#ifndef COMBRO_INCLUDE
#define COMBRO_INCLUDE
/*------------------------------------------------------
 Maximum likelihood estimation 
 of migration rate  and effectice world size
 using a Metropolis-Hastings Monte Carlo algorithm                            
 -------------------------------------------------------                        
 C O M B I N E   L O C I   R O U T I N E S 
 
 
 
 Peter Beerli 1996, Seattle
 beerli@scs.fsu.edu
 
Copyright 1996-2002 Peter Beerli and Joseph Felsenstein, Seattle WA
Copyright 2003-2004 Peter Beerli, Tallahassee FL
 
$Id: combroyden.h 514 2006-11-09 20:14:08Z beerli $
 
-------------------------------------------------------*/

#include "migration.h"

extern long estimateParameter (long rep, long G, world_fmt * world,
                                   option_fmt * options, MYREAL **dd, long chain,
                                   char type, long kind, long repkind);

extern MYREAL calc_loci_like (helper_fmt * helper, MYREAL *param,
                                  MYREAL *lparam);

extern void calc_apgg (MYREAL thetax, MYREAL **apgg, nr_fmt * nr,
                           timearchive_fmt * atl, long which);
extern void set_gamma_param (MYREAL *paramn, MYREAL *paramo, MYREAL *lparamn,
                                 MYREAL *lparamo, MYREAL theta, nr_fmt * nr);
extern void calc_apg0 (MYREAL *apg0, nr_fmt * nr, timearchive_fmt * tyme,
                           MYREAL thetax, MYREAL theta1);
extern void which_calc_like (long repkind);
extern void calc_loci_param (nr_fmt * nr, MYREAL *lparam, MYREAL *olparam,
                                 MYREAL *dv, MYREAL lamda, long nnn);
extern void set_replicates (world_fmt * world, long repkind, long rep,
                                long *repstart, long *repstop);
extern void prepare_broyden (long kind, world_fmt * world,
                                 boolean * multilocus);
extern void simple_loci_derivatives (MYREAL *d, nr_fmt * nr,
                                         timearchive_fmt ** tyme, long locus);
extern void copy_and_clear_d (nr_fmt * nr);
extern void add_back_d (nr_fmt * nr);
extern void setup_parameter0_standard (world_fmt * world, nr_fmt * nr,
                                           long repkind, long repstart,
                                           long repstop, long loci, long kind,
                                           boolean multilocus);

extern void combine_gradient (nr_fmt * nr, helper_fmt * helper, MYREAL *gxv);

extern long maximize (MYREAL **thisparam, world_fmt * world, 
		      nr_fmt * nr,
		      MYREAL **hess,
                          long analystype, long repkind);
extern void set_logparam (MYREAL *loga, MYREAL *a, long size);
extern void set_expparam (MYREAL *expa, MYREAL *a, long size);
extern long do_profiles (world_fmt * world, nr_fmt * nr, MYREAL *likes,
                             MYREAL *normd, long kind, long rep, long repkind);
extern void fill_helper (helper_fmt * helper, MYREAL *param, MYREAL *lparam,
                             world_fmt * world, nr_fmt * nr);

extern void replace_with (int mode, MYREAL *a, MYREAL *b, MYREAL *c, MYREAL m,
                              MYREAL *la, MYREAL *lb, MYREAL *lc, MYREAL ll);
MYREAL quadratic_lamda (MYREAL lamda, MYREAL a, MYREAL b, MYREAL c, MYREAL la,
                        MYREAL lb, MYREAL lc);


#endif /* COMBINE_INCLUDE */