initialized.
       extern char       *getcwd( );    Forecasting file added.
   
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    Revision 1.124  2006/03/22 17:13:53  lievre
 #endif    Parameters are printed with %lf instead of %f (more numbers after the comma).
          return( GLOCK_ERROR_GETCWD );    The log-likelihood is printed in the log file
       }  
       strcpy( name, path );             /* we've got it */    Revision 1.123  2006/03/20 10:52:43  brouard
    } else {                             /* strip direcotry from path */    * imach.c (Module): <title> changed, corresponds to .htm file
       s++;                              /* after this, the filename */    name. <head> headers where missing.
       l2 = strlen( s );                 /* length of filename */  
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    * imach.c (Module): Weights can have a decimal point as for
       strcpy( name, s );                /* save file name */    English (a comma might work with a correct LC_NUMERIC environment,
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    otherwise the weight is truncated).
       dirc[l1-l2] = 0;                  /* add zero */    Modification of warning when the covariates values are not 0 or
    }    1.
    l1 = strlen( dirc );                 /* length of directory */    Version 0.98g
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  
    return( 0 );                         /* we're done */    Revision 1.122  2006/03/20 09:45:41  brouard
 }    (Module): Weights can have a decimal point as for
     English (a comma might work with a correct LC_NUMERIC environment,
     otherwise the weight is truncated).
 /******************************************/    Modification of warning when the covariates values are not 0 or
     1.
 void replace(char *s, char*t)    Version 0.98g
 {  
   int i;    Revision 1.121  2006/03/16 17:45:01  lievre
   int lg=20;    * imach.c (Module): Comments concerning covariates added
   i=0;  
   lg=strlen(t);    * imach.c (Module): refinements in the computation of lli if
   for(i=0; i<= lg; i++) {    status=-2 in order to have more reliable computation if stepm is
     (s[i] = t[i]);    not 1 month. Version 0.98f
     if (t[i]== '\\') s[i]='/';  
   }    Revision 1.120  2006/03/16 15:10:38  lievre
 }    (Module): refinements in the computation of lli if
     status=-2 in order to have more reliable computation if stepm is
 int nbocc(char *s, char occ)    not 1 month. Version 0.98f
 {  
   int i,j=0;    Revision 1.119  2006/03/15 17:42:26  brouard
   int lg=20;    (Module): Bug if status = -2, the loglikelihood was
   i=0;    computed as likelihood omitting the logarithm. Version O.98e
   lg=strlen(s);  
   for(i=0; i<= lg; i++) {    Revision 1.118  2006/03/14 18:20:07  brouard
   if  (s[i] == occ ) j++;    (Module): varevsij Comments added explaining the second
   }    table of variances if popbased=1 .
   return j;    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 }    (Module): Function pstamp added
     (Module): Version 0.98d
 void cutv(char *u,char *v, char*t, char occ)  
 {    Revision 1.117  2006/03/14 17:16:22  brouard
   int i,lg,j,p=0;    (Module): varevsij Comments added explaining the second
   i=0;    table of variances if popbased=1 .
   for(j=0; j<=strlen(t)-1; j++) {    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    (Module): Function pstamp added
   }    (Module): Version 0.98d
   
   lg=strlen(t);    Revision 1.116  2006/03/06 10:29:27  brouard
   for(j=0; j<p; j++) {    (Module): Variance-covariance wrong links and
     (u[j] = t[j]);    varian-covariance of ej. is needed (Saito).
   }  
      u[p]='\0';    Revision 1.115  2006/02/27 12:17:45  brouard
     (Module): One freematrix added in mlikeli! 0.98c
    for(j=0; j<= lg; j++) {  
     if (j>=(p+1))(v[j-p-1] = t[j]);    Revision 1.114  2006/02/26 12:57:58  brouard
   }    (Module): Some improvements in processing parameter
 }    filename with strsep.
   
 /********************** nrerror ********************/    Revision 1.113  2006/02/24 14:20:24  brouard
     (Module): Memory leaks checks with valgrind and:
 void nrerror(char error_text[])    datafile was not closed, some imatrix were not freed and on matrix
 {    allocation too.
   fprintf(stderr,"ERREUR ...\n");  
   fprintf(stderr,"%s\n",error_text);    Revision 1.112  2006/01/30 09:55:26  brouard
   exit(1);    (Module): Back to gnuplot.exe instead of wgnuplot.exe
 }  
 /*********************** vector *******************/    Revision 1.111  2006/01/25 20:38:18  brouard
 double *vector(int nl, int nh)    (Module): Lots of cleaning and bugs added (Gompertz)
 {    (Module): Comments can be added in data file. Missing date values
   double *v;    can be a simple dot '.'.
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  
   if (!v) nrerror("allocation failure in vector");    Revision 1.110  2006/01/25 00:51:50  brouard
   return v-nl+NR_END;    (Module): Lots of cleaning and bugs added (Gompertz)
 }  
     Revision 1.109  2006/01/24 19:37:15  brouard
 /************************ free vector ******************/    (Module): Comments (lines starting with a #) are allowed in data.
 void free_vector(double*v, int nl, int nh)  
 {    Revision 1.108  2006/01/19 18:05:42  lievre
   free((FREE_ARG)(v+nl-NR_END));    Gnuplot problem appeared...
 }    To be fixed
   
 /************************ivector *******************************/    Revision 1.107  2006/01/19 16:20:37  brouard
 int *ivector(long nl,long nh)    Test existence of gnuplot in imach path
 {  
   int *v;    Revision 1.106  2006/01/19 13:24:36  brouard
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    Some cleaning and links added in html output
   if (!v) nrerror("allocation failure in ivector");  
   return v-nl+NR_END;    Revision 1.105  2006/01/05 20:23:19  lievre
 }    *** empty log message ***
   
 /******************free ivector **************************/    Revision 1.104  2005/09/30 16:11:43  lievre
 void free_ivector(int *v, long nl, long nh)    (Module): sump fixed, loop imx fixed, and simplifications.
 {    (Module): If the status is missing at the last wave but we know
   free((FREE_ARG)(v+nl-NR_END));    that the person is alive, then we can code his/her status as -2
 }    (instead of missing=-1 in earlier versions) and his/her
     contributions to the likelihood is 1 - Prob of dying from last
 /******************* imatrix *******************************/    health status (= 1-p13= p11+p12 in the easiest case of somebody in
 int **imatrix(long nrl, long nrh, long ncl, long nch)    the healthy state at last known wave). Version is 0.98
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  
 {    Revision 1.103  2005/09/30 15:54:49  lievre
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    (Module): sump fixed, loop imx fixed, and simplifications.
   int **m;  
      Revision 1.102  2004/09/15 17:31:30  brouard
   /* allocate pointers to rows */    Add the possibility to read data file including tab characters.
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");    Revision 1.101  2004/09/15 10:38:38  brouard
   m += NR_END;    Fix on curr_time
   m -= nrl;  
      Revision 1.100  2004/07/12 18:29:06  brouard
      Add version for Mac OS X. Just define UNIX in Makefile
   /* allocate rows and set pointers to them */  
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    Revision 1.99  2004/06/05 08:57:40  brouard
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    *** empty log message ***
   m[nrl] += NR_END;  
   m[nrl] -= ncl;    Revision 1.98  2004/05/16 15:05:56  brouard
      New version 0.97 . First attempt to estimate force of mortality
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    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 .
   /* return pointer to array of pointers to rows */    This is the basic analysis of mortality and should be done before any
   return m;    other analysis, in order to test if the mortality estimated from the
 }    cross-longitudinal survey is different from the mortality estimated
     from other sources like vital statistic data.
 /****************** free_imatrix *************************/  
 void free_imatrix(m,nrl,nrh,ncl,nch)    The same imach parameter file can be used but the option for mle should be -3.
       int **m;  
       long nch,ncl,nrh,nrl;    Agnès, who wrote this part of the code, tried to keep most of the
      /* free an int matrix allocated by imatrix() */    former routines in order to include the new code within the former code.
 {  
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    The output is very simple: only an estimate of the intercept and of
   free((FREE_ARG) (m+nrl-NR_END));    the slope with 95% confident intervals.
 }  
     Current limitations:
 /******************* matrix *******************************/    A) Even if you enter covariates, i.e. with the
 double **matrix(long nrl, long nrh, long ncl, long nch)    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.
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  
   double **m;    Revision 1.97  2004/02/20 13:25:42  lievre
     Version 0.96d. Population forecasting command line is (temporarily)
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    suppressed.
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;    Revision 1.96  2003/07/15 15:38:55  brouard
   m -= nrl;    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
     rewritten within the same printf. Workaround: many printfs.
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    Revision 1.95  2003/07/08 07:54:34  brouard
   m[nrl] += NR_END;    * imach.c (Repository):
   m[nrl] -= ncl;    (Repository): Using imachwizard code to output a more meaningful covariance
     matrix (cov(a12,c31) instead of numbers.
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  
   return m;    Revision 1.94  2003/06/27 13:00:02  brouard
 }    Just cleaning
   
 /*************************free matrix ************************/    Revision 1.93  2003/06/25 16:33:55  brouard
 void free_matrix(double **m, 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.
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    (Module): Version 0.96b
   free((FREE_ARG)(m+nrl-NR_END));  
 }    Revision 1.92  2003/06/25 16:30:45  brouard
     (Module): On windows (cygwin) function asctime_r doesn't
 /******************* ma3x *******************************/    exist so I changed back to asctime which exists.
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  
 {    Revision 1.91  2003/06/25 15:30:29  brouard
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    * imach.c (Repository): Duplicated warning errors corrected.
   double ***m;    (Repository): Elapsed time after each iteration is now output. It
     helps to forecast when convergence will be reached. Elapsed time
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    is stamped in powell.  We created a new html file for the graphs
   if (!m) nrerror("allocation failure 1 in matrix()");    concerning matrix of covariance. It has extension -cov.htm.
   m += NR_END;  
   m -= nrl;    Revision 1.90  2003/06/24 12:34:15  brouard
     (Module): Some bugs corrected for windows. Also, when
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    mle=-1 a template is output in file "or"mypar.txt with the design
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    of the covariance matrix to be input.
   m[nrl] += NR_END;  
   m[nrl] -= ncl;    Revision 1.89  2003/06/24 12:30:52  brouard
     (Module): Some bugs corrected for windows. Also, when
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    mle=-1 a template is output in file "or"mypar.txt with the design
     of the covariance matrix to be input.
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    Revision 1.88  2003/06/23 17:54:56  brouard
   m[nrl][ncl] += NR_END;    * imach.c (Repository): Create a sub-directory where all the secondary files are. Only imach, htm, gp and r(imach) are on the main directory. Correct time and other things.
   m[nrl][ncl] -= nll;  
   for (j=ncl+1; j<=nch; j++)    Revision 1.87  2003/06/18 12:26:01  brouard
     m[nrl][j]=m[nrl][j-1]+nlay;    Version 0.96
    
   for (i=nrl+1; i<=nrh; i++) {    Revision 1.86  2003/06/17 20:04:08  brouard
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;    (Module): Change position of html and gnuplot routines and added
     for (j=ncl+1; j<=nch; j++)    routine fileappend.
       m[i][j]=m[i][j-1]+nlay;  
   }    Revision 1.85  2003/06/17 13:12:43  brouard
   return m;    * imach.c (Repository): Check when date of death was earlier that
 }    current date of interview. It may happen when the death was just
     prior to the death. In this case, dh was negative and likelihood
 /*************************free ma3x ************************/    was wrong (infinity). We still send an "Error" but patch by
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    assuming that the date of death was just one stepm after the
 {    interview.
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    (Repository): Because some people have very long ID (first column)
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    we changed int to long in num[] and we added a new lvector for
   free((FREE_ARG)(m+nrl-NR_END));    memory allocation. But we also truncated to 8 characters (left
 }    truncation)
     (Repository): No more line truncation errors.
 /***************** f1dim *************************/  
 extern int ncom;    Revision 1.84  2003/06/13 21:44:43  brouard
 extern double *pcom,*xicom;    * imach.c (Repository): Replace "freqsummary" at a correct
 extern double (*nrfunc)(double []);    place. It differs from routine "prevalence" which may be called
      many times. Probs is memory consuming and must be used with
 double f1dim(double x)    parcimony.
 {    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
   int j;  
   double f;    Revision 1.83  2003/06/10 13:39:11  lievre
   double *xt;    *** empty log message ***
    
   xt=vector(1,ncom);    Revision 1.82  2003/06/05 15:57:20  brouard
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    Add log in  imach.c and  fullversion number is now printed.
   f=(*nrfunc)(xt);  
   free_vector(xt,1,ncom);  */
   return f;  /*
 }     Interpolated Markov Chain
   
 /*****************brent *************************/    Short summary of the programme:
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    
 {    This program computes Healthy Life Expectancies from
   int iter;    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
   double a,b,d,etemp;    first survey ("cross") where individuals from different ages are
   double fu,fv,fw,fx;    interviewed on their health status or degree of disability (in the
   double ftemp;    case of a health survey which is our main interest) -2- at least a
   double p,q,r,tol1,tol2,u,v,w,x,xm;    second wave of interviews ("longitudinal") which measure each change
   double e=0.0;    (if any) in individual health status.  Health expectancies are
      computed from the time spent in each health state according to a
   a=(ax < cx ? ax : cx);    model. More health states you consider, more time is necessary to reach the
   b=(ax > cx ? ax : cx);    Maximum Likelihood of the parameters involved in the model.  The
   x=w=v=bx;    simplest model is the multinomial logistic model where pij is the
   fw=fv=fx=(*f)(x);    probability to be observed in state j at the second wave
   for (iter=1;iter<=ITMAX;iter++) {    conditional to be observed in state i at the first wave. Therefore
     xm=0.5*(a+b);    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    'age' is age and 'sex' is a covariate. If you want to have a more
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    complex model than "constant and age", you should modify the program
     printf(".");fflush(stdout);    where the markup *Covariates have to be included here again* invites
 #ifdef DEBUG    you to do it.  More covariates you add, slower the
     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);    convergence.
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  
 #endif    The advantage of this computer programme, compared to a simple
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    multinomial logistic model, is clear when the delay between waves is not
       *xmin=x;    identical for each individual. Also, if a individual missed an
       return fx;    intermediate interview, the information is lost, but taken into
     }    account using an interpolation or extrapolation.  
     ftemp=fu;  
     if (fabs(e) > tol1) {    hPijx is the probability to be observed in state i at age x+h
       r=(x-w)*(fx-fv);    conditional to the observed state i at age x. The delay 'h' can be
       q=(x-v)*(fx-fw);    split into an exact number (nh*stepm) of unobserved intermediate
       p=(x-v)*q-(x-w)*r;    states. This elementary transition (by month, quarter,
       q=2.0*(q-r);    semester or year) is modelled as a multinomial logistic.  The hPx
       if (q > 0.0) p = -p;    matrix is simply the matrix product of nh*stepm elementary matrices
       q=fabs(q);    and the contribution of each individual to the likelihood is simply
       etemp=e;    hPijx.
       e=d;  
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    Also this programme outputs the covariance matrix of the parameters but also
         d=CGOLD*(e=(x >= xm ? a-x : b-x));    of the life expectancies. It also computes the period (stable) prevalence. 
       else {    
         d=p/q;    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
         u=x+d;             Institut national d'études démographiques, Paris.
         if (u-a < tol2 || b-u < tol2)    This software have been partly granted by Euro-REVES, a concerted action
           d=SIGN(tol1,xm-x);    from the European Union.
       }    It is copyrighted identically to a GNU software product, ie programme and
     } else {    software can be distributed freely for non commercial use. Latest version
       d=CGOLD*(e=(x >= xm ? a-x : b-x));    can be accessed at http://euroreves.ined.fr/imach .
     }  
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
     fu=(*f)(u);    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
     if (fu <= fx) {    
       if (u >= x) a=x; else b=x;    **********************************************************************/
       SHFT(v,w,x,u)  /*
         SHFT(fv,fw,fx,fu)    main
         } else {    read parameterfile
           if (u < x) a=u; else b=u;    read datafile
           if (fu <= fw || w == x) {    concatwav
             v=w;    freqsummary
             w=u;    if (mle >= 1)
             fv=fw;      mlikeli
             fw=fu;    print results files
           } else if (fu <= fv || v == x || v == w) {    if mle==1 
             v=u;       computes hessian
             fv=fu;    read end of parameter file: agemin, agemax, bage, fage, estepm
           }        begin-prev-date,...
         }    open gnuplot file
   }    open html file
   nrerror("Too many iterations in brent");    period (stable) prevalence      | pl_nom    1-1 2-2 etc by covariate
   *xmin=x;     for age prevalim()             | #****** V1=0  V2=1  V3=1  V4=0 ******
   return fx;                                    | 65 1 0 2 1 3 1 4 0  0.96326 0.03674
 }      freexexit2 possible for memory heap.
   
 /****************** mnbrak ***********************/    h Pij x                         | pij_nom  ficrestpij
      # Cov Agex agex+h hpijx with i,j= 1-1 1-2     1-3     2-1     2-2     2-3
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,         1  85   85    1.00000             0.00000 0.00000 0.00000 1.00000 0.00000
             double (*func)(double))         1  85   86    0.68299             0.22291 0.09410 0.71093 0.00000 0.28907
 {  
   double ulim,u,r,q, dum;         1  65   99    0.00364             0.00322 0.99314 0.00350 0.00310 0.99340
   double fu;         1  65  100    0.00214             0.00204 0.99581 0.00206 0.00196 0.99597
      variance of p one-step probabilities varprob  | prob_nom   ficresprob #One-step probabilities and stand. devi in ()
   *fa=(*func)(*ax);     Standard deviation of one-step probabilities | probcor_nom   ficresprobcor #One-step probabilities and correlation matrix
   *fb=(*func)(*bx);     Matrix of variance covariance of one-step probabilities |  probcov_nom ficresprobcov #One-step probabilities and covariance matrix
   if (*fb > *fa) {  
     SHFT(dum,*ax,*bx,dum)    forecasting if prevfcast==1 prevforecast call prevalence()
       SHFT(dum,*fb,*fa,dum)    health expectancies
       }    Variance-covariance of DFLE
   *cx=(*bx)+GOLD*(*bx-*ax);    prevalence()
   *fc=(*func)(*cx);     movingaverage()
   while (*fb > *fc) {    varevsij() 
     r=(*bx-*ax)*(*fb-*fc);    if popbased==1 varevsij(,popbased)
     q=(*bx-*cx)*(*fb-*fa);    total life expectancies
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/    Variance of period (stable) prevalence
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));   end
     ulim=(*bx)+GLIMIT*(*cx-*bx);  */
     if ((*bx-u)*(u-*cx) > 0.0) {  
       fu=(*func)(u);  
     } else if ((*cx-u)*(u-ulim) > 0.0) {  
       fu=(*func)(u);   
       if (fu < *fc) {  #include <math.h>
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  #include <stdio.h>
           SHFT(*fb,*fc,fu,(*func)(u))  #include <stdlib.h>
           }  #include <string.h>
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  
       u=ulim;  #ifdef _WIN32
       fu=(*func)(u);  #include <io.h>
     } else {  #else
       u=(*cx)+GOLD*(*cx-*bx);  #include <unistd.h>
       fu=(*func)(u);  #endif
     }  
     SHFT(*ax,*bx,*cx,u)  #include <limits.h>
       SHFT(*fa,*fb,*fc,fu)  #include <sys/types.h>
       }  #include <sys/stat.h>
 }  #include <errno.h>
   /* extern int errno; */
 /*************** linmin ************************/  
   /* #ifdef LINUX */
 int ncom;  /* #include <time.h> */
 double *pcom,*xicom;  /* #include "timeval.h" */
 double (*nrfunc)(double []);  /* #else */
    /* #include <sys/time.h> */
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  /* #endif */
 {  
   double brent(double ax, double bx, double cx,  #include <time.h>
                double (*f)(double), double tol, double *xmin);  
   double f1dim(double x);  #ifdef GSL
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  #include <gsl/gsl_errno.h>
               double *fc, double (*func)(double));  #include <gsl/gsl_multimin.h>
   int j;  #endif
   double xx,xmin,bx,ax;  
   double fx,fb,fa;  /* #include <libintl.h> */
    /* #define _(String) gettext (String) */
   ncom=n;  
   pcom=vector(1,n);  #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
   xicom=vector(1,n);  
   nrfunc=func;  #define GNUPLOTPROGRAM "gnuplot"
   for (j=1;j<=n;j++) {  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
     pcom[j]=p[j];  #define FILENAMELENGTH 132
     xicom[j]=xi[j];  
   }  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
   ax=0.0;  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   xx=1.0;  
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
 #ifdef DEBUG  
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  #define NINTERVMAX 8
 #endif  #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
   for (j=1;j<=n;j++) {  #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
     xi[j] *= xmin;  #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
     p[j] += xi[j];  #define codtabm(h,k)  1 & (h-1) >> (k-1) ;
   }  #define MAXN 20000
   free_vector(xicom,1,n);  #define YEARM 12. /**< Number of months per year */
   free_vector(pcom,1,n);  #define AGESUP 130
 }  #define AGEBASE 40
   #define AGEGOMP 10. /**< Minimal age for Gompertz adjustment */
 /*************** powell ************************/  #ifdef _WIN32
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  #define DIRSEPARATOR '\\'
             double (*func)(double []))  #define CHARSEPARATOR "\\"
 {  #define ODIRSEPARATOR '/'
   void linmin(double p[], double xi[], int n, double *fret,  #else
               double (*func)(double []));  #define DIRSEPARATOR '/'
   int i,ibig,j;  #define CHARSEPARATOR "/"
   double del,t,*pt,*ptt,*xit;  #define ODIRSEPARATOR '\\'
   double fp,fptt;  #endif
   double *xits;  
   pt=vector(1,n);  /* $Id$ */
   ptt=vector(1,n);  /* $State$ */
   xit=vector(1,n);  
   xits=vector(1,n);  char version[]="Imach version 0.98nX, August 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121)";
   *fret=(*func)(p);  char fullversion[]="$Revision$ $Date$"; 
   for (j=1;j<=n;j++) pt[j]=p[j];  char strstart[80];
   for (*iter=1;;++(*iter)) {  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
     fp=(*fret);  int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
     ibig=0;  int nvar=0, nforce=0; /* Number of variables, number of forces */
     del=0.0;  /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
     for (i=1;i<=n;i++)  int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
       printf(" %d %.12f",i, p[i]);  int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
     printf("\n");  int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
     for (i=1;i<=n;i++) {  int cptcovprodnoage=0; /**< Number of covariate products without age */   
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  int cptcoveff=0; /* Total number of covariates to vary for printing results */
       fptt=(*fret);  int cptcov=0; /* Working variable */
 #ifdef DEBUG  int npar=NPARMAX;
       printf("fret=%lf \n",*fret);  int nlstate=2; /* Number of live states */
 #endif  int ndeath=1; /* Number of dead states */
       printf("%d",i);fflush(stdout);  int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
       linmin(p,xit,n,fret,func);  int popbased=0;
       if (fabs(fptt-(*fret)) > del) {  
         del=fabs(fptt-(*fret));  int *wav; /* Number of waves for this individuual 0 is possible */
         ibig=i;  int maxwav=0; /* Maxim number of waves */
       }  int jmin=0, jmax=0; /* min, max spacing between 2 waves */
 #ifdef DEBUG  int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
       printf("%d %.12e",i,(*fret));  int gipmx=0, gsw=0; /* Global variables on the number of contributions 
       for (j=1;j<=n;j++) {                     to the likelihood and the sum of weights (done by funcone)*/
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  int mle=1, weightopt=0;
         printf(" x(%d)=%.12e",j,xit[j]);  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
       }  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
       for(j=1;j<=n;j++)  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
         printf(" p=%.12e",p[j]);             * wave mi and wave mi+1 is not an exact multiple of stepm. */
       printf("\n");  double jmean=1; /* Mean space between 2 waves */
 #endif  double **matprod2(); /* test */
     }  double **oldm, **newm, **savm; /* Working pointers to matrices */
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
 #ifdef DEBUG  /*FILE *fic ; */ /* Used in readdata only */
       int k[2],l;  FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
       k[0]=1;  FILE *ficlog, *ficrespow;
       k[1]=-1;  int globpr=0; /* Global variable for printing or not */
       printf("Max: %.12e",(*func)(p));  double fretone; /* Only one call to likelihood */
       for (j=1;j<=n;j++)  long ipmx=0; /* Number of contributions */
         printf(" %.12e",p[j]);  double sw; /* Sum of weights */
       printf("\n");  char filerespow[FILENAMELENGTH];
       for(l=0;l<=1;l++) {  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
         for (j=1;j<=n;j++) {  FILE *ficresilk;
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  FILE *ficresprobmorprev;
         }  FILE *fichtm, *fichtmcov; /* Html File */
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  FILE *ficreseij;
       }  char filerese[FILENAMELENGTH];
 #endif  FILE *ficresstdeij;
   char fileresstde[FILENAMELENGTH];
   FILE *ficrescveij;
       free_vector(xit,1,n);  char filerescve[FILENAMELENGTH];
       free_vector(xits,1,n);  FILE  *ficresvij;
       free_vector(ptt,1,n);  char fileresv[FILENAMELENGTH];
       free_vector(pt,1,n);  FILE  *ficresvpl;
       return;  char fileresvpl[FILENAMELENGTH];
     }  char title[MAXLINE];
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
     for (j=1;j<=n;j++) {  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
       ptt[j]=2.0*p[j]-pt[j];  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
       xit[j]=p[j]-pt[j];  char command[FILENAMELENGTH];
       pt[j]=p[j];  int  outcmd=0;
     }  
     fptt=(*func)(ptt);  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
     if (fptt < fp) {  
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  char filelog[FILENAMELENGTH]; /* Log file */
       if (t < 0.0) {  char filerest[FILENAMELENGTH];
         linmin(p,xit,n,fret,func);  char fileregp[FILENAMELENGTH];
         for (j=1;j<=n;j++) {  char popfile[FILENAMELENGTH];
           xi[j][ibig]=xi[j][n];  
           xi[j][n]=xit[j];  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
         }  
 #ifdef DEBUG  /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  /* struct timezone tzp; */
         for(j=1;j<=n;j++)  /* extern int gettimeofday(); */
           printf(" %.12e",xit[j]);  struct tm tml, *gmtime(), *localtime();
         printf("\n");  
 #endif  extern time_t time();
       }  
     }  struct tm start_time, end_time, curr_time, last_time, forecast_time;
   }  time_t  rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
 }  struct tm tm;
   
 /**** Prevalence limit ****************/  char strcurr[80], strfor[80];
   
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  char *endptr;
 {  long lval;
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit  double dval;
      matrix by transitions matrix until convergence is reached */  
   #define NR_END 1
   int i, ii,j,k;  #define FREE_ARG char*
   double min, max, maxmin, maxmax,sumnew=0.;  #define FTOL 1.0e-10
   double **matprod2();  
   double **out, cov[NCOVMAX], **pmij();  #define NRANSI 
   double **newm;  #define ITMAX 200 
   double agefin, delaymax=50 ; /* Max number of years to converge */  
   #define TOL 2.0e-4 
   for (ii=1;ii<=nlstate+ndeath;ii++)  
     for (j=1;j<=nlstate+ndeath;j++){  #define CGOLD 0.3819660 
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);  #define ZEPS 1.0e-10 
     }  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
   
    cov[1]=1.;  #define GOLD 1.618034 
    #define GLIMIT 100.0 
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */  #define TINY 1.0e-20 
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){  
     newm=savm;  static double maxarg1,maxarg2;
     /* Covariates have to be included here again */  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
      cov[2]=agefin;  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
      
       for (k=1; k<=cptcovn;k++) {  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  #define rint(a) floor(a+0.5)
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/  
       }  static double sqrarg;
       for (k=1; k<=cptcovage;k++)  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
       for (k=1; k<=cptcovprod;k++)  int agegomp= AGEGOMP;
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  
   int imx; 
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/  int stepm=1;
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/  /* Stepm, step in month: minimum step interpolation*/
   
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  int estepm;
   /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
     savm=oldm;  
     oldm=newm;  int m,nb;
     maxmax=0.;  long *num;
     for(j=1;j<=nlstate;j++){  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
       min=1.;  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
       max=0.;  double **pmmij, ***probs;
       for(i=1; i<=nlstate; i++) {  double *ageexmed,*agecens;
         sumnew=0;  double dateintmean=0;
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  
         prlim[i][j]= newm[i][j]/(1-sumnew);  double *weight;
         max=FMAX(max,prlim[i][j]);  int **s; /* Status */
         min=FMIN(min,prlim[i][j]);  double *agedc;
       }  double  **covar; /**< covar[j,i], value of jth covariate for individual i,
       maxmin=max-min;                    * covar=matrix(0,NCOVMAX,1,n); 
       maxmax=FMAX(maxmax,maxmin);                    * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
     }  double  idx; 
     if(maxmax < ftolpl){  int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
       return prlim;  int *Ndum; /** Freq of modality (tricode */
     }  int **codtab; /**< codtab=imatrix(1,100,1,10); */
   }  int **Tvard, *Tprod, cptcovprod, *Tvaraff;
 }  double *lsurv, *lpop, *tpop;
   
 /*************** transition probabilities ***************/  double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
   double ftolhess; /**< Tolerance for computing hessian */
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  
 {  /**************** split *************************/
   double s1, s2;  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   /*double t34;*/  {
   int i,j,j1, nc, ii, jj;    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
        the name of the file (name), its extension only (ext) and its first part of the name (finame)
     for(i=1; i<= nlstate; i++){    */ 
     for(j=1; j<i;j++){    char  *ss;                            /* pointer */
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    int   l1, l2;                         /* length counters */
         /*s2 += param[i][j][nc]*cov[nc];*/  
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    l1 = strlen(path );                   /* length of path */
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
       }    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
       ps[i][j]=s2;    if ( ss == NULL ) {                   /* no directory, so determine current directory */
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/      strcpy( name, path );               /* we got the fullname name because no directory */
     }      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
     for(j=i+1; j<=nlstate+ndeath;j++){        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){      /* get current working directory */
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];      /*    extern  char* getcwd ( char *buf , int len);*/
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
       }        return( GLOCK_ERROR_GETCWD );
       ps[i][j]=(s2);      }
     }      /* got dirc from getcwd*/
   }      printf(" DIRC = %s \n",dirc);
     /*ps[3][2]=1;*/    } else {                              /* strip direcotry from path */
       ss++;                               /* after this, the filename */
   for(i=1; i<= nlstate; i++){      l2 = strlen( ss );                  /* length of filename */
      s1=0;      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
     for(j=1; j<i; j++)      strcpy( name, ss );         /* save file name */
       s1+=exp(ps[i][j]);      strncpy( dirc, path, l1 - l2 );     /* now the directory */
     for(j=i+1; j<=nlstate+ndeath; j++)      dirc[l1-l2] = 0;                    /* add zero */
       s1+=exp(ps[i][j]);      printf(" DIRC2 = %s \n",dirc);
     ps[i][i]=1./(s1+1.);    }
     for(j=1; j<i; j++)    /* We add a separator at the end of dirc if not exists */
       ps[i][j]= exp(ps[i][j])*ps[i][i];    l1 = strlen( dirc );                  /* length of directory */
     for(j=i+1; j<=nlstate+ndeath; j++)    if( dirc[l1-1] != DIRSEPARATOR ){
       ps[i][j]= exp(ps[i][j])*ps[i][i];      dirc[l1] =  DIRSEPARATOR;
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */      dirc[l1+1] = 0; 
   } /* end i */      printf(" DIRC3 = %s \n",dirc);
     }
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){    ss = strrchr( name, '.' );            /* find last / */
     for(jj=1; jj<= nlstate+ndeath; jj++){    if (ss >0){
       ps[ii][jj]=0;      ss++;
       ps[ii][ii]=1;      strcpy(ext,ss);                     /* save extension */
     }      l1= strlen( name);
   }      l2= strlen(ss)+1;
       strncpy( finame, name, l1-l2);
       finame[l1-l2]= 0;
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){    }
     for(jj=1; jj<= nlstate+ndeath; jj++){  
      printf("%lf ",ps[ii][jj]);    return( 0 );                          /* we're done */
    }  }
     printf("\n ");  
     }  
     printf("\n ");printf("%lf ",cov[2]);*/  /******************************************/
 /*  
   for(i=1; i<= npar; i++) printf("%f ",x[i]);  void replace_back_to_slash(char *s, char*t)
   goto end;*/  {
     return ps;    int i;
 }    int lg=0;
     i=0;
 /**************** Product of 2 matrices ******************/    lg=strlen(t);
     for(i=0; i<= lg; i++) {
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)      (s[i] = t[i]);
 {      if (t[i]== '\\') s[i]='/';
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times    }
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */  }
   /* in, b, out are matrice of pointers which should have been initialized  
      before: only the contents of out is modified. The function returns  char *trimbb(char *out, char *in)
      a pointer to pointers identical to out */  { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
   long i, j, k;    char *s;
   for(i=nrl; i<= nrh; i++)    s=out;
     for(k=ncolol; k<=ncoloh; k++)    while (*in != '\0'){
       for(j=ncl,out[i][k]=0.; j<=nch; j++)      while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
         out[i][k] +=in[i][j]*b[j][k];        in++;
       }
   return out;      *out++ = *in++;
 }    }
     *out='\0';
     return s;
 /************* Higher Matrix Product ***************/  }
   
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )  char *cutl(char *blocc, char *alocc, char *in, char occ)
 {  {
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month    /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ' 
      duration (i.e. until       and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.       gives blocc="abcdef2ghi" and alocc="j".
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step       If occ is not found blocc is null and alocc is equal to in. Returns blocc
      (typically every 2 years instead of every month which is too big).    */
      Model is determined by parameters x and covariates have to be    char *s, *t, *bl;
      included manually here.    t=in;s=in;
     while ((*in != occ) && (*in != '\0')){
      */      *alocc++ = *in++;
     }
   int i, j, d, h, k;    if( *in == occ){
   double **out, cov[NCOVMAX];      *(alocc)='\0';
   double **newm;      s=++in;
     }
   /* Hstepm could be zero and should return the unit matrix */   
   for (i=1;i<=nlstate+ndeath;i++)    if (s == t) {/* occ not found */
     for (j=1;j<=nlstate+ndeath;j++){      *(alocc-(in-s))='\0';
       oldm[i][j]=(i==j ? 1.0 : 0.0);      in=s;
       po[i][j][0]=(i==j ? 1.0 : 0.0);    }
     }    while ( *in != '\0'){
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */      *blocc++ = *in++;
   for(h=1; h <=nhstepm; h++){    }
     for(d=1; d <=hstepm; d++){  
       newm=savm;    *blocc='\0';
       /* Covariates have to be included here again */    return t;
       cov[1]=1.;  }
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;  char *cutv(char *blocc, char *alocc, char *in, char occ)
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  {
       for (k=1; k<=cptcovage;k++)    /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ' 
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];       and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
       for (k=1; k<=cptcovprod;k++)       gives blocc="abcdef2ghi" and alocc="j".
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];       If occ is not found blocc is null and alocc is equal to in. Returns alocc
     */
     char *s, *t;
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/    t=in;s=in;
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/    while (*in != '\0'){
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,      while( *in == occ){
                    pmij(pmmij,cov,ncovmodel,x,nlstate));        *blocc++ = *in++;
       savm=oldm;        s=in;
       oldm=newm;      }
     }      *blocc++ = *in++;
     for(i=1; i<=nlstate+ndeath; i++)    }
       for(j=1;j<=nlstate+ndeath;j++) {    if (s == t) /* occ not found */
         po[i][j][h]=newm[i][j];      *(blocc-(in-s))='\0';
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);    else
          */      *(blocc-(in-s)-1)='\0';
       }    in=s;
   } /* end h */    while ( *in != '\0'){
   return po;      *alocc++ = *in++;
 }    }
   
     *alocc='\0';
 /*************** log-likelihood *************/    return s;
 double func( double *x)  }
 {  
   int i, ii, j, k, mi, d, kk;  int nbocc(char *s, char occ)
   double l, ll[NLSTATEMAX], cov[NCOVMAX];  {
   double **out;    int i,j=0;
   double sw; /* Sum of weights */    int lg=20;
   double lli; /* Individual log likelihood */    i=0;
   long ipmx;    lg=strlen(s);
   /*extern weight */    for(i=0; i<= lg; i++) {
   /* We are differentiating ll according to initial status */    if  (s[i] == occ ) j++;
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    }
   /*for(i=1;i<imx;i++)    return j;
     printf(" %d\n",s[4][i]);  }
   */  
   cov[1]=1.;  /* void cutv(char *u,char *v, char*t, char occ) */
   /* { */
   for(k=1; k<=nlstate; k++) ll[k]=0.;  /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){  /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];  /*      gives u="abcdef2ghi" and v="j" *\/ */
     for(mi=1; mi<= wav[i]-1; mi++){  /*   int i,lg,j,p=0; */
       for (ii=1;ii<=nlstate+ndeath;ii++)  /*   i=0; */
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);  /*   lg=strlen(t); */
       for(d=0; d<dh[mi][i]; d++){  /*   for(j=0; j<=lg-1; j++) { */
         newm=savm;  /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;  /*   } */
         for (kk=1; kk<=cptcovage;kk++) {  
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];  /*   for(j=0; j<p; j++) { */
         }  /*     (u[j] = t[j]); */
          /*   } */
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,  /*      u[p]='\0'; */
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));  
         savm=oldm;  /*    for(j=0; j<= lg; j++) { */
         oldm=newm;  /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
          /*   } */
          /* } */
       } /* end mult */  
        /********************** nrerror ********************/
       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]]);*/  void nrerror(char error_text[])
       ipmx +=1;  {
       sw += weight[i];    fprintf(stderr,"ERREUR ...\n");
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;    fprintf(stderr,"%s\n",error_text);
     } /* end of wave */    exit(EXIT_FAILURE);
   } /* end of individual */  }
   /*********************** vector *******************/
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];  double *vector(int nl, int nh)
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */  {
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */    double *v;
   return -l;    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
 }    if (!v) nrerror("allocation failure in vector");
     return v-nl+NR_END;
   }
 /*********** Maximum Likelihood Estimation ***************/  
   /************************ free vector ******************/
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))  void free_vector(double*v, int nl, int nh)
 {  {
   int i,j, iter;    free((FREE_ARG)(v+nl-NR_END));
   double **xi,*delti;  }
   double fret;  
   xi=matrix(1,npar,1,npar);  /************************ivector *******************************/
   for (i=1;i<=npar;i++)  int *ivector(long nl,long nh)
     for (j=1;j<=npar;j++)  {
       xi[i][j]=(i==j ? 1.0 : 0.0);    int *v;
   printf("Powell\n");    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   powell(p,xi,npar,ftol,&iter,&fret,func);    if (!v) nrerror("allocation failure in ivector");
     return v-nl+NR_END;
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));  }
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f ",iter,func(p));  
   /******************free ivector **************************/
 }  void free_ivector(int *v, long nl, long nh)
   {
 /**** Computes Hessian and covariance matrix ***/    free((FREE_ARG)(v+nl-NR_END));
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))  }
 {  
   double  **a,**y,*x,pd;  /************************lvector *******************************/
   double **hess;  long *lvector(long nl,long nh)
   int i, j,jk;  {
   int *indx;    long *v;
     v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
   double hessii(double p[], double delta, int theta, double delti[]);    if (!v) nrerror("allocation failure in ivector");
   double hessij(double p[], double delti[], int i, int j);    return v-nl+NR_END;
   void lubksb(double **a, int npar, int *indx, double b[]) ;  }
   void ludcmp(double **a, int npar, int *indx, double *d) ;  
   /******************free lvector **************************/
   hess=matrix(1,npar,1,npar);  void free_lvector(long *v, long nl, long nh)
   {
   printf("\nCalculation of the hessian matrix. Wait...\n");    free((FREE_ARG)(v+nl-NR_END));
   for (i=1;i<=npar;i++){  }
     printf("%d",i);fflush(stdout);  
     hess[i][i]=hessii(p,ftolhess,i,delti);  /******************* imatrix *******************************/
     /*printf(" %f ",p[i]);*/  int **imatrix(long nrl, long nrh, long ncl, long nch) 
     /*printf(" %lf ",hess[i][i]);*/       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
   }  { 
      long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
   for (i=1;i<=npar;i++) {    int **m; 
     for (j=1;j<=npar;j++)  {    
       if (j>i) {    /* allocate pointers to rows */ 
         printf(".%d%d",i,j);fflush(stdout);    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
         hess[i][j]=hessij(p,delti,i,j);    if (!m) nrerror("allocation failure 1 in matrix()"); 
         hess[j][i]=hess[i][j];        m += NR_END; 
         /*printf(" %lf ",hess[i][j]);*/    m -= nrl; 
       }    
     }    
   }    /* allocate rows and set pointers to them */ 
   printf("\n");    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
     if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");    m[nrl] += NR_END; 
      m[nrl] -= ncl; 
   a=matrix(1,npar,1,npar);    
   y=matrix(1,npar,1,npar);    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
   x=vector(1,npar);    
   indx=ivector(1,npar);    /* return pointer to array of pointers to rows */ 
   for (i=1;i<=npar;i++)    return m; 
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];  } 
   ludcmp(a,npar,indx,&pd);  
   /****************** free_imatrix *************************/
   for (j=1;j<=npar;j++) {  void free_imatrix(m,nrl,nrh,ncl,nch)
     for (i=1;i<=npar;i++) x[i]=0;        int **m;
     x[j]=1;        long nch,ncl,nrh,nrl; 
     lubksb(a,npar,indx,x);       /* free an int matrix allocated by imatrix() */ 
     for (i=1;i<=npar;i++){  { 
       matcov[i][j]=x[i];    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
     }    free((FREE_ARG) (m+nrl-NR_END)); 
   }  } 
   
   printf("\n#Hessian matrix#\n");  /******************* matrix *******************************/
   for (i=1;i<=npar;i++) {  double **matrix(long nrl, long nrh, long ncl, long nch)
     for (j=1;j<=npar;j++) {  {
       printf("%.3e ",hess[i][j]);    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
     }    double **m;
     printf("\n");  
   }    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     if (!m) nrerror("allocation failure 1 in matrix()");
   /* Recompute Inverse */    m += NR_END;
   for (i=1;i<=npar;i++)    m -= nrl;
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];  
   ludcmp(a,npar,indx,&pd);    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   /*  printf("\n#Hessian matrix recomputed#\n");    m[nrl] += NR_END;
     m[nrl] -= ncl;
   for (j=1;j<=npar;j++) {  
     for (i=1;i<=npar;i++) x[i]=0;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     x[j]=1;    return m;
     lubksb(a,npar,indx,x);    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
     for (i=1;i<=npar;i++){  m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
       y[i][j]=x[i];  that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
       printf("%.3e ",y[i][j]);     */
     }  }
     printf("\n");  
   }  /*************************free matrix ************************/
   */  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   {
   free_matrix(a,1,npar,1,npar);    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   free_matrix(y,1,npar,1,npar);    free((FREE_ARG)(m+nrl-NR_END));
   free_vector(x,1,npar);  }
   free_ivector(indx,1,npar);  
   free_matrix(hess,1,npar,1,npar);  /******************* ma3x *******************************/
   double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
   {
 }    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
     double ***m;
 /*************** hessian matrix ****************/  
 double hessii( double x[], double delta, int theta, double delti[])    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
 {    if (!m) nrerror("allocation failure 1 in matrix()");
   int i;    m += NR_END;
   int l=1, lmax=20;    m -= nrl;
   double k1,k2;  
   double p2[NPARMAX+1];    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   double res;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;    m[nrl] += NR_END;
   double fx;    m[nrl] -= ncl;
   int k=0,kmax=10;  
   double l1;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   
   fx=func(x);    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
   for (i=1;i<=npar;i++) p2[i]=x[i];    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
   for(l=0 ; l <=lmax; l++){    m[nrl][ncl] += NR_END;
     l1=pow(10,l);    m[nrl][ncl] -= nll;
     delts=delt;    for (j=ncl+1; j<=nch; j++) 
     for(k=1 ; k <kmax; k=k+1){      m[nrl][j]=m[nrl][j-1]+nlay;
       delt = delta*(l1*k);    
       p2[theta]=x[theta] +delt;    for (i=nrl+1; i<=nrh; i++) {
       k1=func(p2)-fx;      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
       p2[theta]=x[theta]-delt;      for (j=ncl+1; j<=nch; j++) 
       k2=func(p2)-fx;        m[i][j]=m[i][j-1]+nlay;
       /*res= (k1-2.0*fx+k2)/delt/delt; */    }
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */    return m; 
          /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
 #ifdef DEBUG             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);    */
 #endif  }
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */  
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){  /*************************free ma3x ************************/
         k=kmax;  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
       }  {
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
         k=kmax; l=lmax*10.;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
       }    free((FREE_ARG)(m+nrl-NR_END));
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){  }
         delts=delt;  
       }  /*************** function subdirf ***********/
     }  char *subdirf(char fileres[])
   }  {
   delti[theta]=delts;    /* Caution optionfilefiname is hidden */
   return res;    strcpy(tmpout,optionfilefiname);
      strcat(tmpout,"/"); /* Add to the right */
 }    strcat(tmpout,fileres);
     return tmpout;
 double hessij( double x[], double delti[], int thetai,int thetaj)  }
 {  
   int i;  /*************** function subdirf2 ***********/
   int l=1, l1, lmax=20;  char *subdirf2(char fileres[], char *preop)
   double k1,k2,k3,k4,res,fx;  {
   double p2[NPARMAX+1];    
   int k;    /* Caution optionfilefiname is hidden */
     strcpy(tmpout,optionfilefiname);
   fx=func(x);    strcat(tmpout,"/");
   for (k=1; k<=2; k++) {    strcat(tmpout,preop);
     for (i=1;i<=npar;i++) p2[i]=x[i];    strcat(tmpout,fileres);
     p2[thetai]=x[thetai]+delti[thetai]/k;    return tmpout;
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  }
     k1=func(p2)-fx;  
    /*************** function subdirf3 ***********/
     p2[thetai]=x[thetai]+delti[thetai]/k;  char *subdirf3(char fileres[], char *preop, char *preop2)
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;  {
     k2=func(p2)-fx;    
      /* Caution optionfilefiname is hidden */
     p2[thetai]=x[thetai]-delti[thetai]/k;    strcpy(tmpout,optionfilefiname);
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    strcat(tmpout,"/");
     k3=func(p2)-fx;    strcat(tmpout,preop);
      strcat(tmpout,preop2);
     p2[thetai]=x[thetai]-delti[thetai]/k;    strcat(tmpout,fileres);
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    return tmpout;
     k4=func(p2)-fx;  }
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */  
 #ifdef DEBUG  /***************** f1dim *************************/
     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);  extern int ncom; 
 #endif  extern double *pcom,*xicom;
   }  extern double (*nrfunc)(double []); 
   return res;   
 }  double f1dim(double x) 
   { 
 /************** Inverse of matrix **************/    int j; 
 void ludcmp(double **a, int n, int *indx, double *d)    double f;
 {    double *xt; 
   int i,imax,j,k;   
   double big,dum,sum,temp;    xt=vector(1,ncom); 
   double *vv;    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
      f=(*nrfunc)(xt); 
   vv=vector(1,n);    free_vector(xt,1,ncom); 
   *d=1.0;    return f; 
   for (i=1;i<=n;i++) {  } 
     big=0.0;  
     for (j=1;j<=n;j++)  /*****************brent *************************/
       if ((temp=fabs(a[i][j])) > big) big=temp;  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");  { 
     vv[i]=1.0/big;    int iter; 
   }    double a,b,d,etemp;
   for (j=1;j<=n;j++) {    double fu=0,fv,fw,fx;
     for (i=1;i<j;i++) {    double ftemp;
       sum=a[i][j];    double p,q,r,tol1,tol2,u,v,w,x,xm; 
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];    double e=0.0; 
       a[i][j]=sum;   
     }    a=(ax < cx ? ax : cx); 
     big=0.0;    b=(ax > cx ? ax : cx); 
     for (i=j;i<=n;i++) {    x=w=v=bx; 
       sum=a[i][j];    fw=fv=fx=(*f)(x); 
       for (k=1;k<j;k++)    for (iter=1;iter<=ITMAX;iter++) { 
         sum -= a[i][k]*a[k][j];      xm=0.5*(a+b); 
       a[i][j]=sum;      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
       if ( (dum=vv[i]*fabs(sum)) >= big) {      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
         big=dum;      printf(".");fflush(stdout);
         imax=i;      fprintf(ficlog,".");fflush(ficlog);
       }  #ifdef DEBUG
     }      printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
     if (j != imax) {      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);
       for (k=1;k<=n;k++) {      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
         dum=a[imax][k];  #endif
         a[imax][k]=a[j][k];      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
         a[j][k]=dum;        *xmin=x; 
       }        return fx; 
       *d = -(*d);      } 
       vv[imax]=vv[j];      ftemp=fu;
     }      if (fabs(e) > tol1) { 
     indx[j]=imax;        r=(x-w)*(fx-fv); 
     if (a[j][j] == 0.0) a[j][j]=TINY;        q=(x-v)*(fx-fw); 
     if (j != n) {        p=(x-v)*q-(x-w)*r; 
       dum=1.0/(a[j][j]);        q=2.0*(q-r); 
       for (i=j+1;i<=n;i++) a[i][j] *= dum;        if (q > 0.0) p = -p; 
     }        q=fabs(q); 
   }        etemp=e; 
   free_vector(vv,1,n);  /* Doesn't work */        e=d; 
 ;        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)); 
         else { 
 void lubksb(double **a, int n, int *indx, double b[])          d=p/q; 
 {          u=x+d; 
   int i,ii=0,ip,j;          if (u-a < tol2 || b-u < tol2) 
   double sum;            d=SIGN(tol1,xm-x); 
          } 
   for (i=1;i<=n;i++) {      } else { 
     ip=indx[i];        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
     sum=b[ip];      } 
     b[ip]=b[i];      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
     if (ii)      fu=(*f)(u); 
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];      if (fu <= fx) { 
     else if (sum) ii=i;        if (u >= x) a=x; else b=x; 
     b[i]=sum;        SHFT(v,w,x,u) 
   }          SHFT(fv,fw,fx,fu) 
   for (i=n;i>=1;i--) {          } else { 
     sum=b[i];            if (u < x) a=u; else b=u; 
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];            if (fu <= fw || w == x) { 
     b[i]=sum/a[i][i];              v=w; 
   }              w=u; 
 }              fv=fw; 
               fw=fu; 
 /************ Frequencies ********************/            } else if (fu <= fv || v == x || v == w) { 
 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)              v=u; 
 {  /* Some frequencies */              fv=fu; 
              } 
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;          } 
   double ***freq; /* Frequencies */    } 
   double *pp;    nrerror("Too many iterations in brent"); 
   double pos, k2, dateintsum=0,k2cpt=0;    *xmin=x; 
   FILE *ficresp;    return fx; 
   char fileresp[FILENAMELENGTH];  } 
   
   pp=vector(1,nlstate);  /****************** mnbrak ***********************/
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);  
   strcpy(fileresp,"p");  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
   strcat(fileresp,fileres);              double (*func)(double)) 
   if((ficresp=fopen(fileresp,"w"))==NULL) {  { 
     printf("Problem with prevalence resultfile: %s\n", fileresp);    double ulim,u,r,q, dum;
     exit(0);    double fu; 
   }   
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    *fa=(*func)(*ax); 
   j1=0;    *fb=(*func)(*bx); 
     if (*fb > *fa) { 
   j=cptcoveff;      SHFT(dum,*ax,*bx,dum) 
   if (cptcovn<1) {j=1;ncodemax[1]=1;}        SHFT(dum,*fb,*fa,dum) 
         } 
   for(k1=1; k1<=j;k1++){    *cx=(*bx)+GOLD*(*bx-*ax); 
    for(i1=1; i1<=ncodemax[k1];i1++){    *fc=(*func)(*cx); 
        j1++;    while (*fb > *fc) { 
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);      r=(*bx-*ax)*(*fb-*fc); 
          scanf("%d", i);*/      q=(*bx-*cx)*(*fb-*fa); 
         for (i=-1; i<=nlstate+ndeath; i++)        u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
          for (jk=-1; jk<=nlstate+ndeath; jk++)          (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
            for(m=agemin; m <= agemax+3; m++)      ulim=(*bx)+GLIMIT*(*cx-*bx); 
              freq[i][jk][m]=0;      if ((*bx-u)*(u-*cx) > 0.0) { 
         fu=(*func)(u); 
         dateintsum=0;      } else if ((*cx-u)*(u-ulim) > 0.0) { 
         k2cpt=0;        fu=(*func)(u); 
        for (i=1; i<=imx; i++) {        if (fu < *fc) { 
          bool=1;          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
          if  (cptcovn>0) {            SHFT(*fb,*fc,fu,(*func)(u)) 
            for (z1=1; z1<=cptcoveff; z1++)            } 
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
                bool=0;        u=ulim; 
          }        fu=(*func)(u); 
          if (bool==1) {      } else { 
            for(m=firstpass; m<=lastpass; m++){        u=(*cx)+GOLD*(*cx-*bx); 
              k2=anint[m][i]+(mint[m][i]/12.);        fu=(*func)(u); 
              if ((k2>=dateprev1) && (k2<=dateprev2)) {      } 
                if(agev[m][i]==0) agev[m][i]=agemax+1;      SHFT(*ax,*bx,*cx,u) 
                if(agev[m][i]==1) agev[m][i]=agemax+2;        SHFT(*fa,*fb,*fc,fu) 
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];        } 
                freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];  } 
                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {  
                  dateintsum=dateintsum+k2;  /*************** linmin ************************/
                  k2cpt++;  
                }  int ncom; 
   double *pcom,*xicom;
              }  double (*nrfunc)(double []); 
            }   
          }  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
        }  { 
         if  (cptcovn>0) {    double brent(double ax, double bx, double cx, 
          fprintf(ficresp, "\n#********** Variable ");                 double (*f)(double), double tol, double *xmin); 
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    double f1dim(double x); 
        fprintf(ficresp, "**********\n#");    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
         }                double *fc, double (*func)(double)); 
        for(i=1; i<=nlstate;i++)    int j; 
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);    double xx,xmin,bx,ax; 
        fprintf(ficresp, "\n");    double fx,fb,fa;
           
   for(i=(int)agemin; i <= (int)agemax+3; i++){    ncom=n; 
     if(i==(int)agemax+3)    pcom=vector(1,n); 
       printf("Total");    xicom=vector(1,n); 
     else    nrfunc=func; 
       printf("Age %d", i);    for (j=1;j<=n;j++) { 
     for(jk=1; jk <=nlstate ; jk++){      pcom[j]=p[j]; 
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)      xicom[j]=xi[j]; 
         pp[jk] += freq[jk][m][i];    } 
     }    ax=0.0; 
     for(jk=1; jk <=nlstate ; jk++){    xx=1.0; 
       for(m=-1, pos=0; m <=0 ; m++)    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
         pos += freq[jk][m][i];    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
       if(pp[jk]>=1.e-10)  #ifdef DEBUG
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
       else    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);  #endif
     }    for (j=1;j<=n;j++) { 
       xi[j] *= xmin; 
      for(jk=1; jk <=nlstate ; jk++){      p[j] += xi[j]; 
       for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)    } 
         pp[jk] += freq[jk][m][i];    free_vector(xicom,1,n); 
      }    free_vector(pcom,1,n); 
   } 
     for(jk=1,pos=0; jk <=nlstate ; jk++)  
       pos += pp[jk];  char *asc_diff_time(long time_sec, char ascdiff[])
     for(jk=1; jk <=nlstate ; jk++){  {
       if(pos>=1.e-5)    long sec_left, days, hours, minutes;
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);    days = (time_sec) / (60*60*24);
       else    sec_left = (time_sec) % (60*60*24);
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);    hours = (sec_left) / (60*60) ;
       if( i <= (int) agemax){    sec_left = (sec_left) %(60*60);
         if(pos>=1.e-5){    minutes = (sec_left) /60;
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);    sec_left = (sec_left) % (60);
           probs[i][jk][j1]= pp[jk]/pos;    sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);  
           /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/    return ascdiff;
         }  }
       else  
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);  /*************** powell ************************/
       }  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
     }              double (*func)(double [])) 
     for(jk=-1; jk <=nlstate+ndeath; jk++)  { 
       for(m=-1; m <=nlstate+ndeath; m++)    void linmin(double p[], double xi[], int n, double *fret, 
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);                double (*func)(double [])); 
     if(i <= (int) agemax)    int i,ibig,j; 
       fprintf(ficresp,"\n");    double del,t,*pt,*ptt,*xit;
     printf("\n");    double fp,fptt;
     }    double *xits;
     }    int niterf, itmp;
  }  
   dateintmean=dateintsum/k2cpt;    pt=vector(1,n); 
      ptt=vector(1,n); 
   fclose(ficresp);    xit=vector(1,n); 
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    xits=vector(1,n); 
   free_vector(pp,1,nlstate);    *fret=(*func)(p); 
     for (j=1;j<=n;j++) pt[j]=p[j]; 
   /* End of Freq */      rcurr_time = time(NULL);  
 }    for (*iter=1;;++(*iter)) { 
       fp=(*fret); 
 /************ Prevalence ********************/      ibig=0; 
 void prevalence(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 calagedate)      del=0.0; 
 {  /* Some frequencies */      rlast_time=rcurr_time;
        /* (void) gettimeofday(&curr_time,&tzp); */
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;      rcurr_time = time(NULL);  
   double ***freq; /* Frequencies */      curr_time = *localtime(&rcurr_time);
   double *pp;      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
   double pos, k2;      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
   /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
   pp=vector(1,nlstate);     for (i=1;i<=n;i++) {
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);        printf(" %d %.12f",i, p[i]);
          fprintf(ficlog," %d %.12lf",i, p[i]);
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);        fprintf(ficrespow," %.12lf", p[i]);
   j1=0;      }
        printf("\n");
   j=cptcoveff;      fprintf(ficlog,"\n");
   if (cptcovn<1) {j=1;ncodemax[1]=1;}      fprintf(ficrespow,"\n");fflush(ficrespow);
        if(*iter <=3){
  for(k1=1; k1<=j;k1++){        tml = *localtime(&rcurr_time);
     for(i1=1; i1<=ncodemax[k1];i1++){        strcpy(strcurr,asctime(&tml));
       j1++;  /*       asctime_r(&tm,strcurr); */
          rforecast_time=rcurr_time; 
       for (i=-1; i<=nlstate+ndeath; i++)          itmp = strlen(strcurr);
         for (jk=-1; jk<=nlstate+ndeath; jk++)          if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
           for(m=agemin; m <= agemax+3; m++)          strcurr[itmp-1]='\0';
             freq[i][jk][m]=0;        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
              fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
       for (i=1; i<=imx; i++) {        for(niterf=10;niterf<=30;niterf+=10){
         bool=1;          rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
         if  (cptcovn>0) {          forecast_time = *localtime(&rforecast_time);
           for (z1=1; z1<=cptcoveff; z1++)  /*      asctime_r(&tmf,strfor); */
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])          strcpy(strfor,asctime(&forecast_time));
               bool=0;          itmp = strlen(strfor);
         }          if(strfor[itmp-1]=='\n')
         if (bool==1) {          strfor[itmp-1]='\0';
           for(m=firstpass; m<=lastpass; m++){          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);
             k2=anint[m][i]+(mint[m][i]/12.);          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);
             if ((k2>=dateprev1) && (k2<=dateprev2)) {        }
               if(agev[m][i]==0) agev[m][i]=agemax+1;      }
               if(agev[m][i]==1) agev[m][i]=agemax+2;      for (i=1;i<=n;i++) { 
               freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
               freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];          fptt=(*fret); 
             }  #ifdef DEBUG
           }        printf("fret=%lf \n",*fret);
         }        fprintf(ficlog,"fret=%lf \n",*fret);
       }  #endif
              printf("%d",i);fflush(stdout);
         for(i=(int)agemin; i <= (int)agemax+3; i++){        fprintf(ficlog,"%d",i);fflush(ficlog);
           for(jk=1; jk <=nlstate ; jk++){        linmin(p,xit,n,fret,func); 
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        if (fabs(fptt-(*fret)) > del) { 
               pp[jk] += freq[jk][m][i];          del=fabs(fptt-(*fret)); 
           }          ibig=i; 
           for(jk=1; jk <=nlstate ; jk++){        } 
             for(m=-1, pos=0; m <=0 ; m++)  #ifdef DEBUG
             pos += freq[jk][m][i];        printf("%d %.12e",i,(*fret));
         }        fprintf(ficlog,"%d %.12e",i,(*fret));
                for (j=1;j<=n;j++) {
          for(jk=1; jk <=nlstate ; jk++){          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)          printf(" x(%d)=%.12e",j,xit[j]);
              pp[jk] += freq[jk][m][i];          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
          }        }
                  for(j=1;j<=n;j++) {
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];          printf(" p=%.12e",p[j]);
           fprintf(ficlog," p=%.12e",p[j]);
          for(jk=1; jk <=nlstate ; jk++){                  }
            if( i <= (int) agemax){        printf("\n");
              if(pos>=1.e-5){        fprintf(ficlog,"\n");
                probs[i][jk][j1]= pp[jk]/pos;  #endif
              }      } 
            }      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
          }  #ifdef DEBUG
                  int k[2],l;
         }        k[0]=1;
     }        k[1]=-1;
   }        printf("Max: %.12e",(*func)(p));
          fprintf(ficlog,"Max: %.12e",(*func)(p));
          for (j=1;j<=n;j++) {
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);          printf(" %.12e",p[j]);
   free_vector(pp,1,nlstate);          fprintf(ficlog," %.12e",p[j]);
          }
 }  /* End of Freq */        printf("\n");
         fprintf(ficlog,"\n");
 /************* Waves Concatenation ***************/        for(l=0;l<=1;l++) {
           for (j=1;j<=n;j++) {
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)            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]);
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
      Death is a valid wave (if date is known).          }
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
      and mw[mi+1][i]. dh depends on stepm.        }
      */  #endif
   
   int i, mi, m;  
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;        free_vector(xit,1,n); 
      double sum=0., jmean=0.;*/        free_vector(xits,1,n); 
         free_vector(ptt,1,n); 
   int j, k=0,jk, ju, jl;        free_vector(pt,1,n); 
   double sum=0.;        return; 
   jmin=1e+5;      } 
   jmax=-1;      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
   jmean=0.;      for (j=1;j<=n;j++) { 
   for(i=1; i<=imx; i++){        ptt[j]=2.0*p[j]-pt[j]; 
     mi=0;        xit[j]=p[j]-pt[j]; 
     m=firstpass;        pt[j]=p[j]; 
     while(s[m][i] <= nlstate){      } 
       if(s[m][i]>=1)      fptt=(*func)(ptt); 
         mw[++mi][i]=m;      if (fptt < fp) { 
       if(m >=lastpass)        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
         break;        if (t < 0.0) { 
       else          linmin(p,xit,n,fret,func); 
         m++;          for (j=1;j<=n;j++) { 
     }/* end while */            xi[j][ibig]=xi[j][n]; 
     if (s[m][i] > nlstate){            xi[j][n]=xit[j]; 
       mi++;     /* Death is another wave */          }
       /* if(mi==0)  never been interviewed correctly before death */  #ifdef DEBUG
          /* Only death is a correct wave */          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
       mw[mi][i]=m;          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
     }          for(j=1;j<=n;j++){
             printf(" %.12e",xit[j]);
     wav[i]=mi;            fprintf(ficlog," %.12e",xit[j]);
     if(mi==0)          }
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);          printf("\n");
   }          fprintf(ficlog,"\n");
   #endif
   for(i=1; i<=imx; i++){        }
     for(mi=1; mi<wav[i];mi++){      } 
       if (stepm <=0)    } 
         dh[mi][i]=1;  } 
       else{  
         if (s[mw[mi+1][i]][i] > nlstate) {  /**** Prevalence limit (stable or period prevalence)  ****************/
           if (agedc[i] < 2*AGESUP) {  
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
           if(j==0) j=1;  /* Survives at least one month after exam */  {
           k=k+1;    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
           if (j >= jmax) jmax=j;       matrix by transitions matrix until convergence is reached */
           if (j <= jmin) jmin=j;  
           sum=sum+j;    int i, ii,j,k;
           /* if (j<10) printf("j=%d num=%d ",j,i); */    double min, max, maxmin, maxmax,sumnew=0.;
           }    /* double **matprod2(); */ /* test */
         }    double **out, cov[NCOVMAX+1], **pmij();
         else{    double **newm;
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));    double agefin, delaymax=50 ; /* Max number of years to converge */
           k=k+1;  
           if (j >= jmax) jmax=j;    for (ii=1;ii<=nlstate+ndeath;ii++)
           else if (j <= jmin)jmin=j;      for (j=1;j<=nlstate+ndeath;j++){
           /*   if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           sum=sum+j;      }
         }  
         jk= j/stepm;     cov[1]=1.;
         jl= j -jk*stepm;   
         ju= j -(jk+1)*stepm;   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
         if(jl <= -ju)    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
           dh[mi][i]=jk;      newm=savm;
         else      /* Covariates have to be included here again */
           dh[mi][i]=jk+1;      cov[2]=agefin;
         if(dh[mi][i]==0)      
           dh[mi][i]=1; /* At least one step */      for (k=1; k<=cptcovn;k++) {
       }        cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
     }        /*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]]);*/
   }      }
   jmean=sum/k;      /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);      /* 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]]]; */
 /*********** Tricode ****************************/      
 void tricode(int *Tvar, int **nbcode, int imx)      /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
 {      /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
   int Ndum[20],ij=1, k, j, i;      /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
   int cptcode=0;      /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
   cptcoveff=0;      /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
        out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
   for (k=0; k<19; k++) Ndum[k]=0;      
   for (k=1; k<=7; k++) ncodemax[k]=0;      savm=oldm;
       oldm=newm;
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {      maxmax=0.;
     for (i=1; i<=imx; i++) {      for(j=1;j<=nlstate;j++){
       ij=(int)(covar[Tvar[j]][i]);        min=1.;
       Ndum[ij]++;        max=0.;
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/        for(i=1; i<=nlstate; i++) {
       if (ij > cptcode) cptcode=ij;          sumnew=0;
     }          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
           prlim[i][j]= newm[i][j]/(1-sumnew);
     for (i=0; i<=cptcode; i++) {          /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
       if(Ndum[i]!=0) ncodemax[j]++;          max=FMAX(max,prlim[i][j]);
     }          min=FMIN(min,prlim[i][j]);
     ij=1;        }
         maxmin=max-min;
         maxmax=FMAX(maxmax,maxmin);
     for (i=1; i<=ncodemax[j]; i++) {      }
       for (k=0; k<=19; k++) {      if(maxmax < ftolpl){
         if (Ndum[k] != 0) {        return prlim;
           nbcode[Tvar[j]][ij]=k;      }
           ij++;    }
         }  }
         if (ij > ncodemax[j]) break;  
       }    /*************** transition probabilities ***************/ 
     }  
   }    double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
   {
  for (k=0; k<19; k++) Ndum[k]=0;    /* According to parameters values stored in x and the covariate's values stored in cov,
        computes the probability to be observed in state j being in state i by appying the
  for (i=1; i<=ncovmodel-2; i++) {       model to the ncovmodel covariates (including constant and age).
       ij=Tvar[i];       lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
       Ndum[ij]++;       and, according on how parameters are entered, the position of the coefficient xij(nc) of the
     }       ncth covariate in the global vector x is given by the formula:
        j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
  ij=1;       j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
  for (i=1; i<=10; i++) {       Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
    if((Ndum[i]!=0) && (i<=ncov)){       sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
      Tvaraff[ij]=i;       Outputs ps[i][j] the probability to be observed in j being in j according to
      ij++;       the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
    }    */
  }    double s1, lnpijopii;
      /*double t34;*/
     cptcoveff=ij-1;    int i,j,j1, nc, ii, jj;
 }  
       for(i=1; i<= nlstate; i++){
 /*********** Health Expectancies ****************/        for(j=1; j<i;j++){
           for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)            /*lnpijopii += param[i][j][nc]*cov[nc];*/
 {            lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
   /* Health expectancies */  /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
   int i, j, nhstepm, hstepm, h;          }
   double age, agelim,hf;          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
   double ***p3mat;  /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
          }
   fprintf(ficreseij,"# Health expectancies\n");        for(j=i+1; j<=nlstate+ndeath;j++){
   fprintf(ficreseij,"# Age");          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
   for(i=1; i<=nlstate;i++)            /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
     for(j=1; j<=nlstate;j++)            lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
       fprintf(ficreseij," %1d-%1d",i,j);  /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
   fprintf(ficreseij,"\n");          }
           ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
   hstepm=1*YEARM; /*  Every j years of age (in month) */        }
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */      }
       
   agelim=AGESUP;      for(i=1; i<= nlstate; i++){
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        s1=0;
     /* nhstepm age range expressed in number of stepm */        for(j=1; j<i; j++){
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
     /* Typically if 20 years = 20*12/6=40 stepm */          /*printf("debug1 %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 = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */        for(j=i+1; j<=nlstate+ndeath; j++){
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
     /* Computed by stepm unit matrices, product of hstepm matrices, stored          /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */        }
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);          /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
         ps[i][i]=1./(s1+1.);
         /* Computing other pijs */
     for(i=1; i<=nlstate;i++)        for(j=1; j<i; j++)
       for(j=1; j<=nlstate;j++)          ps[i][j]= exp(ps[i][j])*ps[i][i];
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){        for(j=i+1; j<=nlstate+ndeath; j++)
           eij[i][j][(int)age] +=p3mat[i][j][h];          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 */
     hf=1;      
     if (stepm >= YEARM) hf=stepm/YEARM;      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
     fprintf(ficreseij,"%.0f",age );        for(jj=1; jj<= nlstate+ndeath; jj++){
     for(i=1; i<=nlstate;i++)          ps[ii][jj]=0;
       for(j=1; j<=nlstate;j++){          ps[ii][ii]=1;
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);        }
       }      }
     fprintf(ficreseij,"\n");      
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      
   }      /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
 }      /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
       /*  printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
 /************ 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)      /*   printf("\n "); */
 {      /* } */
   /* Variance of health expectancies */      /* printf("\n ");printf("%lf ",cov[2]);*/
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/      /*
   double **newm;        for(i=1; i<= npar; i++) printf("%f ",x[i]);
   double **dnewm,**doldm;        goto end;*/
   int i, j, nhstepm, hstepm, h;      return ps;
   int k, cptcode;  }
   double *xp;  
   double **gp, **gm;  /**************** Product of 2 matrices ******************/
   double ***gradg, ***trgradg;  
   double ***p3mat;  double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
   double age,agelim;  {
   int theta;    /* 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(...) */
    fprintf(ficresvij,"# Covariances of life expectancies\n");    /* in, b, out are matrice of pointers which should have been initialized 
   fprintf(ficresvij,"# Age");       before: only the contents of out is modified. The function returns
   for(i=1; i<=nlstate;i++)       a pointer to pointers identical to out */
     for(j=1; j<=nlstate;j++)    int i, j, k;
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);    for(i=nrl; i<= nrh; i++)
   fprintf(ficresvij,"\n");      for(k=ncolol; k<=ncoloh; k++){
         out[i][k]=0.;
   xp=vector(1,npar);        for(j=ncl; j<=nch; j++)
   dnewm=matrix(1,nlstate,1,npar);          out[i][k] +=in[i][j]*b[j][k];
   doldm=matrix(1,nlstate,1,nlstate);      }
      return out;
   hstepm=1*YEARM; /* Every year of age */  }
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */  
   agelim = AGESUP;  
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */  /************* Higher Matrix Product ***************/
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */  
     if (stepm >= YEARM) hstepm=1;  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */  {
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    /* Computes the transition matrix starting at age 'age' over 
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);       'nhstepm*hstepm*stepm' months (i.e. until
     gp=matrix(0,nhstepm,1,nlstate);       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
     gm=matrix(0,nhstepm,1,nlstate);       nhstepm*hstepm matrices. 
        Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
     for(theta=1; theta <=npar; theta++){       (typically every 2 years instead of every month which is too big 
       for(i=1; i<=npar; i++){ /* Computes gradient */       for the memory).
         xp[i] = x[i] + (i==theta ?delti[theta]:0);       Model is determined by parameters x and covariates have to be 
       }       included manually here. 
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);    
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);       */
   
       if (popbased==1) {    int i, j, d, h, k;
         for(i=1; i<=nlstate;i++)    double **out, cov[NCOVMAX+1];
           prlim[i][i]=probs[(int)age][i][ij];    double **newm;
       }  
          /* Hstepm could be zero and should return the unit matrix */
       for(j=1; j<= nlstate; j++){    for (i=1;i<=nlstate+ndeath;i++)
         for(h=0; h<=nhstepm; h++){      for (j=1;j<=nlstate+ndeath;j++){
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)        oldm[i][j]=(i==j ? 1.0 : 0.0);
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];        po[i][j][0]=(i==j ? 1.0 : 0.0);
         }      }
       }    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
        for(h=1; h <=nhstepm; h++){
       for(i=1; i<=npar; i++) /* Computes gradient */      for(d=1; d <=hstepm; d++){
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        newm=savm;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          /* Covariates have to be included here again */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        cov[1]=1.;
         cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
       if (popbased==1) {        for (k=1; k<=cptcovn;k++) 
         for(i=1; i<=nlstate;i++)          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
           prlim[i][i]=probs[(int)age][i][ij];        for (k=1; k<=cptcovage;k++)
       }          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
         for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
       for(j=1; j<= nlstate; j++){          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
         for(h=0; h<=nhstepm; h++){  
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)  
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
         }        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
       }        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
                      pmij(pmmij,cov,ncovmodel,x,nlstate));
       for(j=1; j<= nlstate; j++)        savm=oldm;
         for(h=0; h<=nhstepm; h++){        oldm=newm;
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];      }
         }      for(i=1; i<=nlstate+ndeath; i++)
     } /* End theta */        for(j=1;j<=nlstate+ndeath;j++) {
           po[i][j][h]=newm[i][j];
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);          /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
         }
     for(h=0; h<=nhstepm; h++)      /*printf("h=%d ",h);*/
       for(j=1; j<=nlstate;j++)    } /* end h */
         for(theta=1; theta <=npar; theta++)  /*     printf("\n H=%d \n",h); */
           trgradg[h][j][theta]=gradg[h][theta][j];    return po;
   }
     for(i=1;i<=nlstate;i++)  
       for(j=1;j<=nlstate;j++)  
         vareij[i][j][(int)age] =0.;  /*************** log-likelihood *************/
     for(h=0;h<=nhstepm;h++){  double func( double *x)
       for(k=0;k<=nhstepm;k++){  {
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);    int i, ii, j, k, mi, d, kk;
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
         for(i=1;i<=nlstate;i++)    double **out;
           for(j=1;j<=nlstate;j++)    double sw; /* Sum of weights */
             vareij[i][j][(int)age] += doldm[i][j];    double lli; /* Individual log likelihood */
       }    int s1, s2;
     }    double bbh, survp;
     h=1;    long ipmx;
     if (stepm >= YEARM) h=stepm/YEARM;    /*extern weight */
     fprintf(ficresvij,"%.0f ",age );    /* We are differentiating ll according to initial status */
     for(i=1; i<=nlstate;i++)    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
       for(j=1; j<=nlstate;j++){    /*for(i=1;i<imx;i++) 
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);      printf(" %d\n",s[4][i]);
       }    */
     fprintf(ficresvij,"\n");    cov[1]=1.;
     free_matrix(gp,0,nhstepm,1,nlstate);  
     free_matrix(gm,0,nhstepm,1,nlstate);    for(k=1; k<=nlstate; k++) ll[k]=0.;
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);  
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);    if(mle==1){
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   } /* End age */        /* Computes the values of the ncovmodel covariates of the model
             depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
   free_vector(xp,1,npar);           Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
   free_matrix(doldm,1,nlstate,1,npar);           to be observed in j being in i according to the model.
   free_matrix(dnewm,1,nlstate,1,nlstate);         */
         for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
 }          cov[2+k]=covar[Tvar[k]][i];
         }
 /************ Variance of prevlim ******************/        /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 
 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)           is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] 
 {           has been calculated etc */
   /* Variance of prevalence limit */        for(mi=1; mi<= wav[i]-1; mi++){
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/          for (ii=1;ii<=nlstate+ndeath;ii++)
   double **newm;            for (j=1;j<=nlstate+ndeath;j++){
   double **dnewm,**doldm;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   int i, j, nhstepm, hstepm;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   int k, cptcode;            }
   double *xp;          for(d=0; d<dh[mi][i]; d++){
   double *gp, *gm;            newm=savm;
   double **gradg, **trgradg;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   double age,agelim;            for (kk=1; kk<=cptcovage;kk++) {
   int theta;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
                }
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   fprintf(ficresvpl,"# Age");                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   for(i=1; i<=nlstate;i++)            savm=oldm;
       fprintf(ficresvpl," %1d-%1d",i,i);            oldm=newm;
   fprintf(ficresvpl,"\n");          } /* end mult */
         
   xp=vector(1,npar);          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
   dnewm=matrix(1,nlstate,1,npar);          /* But now since version 0.9 we anticipate for bias at large stepm.
   doldm=matrix(1,nlstate,1,nlstate);           * 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 
   hstepm=1*YEARM; /* Every year of age */           * the nearest (and in case of equal distance, to the lowest) interval but now
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */           * we keep into memory the bias bh[mi][i] and also the previous matrix product
   agelim = AGESUP;           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */           * probability in order to take into account the bias as a fraction of the way
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
     if (stepm >= YEARM) hstepm=1;           * -stepm/2 to stepm/2 .
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */           * For stepm=1 the results are the same as for previous versions of Imach.
     gradg=matrix(1,npar,1,nlstate);           * For stepm > 1 the results are less biased than in previous versions. 
     gp=vector(1,nlstate);           */
     gm=vector(1,nlstate);          s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
     for(theta=1; theta <=npar; theta++){          bbh=(double)bh[mi][i]/(double)stepm; 
       for(i=1; i<=npar; i++){ /* Computes gradient */          /* bias bh is positive if real duration
         xp[i] = x[i] + (i==theta ?delti[theta]:0);           * is higher than the multiple of stepm and negative otherwise.
       }           */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          /* 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(i=1;i<=nlstate;i++)          if( s2 > nlstate){ 
         gp[i] = prlim[i][i];            /* i.e. if s2 is a death state and if the date of death is known 
                   then the contribution to the likelihood is the probability to 
       for(i=1; i<=npar; i++) /* Computes gradient */               die between last step unit time and current  step unit time, 
         xp[i] = x[i] - (i==theta ?delti[theta]:0);               which is also equal to probability to die before dh 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);               minus probability to die before dh-stepm . 
       for(i=1;i<=nlstate;i++)               In version up to 0.92 likelihood was computed
         gm[i] = prlim[i][i];          as if date of death was unknown. Death was treated as any other
           health state: the date of the interview describes the actual state
       for(i=1;i<=nlstate;i++)          and not the date of a change in health state. The former idea was
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];          to consider that at each interview the state was recorded
     } /* End theta */          (healthy, disable or death) and IMaCh was corrected; but when we
           introduced the exact date of death then we should have modified
     trgradg =matrix(1,nlstate,1,npar);          the contribution of an exact death to the likelihood. This new
           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
       for(theta=1; theta <=npar; theta++)          and month of death but the probability to survive from last
         trgradg[j][theta]=gradg[theta][j];          interview up to one month before death multiplied by the
           probability to die within a month. Thanks to Chris
     for(i=1;i<=nlstate;i++)          Jackson for correcting this bug.  Former versions increased
       varpl[i][(int)age] =0.;          mortality artificially. The bad side is that we add another loop
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);          which slows down the processing. The difference can be up to 10%
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);          lower mortality.
     for(i=1;i<=nlstate;i++)            */
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */            lli=log(out[s1][s2] - savm[s1][s2]);
   
     fprintf(ficresvpl,"%.0f ",age );  
     for(i=1; i<=nlstate;i++)          } else if  (s2==-2) {
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));            for (j=1,survp=0. ; j<=nlstate; j++) 
     fprintf(ficresvpl,"\n");              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
     free_vector(gp,1,nlstate);            /*survp += out[s1][j]; */
     free_vector(gm,1,nlstate);            lli= log(survp);
     free_matrix(gradg,1,npar,1,nlstate);          }
     free_matrix(trgradg,1,nlstate,1,npar);          
   } /* End age */          else if  (s2==-4) { 
             for (j=3,survp=0. ; j<=nlstate; j++)  
   free_vector(xp,1,npar);              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   free_matrix(doldm,1,nlstate,1,npar);            lli= log(survp); 
   free_matrix(dnewm,1,nlstate,1,nlstate);          } 
   
 }          else if  (s2==-5) { 
             for (j=1,survp=0. ; j<=2; j++)  
 /************ Variance of one-step probabilities  ******************/              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)            lli= log(survp); 
 {          } 
   int i, j;          
   int k=0, cptcode;          else{
   double **dnewm,**doldm;            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, cov[NCOVMAX];          /*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); */
   char fileresprob[FILENAMELENGTH];          ipmx +=1;
           sw += weight[i];
   strcpy(fileresprob,"prob");          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   strcat(fileresprob,fileres);        } /* end of wave */
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {      } /* end of individual */
     printf("Problem with resultfile: %s\n", fileresprob);    }  else if(mle==2){
   }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);        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++)
   xp=vector(1,npar);            for (j=1;j<=nlstate+ndeath;j++){
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));              savm[ii][j]=(ii==j ? 1.0 : 0.0);
              }
   cov[1]=1;          for(d=0; d<=dh[mi][i]; d++){
   for (age=bage; age<=fage; age ++){            newm=savm;
     cov[2]=age;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     gradg=matrix(1,npar,1,9);            for (kk=1; kk<=cptcovage;kk++) {
     trgradg=matrix(1,9,1,npar);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));            }
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));            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++)            oldm=newm;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          } /* end mult */
              
       pmij(pmmij,cov,ncovmodel,xp,nlstate);          s1=s[mw[mi][i]][i];
              s2=s[mw[mi+1][i]][i];
       k=0;          bbh=(double)bh[mi][i]/(double)stepm; 
       for(i=1; i<= (nlstate+ndeath); 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 */
         for(j=1; j<=(nlstate+ndeath);j++){          ipmx +=1;
            k=k+1;          sw += weight[i];
           gp[k]=pmmij[i][j];          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         }        } /* end of wave */
       }      } /* end of individual */
     }  else if(mle==3){  /* exponential inter-extrapolation */
       for(i=1; i<=npar; i++)      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        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++)
       pmij(pmmij,cov,ncovmodel,xp,nlstate);            for (j=1;j<=nlstate+ndeath;j++){
       k=0;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       for(i=1; i<=(nlstate+ndeath); i++){              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         for(j=1; j<=(nlstate+ndeath);j++){            }
           k=k+1;          for(d=0; d<dh[mi][i]; d++){
           gm[k]=pmmij[i][j];            newm=savm;
         }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       }            for (kk=1; kk<=cptcovage;kk++) {
                    cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)            }
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];              out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)            oldm=newm;
       for(theta=1; theta <=npar; theta++)          } /* end mult */
       trgradg[j][theta]=gradg[theta][j];        
            s1=s[mw[mi][i]][i];
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);          s2=s[mw[mi+1][i]][i];
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);          bbh=(double)bh[mi][i]/(double)stepm; 
           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 */
      pmij(pmmij,cov,ncovmodel,x,nlstate);          ipmx +=1;
           sw += weight[i];
      k=0;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
      for(i=1; i<=(nlstate+ndeath); i++){        } /* end of wave */
        for(j=1; j<=(nlstate+ndeath);j++){      } /* end of individual */
          k=k+1;    }else if (mle==4){  /* ml=4 no inter-extrapolation */
          gm[k]=pmmij[i][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++)
      /*printf("\n%d ",(int)age);            for (j=1;j<=nlstate+ndeath;j++){
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                      savm[ii][j]=(ii==j ? 1.0 : 0.0);
             }
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));          for(d=0; d<dh[mi][i]; d++){
      }*/            newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   fprintf(ficresprob,"\n%d ",(int)age);            for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){            }
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);          
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));            oldm=newm;
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));          } /* end mult */
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);        
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);          s1=s[mw[mi][i]][i];
 }          s2=s[mw[mi+1][i]][i];
  free_vector(xp,1,npar);          if( s2 > nlstate){ 
 fclose(ficresprob);            lli=log(out[s1][s2] - savm[s1][s2]);
  exit(0);          }else{
 }            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
           }
 /***********************************************/          ipmx +=1;
 /**************** Main Program *****************/          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]); */
 /*int main(int argc, char *argv[])*/        } /* end of wave */
 int main()      } /* end of individual */
 {    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   double agedeb, agefin,hf;        for(mi=1; mi<= wav[i]-1; mi++){
   double agemin=1.e20, agemax=-1.e20;          for (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
   double fret;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   double **xi,tmp,delta;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             }
   double dum; /* Dummy variable */          for(d=0; d<dh[mi][i]; d++){
   double ***p3mat;            newm=savm;
   int *indx;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   char line[MAXLINE], linepar[MAXLINE];            for (kk=1; kk<=cptcovage;kk++) {
   char title[MAXLINE];              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];            }
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], fileresf[FILENAMELENGTH];          
   char filerest[FILENAMELENGTH];            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   char fileregp[FILENAMELENGTH];                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   char popfile[FILENAMELENGTH];            savm=oldm;
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];            oldm=newm;
   int firstobs=1, lastobs=10;          } /* end mult */
   int sdeb, sfin; /* Status at beginning and end */        
   int c,  h , cpt,l;          s1=s[mw[mi][i]][i];
   int ju,jl, mi;          s2=s[mw[mi+1][i]][i];
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;          ipmx +=1;
   int mobilav=0,popforecast=0;          sw += weight[i];
   int hstepm, nhstepm;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   int *popage;/*boolprev=0 if date and zero if wave*/          /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2;        } /* end of wave */
       } /* end of individual */
   double bage, fage, age, agelim, agebase;    } /* End of if */
   double ftolpl=FTOL;    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   double **prlim;    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   double *severity;    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
   double ***param; /* Matrix of parameters */    return -l;
   double  *p;  }
   double **matcov; /* Matrix of covariance */  
   double ***delti3; /* Scale */  /*************** log-likelihood *************/
   double *delti; /* Scale */  double funcone( double *x)
   double ***eij, ***vareij;  {
   double **varpl; /* Variances of prevalence limits by age */    /* Same as likeli but slower because of a lot of printf and if */
   double *epj, vepp;    int i, ii, j, k, mi, d, kk;
   double kk1, kk2;    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
   double *popeffectif,*popcount;    double **out;
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,jprojmean,mprojmean,anprojmean, calagedate;    double lli; /* Individual log likelihood */
   double yp,yp1,yp2;    double llt;
     int s1, s2;
   char version[80]="Imach version 64b, May 2001, INED-EUROREVES ";    double bbh, survp;
   char *alph[]={"a","a","b","c","d","e"}, str[4];    /*extern weight */
     /* We are differentiating ll according to initial status */
     /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   char z[1]="c", occ;    /*for(i=1;i<imx;i++) 
 #include <sys/time.h>      printf(" %d\n",s[4][i]);
 #include <time.h>    */
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];    cov[1]=1.;
    
   /* long total_usecs;    for(k=1; k<=nlstate; k++) ll[k]=0.;
   struct timeval start_time, end_time;  
      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */      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++)
   printf("\nIMACH, Version 0.7");          for (j=1;j<=nlstate+ndeath;j++){
   printf("\nEnter the parameter file name: ");            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
             savm[ii][j]=(ii==j ? 1.0 : 0.0);
 #ifdef windows          }
   scanf("%s",pathtot);        for(d=0; d<dh[mi][i]; d++){
   getcwd(pathcd, size);          newm=savm;
   /*cygwin_split_path(pathtot,path,optionfile);          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/          for (kk=1; kk<=cptcovage;kk++) {
   /* cutv(path,optionfile,pathtot,'\\');*/            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
           }
 split(pathtot, path,optionfile);          /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
   chdir(path);          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   replace(pathc,path);                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 #endif          /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
 #ifdef unix          /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
   scanf("%s",optionfile);          savm=oldm;
 #endif          oldm=newm;
         } /* end mult */
 /*-------- arguments in the command line --------*/        
         s1=s[mw[mi][i]][i];
   strcpy(fileres,"r");        s2=s[mw[mi+1][i]][i];
   strcat(fileres, optionfile);        bbh=(double)bh[mi][i]/(double)stepm; 
         /* bias is positive if real duration
   /*---------arguments file --------*/         * is higher than the multiple of stepm and negative otherwise.
          */
   if((ficpar=fopen(optionfile,"r"))==NULL)    {        if( s2 > nlstate && (mle <5) ){  /* Jackson */
     printf("Problem with optionfile %s\n",optionfile);          lli=log(out[s1][s2] - savm[s1][s2]);
     goto end;        } else if  (s2==-2) {
   }          for (j=1,survp=0. ; j<=nlstate; j++) 
             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   strcpy(filereso,"o");          lli= log(survp);
   strcat(filereso,fileres);        }else if (mle==1){
   if((ficparo=fopen(filereso,"w"))==NULL) {          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
     printf("Problem with Output resultfile: %s\n", filereso);goto end;        } else if(mle==2){
   }          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
         } else if(mle==3){  /* exponential inter-extrapolation */
   /* Reads comments: lines beginning with '#' */          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 */
   while((c=getc(ficpar))=='#' && c!= EOF){        } else if (mle==4){  /* mle=4 no inter-extrapolation */
     ungetc(c,ficpar);          lli=log(out[s1][s2]); /* Original formula */
     fgets(line, MAXLINE, ficpar);        } else{  /* mle=0 back to 1 */
     puts(line);          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
     fputs(line,ficparo);          /*lli=log(out[s1][s2]); */ /* Original formula */
   }        } /* End of if */
   ungetc(c,ficpar);        ipmx +=1;
         sw += weight[i];
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncov, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate,ndeath, maxwav, mle, weightopt,model);        /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncov,nlstate,ndeath,maxwav, mle, weightopt,model);        if(globpr){
 while((c=getc(ficpar))=='#' && c!= EOF){          fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
     ungetc(c,ficpar);   %11.6f %11.6f %11.6f ", \
     fgets(line, MAXLINE, ficpar);                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
     puts(line);                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
     fputs(line,ficparo);          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
   }            llt +=ll[k]*gipmx/gsw;
   ungetc(c,ficpar);            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
            }
              fprintf(ficresilk," %10.6f\n", -llt);
   covar=matrix(0,NCOVMAX,1,n);        }
   cptcovn=0;      } /* end of wave */
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;    } /* end of individual */
     for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   ncovmodel=2+cptcovn;    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
      if(globpr==0){ /* First time we count the contributions and weights */
   /* Read guess parameters */      gipmx=ipmx;
   /* Reads comments: lines beginning with '#' */      gsw=sw;
   while((c=getc(ficpar))=='#' && c!= EOF){    }
     ungetc(c,ficpar);    return -l;
     fgets(line, MAXLINE, ficpar);  }
     puts(line);  
     fputs(line,ficparo);  
   }  /*************** function likelione ***********/
   ungetc(c,ficpar);  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
    {
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    /* This routine should help understanding what is done with 
     for(i=1; i <=nlstate; i++)       the selection of individuals/waves and
     for(j=1; j <=nlstate+ndeath-1; j++){       to check the exact contribution to the likelihood.
       fscanf(ficpar,"%1d%1d",&i1,&j1);       Plotting could be done.
       fprintf(ficparo,"%1d%1d",i1,j1);     */
       printf("%1d%1d",i,j);    int k;
       for(k=1; k<=ncovmodel;k++){  
         fscanf(ficpar," %lf",&param[i][j][k]);    if(*globpri !=0){ /* Just counts and sums, no printings */
         printf(" %lf",param[i][j][k]);      strcpy(fileresilk,"ilk"); 
         fprintf(ficparo," %lf",param[i][j][k]);      strcat(fileresilk,fileres);
       }      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
       fscanf(ficpar,"\n");        printf("Problem with resultfile: %s\n", fileresilk);
       printf("\n");        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
       fprintf(ficparo,"\n");      }
     }      fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
        fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;      /*  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++) 
   p=param[1][1];        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
        fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
   /* Reads comments: lines beginning with '#' */    }
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);    *fretone=(*funcone)(p);
     fgets(line, MAXLINE, ficpar);    if(*globpri !=0){
     puts(line);      fclose(ficresilk);
     fputs(line,ficparo);      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
   }      fflush(fichtm); 
   ungetc(c,ficpar);    } 
     return;
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);  }
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */  
   for(i=1; i <=nlstate; i++){  
     for(j=1; j <=nlstate+ndeath-1; j++){  /*********** Maximum Likelihood Estimation ***************/
       fscanf(ficpar,"%1d%1d",&i1,&j1);  
       printf("%1d%1d",i,j);  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
       fprintf(ficparo,"%1d%1d",i1,j1);  {
       for(k=1; k<=ncovmodel;k++){    int i,j, iter;
         fscanf(ficpar,"%le",&delti3[i][j][k]);    double **xi;
         printf(" %le",delti3[i][j][k]);    double fret;
         fprintf(ficparo," %le",delti3[i][j][k]);    double fretone; /* Only one call to likelihood */
       }    /*  char filerespow[FILENAMELENGTH];*/
       fscanf(ficpar,"\n");    xi=matrix(1,npar,1,npar);
       printf("\n");    for (i=1;i<=npar;i++)
       fprintf(ficparo,"\n");      for (j=1;j<=npar;j++)
     }        xi[i][j]=(i==j ? 1.0 : 0.0);
   }    printf("Powell\n");  fprintf(ficlog,"Powell\n");
   delti=delti3[1][1];    strcpy(filerespow,"pow"); 
      strcat(filerespow,fileres);
   /* Reads comments: lines beginning with '#' */    if((ficrespow=fopen(filerespow,"w"))==NULL) {
   while((c=getc(ficpar))=='#' && c!= EOF){      printf("Problem with resultfile: %s\n", filerespow);
     ungetc(c,ficpar);      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
     fgets(line, MAXLINE, ficpar);    }
     puts(line);    fprintf(ficrespow,"# Powell\n# iter -2*LL");
     fputs(line,ficparo);    for (i=1;i<=nlstate;i++)
   }      for(j=1;j<=nlstate+ndeath;j++)
   ungetc(c,ficpar);        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
      fprintf(ficrespow,"\n");
   matcov=matrix(1,npar,1,npar);  
   for(i=1; i <=npar; i++){    powell(p,xi,npar,ftol,&iter,&fret,func);
     fscanf(ficpar,"%s",&str);  
     printf("%s",str);    free_matrix(xi,1,npar,1,npar);
     fprintf(ficparo,"%s",str);    fclose(ficrespow);
     for(j=1; j <=i; j++){    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
       fscanf(ficpar," %le",&matcov[i][j]);    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
       printf(" %.5le",matcov[i][j]);    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
       fprintf(ficparo," %.5le",matcov[i][j]);  
     }  }
     fscanf(ficpar,"\n");  
     printf("\n");  /**** Computes Hessian and covariance matrix ***/
     fprintf(ficparo,"\n");  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
   }  {
   for(i=1; i <=npar; i++)    double  **a,**y,*x,pd;
     for(j=i+1;j<=npar;j++)    double **hess;
       matcov[i][j]=matcov[j][i];    int i, j,jk;
        int *indx;
   printf("\n");  
     double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
     double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
     /*-------- data file ----------*/    void lubksb(double **a, int npar, int *indx, double b[]) ;
     if((ficres =fopen(fileres,"w"))==NULL) {    void ludcmp(double **a, int npar, int *indx, double *d) ;
       printf("Problem with resultfile: %s\n", fileres);goto end;    double gompertz(double p[]);
     }    hess=matrix(1,npar,1,npar);
     fprintf(ficres,"#%s\n",version);  
        printf("\nCalculation of the hessian matrix. Wait...\n");
     if((fic=fopen(datafile,"r"))==NULL)    {    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
       printf("Problem with datafile: %s\n", datafile);goto end;    for (i=1;i<=npar;i++){
     }      printf("%d",i);fflush(stdout);
       fprintf(ficlog,"%d",i);fflush(ficlog);
     n= lastobs;     
     severity = vector(1,maxwav);       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
     outcome=imatrix(1,maxwav+1,1,n);      
     num=ivector(1,n);      /*  printf(" %f ",p[i]);
     moisnais=vector(1,n);          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
     annais=vector(1,n);    }
     moisdc=vector(1,n);    
     andc=vector(1,n);    for (i=1;i<=npar;i++) {
     agedc=vector(1,n);      for (j=1;j<=npar;j++)  {
     cod=ivector(1,n);        if (j>i) { 
     weight=vector(1,n);          printf(".%d%d",i,j);fflush(stdout);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
     mint=matrix(1,maxwav,1,n);          hess[i][j]=hessij(p,delti,i,j,func,npar);
     anint=matrix(1,maxwav,1,n);          
     s=imatrix(1,maxwav+1,1,n);          hess[j][i]=hess[i][j];    
     adl=imatrix(1,maxwav+1,1,n);              /*printf(" %lf ",hess[i][j]);*/
     tab=ivector(1,NCOVMAX);        }
     ncodemax=ivector(1,8);      }
     }
     i=1;    printf("\n");
     while (fgets(line, MAXLINE, fic) != NULL)    {    fprintf(ficlog,"\n");
       if ((i >= firstobs) && (i <=lastobs)) {  
            printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
         for (j=maxwav;j>=1;j--){    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);    
           strcpy(line,stra);    a=matrix(1,npar,1,npar);
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    y=matrix(1,npar,1,npar);
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    x=vector(1,npar);
         }    indx=ivector(1,npar);
            for (i=1;i<=npar;i++)
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);    ludcmp(a,npar,indx,&pd);
   
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);    for (j=1;j<=npar;j++) {
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);      for (i=1;i<=npar;i++) x[i]=0;
       x[j]=1;
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);      lubksb(a,npar,indx,x);
         for (j=ncov;j>=1;j--){      for (i=1;i<=npar;i++){ 
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);        matcov[i][j]=x[i];
         }      }
         num[i]=atol(stra);    }
          
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){    printf("\n#Hessian matrix#\n");
           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;}*/    fprintf(ficlog,"\n#Hessian matrix#\n");
     for (i=1;i<=npar;i++) { 
         i=i+1;      for (j=1;j<=npar;j++) { 
       }        printf("%.3e ",hess[i][j]);
     }        fprintf(ficlog,"%.3e ",hess[i][j]);
     /* printf("ii=%d", ij);      }
        scanf("%d",i);*/      printf("\n");
   imx=i-1; /* Number of individuals */      fprintf(ficlog,"\n");
     }
   /* for (i=1; i<=imx; i++){  
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;    /* Recompute Inverse */
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;    for (i=1;i<=npar;i++)
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
     }    ludcmp(a,npar,indx,&pd);
   
     for (i=1; i<=imx; i++)    /*  printf("\n#Hessian matrix recomputed#\n");
     if (covar[1][i]==0) printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));*/  
     for (j=1;j<=npar;j++) {
   /* Calculation of the number of parameter from char model*/      for (i=1;i<=npar;i++) x[i]=0;
   Tvar=ivector(1,15);      x[j]=1;
   Tprod=ivector(1,15);      lubksb(a,npar,indx,x);
   Tvaraff=ivector(1,15);      for (i=1;i<=npar;i++){ 
   Tvard=imatrix(1,15,1,2);        y[i][j]=x[i];
   Tage=ivector(1,15);              printf("%.3e ",y[i][j]);
            fprintf(ficlog,"%.3e ",y[i][j]);
   if (strlen(model) >1){      }
     j=0, j1=0, k1=1, k2=1;      printf("\n");
     j=nbocc(model,'+');      fprintf(ficlog,"\n");
     j1=nbocc(model,'*');    }
     cptcovn=j+1;    */
     cptcovprod=j1;  
        free_matrix(a,1,npar,1,npar);
        free_matrix(y,1,npar,1,npar);
     strcpy(modelsav,model);    free_vector(x,1,npar);
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){    free_ivector(indx,1,npar);
       printf("Error. Non available option model=%s ",model);    free_matrix(hess,1,npar,1,npar);
       goto end;  
     }  
      }
     for(i=(j+1); i>=1;i--){  
       cutv(stra,strb,modelsav,'+');  /*************** hessian matrix ****************/
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/  {
       /*scanf("%d",i);*/    int i;
       if (strchr(strb,'*')) {    int l=1, lmax=20;
         cutv(strd,strc,strb,'*');    double k1,k2;
         if (strcmp(strc,"age")==0) {    double p2[MAXPARM+1]; /* identical to x */
           cptcovprod--;    double res;
           cutv(strb,stre,strd,'V');    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
           Tvar[i]=atoi(stre);    double fx;
           cptcovage++;    int k=0,kmax=10;
             Tage[cptcovage]=i;    double l1;
             /*printf("stre=%s ", stre);*/  
         }    fx=func(x);
         else if (strcmp(strd,"age")==0) {    for (i=1;i<=npar;i++) p2[i]=x[i];
           cptcovprod--;    for(l=0 ; l <=lmax; l++){  /* Enlarging the zone around the Maximum */
           cutv(strb,stre,strc,'V');      l1=pow(10,l);
           Tvar[i]=atoi(stre);      delts=delt;
           cptcovage++;      for(k=1 ; k <kmax; k=k+1){
           Tage[cptcovage]=i;        delt = delta*(l1*k);
         }        p2[theta]=x[theta] +delt;
         else {        k1=func(p2)-fx;   /* Might be negative if too close to the theoretical maximum */
           cutv(strb,stre,strc,'V');        p2[theta]=x[theta]-delt;
           Tvar[i]=ncov+k1;        k2=func(p2)-fx;
           cutv(strb,strc,strd,'V');        /*res= (k1-2.0*fx+k2)/delt/delt; */
           Tprod[k1]=i;        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
           Tvard[k1][1]=atoi(strc);        
           Tvard[k1][2]=atoi(stre);  #ifdef DEBUGHESS
           Tvar[cptcovn+k2]=Tvard[k1][1];        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);
           Tvar[cptcovn+k2+1]=Tvard[k1][2];        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 (k=1; k<=lastobs;k++)  #endif
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
           k1++;        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
           k2=k2+2;          k=kmax;
         }        }
       }        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
       else {          k=kmax; l=lmax*10.;
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/        }
        /*  scanf("%d",i);*/        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
       cutv(strd,strc,strb,'V');          delts=delt;
       Tvar[i]=atoi(strc);        }
       }      }
       strcpy(modelsav,stra);      }
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);    delti[theta]=delts;
         scanf("%d",i);*/    return res; 
     }    
 }  }
    
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
   printf("cptcovprod=%d ", cptcovprod);  {
   scanf("%d ",i);*/    int i;
     fclose(fic);    int l=1, l1, lmax=20;
     double k1,k2,k3,k4,res,fx;
     /*  if(mle==1){*/    double p2[MAXPARM+1];
     if (weightopt != 1) { /* Maximisation without weights*/    int k;
       for(i=1;i<=n;i++) weight[i]=1.0;  
     }    fx=func(x);
     /*-calculation of age at interview from date of interview and age at death -*/    for (k=1; k<=2; k++) {
     agev=matrix(1,maxwav,1,imx);      for (i=1;i<=npar;i++) p2[i]=x[i];
       p2[thetai]=x[thetai]+delti[thetai]/k;
    for (i=1; i<=imx; i++)      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
      for(m=2; (m<= maxwav); m++)      k1=func(p2)-fx;
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){    
          anint[m][i]=9999;      p2[thetai]=x[thetai]+delti[thetai]/k;
          s[m][i]=-1;      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
        }      k2=func(p2)-fx;
        
     for (i=1; i<=imx; i++)  {      p2[thetai]=x[thetai]-delti[thetai]/k;
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       for(m=1; (m<= maxwav); m++){      k3=func(p2)-fx;
         if(s[m][i] >0){    
           if (s[m][i] == nlstate+1) {      p2[thetai]=x[thetai]-delti[thetai]/k;
             if(agedc[i]>0)      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
               if(moisdc[i]!=99 && andc[i]!=9999)      k4=func(p2)-fx;
               agev[m][i]=agedc[i];      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
             else {  #ifdef DEBUG
               if (andc[i]!=9999){      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);
               printf("Warning negative age at death: %d line:%d\n",num[i],i);      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);
               agev[m][i]=-1;  #endif
               }    }
             }    return res;
           }  }
           else if(s[m][i] !=9){ /* Should no more exist */  
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);  /************** Inverse of matrix **************/
             if(mint[m][i]==99 || anint[m][i]==9999)  void ludcmp(double **a, int n, int *indx, double *d) 
               agev[m][i]=1;  { 
             else if(agev[m][i] <agemin){    int i,imax,j,k; 
               agemin=agev[m][i];    double big,dum,sum,temp; 
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/    double *vv; 
             }   
             else if(agev[m][i] >agemax){    vv=vector(1,n); 
               agemax=agev[m][i];    *d=1.0; 
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/    for (i=1;i<=n;i++) { 
             }      big=0.0; 
             /*agev[m][i]=anint[m][i]-annais[i];*/      for (j=1;j<=n;j++) 
             /*   agev[m][i] = age[i]+2*m;*/        if ((temp=fabs(a[i][j])) > big) big=temp; 
           }      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
           else { /* =9 */      vv[i]=1.0/big; 
             agev[m][i]=1;    } 
             s[m][i]=-1;    for (j=1;j<=n;j++) { 
           }      for (i=1;i<j;i++) { 
         }        sum=a[i][j]; 
         else /*= 0 Unknown */        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
           agev[m][i]=1;        a[i][j]=sum; 
       }      } 
          big=0.0; 
     }      for (i=j;i<=n;i++) { 
     for (i=1; i<=imx; i++)  {        sum=a[i][j]; 
       for(m=1; (m<= maxwav); m++){        for (k=1;k<j;k++) 
         if (s[m][i] > (nlstate+ndeath)) {          sum -= a[i][k]*a[k][j]; 
           printf("Error: Wrong value in nlstate or ndeath\n");          a[i][j]=sum; 
           goto end;        if ( (dum=vv[i]*fabs(sum)) >= big) { 
         }          big=dum; 
       }          imax=i; 
     }        } 
       } 
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);      if (j != imax) { 
         for (k=1;k<=n;k++) { 
     free_vector(severity,1,maxwav);          dum=a[imax][k]; 
     free_imatrix(outcome,1,maxwav+1,1,n);          a[imax][k]=a[j][k]; 
     free_vector(moisnais,1,n);          a[j][k]=dum; 
     free_vector(annais,1,n);        } 
     /* free_matrix(mint,1,maxwav,1,n);        *d = -(*d); 
        free_matrix(anint,1,maxwav,1,n);*/        vv[imax]=vv[j]; 
     free_vector(moisdc,1,n);      } 
     free_vector(andc,1,n);      indx[j]=imax; 
       if (a[j][j] == 0.0) a[j][j]=TINY; 
          if (j != n) { 
     wav=ivector(1,imx);        dum=1.0/(a[j][j]); 
     dh=imatrix(1,lastpass-firstpass+1,1,imx);        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
     mw=imatrix(1,lastpass-firstpass+1,1,imx);      } 
        } 
     /* Concatenates waves */    free_vector(vv,1,n);  /* Doesn't work */
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);  ;
   } 
   
       Tcode=ivector(1,100);  void lubksb(double **a, int n, int *indx, double b[]) 
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);  { 
       ncodemax[1]=1;    int i,ii=0,ip,j; 
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);    double sum; 
         
    codtab=imatrix(1,100,1,10);    for (i=1;i<=n;i++) { 
    h=0;      ip=indx[i]; 
    m=pow(2,cptcoveff);      sum=b[ip]; 
        b[ip]=b[i]; 
    for(k=1;k<=cptcoveff; k++){      if (ii) 
      for(i=1; i <=(m/pow(2,k));i++){        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
        for(j=1; j <= ncodemax[k]; j++){      else if (sum) ii=i; 
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){      b[i]=sum; 
            h++;    } 
            if (h>m) h=1;codtab[h][k]=j;    for (i=n;i>=1;i--) { 
          }      sum=b[i]; 
        }      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
      }      b[i]=sum/a[i][i]; 
    }    } 
      } 
    /* Calculates basic frequencies. Computes observed prevalence at single age  
        and prints on file fileres'p'. */  void pstamp(FILE *fichier)
   {
        fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
      }
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  /************ Frequencies ********************/
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  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[])
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  {  /* Some frequencies */
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    
          int i, m, jk, k1,i1, j1, bool, z1,j;
     /* For Powell, parameters are in a vector p[] starting at p[1]    int first;
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */    double ***freq; /* Frequencies */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */    double *pp, **prop;
     double pos,posprop, k2, dateintsum=0,k2cpt=0;
     if(mle==1){    char fileresp[FILENAMELENGTH];
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);    
     }    pp=vector(1,nlstate);
        prop=matrix(1,nlstate,iagemin,iagemax+3);
     /*--------- results files --------------*/    strcpy(fileresp,"p");
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, mle,weightopt,model);    strcat(fileresp,fileres);
      if((ficresp=fopen(fileresp,"w"))==NULL) {
       printf("Problem with prevalence resultfile: %s\n", fileresp);
    jk=1;      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
    fprintf(ficres,"# Parameters\n");      exit(0);
    printf("# Parameters\n");    }
    for(i=1,jk=1; i <=nlstate; i++){    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
      for(k=1; k <=(nlstate+ndeath); k++){    j1=0;
        if (k != i)    
          {    j=cptcoveff;
            printf("%d%d ",i,k);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
            fprintf(ficres,"%1d%1d ",i,k);  
            for(j=1; j <=ncovmodel; j++){    first=1;
              printf("%f ",p[jk]);  
              fprintf(ficres,"%f ",p[jk]);    /* for(k1=1; k1<=j ; k1++){   /* Loop on covariates */
              jk++;    /*  for(i1=1; i1<=ncodemax[k1];i1++){ /* Now it is 2 */
            }    /*    j1++;
            printf("\n");  */
            fprintf(ficres,"\n");    for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
          }        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
      }          scanf("%d", i);*/
    }        for (i=-5; i<=nlstate+ndeath; i++)  
  if(mle==1){          for (jk=-5; jk<=nlstate+ndeath; jk++)  
     /* Computing hessian and covariance matrix */            for(m=iagemin; m <= iagemax+3; m++)
     ftolhess=ftol; /* Usually correct */              freq[i][jk][m]=0;
     hesscov(matcov, p, npar, delti, ftolhess, func);        
  }        for (i=1; i<=nlstate; i++)  
     fprintf(ficres,"# Scales\n");          for(m=iagemin; m <= iagemax+3; m++)
     printf("# Scales\n");            prop[i][m]=0;
      for(i=1,jk=1; i <=nlstate; i++){        
       for(j=1; j <=nlstate+ndeath; j++){        dateintsum=0;
         if (j!=i) {        k2cpt=0;
           fprintf(ficres,"%1d%1d",i,j);        for (i=1; i<=imx; i++) {
           printf("%1d%1d",i,j);          bool=1;
           for(k=1; k<=ncovmodel;k++){          if  (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
             printf(" %.5e",delti[jk]);            for (z1=1; z1<=cptcoveff; z1++)       
             fprintf(ficres," %.5e",delti[jk]);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
             jk++;                  /* Tests if the value of each of the covariates of i is equal to filter j1 */
           }                bool=0;
           printf("\n");                /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtab[%d][%d]=%d, nbcode[Tvaraff][codtab[%d][%d]=%d, j1=%d\n", 
           fprintf(ficres,"\n");                  bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
         }                  j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
       }                /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
      }              } 
              }
     k=1;   
     fprintf(ficres,"# Covariance\n");          if (bool==1){
     printf("# Covariance\n");            for(m=firstpass; m<=lastpass; m++){
     for(i=1;i<=npar;i++){              k2=anint[m][i]+(mint[m][i]/12.);
       /*  if (k>nlstate) k=1;              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
       i1=(i-1)/(ncovmodel*nlstate)+1;                if(agev[m][i]==0) agev[m][i]=iagemax+1;
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
       printf("%s%d%d",alph[k],i1,tab[i]);*/                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
       fprintf(ficres,"%3d",i);                if (m<lastpass) {
       printf("%3d",i);                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
       for(j=1; j<=i;j++){                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
         fprintf(ficres," %.5e",matcov[i][j]);                }
         printf(" %.5e",matcov[i][j]);                
       }                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
       fprintf(ficres,"\n");                  dateintsum=dateintsum+k2;
       printf("\n");                  k2cpt++;
       k++;                }
     }                /*}*/
                }
     while((c=getc(ficpar))=='#' && c!= EOF){          }
       ungetc(c,ficpar);        } /* end i */
       fgets(line, MAXLINE, ficpar);         
       puts(line);        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
       fputs(line,ficparo);        pstamp(ficresp);
     }        if  (cptcovn>0) {
     ungetc(c,ficpar);          fprintf(ficresp, "\n#********** Variable "); 
            for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);          fprintf(ficresp, "**********\n#");
              fprintf(ficlog, "\n#********** Variable "); 
     if (fage <= 2) {          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       bage = agemin;          fprintf(ficlog, "**********\n#");
       fage = agemax;        }
     }        for(i=1; i<=nlstate;i++) 
           fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
     fprintf(ficres,"# agemin agemax for life expectancy.\n");        fprintf(ficresp, "\n");
         
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);        for(i=iagemin; i <= iagemax+3; i++){
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);          if(i==iagemax+3){
              fprintf(ficlog,"Total");
     while((c=getc(ficpar))=='#' && c!= EOF){          }else{
     ungetc(c,ficpar);            if(first==1){
     fgets(line, MAXLINE, ficpar);              first=0;
     puts(line);              printf("See log file for details...\n");
     fputs(line,ficparo);            }
   }            fprintf(ficlog,"Age %d", i);
   ungetc(c,ficpar);          }
            for(jk=1; jk <=nlstate ; jk++){
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mob_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mob_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);              pp[jk] += freq[jk][m][i]; 
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mob_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);          }
                for(jk=1; jk <=nlstate ; jk++){
   while((c=getc(ficpar))=='#' && c!= EOF){            for(m=-1, pos=0; m <=0 ; m++)
     ungetc(c,ficpar);              pos += freq[jk][m][i];
     fgets(line, MAXLINE, ficpar);            if(pp[jk]>=1.e-10){
     puts(line);              if(first==1){
     fputs(line,ficparo);                printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   }              }
   ungetc(c,ficpar);              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
              }else{
               if(first==1)
    dateprev1=anprev1+mprev1/12.+jprev1/365.;                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
    dateprev2=anprev2+mprev2/12.+jprev2/365.;              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
             }
   fscanf(ficpar,"pop_based=%d\n",&popbased);          }
    fprintf(ficparo,"pop_based=%d\n",popbased);    
    fprintf(ficres,"pop_based=%d\n",popbased);            for(jk=1; jk <=nlstate ; jk++){
             for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
   while((c=getc(ficpar))=='#' && c!= EOF){              pp[jk] += freq[jk][m][i];
     ungetc(c,ficpar);          }       
     fgets(line, MAXLINE, ficpar);          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
     puts(line);            pos += pp[jk];
     fputs(line,ficparo);            posprop += prop[jk][i];
   }          }
   ungetc(c,ficpar);          for(jk=1; jk <=nlstate ; jk++){
   fscanf(ficpar,"popforecast=%d popfile=%s starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf\n",&popforecast,popfile,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2);            if(pos>=1.e-5){
 fprintf(ficparo,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);              if(first==1)
 fprintf(ficres,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
               fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2);            }else{
               if(first==1)
  /*------------ gnuplot -------------*/                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
 chdir(pathcd);              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   if((ficgp=fopen("graph.plt","w"))==NULL) {            }
     printf("Problem with file graph.gp");goto end;            if( i <= iagemax){
   }              if(pos>=1.e-5){
 #ifdef windows                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
   fprintf(ficgp,"cd \"%s\" \n",pathc);                /*probs[i][jk][j1]= pp[jk]/pos;*/
 #endif                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
 m=pow(2,cptcoveff);              }
                else
  /* 1eme*/                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
   for (cpt=1; cpt<= nlstate ; cpt ++) {            }
    for (k1=1; k1<= m ; k1 ++) {          }
           
 #ifdef windows          for(jk=-1; jk <=nlstate+ndeath; jk++)
     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",agemin,fage,fileres,k1-1,k1-1);            for(m=-1; m <=nlstate+ndeath; m++)
 #endif              if(freq[jk][m][i] !=0 ) {
 #ifdef unix              if(first==1)
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
 #endif                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
               }
 for (i=1; i<= nlstate ; i ++) {          if(i <= iagemax)
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");            fprintf(ficresp,"\n");
   else fprintf(ficgp," \%%*lf (\%%*lf)");          if(first==1)
 }            printf("Others in log...\n");
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);          fprintf(ficlog,"\n");
     for (i=1; i<= nlstate ; i ++) {        }
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        /*}*/
   else fprintf(ficgp," \%%*lf (\%%*lf)");    }
 }    dateintmean=dateintsum/k2cpt; 
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);   
      for (i=1; i<= nlstate ; i ++) {    fclose(ficresp);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
   else fprintf(ficgp," \%%*lf (\%%*lf)");    free_vector(pp,1,nlstate);
 }      free_matrix(prop,1,nlstate,iagemin, iagemax+3);
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));    /* End of Freq */
 #ifdef unix  }
 fprintf(ficgp,"\nset ter gif small size 400,300");  
 #endif  /************ Prevalence ********************/
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);  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)
    }  {  
   }    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
   /*2 eme*/       in each health status at the date of interview (if between dateprev1 and dateprev2).
        We still use firstpass and lastpass as another selection.
   for (k1=1; k1<= m ; k1 ++) {    */
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);   
        int i, m, jk, k1, i1, j1, bool, z1,j;
     for (i=1; i<= nlstate+1 ; i ++) {    double ***freq; /* Frequencies */
       k=2*i;    double *pp, **prop;
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);    double pos,posprop; 
       for (j=1; j<= nlstate+1 ; j ++) {    double  y2; /* in fractional years */
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    int iagemin, iagemax;
   else fprintf(ficgp," \%%*lf (\%%*lf)");    int first; /** to stop verbosity which is redirected to log file */
 }    
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");    iagemin= (int) agemin;
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);    iagemax= (int) agemax;
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);    /*pp=vector(1,nlstate);*/
       for (j=1; j<= nlstate+1 ; j ++) {    prop=matrix(1,nlstate,iagemin,iagemax+3); 
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
         else fprintf(ficgp," \%%*lf (\%%*lf)");    j1=0;
 }      
       fprintf(ficgp,"\" t\"\" w l 0,");    /*j=cptcoveff;*/
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
       for (j=1; j<= nlstate+1 ; j ++) {    
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    first=1;
   else fprintf(ficgp," \%%*lf (\%%*lf)");    for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
 }        /*for(i1=1; i1<=ncodemax[k1];i1++){
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");        j1++;*/
       else fprintf(ficgp,"\" t\"\" w l 0,");        
     }        for (i=1; i<=nlstate; i++)  
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);          for(m=iagemin; m <= iagemax+3; m++)
   }            prop[i][m]=0.0;
         
   /*3eme*/        for (i=1; i<=imx; i++) { /* Each individual */
           bool=1;
   for (k1=1; k1<= m ; k1 ++) {          if  (cptcovn>0) {
     for (cpt=1; cpt<= nlstate ; cpt ++) {            for (z1=1; z1<=cptcoveff; z1++) 
       k=2+nlstate*(cpt-1);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k1-1,k1-1,k,cpt);                bool=0;
       for (i=1; i< nlstate ; i ++) {          } 
         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);          if (bool==1) { 
       }            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
     }              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
   }                if(agev[m][i]==0) agev[m][i]=iagemax+1;
                  if(agev[m][i]==1) agev[m][i]=iagemax+2;
   /* CV preval stat */                if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
   for (k1=1; k1<= m ; k1 ++) {                if (s[m][i]>0 && s[m][i]<=nlstate) { 
     for (cpt=1; cpt<nlstate ; cpt ++) {                  /*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]]);*/
       k=3;                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);                  prop[s[m][i]][iagemax+3] += weight[i]; 
       for (i=1; i< nlstate ; i ++)                } 
         fprintf(ficgp,"+$%d",k+i+1);              }
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);            } /* end selection of waves */
                }
       l=3+(nlstate+ndeath)*cpt;        }
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);        for(i=iagemin; i <= iagemax+3; i++){  
       for (i=1; i< nlstate ; i ++) {          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
         l=3+(nlstate+ndeath)*cpt;            posprop += prop[jk][i]; 
         fprintf(ficgp,"+$%d",l+i+1);          } 
       }          
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);            for(jk=1; jk <=nlstate ; jk++){     
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);            if( i <=  iagemax){ 
     }              if(posprop>=1.e-5){ 
   }                  probs[i][jk][j1]= prop[jk][i]/posprop;
               } else{
   /* proba elementaires */                if(first==1){
    for(i=1,jk=1; i <=nlstate; i++){                  first=0;
     for(k=1; k <=(nlstate+ndeath); k++){                  printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others on log file...\n",jk,i,j1,probs[i][jk][j1]);
       if (k != i) {                }
         for(j=1; j <=ncovmodel; j++){              }
           /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/            } 
           /*fprintf(ficgp,"%s",alph[1]);*/          }/* end jk */ 
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);        }/* end i */ 
           jk++;      /*} *//* end i1 */
           fprintf(ficgp,"\n");    } /* end j1 */
         }    
       }    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
     }    /*free_vector(pp,1,nlstate);*/
     }    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
   }  /* End of prevalence */
   for(jk=1; jk <=m; jk++) {  
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);  /************* Waves Concatenation ***************/
    i=1;  
    for(k2=1; k2<=nlstate; k2++) {  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)
      k3=i;  {
      for(k=1; k<=(nlstate+ndeath); k++) {    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
        if (k != k2){       Death is a valid wave (if date is known).
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
 ij=1;       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
         for(j=3; j <=ncovmodel; j++) {       and mw[mi+1][i]. dh depends on stepm.
           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]]]);  
             ij++;    int i, mi, m;
           }    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
           else       double sum=0., jmean=0.;*/
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    int first;
         }    int j, k=0,jk, ju, jl;
           fprintf(ficgp,")/(1");    double sum=0.;
            first=0;
         for(k1=1; k1 <=nlstate; k1++){      jmin=1e+5;
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);    jmax=-1;
 ij=1;    jmean=0.;
           for(j=3; j <=ncovmodel; j++){    for(i=1; i<=imx; i++){
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {      mi=0;
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);      m=firstpass;
             ij++;      while(s[m][i] <= nlstate){
           }        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
           else          mw[++mi][i]=m;
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);        if(m >=lastpass)
           }          break;
           fprintf(ficgp,")");        else
         }          m++;
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);      }/* end while */
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");      if (s[m][i] > nlstate){
         i=i+ncovmodel;        mi++;     /* Death is another wave */
        }        /* if(mi==0)  never been interviewed correctly before death */
      }           /* Only death is a correct wave */
    }        mw[mi][i]=m;
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);      }
   }  
          wav[i]=mi;
   fclose(ficgp);      if(mi==0){
            nbwarn++;
 chdir(path);        if(first==0){
              printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
     free_ivector(wav,1,imx);          first=1;
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);        }
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);          if(first==1){
     free_ivector(num,1,n);          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
     free_vector(agedc,1,n);        }
     /*free_matrix(covar,1,NCOVMAX,1,n);*/      } /* end mi==0 */
     fclose(ficparo);    } /* End individuals */
     fclose(ficres);  
     /*  }*/    for(i=1; i<=imx; i++){
          for(mi=1; mi<wav[i];mi++){
    /*________fin mle=1_________*/        if (stepm <=0)
              dh[mi][i]=1;
         else{
            if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
     /* No more information from the sample is required now */            if (agedc[i] < 2*AGESUP) {
   /* Reads comments: lines beginning with '#' */              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
   while((c=getc(ficpar))=='#' && c!= EOF){              if(j==0) j=1;  /* Survives at least one month after exam */
     ungetc(c,ficpar);              else if(j<0){
     fgets(line, MAXLINE, ficpar);                nberr++;
     puts(line);                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]);
     fputs(line,ficparo);                j=1; /* Temporary Dangerous patch */
   }                printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
   ungetc(c,ficpar);                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);
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);              }
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);              k=k+1;
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);              if (j >= jmax){
 /*--------- index.htm --------*/                jmax=j;
                 ijmax=i;
   strcpy(optionfilehtm,optionfile);              }
   strcat(optionfilehtm,".htm");              if (j <= jmin){
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {                jmin=j;
     printf("Problem with %s \n",optionfilehtm);goto end;                ijmin=i;
   }              }
               sum=sum+j;
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.7 </font> <hr size=\"2\" color=\"#EC5E5E\">              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
 Titre=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
 Total number of observations=%d <br>            }
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>          }
 <hr  size=\"2\" color=\"#EC5E5E\">          else{
 <li>Outputs files<br><br>\n            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n  /*        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]); */
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>  
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>            k=k+1;
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>            if (j >= jmax) {
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>              jmax=j;
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>              ijmax=i;
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>            }
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>            else if (j <= jmin){
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>              jmin=j;
         - Prevalences and population forecasting: <a href=\"f%s\">f%s</a> <br>              ijmin=i;
 <br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);            }
             /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
  fprintf(fichtm," <li>Graphs</li><p>");            /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
             if(j<0){
  m=cptcoveff;              nberr++;
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}              printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
               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]);
  j1=0;            }
  for(k1=1; k1<=m;k1++){            sum=sum+j;
    for(i1=1; i1<=ncodemax[k1];i1++){          }
        j1++;          jk= j/stepm;
        if (cptcovn > 0) {          jl= j -jk*stepm;
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");          ju= j -(jk+1)*stepm;
          for (cpt=1; cpt<=cptcoveff;cpt++)          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[j1][cpt]]);            if(jl==0){
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");              dh[mi][i]=jk;
        }              bh[mi][i]=0;
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>            }else{ /* We want a negative bias in order to only have interpolation ie
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);                        * to avoid the price of an extra matrix product in likelihood */
        for(cpt=1; cpt<nlstate;cpt++){              dh[mi][i]=jk+1;
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>              bh[mi][i]=ju;
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);            }
        }          }else{
     for(cpt=1; cpt<=nlstate;cpt++) {            if(jl <= -ju){
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident              dh[mi][i]=jk;
 interval) in state (%d): v%s%d%d.gif <br>              bh[mi][i]=jl;       /* bias is positive if real duration
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);                                     * is higher than the multiple of stepm and negative otherwise.
      }                                   */
      for(cpt=1; cpt<=nlstate;cpt++) {            }
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>            else{
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);              dh[mi][i]=jk+1;
      }              bh[mi][i]=ju;
      fprintf(fichtm,"\n<br>- Total life expectancy by age and            }
 health expectancies in states (1) and (2): e%s%d.gif<br>            if(dh[mi][i]==0){
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);              dh[mi][i]=1; /* At least one step */
 fprintf(fichtm,"\n</body>");              bh[mi][i]=ju; /* At least one step */
    }              /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
  }            }
 fclose(fichtm);          } /* end if mle */
         }
   /*--------------- Prevalence limit --------------*/      } /* end wave */
      }
   strcpy(filerespl,"pl");    jmean=sum/k;
   strcat(filerespl,fileres);    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);
   if((ficrespl=fopen(filerespl,"w"))==NULL) {    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);
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;   }
   }  
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);  /*********** Tricode ****************************/
   fprintf(ficrespl,"#Prevalence limit\n");  void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
   fprintf(ficrespl,"#Age ");  {
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);    /**< Uses cptcovn+2*cptcovprod as the number of covariates */
   fprintf(ficrespl,"\n");    /*      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]
   prlim=matrix(1,nlstate,1,nlstate);     * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    /* nbcode[Tvar[j]][1]= 
   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 */    int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    int modmaxcovj=0; /* Modality max of covariates j */
   k=0;    int cptcode=0; /* Modality max of covariates j */
   agebase=agemin;    int modmincovj=0; /* Modality min of covariates j */
   agelim=agemax;  
   ftolpl=1.e-10;  
   i1=cptcoveff;    cptcoveff=0; 
   if (cptcovn < 1){i1=1;}   
     for (k=-1; k < maxncov; k++) Ndum[k]=0;
   for(cptcov=1;cptcov<=i1;cptcov++){    for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  
         k=k+1;    /* Loop on covariates without age and products */
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/    for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */
         fprintf(ficrespl,"\n#******");      for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the 
         for(j=1;j<=cptcoveff;j++)                                 modality of this covariate Vj*/ 
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
         fprintf(ficrespl,"******\n");                                      * If product of Vn*Vm, still boolean *:
                                              * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
         for (age=agebase; age<=agelim; age++){                                      * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);        /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
           fprintf(ficrespl,"%.0f",age );                                        modality of the nth covariate of individual i. */
           for(i=1; i<=nlstate;i++)        if (ij > modmaxcovj)
           fprintf(ficrespl," %.5f", prlim[i][i]);          modmaxcovj=ij; 
           fprintf(ficrespl,"\n");        else if (ij < modmincovj) 
         }          modmincovj=ij; 
       }        if ((ij < -1) && (ij > NCOVMAX)){
     }          printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
   fclose(ficrespl);          exit(1);
         }else
   /*------------- h Pij x at various ages ------------*/        Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
          /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
   if((ficrespij=fopen(filerespij,"w"))==NULL) {        /* getting the maximum value of the modality of the covariate
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;           (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
   }           female is 1, then modmaxcovj=1.*/
   printf("Computing pij: result on file '%s' \n", filerespij);      }
        printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
   stepsize=(int) (stepm+YEARM-1)/YEARM;      cptcode=modmaxcovj;
   /*if (stepm<=24) stepsize=2;*/      /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
      /*for (i=0; i<=cptcode; i++) {*/
   agelim=AGESUP;      for (i=modmincovj;  i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
   hstepm=stepsize*YEARM; /* Every year of age */        printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */        if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
            ncodemax[j]++;  /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
   k=0;        }
   for(cptcov=1;cptcov<=i1;cptcov++){        /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){           historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
       k=k+1;      } /* Ndum[-1] number of undefined modalities */
         fprintf(ficrespij,"\n#****** ");  
         for(j=1;j<=cptcoveff;j++)      /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
         fprintf(ficrespij,"******\n");      /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
                 modmincovj=3; modmaxcovj = 7;
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */         There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */         which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy 
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */         variables V1_1 and V1_2.
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);         nbcode[Tvar[j]][ij]=k;
           oldm=oldms;savm=savms;         nbcode[Tvar[j]][1]=0;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);           nbcode[Tvar[j]][2]=1;
           fprintf(ficrespij,"# Age");         nbcode[Tvar[j]][3]=2;
           for(i=1; i<=nlstate;i++)      */
             for(j=1; j<=nlstate+ndeath;j++)      ij=1; /* ij is similar to i but can jumps over null modalities */
               fprintf(ficrespij," %1d-%1d",i,j);      for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
           fprintf(ficrespij,"\n");        for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
           for (h=0; h<=nhstepm; h++){          /*recode from 0 */
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );          if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
             for(i=1; i<=nlstate;i++)            nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode. 
               for(j=1; j<=nlstate+ndeath;j++)                                       k is a modality. If we have model=V1+V1*sex 
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);                                       then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
             fprintf(ficrespij,"\n");            ij++;
           }          }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          if (ij > ncodemax[j]) break; 
           fprintf(ficrespij,"\n");        }  /* end of loop on */
         }      } /* end of loop on modality */ 
     }    } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/  
   }    
    for (k=-1; k< maxncov; k++) Ndum[k]=0; 
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/    
     for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */ 
   fclose(ficrespij);     /* 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 */ 
   /*---------- Forecasting ------------------*/     Ndum[ij]++; 
   calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;   } 
   
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);   ij=1;
    for (i=0; i<=  maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
      /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
   strcpy(fileresf,"f");     if((Ndum[i]!=0) && (i<=ncovcol)){
   strcat(fileresf,fileres);       /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
   if((ficresf=fopen(fileresf,"w"))==NULL) {       Tvaraff[ij]=i; /*For printing (unclear) */
     printf("Problem with forecast resultfile: %s\n", fileresf);goto end;       ij++;
   }     }else
   printf("Computing forecasting: result on file '%s' \n", fileresf);         Tvaraff[ij]=0;
    }
   free_matrix(mint,1,maxwav,1,n);   ij--;
   free_matrix(anint,1,maxwav,1,n);   cptcoveff=ij; /*Number of total covariates*/
   free_matrix(agev,1,maxwav,1,imx);  
   /* Mobile average */  }
   
   if (cptcoveff==0) ncodemax[cptcoveff]=1;  
   /*********** Health Expectancies ****************/
   if (mobilav==1) {  
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
     for (agedeb=bage+3; agedeb<=fage-2; agedeb++)  
       for (i=1; i<=nlstate;i++)  {
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)    /* Health expectancies, no variances */
           mobaverage[(int)agedeb][i][cptcod]=0.;    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
        int nhstepma, nstepma; /* Decreasing with age */
     for (agedeb=bage+4; agedeb<=fage; agedeb++){    double age, agelim, hf;
       for (i=1; i<=nlstate;i++){    double ***p3mat;
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    double eip;
           for (cpt=0;cpt<=4;cpt++){  
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];    pstamp(ficreseij);
           }    fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;    fprintf(ficreseij,"# Age");
         }    for(i=1; i<=nlstate;i++){
       }      for(j=1; j<=nlstate;j++){
     }          fprintf(ficreseij," e%1d%1d ",i,j);
   }      }
       fprintf(ficreseij," e%1d. ",i);
   stepsize=(int) (stepm+YEARM-1)/YEARM;    }
   if (stepm<=12) stepsize=1;    fprintf(ficreseij,"\n");
   
   agelim=AGESUP;    
   /*hstepm=stepsize*YEARM; *//* Every year of age */    if(estepm < stepm){
   hstepm=1;      printf ("Problem %d lower than %d\n",estepm, stepm);
   hstepm=hstepm/stepm; /* Typically 2 years, = 2 years/6 months = 4 */    }
   yp1=modf(dateintmean,&yp);    else  hstepm=estepm;   
   anprojmean=yp;    /* We compute the life expectancy from trapezoids spaced every estepm months
   yp2=modf((yp1*12),&yp);     * This is mainly to measure the difference between two models: for example
   mprojmean=yp;     * if stepm=24 months pijx are given only every 2 years and by summing them
   yp1=modf((yp2*30.5),&yp);     * we are calculating an estimate of the Life Expectancy assuming a linear 
   jprojmean=yp;     * progression in between and thus overestimating or underestimating according
   if(jprojmean==0) jprojmean=1;     * to the curvature of the survival function. If, for the same date, we 
   if(mprojmean==0) jprojmean=1;     * estimate the model with stepm=1 month, we can keep estepm to 24 months
      * to compare the new estimate of Life expectancy with the same linear 
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);     * hypothesis. A more precise result, taking into account a more precise
      * curvature will be obtained if estepm is as small as stepm. */
   if (popforecast==1) {  
     if((ficpop=fopen(popfile,"r"))==NULL)    {    /* For example we decided to compute the life expectancy with the smallest unit */
       printf("Problem with population file : %s\n",popfile);goto end;    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
     }       nhstepm is the number of hstepm from age to agelim 
     popage=ivector(0,AGESUP);       nstepm is the number of stepm from age to agelin. 
     popeffectif=vector(0,AGESUP);       Look at hpijx to understand the reason of that which relies in memory size
     popcount=vector(0,AGESUP);       and note for a fixed period like estepm months */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
     i=1;         survival function given by stepm (the optimization length). Unfortunately it
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF)       means that if the survival funtion is printed only each two years of age and if
       {       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
         i=i+1;       results. So we changed our mind and took the option of the best precision.
       }    */
     imx=i;    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
      
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];    agelim=AGESUP;
   }    /* If stepm=6 months */
       /* Computed by stepm unit matrices, product of hstepm matrices, stored
   for(cptcov=1;cptcov<=i1;cptcov++){         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      
       k=k+1;  /* nhstepm age range expressed in number of stepm */
       fprintf(ficresf,"\n#******");    nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
       for(j=1;j<=cptcoveff;j++) {    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    /* if (stepm >= YEARM) hstepm=1;*/
       }    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       fprintf(ficresf,"******\n");    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       fprintf(ficresf,"# StartingAge FinalAge");  
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);    for (age=bage; age<=fage; age ++){ 
       if (popforecast==1)  fprintf(ficresf," [Population]");      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
        /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       for (cpt=0; cpt<=5;cpt++) {      /* if (stepm >= YEARM) hstepm=1;*/
         fprintf(ficresf,"\n");      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
   fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);    
       for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(bage-((int)calagedate %12)/12.); agedeb--){ /* If stepm=6 months */      /* If stepm=6 months */
         nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);      /* Computed by stepm unit matrices, product of hstepma matrices, stored
         nhstepm = nhstepm/hstepm;         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
         /*printf("agedeb=%.lf stepm=%d hstepm=%d nhstepm=%d \n",agedeb,stepm,hstepm,nhstepm);*/      
       hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      
         oldm=oldms;savm=savms;      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
         hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        
                      printf("%d|",(int)age);fflush(stdout);
         for (h=0; h<=nhstepm; h++){      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
           if (h==(int) (calagedate+YEARM*cpt)) {      
             fprintf(ficresf,"\n %.f ",agedeb+h*hstepm/YEARM*stepm);      /* Computing expectancies */
           }      for(i=1; i<=nlstate;i++)
           for(j=1; j<=nlstate+ndeath;j++) {        for(j=1; j<=nlstate;j++)
             kk1=0.;kk2=0;          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
             for(i=1; i<=nlstate;i++) {                    eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
               if (mobilav==1)            
                 kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];            /* 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]);*/
               else {  
                 kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];          }
                 /* fprintf(ficresf," p3=%.3f p=%.3f ", p3mat[i][j][h], probs[(int)(agedeb)+1][i][cptcod]);*/  
               }      fprintf(ficreseij,"%3.0f",age );
       for(i=1; i<=nlstate;i++){
               if (popforecast==1) kk2=kk1*popeffectif[(int)agedeb];        eip=0;
             }        for(j=1; j<=nlstate;j++){
                    eip +=eij[i][j][(int)age];
             if (h==(int)(calagedate+12*cpt)){          fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
               fprintf(ficresf," %.3f", kk1);        }
                      fprintf(ficreseij,"%9.4f", eip );
               if (popforecast==1) fprintf(ficresf," [%.f]", kk2);      }
             }      fprintf(ficreseij,"\n");
           }      
         }    }
         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       }    printf("\n");
       }    fprintf(ficlog,"\n");
     }    
   }  }
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  
   if (popforecast==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[] )
     free_ivector(popage,0,AGESUP);  
     free_vector(popeffectif,0,AGESUP);  {
     free_vector(popcount,0,AGESUP);    /* Covariances of health expectancies eij and of total life expectancies according
   }     to initial status i, ei. .
   free_imatrix(s,1,maxwav+1,1,n);    */
   free_vector(weight,1,n);    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
   fclose(ficresf);    int nhstepma, nstepma; /* Decreasing with age */
   /*---------- Health expectancies and variances ------------*/    double age, agelim, hf;
     double ***p3matp, ***p3matm, ***varhe;
   strcpy(filerest,"t");    double **dnewm,**doldm;
   strcat(filerest,fileres);    double *xp, *xm;
   if((ficrest=fopen(filerest,"w"))==NULL) {    double **gp, **gm;
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;    double ***gradg, ***trgradg;
   }    int theta;
   printf("Computing Total LEs with variances: file '%s' \n", filerest);  
     double eip, vip;
   
   strcpy(filerese,"e");    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
   strcat(filerese,fileres);    xp=vector(1,npar);
   if((ficreseij=fopen(filerese,"w"))==NULL) {    xm=vector(1,npar);
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);    dnewm=matrix(1,nlstate*nlstate,1,npar);
   }    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);    
     pstamp(ficresstdeij);
  strcpy(fileresv,"v");    fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
   strcat(fileresv,fileres);    fprintf(ficresstdeij,"# Age");
   if((ficresvij=fopen(fileresv,"w"))==NULL) {    for(i=1; i<=nlstate;i++){
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);      for(j=1; j<=nlstate;j++)
   }        fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);      fprintf(ficresstdeij," e%1d. ",i);
     }
   k=0;    fprintf(ficresstdeij,"\n");
   for(cptcov=1;cptcov<=i1;cptcov++){  
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    pstamp(ficrescveij);
       k=k+1;    fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
       fprintf(ficrest,"\n#****** ");    fprintf(ficrescveij,"# Age");
       for(j=1;j<=cptcoveff;j++)    for(i=1; i<=nlstate;i++)
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      for(j=1; j<=nlstate;j++){
       fprintf(ficrest,"******\n");        cptj= (j-1)*nlstate+i;
         for(i2=1; i2<=nlstate;i2++)
       fprintf(ficreseij,"\n#****** ");          for(j2=1; j2<=nlstate;j2++){
       for(j=1;j<=cptcoveff;j++)            cptj2= (j2-1)*nlstate+i2;
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);            if(cptj2 <= cptj)
       fprintf(ficreseij,"******\n");              fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
           }
       fprintf(ficresvij,"\n#****** ");      }
       for(j=1;j<=cptcoveff;j++)    fprintf(ficrescveij,"\n");
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);    
       fprintf(ficresvij,"******\n");    if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    }
       oldm=oldms;savm=savms;    else  hstepm=estepm;   
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);      /* We compute the life expectancy from trapezoids spaced every estepm months
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);     * This is mainly to measure the difference between two models: for example
       oldm=oldms;savm=savms;     * if stepm=24 months pijx are given only every 2 years and by summing them
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);     * we are calculating an estimate of the Life Expectancy assuming a linear 
           * progression in between and thus overestimating or underestimating according
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");     * to the curvature of the survival function. If, for the same date, we 
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);     * estimate the model with stepm=1 month, we can keep estepm to 24 months
       fprintf(ficrest,"\n");     * to compare the new estimate of Life expectancy with the same linear 
             * hypothesis. A more precise result, taking into account a more precise
       hf=1;     * curvature will be obtained if estepm is as small as stepm. */
       if (stepm >= YEARM) hf=stepm/YEARM;  
       epj=vector(1,nlstate+1);    /* For example we decided to compute the life expectancy with the smallest unit */
       for(age=bage; age <=fage ;age++){    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);       nhstepm is the number of hstepm from age to agelim 
         if (popbased==1) {       nstepm is the number of stepm from age to agelin. 
           for(i=1; i<=nlstate;i++)       Look at hpijx to understand the reason of that which relies in memory size
             prlim[i][i]=probs[(int)age][i][k];       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
         fprintf(ficrest," %.0f",age);       means that if the survival funtion is printed only each two years of age and if
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
           for(i=1, epj[j]=0.;i <=nlstate;i++) {       results. So we changed our mind and took the option of the best precision.
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];    */
           }    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
           epj[nlstate+1] +=epj[j];  
         }    /* If stepm=6 months */
         for(i=1, vepp=0.;i <=nlstate;i++)    /* nhstepm age range expressed in number of stepm */
           for(j=1;j <=nlstate;j++)    agelim=AGESUP;
             vepp += vareij[i][j][(int)age];    nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
         for(j=1;j <=nlstate;j++){    /* if (stepm >= YEARM) hstepm=1;*/
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
         }    
         fprintf(ficrest,"\n");    p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       }    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);
   
     for (age=bage; age<=fage; age ++){ 
  fclose(ficreseij);      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
  fclose(ficresvij);      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   fclose(ficrest);      /* if (stepm >= YEARM) hstepm=1;*/
   fclose(ficpar);      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
   free_vector(epj,1,nlstate+1);  
   /*  scanf("%d ",i); */      /* If stepm=6 months */
       /* Computed by stepm unit matrices, product of hstepma matrices, stored
   /*------- Variance limit prevalence------*/           in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
       
 strcpy(fileresvpl,"vpl");      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   strcat(fileresvpl,fileres);  
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {      /* Computing  Variances of health expectancies */
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
     exit(0);         decrease memory allocation */
   }      for(theta=1; theta <=npar; theta++){
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);        for(i=1; i<=npar; i++){ 
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
  k=0;          xm[i] = x[i] - (i==theta ?delti[theta]:0);
  for(cptcov=1;cptcov<=i1;cptcov++){        }
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
      k=k+1;        hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
      fprintf(ficresvpl,"\n#****** ");    
      for(j=1;j<=cptcoveff;j++)        for(j=1; j<= nlstate; j++){
        fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          for(i=1; i<=nlstate; i++){
      fprintf(ficresvpl,"******\n");            for(h=0; h<=nhstepm-1; h++){
                    gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
      varpl=matrix(1,nlstate,(int) bage, (int) fage);              gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
      oldm=oldms;savm=savms;            }
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);          }
    }        }
  }       
         for(ij=1; ij<= nlstate*nlstate; ij++)
   fclose(ficresvpl);          for(h=0; h<=nhstepm-1; h++){
             gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
   /*---------- End : free ----------------*/          }
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);      }/* End theta */
        
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);      
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);      for(h=0; h<=nhstepm-1; h++)
          for(j=1; j<=nlstate*nlstate;j++)
            for(theta=1; theta <=npar; theta++)
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);            trgradg[h][j][theta]=gradg[h][theta][j];
   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);       for(ij=1;ij<=nlstate*nlstate;ij++)
          for(ji=1;ji<=nlstate*nlstate;ji++)
   free_matrix(matcov,1,npar,1,npar);          varhe[ij][ji][(int)age] =0.;
   free_vector(delti,1,npar);  
         printf("%d|",(int)age);fflush(stdout);
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
        for(h=0;h<=nhstepm-1;h++){
   printf("End of Imach\n");        for(k=0;k<=nhstepm-1;k++){
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
            matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
   /* 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);*/          for(ij=1;ij<=nlstate*nlstate;ij++)
   /*printf("Total time was %d uSec.\n", total_usecs);*/            for(ji=1;ji<=nlstate*nlstate;ji++)
   /*------ End -----------*/              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
         }
       }
  end:  
 #ifdef windows      /* Computing expectancies */
  chdir(pathcd);      hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
 #endif      for(i=1; i<=nlstate;i++)
          for(j=1; j<=nlstate;j++)
  system("..\\gp37mgw\\wgnuplot graph.plt");          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;
 #ifdef windows            
   while (z[0] != 'q') {            /* 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]);*/
     chdir(pathcd);  
     printf("\nType e to edit output files, c to start again, and q for exiting: ");          }
     scanf("%s",z);  
     if (z[0] == 'c') system("./imach");      fprintf(ficresstdeij,"%3.0f",age );
     else if (z[0] == 'e') {      for(i=1; i<=nlstate;i++){
       chdir(path);        eip=0.;
       system(optionfilehtm);        vip=0.;
     }        for(j=1; j<=nlstate;j++){
     else if (z[0] == 'q') exit(0);          eip += eij[i][j][(int)age];
   }          for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
 #endif            vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
 }          fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
         }
         fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
       }
       fprintf(ficresstdeij,"\n");
   
       fprintf(ficrescveij,"%3.0f",age );
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
           cptj= (j-1)*nlstate+i;
           for(i2=1; i2<=nlstate;i2++)
             for(j2=1; j2<=nlstate;j2++){
               cptj2= (j2-1)*nlstate+i2;
               if(cptj2 <= cptj)
                 fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
             }
         }
       fprintf(ficrescveij,"\n");
      
     }
     free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
     free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
     free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
     free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     printf("\n");
     fprintf(ficlog,"\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);
   }
   
   /************ Variance ******************/
   void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
   {
     /* Variance of health expectancies */
     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
     /* double **newm;*/
     double **dnewm,**doldm;
     double **dnewmp,**doldmp;
     int i, j, nhstepm, hstepm, h, nstepm ;
     int k, cptcode;
     double *xp;
     double **gp, **gm;  /* for var eij */
     double ***gradg, ***trgradg; /*for var eij */
     double **gradgp, **trgradgp; /* for var p point j */
     double *gpp, *gmp; /* for var p point j */
     double **varppt; /* for var p point j nlstate to nlstate+ndeath */
     double ***p3mat;
     double age,agelim, hf;
     double ***mobaverage;
     int theta;
     char digit[4];
     char digitp[25];
   
     char fileresprobmorprev[FILENAMELENGTH];
   
     if(popbased==1){
       if(mobilav!=0)
         strcpy(digitp,"-populbased-mobilav-");
       else strcpy(digitp,"-populbased-nomobil-");
     }
     else 
       strcpy(digitp,"-stablbased-");
   
     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);
       }
     }
   
     strcpy(fileresprobmorprev,"prmorprev"); 
     sprintf(digit,"%-d",ij);
     /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
     strcat(fileresprobmorprev,digit); /* Tvar to be done */
     strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
     strcat(fileresprobmorprev,fileres);
     if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobmorprev);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
     }
     printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
    
     fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     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);
     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
       fprintf(ficresprobmorprev," p.%-d SE",j);
       for(i=1; i<=nlstate;i++)
         fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
     }  
     fprintf(ficresprobmorprev,"\n");
     fprintf(ficgp,"\n# Routine varevsij");
     /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
     fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
     fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
   /*   } */
     varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     pstamp(ficresvij);
     fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
     if(popbased==1)
       fprintf(ficresvij,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d\n",mobilav);
     else
       fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
     fprintf(ficresvij,"# Age");
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++)
         fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
     fprintf(ficresvij,"\n");
   
     xp=vector(1,npar);
     dnewm=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
     dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
     doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   
     gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
     gpp=vector(nlstate+1,nlstate+ndeath);
     gmp=vector(nlstate+1,nlstate+ndeath);
     trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
     /* For example we decided to compute the life expectancy with the smallest unit */
     /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
        nhstepm is the number of hstepm from age to agelim 
        nstepm is the number of stepm from age to agelin. 
        Look at function hpijx to understand why (it is linked to memory size questions) */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
        survival function given by stepm (the optimization length). Unfortunately it
        means that if the survival funtion is printed every two years of age and if
        you sum them up and add 1 year (area under the trapezoids) you won't get the same 
        results. So we changed our mind and took the option of the best precision.
     */
     hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     agelim = AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
       gp=matrix(0,nhstepm,1,nlstate);
       gm=matrix(0,nhstepm,1,nlstate);
   
   
       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   
         if (popbased==1) {
           if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=mobaverage[(int)age][i][ij];
           }
         }
     
         for(j=1; j<= nlstate; j++){
           for(h=0; h<=nhstepm; h++){
             for(i=1, gp[h][j]=0.;i<=nlstate;i++)
               gp[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
         }
         /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
         */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
           for(i=1,gpp[j]=0.; i<= nlstate; i++)
             gpp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
         /* end probability of death */
   
         for(i=1; i<=npar; i++) /* Computes gradient x - delta */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
    
         if (popbased==1) {
           if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=mobaverage[(int)age][i][ij];
           }
         }
   
         for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
           for(h=0; h<=nhstepm; h++){
             for(i=1, gm[h][j]=0.;i<=nlstate;i++)
               gm[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
         }
         /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
         */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
           for(i=1,gmp[j]=0.; i<= nlstate; i++)
            gmp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
         /* end probability of death */
   
         for(j=1; j<= nlstate; j++) /* vareij */
           for(h=0; h<=nhstepm; h++){
             gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
           }
   
         for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
           gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
         }
   
       } /* End theta */
   
       trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   
       for(h=0; h<=nhstepm; h++) /* veij */
         for(j=1; j<=nlstate;j++)
           for(theta=1; theta <=npar; theta++)
             trgradg[h][j][theta]=gradg[h][theta][j];
   
       for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
         for(theta=1; theta <=npar; theta++)
           trgradgp[j][theta]=gradgp[theta][j];
     
   
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       for(i=1;i<=nlstate;i++)
         for(j=1;j<=nlstate;j++)
           vareij[i][j][(int)age] =0.;
   
       for(h=0;h<=nhstepm;h++){
         for(k=0;k<=nhstepm;k++){
           matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
           matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
           for(i=1;i<=nlstate;i++)
             for(j=1;j<=nlstate;j++)
               vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
         }
       }
     
       /* pptj */
       matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
       matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
       for(j=nlstate+1;j<=nlstate+ndeath;j++)
         for(i=nlstate+1;i<=nlstate+ndeath;i++)
           varppt[j][i]=doldmp[j][i];
       /* end ppptj */
       /*  x centered again */
       hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
       prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
    
       if (popbased==1) {
         if(mobilav ==0){
           for(i=1; i<=nlstate;i++)
             prlim[i][i]=probs[(int)age][i][ij];
         }else{ /* mobilav */ 
           for(i=1; i<=nlstate;i++)
             prlim[i][i]=mobaverage[(int)age][i][ij];
         }
       }
                
       /* This for computing probability of death (h=1 means
          computed over hstepm (estepm) matrices product = hstepm*stepm months) 
          as a weighted average of prlim.
       */
       for(j=nlstate+1;j<=nlstate+ndeath;j++){
         for(i=1,gmp[j]=0.;i<= nlstate; i++) 
           gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
       }    
       /* end probability of death */
   
       fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
       for(j=nlstate+1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
         for(i=1; i<=nlstate;i++){
           fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
         }
       } 
       fprintf(ficresprobmorprev,"\n");
   
       fprintf(ficresvij,"%.0f ",age );
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
           fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
         }
       fprintf(ficresvij,"\n");
       free_matrix(gp,0,nhstepm,1,nlstate);
       free_matrix(gm,0,nhstepm,1,nlstate);
       free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
       free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
       free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     } /* End age */
     free_vector(gpp,nlstate+1,nlstate+ndeath);
     free_vector(gmp,nlstate+1,nlstate+ndeath);
     free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
     free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
     /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
     fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
   /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
   /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
   /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
     fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
     fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
     fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
     /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
   */
   /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
     fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
   
     free_vector(xp,1,npar);
     free_matrix(doldm,1,nlstate,1,nlstate);
     free_matrix(dnewm,1,nlstate,1,npar);
     free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
     free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficresprobmorprev);
     fflush(ficgp);
     fflush(fichtm); 
   }  /* end varevsij */
   
   /************ Variance of prevlim ******************/
   void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, char strstart[])
   {
     /* Variance of prevalence limit */
     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
     double **newm;
     double **dnewm,**doldm;
     int i, j, nhstepm, hstepm;
     int k, cptcode;
     double *xp;
     double *gp, *gm;
     double **gradg, **trgradg;
     double age,agelim;
     int theta;
     
     pstamp(ficresvpl);
     fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
     fprintf(ficresvpl,"# Age");
     for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %1d-%1d",i,i);
     fprintf(ficresvpl,"\n");
   
     xp=vector(1,npar);
     dnewm=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
     
     hstepm=1*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
     agelim = AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       if (stepm >= YEARM) hstepm=1;
       nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
       gradg=matrix(1,npar,1,nlstate);
       gp=vector(1,nlstate);
       gm=vector(1,nlstate);
   
       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient */
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=nlstate;i++)
           gp[i] = prlim[i][i];
       
         for(i=1; i<=npar; i++) /* Computes gradient */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=nlstate;i++)
           gm[i] = prlim[i][i];
   
         for(i=1;i<=nlstate;i++)
           gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
       } /* End theta */
   
       trgradg =matrix(1,nlstate,1,npar);
   
       for(j=1; j<=nlstate;j++)
         for(theta=1; theta <=npar; theta++)
           trgradg[j][theta]=gradg[theta][j];
   
       for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] =0.;
       matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
       matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
       for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   
       fprintf(ficresvpl,"%.0f ",age );
       for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
       fprintf(ficresvpl,"\n");
       free_vector(gp,1,nlstate);
       free_vector(gm,1,nlstate);
       free_matrix(gradg,1,npar,1,nlstate);
       free_matrix(trgradg,1,nlstate,1,npar);
     } /* End age */
   
     free_vector(xp,1,npar);
     free_matrix(doldm,1,nlstate,1,npar);
     free_matrix(dnewm,1,nlstate,1,nlstate);
   
   }
   
   /************ Variance of one-step probabilities  ******************/
   void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
   {
     int i, j=0,  i1, k1, l1, t, tj;
     int k2, l2, j1,  z1;
     int k=0,l, cptcode;
     int first=1, first1, first2;
     double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
     double **dnewm,**doldm;
     double *xp;
     double *gp, *gm;
     double **gradg, **trgradg;
     double **mu;
     double age,agelim, cov[NCOVMAX+1];
     double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
     int theta;
     char fileresprob[FILENAMELENGTH];
     char fileresprobcov[FILENAMELENGTH];
     char fileresprobcor[FILENAMELENGTH];
     double ***varpij;
   
     strcpy(fileresprob,"prob"); 
     strcat(fileresprob,fileres);
     if((ficresprob=fopen(fileresprob,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprob);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
     }
     strcpy(fileresprobcov,"probcov"); 
     strcat(fileresprobcov,fileres);
     if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcov);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
     }
     strcpy(fileresprobcor,"probcor"); 
     strcat(fileresprobcor,fileres);
     if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcor);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
     }
     printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     pstamp(ficresprob);
     fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
     fprintf(ficresprob,"# Age");
     pstamp(ficresprobcov);
     fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
     fprintf(ficresprobcov,"# Age");
     pstamp(ficresprobcor);
     fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
     fprintf(ficresprobcor,"# Age");
   
   
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprob," p%1d-%1d (SE)",i,j);
         fprintf(ficresprobcov," p%1d-%1d ",i,j);
         fprintf(ficresprobcor," p%1d-%1d ",i,j);
       }  
    /* fprintf(ficresprob,"\n");
     fprintf(ficresprobcov,"\n");
     fprintf(ficresprobcor,"\n");
    */
     xp=vector(1,npar);
     dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
     varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
     first=1;
     fprintf(ficgp,"\n# Routine varprob");
     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
     fprintf(fichtm,"\n");
   
     fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
     fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
     file %s<br>\n",optionfilehtmcov);
     fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
   and drawn. It helps understanding how is the covariance between two incidences.\
    They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
     fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
   It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
   would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
   standard deviations wide on each axis. <br>\
    Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
    and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
   To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
   
     cov[1]=1;
     /* tj=cptcoveff; */
     tj = (int) pow(2,cptcoveff);
     if (cptcovn<1) {tj=1;ncodemax[1]=1;}
     j1=0;
     for(j1=1; j1<=tj;j1++){
       /*for(i1=1; i1<=ncodemax[t];i1++){ */
       /*j1++;*/
         if  (cptcovn>0) {
           fprintf(ficresprob, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprob, "**********\n#\n");
           fprintf(ficresprobcov, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcov, "**********\n#\n");
           
           fprintf(ficgp, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficgp, "**********\n#\n");
           
           
           fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
           
           fprintf(ficresprobcor, "\n#********** Variable ");    
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcor, "**********\n#");    
         }
         
         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
         gp=vector(1,(nlstate)*(nlstate+ndeath));
         gm=vector(1,(nlstate)*(nlstate+ndeath));
         for (age=bage; age<=fage; age ++){ 
           cov[2]=age;
           for (k=1; k<=cptcovn;k++) {
             cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
                                                            * 1  1 1 1 1
                                                            * 2  2 1 1 1
                                                            * 3  1 2 1 1
                                                            */
             /* nbcode[1][1]=0 nbcode[1][2]=1;*/
           }
           for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
           for (k=1; k<=cptcovprod;k++)
             cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
           
       
           for(theta=1; theta <=npar; theta++){
             for(i=1; i<=npar; i++)
               xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
             
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             
             k=0;
             for(i=1; i<= (nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gp[k]=pmmij[i][j];
               }
             }
             
             for(i=1; i<=npar; i++)
               xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
       
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             k=0;
             for(i=1; i<=(nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gm[k]=pmmij[i][j];
               }
             }
        
             for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
               gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
           }
   
           for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
             for(theta=1; theta <=npar; theta++)
               trgradg[j][theta]=gradg[theta][j];
           
           matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
           matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
   
           pmij(pmmij,cov,ncovmodel,x,nlstate);
           
           k=0;
           for(i=1; i<=(nlstate); i++){
             for(j=1; j<=(nlstate+ndeath);j++){
               k=k+1;
               mu[k][(int) age]=pmmij[i][j];
             }
           }
           for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
             for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
               varpij[i][j][(int)age] = doldm[i][j];
   
           /*printf("\n%d ",(int)age);
             for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             }*/
   
           fprintf(ficresprob,"\n%d ",(int)age);
           fprintf(ficresprobcov,"\n%d ",(int)age);
           fprintf(ficresprobcor,"\n%d ",(int)age);
   
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
             fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
             fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
           }
           i=0;
           for (k=1; k<=(nlstate);k++){
             for (l=1; l<=(nlstate+ndeath);l++){ 
               i++;
               fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
               fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
               for (j=1; j<=i;j++){
                 /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
                 fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
                 fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
               }
             }
           }/* end of loop for state */
         } /* end of loop for age */
         free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
         free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
         free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
         free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
         
         /* Confidence intervalle of pij  */
         /*
           fprintf(ficgp,"\nunset parametric;unset label");
           fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
           fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
           fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
           fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
           fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
           fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
         */
   
         /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
         first1=1;first2=2;
         for (k2=1; k2<=(nlstate);k2++){
           for (l2=1; l2<=(nlstate+ndeath);l2++){ 
             if(l2==k2) continue;
             j=(k2-1)*(nlstate+ndeath)+l2;
             for (k1=1; k1<=(nlstate);k1++){
               for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                 if(l1==k1) continue;
                 i=(k1-1)*(nlstate+ndeath)+l1;
                 if(i<=j) continue;
                 for (age=bage; age<=fage; age ++){ 
                   if ((int)age %5==0){
                     v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                     v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     mu1=mu[i][(int) age]/stepm*YEARM ;
                     mu2=mu[j][(int) age]/stepm*YEARM;
                     c12=cv12/sqrt(v1*v2);
                     /* Computing eigen value of matrix of covariance */
                     lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     if ((lc2 <0) || (lc1 <0) ){
                       if(first2==1){
                         first1=0;
                       printf("Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS. See log file for details...\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);
                       }
                       fprintf(ficlog,"Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS.\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);fflush(ficlog);
                       /* lc1=fabs(lc1); */ /* If we want to have them positive */
                       /* lc2=fabs(lc2); */
                     }
   
                     /* Eigen vectors */
                     v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                     /*v21=sqrt(1.-v11*v11); *//* error */
                     v21=(lc1-v1)/cv12*v11;
                     v12=-v21;
                     v22=v11;
                     tnalp=v21/v11;
                     if(first1==1){
                       first1=0;
                       printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     }
                     fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     /*printf(fignu*/
                     /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                     /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                     if(first==1){
                       first=0;
                       fprintf(ficgp,"\nset parametric;unset label");
                       fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
                       fprintf(ficgp,"\nset ter png small size 320, 240");
                       fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
    :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
   %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }else{
                       first=0;
                       fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }/* if first */
                   } /* age mod 5 */
                 } /* end loop age */
                 fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                 first=1;
               } /*l12 */
             } /* k12 */
           } /*l1 */
         }/* k1 */
         /* } /* loop covariates */
     }
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
     free_vector(xp,1,npar);
     fclose(ficresprob);
     fclose(ficresprobcov);
     fclose(ficresprobcor);
     fflush(ficgp);
     fflush(fichtmcov);
   }
   
   
   /******************* Printing html file ***********/
   void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                     int popforecast, int estepm ,\
                     double jprev1, double mprev1,double anprev1, \
                     double jprev2, double mprev2,double anprev2){
     int jj1, k1, i1, cpt;
   
      fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
      <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
   </ul>");
      fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
    - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
              jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
      fprintf(fichtm,"\
    - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
              stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
      fprintf(fichtm,"\
    - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
              subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
      fprintf(fichtm,"\
    - (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n",
              estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
      fprintf(fichtm,"\
    - Population projections by age and states: \
      <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
   
   fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
    m=pow(2,cptcoveff);
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        /* Pij */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d_1.png\">%s%d_1.png</a><br> \
   <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
        /* Quasi-incidences */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
    before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d_2.png\">%s%d_2.png</a><br> \
   <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
          /* Period (stable) prevalence in each health state */
          for(cpt=1; cpt<=nlstate;cpt++){
            fprintf(fichtm,"<br>- Convergence from each state (1 to %d) to period (stable) prevalence in state %d <a href=\"%s%d_%d.png\">%s%d_%d.png</a><br> \
   <img src=\"%s%d_%d.png\">",nlstate, cpt, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
          }
        for(cpt=1; cpt<=nlstate;cpt++) {
           fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
   <img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
        }
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
   
   
    fprintf(fichtm,"\
   \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
    - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
   
    fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
    fprintf(fichtm,"\
    - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
   
    fprintf(fichtm,"\
    - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
    fprintf(fichtm,"\
    - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
            estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
    fprintf(fichtm,"\
    - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",
            estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
    fprintf(fichtm,"\
    - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
            subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   
   /*  if(popforecast==1) fprintf(fichtm,"\n */
   /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
   /*      <br>",fileres,fileres,fileres,fileres); */
   /*  else  */
   /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
    fflush(fichtm);
    fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   
    m=pow(2,cptcoveff);
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        for(cpt=1; cpt<=nlstate;cpt++) {
          fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
   prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
   <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
        }
        fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
   true period expectancies (those weighted with period prevalences are also\
    drawn in addition to the population based expectancies computed using\
    observed and cahotic prevalences: %s%d.png<br>\
   <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
    fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m0,cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
     int ng=0;
   /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   /*     printf("Problem with file %s",optionfilegnuplot); */
   /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   /*   } */
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
     m=pow(2,cptcoveff);
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
    /* 1eme*/
     fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
     for (cpt=1; cpt<= nlstate ; cpt ++) {
       for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
        fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
        fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
        fprintf(ficgp,"set xlabel \"Age\" \n\
   set ylabel \"Probability\" \n\
   set ter png small size 320, 240\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else        fprintf(ficgp," \%%*lf (\%%*lf)");
        }
        fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        } 
        fprintf(ficgp,"\" t\"95\%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }  
        fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
      }
     }
     /*2 eme*/
     fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
     for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
       fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
       
       for (i=1; i<= nlstate+1 ; i ++) {
         k=2*i;
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         fprintf(ficgp,"\" t\"\" w l lt 0,");
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
         else fprintf(ficgp,"\" t\"\" w l lt 0,");
       }
     }
     
     /*3eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<= nlstate ; cpt ++) {
         /*       k=2+nlstate*(2*cpt-2); */
         k=2+(nlstate+1)*(cpt-1);
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
         fprintf(ficgp,"set ter png small size 320, 240\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           
         */
         for (i=1; i< nlstate ; i ++) {
           fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1);
           /*      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
           
         } 
         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
       }
     }
     
     /* CV preval stable (period) */
     for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
         k=3;
         fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
         fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   set ter png small size 320, 240\n\
   unset log y\n\
   plot [%.f:%.f]  ", ageminpar, agemaxpar);
         for (i=1; i<= nlstate ; i ++){
           if(i==1)
             fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
           else
             fprintf(ficgp,", '' ");
           l=(nlstate+ndeath)*(i-1)+1;
           fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
           for (j=1; j<= (nlstate-1) ; j ++)
             fprintf(ficgp,"+$%d",k+l+j);
           fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
         } /* nlstate */
         fprintf(ficgp,"\n");
       } /* end cpt state*/ 
     } /* end covariate */  
     
     /* proba elementaires */
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             jk++; 
             fprintf(ficgp,"\n");
           }
         }
       }
      }
     /*goto avoid;*/
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        for(jk=1; jk <=m; jk++) {
          fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
          if (ng==2)
            fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
          else
            fprintf(ficgp,"\nset title \"Probability\"\n");
          fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
          for(k2=1; k2<=nlstate; k2++) {
            k3=i;
            for(k=1; k<=(nlstate+ndeath); k++) {
              if (k != k2){
                if(ng==2)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                else
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;/* To be checked else nbcode[0][0] wrong */
                for(j=3; j <=ncovmodel; j++) {
                  /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /\* Bug valgrind *\/ */
                  /*        /\*fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);*\/ */
                  /*        ij++; */
                  /* } */
                  /* else */
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
                fprintf(ficgp,")/(1");
                
                for(k1=1; k1 <=nlstate; k1++){   
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
                  for(j=3; j <=ncovmodel; j++){
                    /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { */
                    /*   fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); */
                    /*   ij++; */
                    /* } */
                    /* else */
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                  }
                  fprintf(ficgp,")");
                }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
              }
            } /* end k */
          } /* end k2 */
        } /* end jk */
      } /* end ng */
    avoid:
      fflush(ficgp); 
   }  /* end gnuplot */
   
   
   /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
     int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
     double age;
   
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          we use a 5 terms etc. until the borders are no more concerned. 
       */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
           }
         }/* end age */
       }/* end mob */
     }else return -1;
     return 0;
   }/* End movingaverage */
   
   
   /************** Forecasting ******************/
   prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
     int *popage;
     double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   
   
   /**************** function prwizard **********************/
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     /* Wizard to print covariance matrix template */
   
     char ca[32], cb[32], cc[32];
     int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
   } /* end of prwizard */
   /******************* Gompertz Likelihood ******************************/
   double gompertz(double x[])
   { 
     double A,B,L=0.0,sump=0.,num=0.;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
   
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
                +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           L=L+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
    
     return -2*L*num/sump;
   }
   
   #ifdef GSL
   /******************* Gompertz_f Likelihood ******************************/
   double gompertz_f(const gsl_vector *v, void *params)
   { 
     double A,B,LL=0.0,sump=0.,num=0.;
     double *x= (double *) v->data;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
     printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
                +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           LL=LL+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
     printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
    
     return -2*LL*num/sump;
   }
   #endif
   
   /******************* Printing html file ***********/
   void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,  double p[],double **matcov,double agemortsup){
     int i,k;
   
     fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
     fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
     for (i=1;i<=2;i++) 
       fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
     fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
     fprintf(fichtm,"</ul>");
   
   fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
   
    fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
   
    for (k=agegomp;k<(agemortsup-2);k++) 
      fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
   
    
     fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
     fprintf(ficgp,"set out \"graphmort.png\"\n "); 
     fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
     fprintf(ficgp, "set ter png small size 320, 240\n set log y\n"); 
     /* fprintf(ficgp, "set size 0.65,0.65\n"); */
     fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
   
   } 
   
   int readdata(char datafile[], int firstobs, int lastobs, int *imax)
   {
   
     /*-------- data file ----------*/
     FILE *fic;
     char dummy[]="                         ";
     int i, j, n;
     int linei, month, year,iout;
     char line[MAXLINE], linetmp[MAXLINE];
     char stra[80], strb[80];
     char *stratrunc;
     int lstra;
   
   
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem while opening datafile: %s\n", datafile);return 1;
       fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
     }
   
     i=1;
     linei=0;
     while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
       linei=linei+1;
       for(j=strlen(line); j>=0;j--){  /* Untabifies line */
         if(line[j] == '\t')
           line[j] = ' ';
       }
       for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
         ;
       };
       line[j+1]=0;  /* Trims blanks at end of line */
       if(line[0]=='#'){
         fprintf(ficlog,"Comment line\n%s\n",line);
         printf("Comment line\n%s\n",line);
         continue;
       }
       trimbb(linetmp,line); /* Trims multiple blanks in line */
       for (j=0; line[j]!='\0';j++){
         line[j]=linetmp[j];
       }
     
   
       for (j=maxwav;j>=1;j--){
         cutv(stra, strb, line, ' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
         /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
             fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);
             return 1;
           }
         }
         s[j][i]=lval;
         
         strcpy(line,stra);
         cutv(stra, strb,line,' ');
         if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
         }
         else  if(iout=sscanf(strb,"%s.",dummy) != 0){
           month=99;
           year=9999;
         }else{
           printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);fflush(ficlog);
           return 1;
         }
         anint[j][i]= (double) year; 
         mint[j][i]= (double)month; 
         strcpy(line,stra);
       } /* ENd Waves */
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.",dummy) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
       }
       andc[i]=(double) year; 
       moisdc[i]=(double) month; 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.", dummy) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
       }
       if (year==9999) {
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given.  Exiting.\n",strb, linei,i,line);
         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
   
       }
       annais[i]=(double)(year);
       moisnais[i]=(double)(month); 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       errno=0;
       dval=strtod(strb,&endptr); 
       if( strb[0]=='\0' || (*endptr != '\0')){
         printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fprintf(ficlog,"Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fflush(ficlog);
         return 1;
       }
       weight[i]=dval; 
       strcpy(line,stra);
       
       for (j=ncovcol;j>=1;j--){
         cutv(stra, strb,line,' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);
             fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);fflush(ficlog);
             return 1;
           }
         }
         if(lval <-1 || lval >1){
           printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);
           fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
           return 1;
         }
         covar[j][i]=(double)(lval);
         strcpy(line,stra);
       }  
       lstra=strlen(stra);
        
       if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
         stratrunc = &(stra[lstra-9]);
         num[i]=atol(stratrunc);
       }
       else
         num[i]=atol(stra);
       /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
         printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
       
       i=i+1;
     } /* End loop reading  data */
   
     *imax=i-1; /* Number of individuals */
     fclose(fic);
    
     return (0);
     endread:
       printf("Exiting readdata: ");
       fclose(fic);
       return (1);
   
   
   
   }
   void removespace(char *str) {
     char *p1 = str, *p2 = str;
     do
       while (*p2 == ' ')
         p2++;
     while (*p1++ = *p2++);
   }
   
   int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
      * Model  V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age
      * - cptcovt total number of covariates of the model nbocc(+)+1 = 8
      * - cptcovn or number of covariates k of the models excluding age*products =6
      * - cptcovage number of covariates with age*products =2
      * - cptcovs number of simple covariates
      * - Tvar[k] is the id of the kth covariate Tvar[1]@12 {1, 2, 3, 8, 10, 11, 8, 3, 7, 8, 5, 6}, thus Tvar[5=V7*V8]=10
      *     which is a new column after the 9 (ncovcol) variables. 
      * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
      * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
      *    Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
      * - Tvard[k]  p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
    */
   {
     int i, j, k, ks;
     int i1, j1, k1, k2;
     char modelsav[80];
     char stra[80], strb[80], strc[80], strd[80],stre[80];
   
     /*removespace(model);*/
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
       j=nbocc(model,'+'); /**< j=Number of '+' */
       j1=nbocc(model,'*'); /**< j1=Number of '*' */
       cptcovs=j+1-j1; /**<  Number of simple covariates V1+V2*age+V3 +V3*V4=> V1 + V3 =2  */
       cptcovt= j+1; /* Number of total covariates in the model V1 + V2*age+ V3 + V3*V4=> 4*/
                     /* including age products which are counted in cptcovage.
                     /* but the covariates which are products must be treated separately: ncovn=4- 2=2 (V1+V3). */
       cptcovprod=j1; /**< Number of products  V1*V2 +v3*age = 2 */
       cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1  */
       strcpy(modelsav,model); 
       if (strstr(model,"AGE") !=0){
         printf("Error. AGE must be in lower case 'age' model=%s ",model);
         fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
         return 1;
       }
       if (strstr(model,"v") !=0){
         printf("Error. 'v' must be in upper case 'V' model=%s ",model);
         fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
         return 1;
       }
       
       /*   Design
        *  V1   V2   V3   V4  V5  V6  V7  V8  V9 Weight
        *  <          ncovcol=8                >
        * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
        *   k=  1    2      3       4     5       6      7        8
        *  cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
        *  covar[k,i], value of kth covariate if not including age for individual i:
        *       covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
        *  Tvar[k] # of the kth covariate:  Tvar[1]=2  Tvar[4]=3 Tvar[8]=8
        *       if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and 
        *  Tage[++cptcovage]=k
        *       if products, new covar are created after ncovcol with k1
        *  Tvar[k]=ncovcol+k1; # of the kth covariate product:  Tvar[5]=ncovcol+1=10  Tvar[6]=ncovcol+1=11
        *  Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
        *  Tvard[k1][1]=m Tvard[k1][2]=m; Tvard[1][1]=5 (V5) Tvard[1][2]=6 Tvard[2][1]=7 (V7) Tvard[2][2]=8
        *  Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
        *  Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
        *  V1   V2   V3   V4  V5  V6  V7  V8  V9  V10  V11
        *  <          ncovcol=8                >
        *       Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8    d1   d1   d2  d2
        *          k=  1    2      3       4     5       6      7        8    9   10   11  12
        *     Tvar[k]= 2    1      3       3    10      11      8        8    5    6    7   8
        * p Tvar[1]@12={2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
        * p Tprod[1]@2={                         6, 5}
        *p Tvard[1][1]@4= {7, 8, 5, 6}
        * covar[k][i]= V2   V1      ?      V3    V5*V6?   V7*V8?  ?       V8   
        *  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
        *How to reorganize?
        * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
        * Tvars {2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
        *       {2,   1,     4,      8,    5,      6,     3,       7}
        * Struct []
        */
   
       /* This loop fills the array Tvar from the string 'model'.*/
       /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
       /*   modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4  */
       /*  k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
       /*  k=3 V4 Tvar[k=3]= 4 (from V4) */
       /*  k=2 V1 Tvar[k=2]= 1 (from V1) */
       /*  k=1 Tvar[1]=2 (from V2) */
       /*  k=5 Tvar[5] */
       /* for (k=1; k<=cptcovn;k++) { */
       /*  cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
       /*  } */
       /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
       /*
        * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
       for(k=cptcovt; k>=1;k--) /**< Number of covariates */
           Tvar[k]=0;
       cptcovage=0;
       for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
         cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' 
                                        modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
           cutl(strc,strd,strb,'*'); /**< strd*strc  Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
           if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
             /* covar is not filled and then is empty */
             cptcovprod--;
             cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
             Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2 */
             cptcovage++; /* Sums the number of covariates which include age as a product */
             Tage[cptcovage]=k;  /* Tage[1] = 4 */
             /*printf("stre=%s ", stre);*/
           } else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutl(stre,strb,strc,'V');
             Tvar[k]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=k;
           } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/
             /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
             cptcovn++;
             cptcovprodnoage++;k1++;
             cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
             Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
                                     because this model-covariate is a construction we invent a new column
                                     ncovcol + k1
                                     If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
                                     Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
             cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */
             Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
             Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
             k2=k2+2;
             Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
             Tvar[cptcovt+k2+1]=Tvard[k1][2];  /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
             for (i=1; i<=lastobs;i++){
               /* Computes the new covariate which is a product of
                  covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
               covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
             }
           } /* End age is not in the model */
         } /* End if model includes a product */
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
           cutl(strd,strc,strb,'V');
           ks++; /**< Number of simple covariates */
           cptcovn++;
           Tvar[k]=atoi(strd);
         }
         strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+V1+V4 */ 
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);*/
   
   
     return (0); /* with covar[new additional covariate if product] and Tage if age */ 
     endread:
       printf("Exiting decodemodel: ");
       return (1);
   }
   
   calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
   {
     int i, m;
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           *nberr++;
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           *nberr++;
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if ((int)andc[i]!=9999){
                   nbwarn++;
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] < *agemin){ 
               *agemin=agev[m][i];
               printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
             }
             else if(agev[m][i] >*agemax){
               *agemax=agev[m][i];
               /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           *nberr++;
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           return 1;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax); 
   
     return (0);
     endread:
       printf("Exiting calandcheckages: ");
       return (1);
   }
   
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
   #ifdef GSL
     const gsl_multimin_fminimizer_type *T;
     size_t iteri = 0, it;
     int rval = GSL_CONTINUE;
     int status = GSL_SUCCESS;
     double ssval;
   #endif
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
     int linei, month, year,iout;
     int jj, ll, li, lj, lk, imk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int itimes;
     int NDIM=2;
     int vpopbased=0;
   
     char ca[32], cb[32], cc[32];
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     struct stat info;
     double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE], pathimach[MAXLINE]; 
     char **bp, *tok, *val; /* pathtot */
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,*tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     int agemortsup;
     float  sumlpop=0.;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
     double **ximort;
     char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
     int *dcwave;
   
     char z[1]="c", occ;
   
     /*char  *strt;*/
     char strtend[80];
   
     long total_usecs;
    
   /*   setlocale (LC_ALL, ""); */
   /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   /*   textdomain (PACKAGE); */
   /*   setlocale (LC_CTYPE, ""); */
   /*   setlocale (LC_MESSAGES, ""); */
   
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     rstart_time = time(NULL);  
     /*  (void) gettimeofday(&start_time,&tzp);*/
     start_time = *localtime(&rstart_time);
     curr_time=start_time;
     /*tml = *localtime(&start_time.tm_sec);*/
     /* strcpy(strstart,asctime(&tml)); */
     strcpy(strstart,asctime(&start_time));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tm_sec = tp.tm_sec +86400; */
   /*  tm = *localtime(&start_time.tm_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tm_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     nberr=0; /* Number of errors and warnings */
     nbwarn=0;
     getcwd(pathcd, size);
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       fgets(pathr,FILENAMELENGTH,stdin);
       i=strlen(pathr);
       if(pathr[i-1]=='\n')
         pathr[i-1]='\0';
       i=strlen(pathr);
       if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
         pathr[i-1]='\0';
      for (tok = pathr; tok != NULL; ){
         printf("Pathr |%s|\n",pathr);
         while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
         printf("val= |%s| pathr=%s\n",val,pathr);
         strcpy (pathtot, val);
         if(pathr[0] == '\0') break; /* Dirty */
       }
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     /* Split argv[0], imach program to get pathimach */
     printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
     split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
     printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
    /*   strcpy(pathimach,argv[0]); */
     /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path); /* Can be a relative path */
     if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
       printf("Current directory %s!\n",pathcd);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s\n%s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: \n");
     fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     printf("Local time (at start):%s",strstart);
     fprintf(ficlog,"Local time (at start): %s",strstart);
     fflush(ficlog);
   /*   (void) gettimeofday(&curr_time,&tzp); */
   /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
       fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
       fflush(ficlog);
       /* goto end; */
       exit(70); 
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       fputs(line,stdout);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       fputs(line, stdout);
       //puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n);  /**< used in readdata */
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
     /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
        v1+v2*age+v2*v3 makes cptcovn = 3
     */
     if (strlen(model)>1) 
       ncovmodel=2+nbocc(model,'+')+1; /*Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7*/
     else
       ncovmodel=2;
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
     npar= nforce*ncovmodel; /* Number of parameters like aij*/
     if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
       printf("Too complex model for current IMaCh: npar=(nlstate+ndeath-1)*nlstate*ncovmodel=%d >= %d(MAXPARM) or nlstate=%d >= %d(NLSTATEMAX) or ndeath=%d >= %d(NDEATHMAX) or ncovmodel=(k+age+#of+signs)=%d(NCOVMAX) >= %d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fprintf(ficlog,"Too complex model for current IMaCh: %d >=%d(MAXPARM) or %d >=%d(NLSTATEMAX) or %d >=%d(NDEATHMAX) or %d(NCOVMAX) >=%d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fflush(stdout);
       fclose (ficlog);
       goto end;
     }
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     delti=delti3[1][1];
     /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
     if(mle==-1){ /* Print a wizard for help writing covariance matrix */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       fclose (ficparo);
       fclose (ficlog);
       goto end;
       exit(0);
     }
     else if(mle==-3) {
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       matcov=matrix(1,npar,1,npar);
     }
     else{
       /* Read guessed parameters */
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
       
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       for(i=1; i <=nlstate; i++){
         j=0;
         for(jj=1; jj <=nlstate+ndeath; jj++){
           if(jj==i) continue;
           j++;
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1 != i) && (j1 != j)){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
   It might be a problem of design; if ncovcol and the model are correct\n \
   run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           fprintf(ficparo,"%1d%1d",i1,j1);
           if(mle==1)
             printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar," %lf",&param[i][j][k]);
             if(mle==1){
               printf(" %lf",param[i][j][k]);
               fprintf(ficlog," %lf",param[i][j][k]);
             }
             else
               fprintf(ficlog," %lf",param[i][j][k]);
             fprintf(ficparo," %lf",param[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           if(mle==1)
             printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficparo,"\n");
         }
       }  
       fflush(ficlog);
   
       /* Reads scales values */
       p=param[1][1];
       
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
   
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath-1; j++){
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1-i)*(j1-j)!=0){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           printf("%1d%1d",i,j);
           fprintf(ficparo,"%1d%1d",i1,j1);
           fprintf(ficlog,"%1d%1d",i1,j1);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar,"%le",&delti3[i][j][k]);
             printf(" %le",delti3[i][j][k]);
             fprintf(ficparo," %le",delti3[i][j][k]);
             fprintf(ficlog," %le",delti3[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           printf("\n");
           fprintf(ficparo,"\n");
           fprintf(ficlog,"\n");
         }
       }
       fflush(ficlog);
   
       /* Reads covariance matrix */
       delti=delti3[1][1];
   
   
       /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
     
       matcov=matrix(1,npar,1,npar);
       for(i=1; i <=npar; i++)
         for(j=1; j <=npar; j++) matcov[i][j]=0.;
         
       for(i=1; i <=npar; i++){
         fscanf(ficpar,"%s",str);
         if(mle==1)
           printf("%s",str);
         fprintf(ficlog,"%s",str);
         fprintf(ficparo,"%s",str);
         for(j=1; j <=i; j++){
           fscanf(ficpar," %le",&matcov[i][j]);
           if(mle==1){
             printf(" %.5le",matcov[i][j]);
           }
           fprintf(ficlog," %.5le",matcov[i][j]);
           fprintf(ficparo," %.5le",matcov[i][j]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
       for(i=1; i <=npar; i++)
         for(j=i+1;j<=npar;j++)
           matcov[i][j]=matcov[j][i];
       
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       
       fflush(ficlog);
       
       /*-------- Rewriting parameter file ----------*/
       strcpy(rfileres,"r");    /* "Rparameterfile */
       strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
       strcat(rfileres,".");    /* */
       strcat(rfileres,optionfilext);    /* Other files have txt extension */
       if((ficres =fopen(rfileres,"w"))==NULL) {
         printf("Problem writing new parameter file: %s\n", fileres);goto end;
         fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
       }
       fprintf(ficres,"#%s\n",version);
     }    /* End of mle != -3 */
   
   
     n= lastobs;
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */ 
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
   
     /* Reads data from file datafile */
     if (readdata(datafile, firstobs, lastobs, &imx)==1)
       goto end;
   
     /* Calculation of the number of parameters from char model */
       /*    modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 
           k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
           k=3 V4 Tvar[k=3]= 4 (from V4)
           k=2 V1 Tvar[k=2]= 1 (from V1)
           k=1 Tvar[1]=2 (from V2)
       */
     Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
     /*  V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs). 
         For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4, 
         Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
     */
     /* For model-covariate k tells which data-covariate to use but
       because this model-covariate is a construction we invent a new column
       ncovcol + k1
       If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
       Tvar[3=V1*V4]=4+1 etc */
     Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
     /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
        if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2)
     */
     Tvaraff=ivector(1,NCOVMAX); /* Unclear */
     Tvard=imatrix(1,NCOVMAX,1,2); /* n=Tvard[k1][1]  and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm
                               * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd. 
                               * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
     Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
                            4 covariates (3 plus signs)
                            Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
                         */  
   
     if(decodemodel(model, lastobs) == 1)
       goto end;
   
     if((double)(lastobs-imx)/(double)imx > 1.10){
       nbwarn++;
       printf("Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
       fprintf(ficlog,"Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
     }
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
       for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
     }
   
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
       goto end;
   
   
     agegomp=(int)agemin;
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
     /* */
     
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
     /* */
    
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     Ndum =ivector(-1,NCOVMAX);  
     if (ncovmodel > 2)
       tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
   
     codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
     /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
     h=0;
   
   
     /*if (cptcovn > 0) */
         
    
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
       for(i=1; i <=pow(2,cptcoveff-k);i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */ 
         for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
           for(cpt=1; cpt <=pow(2,k-1); cpt++){  /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */ 
             h++;
             if (h>m) 
               h=1;
             /**< codtab(h,k)  k   = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
              *     h     1     2     3     4
              *______________________________  
              *     1 i=1 1 i=1 1 i=1 1 i=1 1
              *     2     2     1     1     1
              *     3 i=2 1     2     1     1
              *     4     2     2     1     1
              *     5 i=3 1 i=2 1     2     1
              *     6     2     1     2     1
              *     7 i=4 1     2     2     1
              *     8     2     2     2     1
              *     9 i=5 1 i=3 1 i=2 1     1
              *    10     2     1     1     1
              *    11 i=6 1     2     1     1
              *    12     2     2     1     1
              *    13 i=7 1 i=4 1     2     1    
              *    14     2     1     2     1
              *    15 i=8 1     2     2     1
              *    16     2     2     2     1
              */
             codtab[h][k]=j;
             /*codtab[h][Tvar[k]]=j;*/
             printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]);
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
          printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
   
    free_ivector(Ndum,-1,NCOVMAX);
   
   
       
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     if(mle==-3)
       strcat(optionfilegnuplot,"-mort");
     strcat(optionfilegnuplot,".gp");
   
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       //fprintf(ficgp,"set missing 'NaNq'\n");
       fprintf(ficgp,"set datafile missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname); /* Main html file */
     if(mle==-3)
       strcat(optionfilehtm,"-mort");
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm);
       exit(0);
     }
   
     strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
     strcat(optionfilehtmcov,"-cov.htm");
     if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtmcov), exit(0);
     }
     else{
     fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
             optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
    - Log file of the run: <a href=\"%s\">%s</a><br>\n\
    - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
    - Date and time at start: %s</ul>\n",\
             optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
             optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
             fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
     chdir(optionfilefiname); /* Move to directory named optionfile */
     
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
   
     fprintf(fichtm,"\n");
     fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
             imx,agemin,agemax,jmin,jmax,jmean);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
   
     if (mle==-3){
       ximort=matrix(1,NDIM,1,NDIM); 
   /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
       cens=ivector(1,n);
       ageexmed=vector(1,n);
       agecens=vector(1,n);
       dcwave=ivector(1,n);
    
       for (i=1; i<=imx; i++){
         dcwave[i]=-1;
         for (m=firstpass; m<=lastpass; m++)
           if (s[m][i]>nlstate) {
             dcwave[i]=m;
             /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
             break;
           }
       }
   
       for (i=1; i<=imx; i++) {
         if (wav[i]>0){
           ageexmed[i]=agev[mw[1][i]][i];
           j=wav[i];
           agecens[i]=1.; 
   
           if (ageexmed[i]> 1 && wav[i] > 0){
             agecens[i]=agev[mw[j][i]][i];
             cens[i]= 1;
           }else if (ageexmed[i]< 1) 
             cens[i]= -1;
           if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
             cens[i]=0 ;
         }
         else cens[i]=-1;
       }
       
       for (i=1;i<=NDIM;i++) {
         for (j=1;j<=NDIM;j++)
           ximort[i][j]=(i == j ? 1.0 : 0.0);
       }
       
       /*p[1]=0.0268; p[NDIM]=0.083;*/
       /*printf("%lf %lf", p[1], p[2]);*/
       
       
   #ifdef GSL
       printf("GSL optimization\n");  fprintf(ficlog,"Powell\n");
   #elsedef
       printf("Powell\n");  fprintf(ficlog,"Powell\n");
   #endif
       strcpy(filerespow,"pow-mort"); 
       strcat(filerespow,fileres);
       if((ficrespow=fopen(filerespow,"w"))==NULL) {
         printf("Problem with resultfile: %s\n", filerespow);
         fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
       }
   #ifdef GSL
       fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
   #elsedef
       fprintf(ficrespow,"# Powell\n# iter -2*LL");
   #endif
       /*  for (i=1;i<=nlstate;i++)
           for(j=1;j<=nlstate+ndeath;j++)
           if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       */
       fprintf(ficrespow,"\n");
   #ifdef GSL
       /* gsl starts here */ 
       T = gsl_multimin_fminimizer_nmsimplex;
       gsl_multimin_fminimizer *sfm = NULL;
       gsl_vector *ss, *x;
       gsl_multimin_function minex_func;
   
       /* Initial vertex size vector */
       ss = gsl_vector_alloc (NDIM);
       
       if (ss == NULL){
         GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
       }
       /* Set all step sizes to 1 */
       gsl_vector_set_all (ss, 0.001);
   
       /* Starting point */
       
       x = gsl_vector_alloc (NDIM);
       
       if (x == NULL){
         gsl_vector_free(ss);
         GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
       }
     
       /* Initialize method and iterate */
       /*     p[1]=0.0268; p[NDIM]=0.083; */
   /*     gsl_vector_set(x, 0, 0.0268); */
   /*     gsl_vector_set(x, 1, 0.083); */
       gsl_vector_set(x, 0, p[1]);
       gsl_vector_set(x, 1, p[2]);
   
       minex_func.f = &gompertz_f;
       minex_func.n = NDIM;
       minex_func.params = (void *)&p; /* ??? */
       
       sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
       gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
       
       printf("Iterations beginning .....\n\n");
       printf("Iter. #    Intercept       Slope     -Log Likelihood     Simplex size\n");
   
       iteri=0;
       while (rval == GSL_CONTINUE){
         iteri++;
         status = gsl_multimin_fminimizer_iterate(sfm);
         
         if (status) printf("error: %s\n", gsl_strerror (status));
         fflush(0);
         
         if (status) 
           break;
         
         rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
         ssval = gsl_multimin_fminimizer_size (sfm);
         
         if (rval == GSL_SUCCESS)
           printf ("converged to a local maximum at\n");
         
         printf("%5d ", iteri);
         for (it = 0; it < NDIM; it++){
           printf ("%10.5f ", gsl_vector_get (sfm->x, it));
         }
         printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
       }
       
       printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
       
       gsl_vector_free(x); /* initial values */
       gsl_vector_free(ss); /* inital step size */
       for (it=0; it<NDIM; it++){
         p[it+1]=gsl_vector_get(sfm->x,it);
         fprintf(ficrespow," %.12lf", p[it]);
       }
       gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1)  */
   #endif
   #ifdef POWELL
        powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
   #endif  
       fclose(ficrespow);
       
       hesscov(matcov, p, NDIM, delti, 1e-4, gompertz); 
   
       for(i=1; i <=NDIM; i++)
         for(j=i+1;j<=NDIM;j++)
           matcov[i][j]=matcov[j][i];
       
       printf("\nCovariance matrix\n ");
       for(i=1; i <=NDIM; i++) {
         for(j=1;j<=NDIM;j++){ 
           printf("%f ",matcov[i][j]);
         }
         printf("\n ");
       }
       
       printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
       for (i=1;i<=NDIM;i++) 
         printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
   
       lsurv=vector(1,AGESUP);
       lpop=vector(1,AGESUP);
       tpop=vector(1,AGESUP);
       lsurv[agegomp]=100000;
       
       for (k=agegomp;k<=AGESUP;k++) {
         agemortsup=k;
         if (p[1]*exp(p[2]*(k-agegomp))>1) break;
       }
       
       for (k=agegomp;k<agemortsup;k++)
         lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
       
       for (k=agegomp;k<agemortsup;k++){
         lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
         sumlpop=sumlpop+lpop[k];
       }
       
       tpop[agegomp]=sumlpop;
       for (k=agegomp;k<(agemortsup-3);k++){
         /*  tpop[k+1]=2;*/
         tpop[k+1]=tpop[k]-lpop[k];
       }
       
       
       printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
       for (k=agegomp;k<(agemortsup-2);k++) 
         printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
       
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
                        stepm, weightopt,\
                        model,imx,p,matcov,agemortsup);
       
       free_vector(lsurv,1,AGESUP);
       free_vector(lpop,1,AGESUP);
       free_vector(tpop,1,AGESUP);
   #ifdef GSL
       free_ivector(cens,1,n);
       free_vector(agecens,1,n);
       free_ivector(dcwave,1,n);
       free_matrix(ximort,1,NDIM,1,NDIM);
   #endif
     } /* Endof if mle==-3 */
     
     else{ /* For mle >=1 */
       globpr=0;/* debug */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       globpr=1; /* to print the contributions */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       if(mle>=1){ /* Could be 1 or 2 */
         mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
       }
       
       /*--------- results files --------------*/
       fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
       
       
       fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(k=1; k <=(nlstate+ndeath); k++){
           if (k != i) {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%lf ",p[jk]);
               fprintf(ficlog,"%lf ",p[jk]);
               fprintf(ficres,"%lf ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       if(mle!=0){
         /* Computing hessian and covariance matrix */
         ftolhess=ftol; /* Usually correct */
         hesscov(matcov, p, npar, delti, ftolhess, func);
       }
       fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
       printf("# Scales (for hessian or gradient estimation)\n");
       fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if (j!=i) {
             fprintf(ficres,"%1d%1d",i,j);
             printf("%1d%1d",i,j);
             fprintf(ficlog,"%1d%1d",i,j);
             for(k=1; k<=ncovmodel;k++){
               printf(" %.5e",delti[jk]);
               fprintf(ficlog," %.5e",delti[jk]);
               fprintf(ficres," %.5e",delti[jk]);
               jk++;
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       
       fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       if(mle>=1)
         printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       /* # 121 Var(a12)\n\ */
       /* # 122 Cov(b12,a12) Var(b12)\n\ */
       /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
       /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
       /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
       /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
       /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
       /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
       
       
       /* Just to have a covariance matrix which will be more understandable
          even is we still don't want to manage dictionary of variables
       */
       for(itimes=1;itimes<=2;itimes++){
         jj=0;
         for(i=1; i <=nlstate; i++){
           for(j=1; j <=nlstate+ndeath; j++){
             if(j==i) continue;
             for(k=1; k<=ncovmodel;k++){
               jj++;
               ca[0]= k+'a'-1;ca[1]='\0';
               if(itimes==1){
                 if(mle>=1)
                   printf("#%1d%1d%d",i,j,k);
                 fprintf(ficlog,"#%1d%1d%d",i,j,k);
                 fprintf(ficres,"#%1d%1d%d",i,j,k);
               }else{
                 if(mle>=1)
                   printf("%1d%1d%d",i,j,k);
                 fprintf(ficlog,"%1d%1d%d",i,j,k);
                 fprintf(ficres,"%1d%1d%d",i,j,k);
               }
               ll=0;
               for(li=1;li <=nlstate; li++){
                 for(lj=1;lj <=nlstate+ndeath; lj++){
                   if(lj==li) continue;
                   for(lk=1;lk<=ncovmodel;lk++){
                     ll++;
                     if(ll<=jj){
                       cb[0]= lk +'a'-1;cb[1]='\0';
                       if(ll<jj){
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }else{
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }
                     }
                   } /* end lk */
                 } /* end lj */
               } /* end li */
               if(mle>=1)
                 printf("\n");
               fprintf(ficlog,"\n");
               fprintf(ficres,"\n");
               numlinepar++;
             } /* end k*/
           } /*end j */
         } /* end i */
       } /* end itimes */
       
       fflush(ficlog);
       fflush(ficres);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       estepm=0;
       fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
       if (estepm==0 || estepm < stepm) estepm=stepm;
       if (fage <= 2) {
         bage = ageminpar;
         fage = agemaxpar;
       }
       
       fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
       fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
       fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       
       dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
       dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
       
       fscanf(ficpar,"pop_based=%d\n",&popbased);
       fprintf(ficparo,"pop_based=%d\n",popbased);   
       fprintf(ficres,"pop_based=%d\n",popbased);   
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
       fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       /* day and month of proj2 are not used but only year anproj2.*/
       
       
       
        /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
       /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                    model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                    jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
         
      /*------------ free_vector  -------------*/
      /*  chdir(path); */
    
       free_ivector(wav,1,imx);
       free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
       free_lvector(num,1,n);
       free_vector(agedc,1,n);
       /*free_matrix(covar,0,NCOVMAX,1,n);*/
       /*free_matrix(covar,1,NCOVMAX,1,n);*/
       fclose(ficparo);
       fclose(ficres);
   
   
       /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
   #include "prevlim.h"  /* Use ficrespl, ficlog */
       fclose(ficrespl);
   
   #ifdef FREEEXIT2
   #include "freeexit2.h"
   #endif
   
       /*------------- h Pij x at various ages ------------*/
   #include "hpijx.h"
       fclose(ficrespij);
   
     /*-------------- Variance of one-step probabilities---*/
       k=1;
       varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
   
   
       probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for(i=1;i<=AGESUP;i++)
         for(j=1;j<=NCOVMAX;j++)
           for(k=1;k<=NCOVMAX;k++)
             probs[i][j][k]=0.;
   
       /*---------- Forecasting ------------------*/
       /*if((stepm == 1) && (strcmp(model,".")==0)){*/
       if(prevfcast==1){
         /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
         /*      }  */
         /*      else{ */
         /*        erreur=108; */
         /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*      } */
       }
     
   
       /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
   
       prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
       /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
           ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
       */
   
       if (mobilav!=0) {
         mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
           fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
           printf(" Error in movingaverage mobilav=%d\n",mobilav);
         }
       }
   
   
       /*---------- Health expectancies, no variances ------------*/
   
       strcpy(filerese,"e");
       strcat(filerese,fileres);
       if((ficreseij=fopen(filerese,"w"))==NULL) {
         printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
         fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       }
       printf("Computing Health Expectancies: result on file '%s' \n", filerese);
       fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficreseij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficreseij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);  
         
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         /*}*/
       }
       fclose(ficreseij);
   
   
       /*---------- Health expectancies and variances ------------*/
   
   
       strcpy(filerest,"t");
       strcat(filerest,fileres);
       if((ficrest=fopen(filerest,"w"))==NULL) {
         printf("Problem with total LE resultfile: %s\n", filerest);goto end;
         fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
       }
       printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
       fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
   
   
       strcpy(fileresstde,"stde");
       strcat(fileresstde,fileres);
       if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
         printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
         fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
       }
       printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
       fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
   
       strcpy(filerescve,"cve");
       strcat(filerescve,fileres);
       if((ficrescveij=fopen(filerescve,"w"))==NULL) {
         printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
         fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
       }
       printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
       fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
   
       strcpy(fileresv,"v");
       strcat(fileresv,fileres);
       if((ficresvij=fopen(fileresv,"w"))==NULL) {
         printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
         fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
       }
       printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
       fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficrest,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrest,"******\n");
   
           fprintf(ficresstdeij,"\n#****** ");
           fprintf(ficrescveij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficresstdeij,"******\n");
           fprintf(ficrescveij,"******\n");
   
           fprintf(ficresvij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);  
           /*
            */
           /* goto endfree; */
    
           vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           pstamp(ficrest);
   
   
           for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
             oldm=oldms;savm=savms; /* Segmentation fault */
             varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart);
             fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");
             if(vpopbased==1)
               fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
             else
               fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
             fprintf(ficrest,"# Age e.. (std) ");
             for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
             fprintf(ficrest,"\n");
   
             epj=vector(1,nlstate+1);
             for(age=bage; age <=fage ;age++){
               prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
               if (vpopbased==1) {
                 if(mobilav ==0){
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=probs[(int)age][i][k];
                 }else{ /* mobilav */ 
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=mobaverage[(int)age][i][k];
                 }
               }
           
               fprintf(ficrest," %4.0f",age);
               for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
                 for(i=1, epj[j]=0.;i <=nlstate;i++) {
                   epj[j] += prlim[i][i]*eij[i][j][(int)age];
                   /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
                 }
                 epj[nlstate+1] +=epj[j];
               }
   
               for(i=1, vepp=0.;i <=nlstate;i++)
                 for(j=1;j <=nlstate;j++)
                   vepp += vareij[i][j][(int)age];
               fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
               for(j=1;j <=nlstate;j++){
                 fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
               }
               fprintf(ficrest,"\n");
             }
           }
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_vector(epj,1,nlstate+1);
         /*}*/
       }
       free_vector(weight,1,n);
       free_imatrix(Tvard,1,NCOVMAX,1,2);
       free_imatrix(s,1,maxwav+1,1,n);
       free_matrix(anint,1,maxwav,1,n); 
       free_matrix(mint,1,maxwav,1,n);
       free_ivector(cod,1,n);
       free_ivector(tab,1,NCOVMAX);
       fclose(ficresstdeij);
       fclose(ficrescveij);
       fclose(ficresvij);
       fclose(ficrest);
       fclose(ficpar);
     
       /*------- Variance of period (stable) prevalence------*/   
   
       strcpy(fileresvpl,"vpl");
       strcat(fileresvpl,fileres);
       if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
         printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
         exit(0);
       }
       printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
   
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficresvpl,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvpl,"******\n");
         
           varpl=matrix(1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
           free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
         /*}*/
       }
   
       fclose(ficresvpl);
   
       /*---------- End : free ----------------*/
       if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
     }  /* mle==-3 arrives here for freeing */
    endfree:
       free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
       free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(covar,0,NCOVMAX,1,n);
       free_matrix(matcov,1,npar,1,npar);
       /*free_vector(delti,1,npar);*/
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       free_matrix(agev,1,maxwav,1,imx);
       free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   
       free_ivector(ncodemax,1,NCOVMAX);
       free_ivector(Tvar,1,NCOVMAX);
       free_ivector(Tprod,1,NCOVMAX);
       free_ivector(Tvaraff,1,NCOVMAX);
       free_ivector(Tage,1,NCOVMAX);
   
       free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
       free_imatrix(codtab,1,100,1,10);
     fflush(fichtm);
     fflush(ficgp);
     
   
     if((nberr >0) || (nbwarn>0)){
       printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
       fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
     }else{
       printf("End of Imach\n");
       fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     /*(void) gettimeofday(&end_time,&tzp);*/
     rend_time = time(NULL);  
     end_time = *localtime(&rend_time);
     /* tml = *localtime(&end_time.tm_sec); */
     strcpy(strtend,asctime(&end_time));
     printf("Local time at start %s\nLocal time at end   %s",strstart, strtend); 
     fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
     printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
   
     printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
     fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
     fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
     /*  printf("Total time was %d uSec.\n", total_usecs);*/
   /*   if(fileappend(fichtm,optionfilehtm)){ */
     fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtm);
     fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtmcov);
     fclose(ficgp);
     fclose(ficlog);
     /*------ End -----------*/
   
   
      printf("Before Current directory %s!\n",pathcd);
      if(chdir(pathcd) != 0)
       printf("Can't move to directory %s!\n",path);
     if(getcwd(pathcd,MAXLINE) > 0)
       printf("Current directory %s!\n",pathcd);
     /*strcat(plotcmd,CHARSEPARATOR);*/
     sprintf(plotcmd,"gnuplot");
   #ifdef _WIN32
     sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
   #endif
     if(!stat(plotcmd,&info)){
       printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
       if(!stat(getenv("GNUPLOTBIN"),&info)){
         printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #ifdef __unix
       strcpy(plotcmd,GNUPLOTPROGRAM);
       if(!stat(plotcmd,&info)){
         printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #endif
     }else
       strcpy(pplotcmd,plotcmd);
     
     sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
     printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
   
     if((outcmd=system(plotcmd)) != 0){
       printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
       printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
       sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
       if((outcmd=system(plotcmd)) != 0)
         printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
     }
     printf(" Successful, please wait...");
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
       scanf("%s",z);
   /*     if (z[0] == 'c') system("./imach"); */
       if (z[0] == 'e') {
   #ifdef __APPLE__
         sprintf(pplotcmd, "open %s", optionfilehtm);
   #elif __linux
         sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
   #else
         sprintf(pplotcmd, "%s", optionfilehtm);
   #endif
         printf("Starting browser with: %s",pplotcmd);fflush(stdout);
         system(pplotcmd);
       }
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     end:
     while (z[0] != 'q') {
       printf("\nType  q for exiting: ");
       scanf("%s",z);
     }
   }

Removed from v.1.20  
changed lines
  Added in v.1.159


FreeBSD-CVSweb <freebsd-cvsweb@FreeBSD.org>