initial_params Class Reference

Description not yet available. More...

#include <admodel.h>

Public Member Functions
	initial_params (void)
	Default constructor. More...
virtual void	add_to_list (void)
virtual void	add_value (const dvector &, const int &)=0
virtual void	add_value (const dvector &, const dvector &, const int &, const double &, const dvector &)=0
void	allocate (int _phase_start)
virtual void	bsave_value (uostream &uos)=0
virtual void	copy_value_to_vector (const dvector &, const int &)=0
virtual void	curv_scale (const dvector &d, const dvector &x, const int &ii)=0
virtual void	dev_correction (const dmatrix &, const int &)=0
double	get_initial_value (void)
virtual void	get_jacobian (const dvector &, const dvector &, const int &)=0
int	get_phase_start (void)
double	get_scalefactor ()
virtual void	hess_scale (const dvector &d, const dvector &x, const int &ii)=0
virtual const char *	label ()=0
virtual void	mc_scale (const dvector &d, const dvector &x, const int &ii)=0
virtual void	pvm_pack (void)=0
virtual void	pvm_unpack (void)=0
void	restore_phase_start (void)
virtual void	restore_value (const ifstream &ifs)=0
virtual void	restore_value_from_vector (const dvector &, const int &)=0
virtual void	save_value (ofstream &ofs)=0
virtual void	save_value (const ofstream &ofs, int prec)=0
virtual void	save_value (const ofstream &ofs, int prec, const dvector &, int &offset)=0
virtual void	sd_scale (const dvector &d, const dvector &x, const int &ii)=0
virtual void	sd_vscale (const dvar_vector &d, const dvar_vector &x, const int &ii)=0
void	set_active_flag (void)
void	set_inactive_flag (void)
void	set_initial_value (double x)
virtual void	set_only_random_effects_active ()
virtual void	set_only_random_effects_inactive ()
void	set_phase_start (int x)
virtual void	set_random_effects_active ()
virtual void	set_random_effects_inactive ()
void	set_scalefactor (const double)
virtual void	set_simulation_bounds (const dmatrix &symbds, const int &ii)=0
virtual void	set_value (const dvar_vector &, const int &, const dvariable &pen)=0
virtual void	set_value_inv (const dvector &, const int &)=0
virtual void	setshare (const index_type &sf, const index_type &af)
virtual void	shared_set_value (const dvar_vector &, const int &, const dvariable &pen)
virtual void	shared_set_value_inv (const dvector &, const int &)
virtual int	shared_size_count (void)
virtual unsigned int	size_count () const =0

Static Public Member Functions
static void	add_random_vector (const dvector &x)
	Author: David Fournier Copyright (c) 2008-2012 Regents of the University of California. More...
static void	add_random_vector (const dvector &y, const dvector &x, const double &ll, const dvector &diag)
static void	copy_all_values (const dvector &x, const int &ii)
static int	correct_for_dev_objects (const dmatrix &H)
static void	get_jacobian_value (const dvector &y, const dvector &jac)
static adstring	get_reportfile_name (void)
static int	montecarlo_scale (const dvector &d, const dvector &x)
	Description not yet available. More...
static int	num_active_calc (void)
static int	nvarcalc ()
static int	nvarcalc_all (void)
	Description not yet available. More...
static void	read (void)
static dvariable	reset (const dvar_vector &x)
static dvariable	reset (const dvector &x)
static dvariable	reset (const dvar_vector &x, const dvector &pen)
static dvariable	reset1 (const dvar_vector &x, const dvector &g)
static dvariable	reset_all (const dvar_vector &x, const dvector &pen)
	Description not yet available. More...
static void	restore (const ifstream &ifs)
static void	restore_all_values (const dvector &x, const int &ii)
static void	restore_start_phase (void)
static void	save (void)
static void	save (const ofstream &ofs, int prec)
	Author: David Fournier Copyright (c) 2008-2014 Regents of the University of California. More...
static void	save_all (const ofstream &_ofs, int prec, const dvector &g)
	Write all values of g into output stream _ofs. More...
static void	set_active_only_random_effects (void)
static void	set_active_random_effects (void)
static void	set_all_simulation_bounds (const dmatrix &symbds)
static void	set_all_simulation_bounds (const dmatrix &symbds, const dvector &)
static void	set_inactive_only_random_effects (void)
static void	set_inactive_random_effects (void)
static int	stddev_curvscale (const dvector &d, const dvector &x)
static int	stddev_scale (const dvector &d, const dvector &x)
static int	stddev_vscale (const dvar_vector &d, const dvar_vector &x)
static void	xinit (const dvector &x)
static void	xinit1 (const dvector &x, const dvector &g)
static void	xinit_all (const dvector &x)
	Description not yet available. More...

Public Attributes
int	phase_save
int	phase_start
int	phase_stop

Static Public Attributes
static int	current_phase =1
static bool	in_hessian_phase = false
static int	max_num_initial_params = 0
static int	max_number_phases =1
static int	mc_phase =0
static int	mceval_phase =0
static int	num_active_initial_params
static int	num_initial_params = 0
static int	restart_phase =0
static int	sd_phase =0
static int	straight_through_flag =0
static adlist_ptr	varsptr

Protected Member Functions
virtual	~initial_params ()
	Destructor. More...

Protected Attributes
int	active_flag
double	initial_value
int	initial_value_flag
double	scalefactor
shareinfo *	share_flags

Friends
int	active (const initial_params &ip)
class	function_minimizer

Detailed Description

Description not yet available.

Parameters

Definition at line 814 of file admodel.h.

Constructor & Destructor Documentation

initial_params::~initial_params ( )

protectedvirtual

Destructor.

Definition at line 56 of file model.cpp.

initial_params::initial_params

(

void

)

Default constructor.

Definition at line 76 of file model.cpp.

Member Function Documentation

void initial_params::add_random_vector ( const dvector &  x )

static

Author: David Fournier Copyright (c) 2008-2012 Regents of the University of California.

Definition at line 7 of file mod_mc1.cpp.

Referenced by function_minimizer::mcmc_routine(), function_minimizer::monte_carlo_routine(), and function_minimizer::rwm_mcmc_routine().

void initial_params::add_random_vector ( const dvector &  y, const dvector &  x, const double &  ll, const dvector &  diag  )

static

Definition at line 9 of file mod_mc3.cpp.

void initial_params::add_to_list ( void  )

virtual

Definition at line 129 of file model.cpp.

Referenced by allocate().

virtual void initial_params::add_value ( const dvector &  , const int &    )

pure virtual

Implemented in param_init_d3array, param_init_bounded_matrix, param_init_matrix, param_init_bounded_number, param_init_number, param_init_bounded_vector, and param_init_vector.

Referenced by add_random_vector().

virtual void initial_params::add_value ( const dvector &  , const dvector &  , const int &  , const double &  , const dvector &    )

pure virtual

Implemented in param_init_d3array, param_init_bounded_matrix, param_init_matrix, param_init_bounded_number, param_init_number, param_init_bounded_vector, and param_init_vector.

void initial_params::allocate

(

int

_phase_start

)

Definition at line 117 of file model.cpp.

Referenced by param_init_vector::allocate(), dll_param_init_vector::allocate(), param_init_bounded_vector::allocate(), dll_param_init_bounded_vector::allocate(), param_init_number::allocate(), dll_param_init_number::allocate(), param_init_bounded_number::allocate(), dll_param_init_bounded_number::allocate(), param_init_matrix::allocate(), dll_param_init_matrix::allocate(), param_init_bounded_matrix::allocate(), param_init_d3array::allocate(), and dll_param_init_d3array::allocate().

virtual void initial_params::bsave_value ( uostream &  uos )

pure virtual

Implemented in param_init_d3array, param_init_matrix, param_init_number, param_init_bounded_vector, and param_init_vector.

Referenced by save().

void initial_params::copy_all_values ( const dvector &  x, const int &  ii  )

static

Definition at line 9 of file model3.cpp.

Referenced by function_minimizer::build_tree(), function_minimizer::hess_routine_noparallel(), function_minimizer::hess_routine_noparallel_random_effects(), function_minimizer::hess_step(), function_minimizer::hybrid_mcmc_routine(), function_minimizer::likeprof_routine(), function_minimizer::mcmc_routine(), function_minimizer::monte_carlo_routine(), function_minimizer::rwm_mcmc_routine(), function_minimizer::sd_routine(), and function_minimizer::shmc_mcmc_routine().

virtual void initial_params::copy_value_to_vector ( const dvector &  , const int &    )

pure virtual

Implemented in param_init_d3array, param_init_matrix, param_init_bounded_number, param_init_number, param_init_bounded_vector, and param_init_vector.

Referenced by copy_all_values().

int initial_params::correct_for_dev_objects ( const dmatrix &  H )

static

Definition at line 137 of file model.cpp.

virtual void initial_params::curv_scale ( const dvector &  d, const dvector &  x, const int &  ii  )

pure virtual

Implemented in param_init_d3array, param_init_bounded_matrix, param_init_matrix, param_init_bounded_number, param_init_number, param_init_bounded_vector, and param_init_vector.

Referenced by stddev_curvscale().

virtual void initial_params::dev_correction ( const dmatrix &  , const int &    )

pure virtual

Implemented in param_init_d3array, param_init_matrix, param_init_number, param_init_bounded_dev_vector, param_init_bounded_vector, and param_init_vector.

Referenced by correct_for_dev_objects().

double initial_params::get_initial_value

(

void

)

Definition at line 96 of file model.cpp.

virtual void initial_params::get_jacobian ( const dvector &  , const dvector &  , const int &    )

pure virtual

Implemented in param_init_d3array, param_init_bounded_matrix, param_init_matrix, param_init_bounded_number, param_init_number, param_init_bounded_vector, and param_init_vector.

Referenced by get_jacobian_value().

void initial_params::get_jacobian_value ( const dvector &  y, const dvector &  jac  )

static

Definition at line 21 of file mod_mc3.cpp.

int initial_params::get_phase_start

(

void

)

Definition at line 107 of file model.cpp.

adstring initial_params::get_reportfile_name ( void  )

static

Definition at line 1267 of file model.cpp.

double initial_params::get_scalefactor

(

void

)

Definition at line 30 of file model.cpp.

virtual void initial_params::hess_scale ( const dvector &  d, const dvector &  x, const int &  ii  )

pure virtual

Implemented in param_init_d3array, param_init_bounded_matrix, param_init_matrix, param_init_bounded_number, param_init_number, param_init_bounded_vector, and param_init_vector.

virtual const char* initial_params::label ( )

pure virtual

Implemented in param_init_d3array, param_init_matrix, param_init_bounded_number, param_init_number, param_init_bounded_vector, and param_init_vector.

Referenced by check_for_params_on_bounds(), and get_param_names().

virtual void initial_params::mc_scale ( const dvector &  d, const dvector &  x, const int &  ii  )

pure virtual

Implemented in param_init_d3array, param_init_bounded_matrix, param_init_matrix, param_init_bounded_number, param_init_number, param_init_bounded_vector, and param_init_vector.

Referenced by montecarlo_scale().

int initial_params::montecarlo_scale ( const dvector &  d, const dvector &  x  )

static

Description not yet available.

Parameters

Definition at line 15 of file mc_scale.cpp.

Referenced by function_minimizer::monte_carlo_routine().

int initial_params::num_active_calc ( void  )

static

Definition at line 177 of file model.cpp.

Referenced by function_minimizer::sd_routine().

int initial_params::nvarcalc ( )

static

Definition at line 152 of file model.cpp.

Referenced by calculate_importance_sample(), calculate_importance_sample_block_diagonal(), calculate_importance_sample_block_diagonal_funnel(), calculate_importance_sample_block_diagonal_option2(), calculate_importance_sample_block_diagonal_option_antithetical(), calculate_importance_sample_funnel(), calculate_importance_sample_shess(), calculate_laplace_approximation(), check_for_params_on_bounds(), laplace_approximation_calculator::default_calculations(), function_minimizer::dep_hess_routine(), function_minimizer::depvars_routine(), do_gauss_hermite_block_diagonal(), do_gauss_hermite_block_diagonal_multi(), laplace_approximation_calculator::do_one_feval(), evaluate_function(), evaluate_function_gradient(), evaluate_function_no_derivatives(), evaluate_function_quiet(), evaluate_function_with_quadprior(), fmmt1::fmin2(), get_param_names(), function_minimizer::hess_determinant(), function_minimizer::hess_inv(), function_minimizer::hess_routine_and_constraint(), function_minimizer::hess_routine_noparallel(), function_minimizer::hess_routine_noparallel_random_effects(), function_minimizer::hess_routine_slave_random_effects(), function_minimizer::hess_step(), function_minimizer::hybrid_mcmc_routine(), function_minimizer::likeprof_routine(), function_minimizer::limited_memory_quasi_newton(), function_minimizer::limited_memory_quasi_newton_block(), function_minimizer::mcmc_eval(), function_minimizer::mcmc_routine(), function_minimizer::minimize(), function_minimizer::monte_carlo_routine(), function_minimizer::normalize_posterior_distribution(), function_minimizer::nuts_mcmc_routine(), function_minimizer::prof_minimize(), function_minimizer::prof_minimize_re(), function_minimizer::projected_hess_determinant(), function_minimizer::quasi_newton_block(), function_minimizer::rwm_mcmc_routine(), save(), function_minimizer::sd_routine(), function_minimizer::shmc_mcmc_routine(), function_minimizer::trust_region_update(), and function_minimizer::unrestricted_hess_determinant().

int initial_params::nvarcalc_all ( void  )

static

Description not yet available.

Parameters

Definition at line 17 of file nvarcall.cpp.

Referenced by laplace_approximation_calculator::do_one_feval(), laplace_approximation_calculator::get_hessian_components_banded_lme(), function_minimizer::limited_memory_quasi_newton_block(), function_minimizer::prof_minimize_re(), function_minimizer::quasi_newton_block(), and function_minimizer::trust_region_update().

virtual void initial_params::pvm_pack ( void  )

pure virtual

Implemented in param_init_d3array, param_init_bounded_matrix, param_init_matrix, param_init_bounded_number, param_init_number, param_init_bounded_vector, and param_init_vector.

virtual void initial_params::pvm_unpack ( void  )

pure virtual

Implemented in param_init_d3array, param_init_bounded_matrix, param_init_matrix, param_init_bounded_number, param_init_number, param_init_bounded_vector, and param_init_vector.

static void initial_params::read ( void  )

static

dvariable initial_params::reset ( const dvar_vector &  x )

static

Definition at line 345 of file model.cpp.

Referenced by function_minimizer::adamoeba(), function_minimizer::amxxx(), laplace_approximation_calculator::banded_calculations(), laplace_approximation_calculator::banded_calculations_lme(), laplace_approximation_calculator::block_diagonal_calculations(), calculate_importance_sample(), calculate_importance_sample_block_diagonal(), calculate_importance_sample_block_diagonal_funnel(), calculate_importance_sample_block_diagonal_option2(), calculate_importance_sample_block_diagonal_option_antithetical(), calculate_importance_sample_funnel(), calculate_importance_sample_shess(), calculate_laplace_approximation(), laplace_approximation_calculator::default_calculations(), laplace_approximation_calculator::default_calculations_check_derivatives(), function_minimizer::dep_hess_routine(), function_minimizer::depvars_routine(), do_evaluation(), do_gauss_hermite_block_diagonal(), do_gauss_hermite_block_diagonal_multi(), laplace_approximation_calculator::do_one_feval(), evaluate_function(), evaluate_function_gradient(), evaluate_function_no_derivatives(), evaluate_function_quiet(), evaluate_function_with_quadprior(), laplace_approximation_calculator::get_fx_fu(), laplace_approximation_calculator::get_gradient_lme(), laplace_approximation_calculator::get_gradient_lme_hp(), laplace_approximation_calculator::get_hessian_from_components_lme(), function_minimizer::get_hybrid_monte_carlo_value(), function_minimizer::get_monte_carlo_value(), function_minimizer::get_particular_grad(), laplace_approximation_calculator::get_uhat_lm_newton2(), laplace_approximation_calculator::get_uhat_quasi_newton(), laplace_approximation_calculator::get_uhat_quasi_newton_block_diagonal(), function_minimizer::hess_routine_and_constraint(), function_minimizer::hess_routine_noparallel(), function_minimizer::hess_routine_slave_random_effects(), function_minimizer::hess_step(), function_minimizer::hybrid_mcmc_routine(), function_minimizer::limited_memory_quasi_newton(), function_minimizer::limited_memory_quasi_newton_block(), function_minimizer::mcmc_routine(), function_minimizer::minimize(), function_minimizer::neldmead(), function_minimizer::nuts_mcmc_routine(), function_minimizer::prof_minimize(), function_minimizer::prof_minimize_re(), function_minimizer::pvm_master_get_monte_carlo_value(), function_minimizer::pvm_slave_get_monte_carlo_value(), function_minimizer::quasi_newton_block(), function_minimizer::rwm_mcmc_routine(), function_minimizer::set_initial_simplex(), and laplace_approximation_calculator::test_trust_region_method().

dvariable initial_params::reset ( const dvector &  x )

static

Definition at line 369 of file model.cpp.

dvariable initial_params::reset ( const dvar_vector &  x, const dvector &  pen  )

static

Definition at line 312 of file model.cpp.

dvariable initial_params::reset1 ( const dvar_vector &  x, const dvector &  g  )

static

Definition at line 330 of file model.cpp.

dvariable initial_params::reset_all ( const dvar_vector &  x, const dvector &  __pen  )

static

Description not yet available.

Parameters

Definition at line 45 of file nvarcall.cpp.

void initial_params::restore ( const ifstream &  ifs )

static

Definition at line 9 of file model13.cpp.

void initial_params::restore_all_values ( const dvector &  x, const int &  ii  )

static

Definition at line 105 of file model3.cpp.

Referenced by function_minimizer::hess_step(), function_minimizer::hybrid_mcmc_routine(), function_minimizer::likeprof_routine(), function_minimizer::mcmc_eval(), function_minimizer::mcmc_routine(), function_minimizer::monte_carlo_routine(), function_minimizer::nuts_mcmc_routine(), and function_minimizer::rwm_mcmc_routine().

void initial_params::restore_phase_start

(

void

)

Definition at line 283 of file model.cpp.

Referenced by restore_start_phase().

void initial_params::restore_start_phase ( void  )

static

Definition at line 275 of file model.cpp.

Referenced by function_minimizer::depvars_routine(), laplace_approximation_calculator::get_gradient_lme_hp(), function_minimizer::hybrid_mcmc_routine(), function_minimizer::limited_memory_quasi_newton_block(), function_minimizer::mcmc_routine(), function_minimizer::nuts_mcmc_routine(), function_minimizer::prof_minimize_re(), function_minimizer::quasi_newton_block(), function_minimizer::rwm_mcmc_routine(), function_minimizer::sd_routine(), function_minimizer::shmc_mcmc_routine(), and function_minimizer::trust_region_update().

virtual void initial_params::restore_value ( const ifstream &  ifs )

pure virtual

Implemented in param_init_d3array, param_init_matrix, param_init_number, param_init_bounded_vector, and param_init_vector.

Referenced by restore().

virtual void initial_params::restore_value_from_vector ( const dvector &  , const int &    )

pure virtual

Implemented in param_init_d3array, param_init_matrix, param_init_bounded_number, param_init_number, param_init_bounded_vector, and param_init_vector.

Referenced by restore_all_values().

void initial_params::save ( void  )

static

Definition at line 382 of file model.cpp.

Referenced by function_minimizer::minimize().

void initial_params::save ( const ofstream &  _ofs, int  precision  )

static

Author: David Fournier Copyright (c) 2008-2014 Regents of the University of California.

Write values of param_init_number into output stream _ofs.

Parameters

_ofs	output stream
precision	sets the floating point precision

Definition at line 13 of file model12.cpp.

void initial_params::save_all ( const ofstream &  _ofs, int  precision, const dvector &  g  )

static

Write all values of g into output stream _ofs.

Note:** precision is hardcoded to 6.

Parameters

_ofs	output stream
precision	sets the floating point precision
g	the data to output

Definition at line 161 of file model12.cpp.

virtual void initial_params::save_value ( ofstream &  ofs )

pure virtual

Implemented in param_init_d3array, param_init_matrix, param_init_number, param_init_bounded_vector, and param_init_vector.

Referenced by save(), and save_all().

virtual void initial_params::save_value ( const ofstream &  ofs, int  prec  )

pure virtual

Implemented in param_init_d3array, param_init_matrix, param_init_number, param_init_bounded_vector, and param_init_vector.

virtual void initial_params::save_value ( const ofstream &  ofs, int  prec, const dvector &  , int &  offset  )

pure virtual

Implemented in param_init_d3array, param_init_matrix, param_init_number, param_init_bounded_vector, and param_init_vector.

virtual void initial_params::sd_scale ( const dvector &  d, const dvector &  x, const int &  ii  )

pure virtual

Implemented in param_init_d3array, param_init_bounded_matrix, param_init_matrix, param_init_bounded_number, param_init_number, param_init_bounded_vector, and param_init_vector.

Referenced by stddev_scale().

virtual void initial_params::sd_vscale ( const dvar_vector &  d, const dvar_vector &  x, const int &  ii  )

pure virtual

Implemented in param_init_d3array, param_init_bounded_matrix, param_init_matrix, param_init_bounded_number, param_init_number, param_init_bounded_vector, and param_init_vector.

Referenced by stddev_vscale().

void initial_params::set_active_flag

(

void

)

Definition at line 427 of file model.cpp.

Referenced by xinit(), and xinit1().

void initial_params::set_active_only_random_effects ( void  )

static

Definition at line 251 of file model.cpp.

Referenced by laplace_approximation_calculator::banded_calculations(), laplace_approximation_calculator::banded_calculations_lme(), laplace_approximation_calculator::block_diagonal_calculations(), laplace_approximation_calculator::default_calculations(), laplace_approximation_calculator::default_calculations_check_derivatives(), function_minimizer::limited_memory_quasi_newton_block(), function_minimizer::prof_minimize_re(), function_minimizer::quasi_newton_block(), and function_minimizer::trust_region_update().

void initial_params::set_active_random_effects ( void  )

static

Definition at line 267 of file model.cpp.

Referenced by calculate_importance_sample(), calculate_importance_sample_block_diagonal(), calculate_importance_sample_block_diagonal_funnel(), calculate_importance_sample_block_diagonal_option2(), calculate_importance_sample_block_diagonal_option_antithetical(), calculate_importance_sample_funnel(), calculate_importance_sample_shess(), calculate_laplace_approximation(), laplace_approximation_calculator::default_calculations(), do_gauss_hermite_block_diagonal(), do_gauss_hermite_block_diagonal_multi(), laplace_approximation_calculator::do_one_feval(), laplace_approximation_calculator::get_fx_fu(), function_minimizer::hybrid_mcmc_routine(), function_minimizer::mcmc_eval(), function_minimizer::mcmc_routine(), function_minimizer::nuts_mcmc_routine(), function_minimizer::rwm_mcmc_routine(), function_minimizer::sd_routine(), and function_minimizer::shmc_mcmc_routine().

void initial_params::set_all_simulation_bounds ( const dmatrix &  symbds )

static

Definition at line 25 of file montebds.cpp.

Referenced by function_minimizer::mcmc_routine(), and function_minimizer::rwm_mcmc_routine().

static void initial_params::set_all_simulation_bounds ( const dmatrix &  symbds, const dvector &    )

static

void initial_params::set_inactive_flag

(

void

)

Definition at line 432 of file model.cpp.

void initial_params::set_inactive_only_random_effects ( void  )

static

Definition at line 259 of file model.cpp.

Referenced by laplace_approximation_calculator::banded_calculations(), laplace_approximation_calculator::banded_calculations_lme(), laplace_approximation_calculator::block_diagonal_calculations(), calculate_importance_sample(), calculate_importance_sample_block_diagonal(), calculate_importance_sample_block_diagonal_funnel(), calculate_importance_sample_block_diagonal_option2(), calculate_importance_sample_block_diagonal_option_antithetical(), calculate_importance_sample_funnel(), calculate_importance_sample_shess(), calculate_laplace_approximation(), laplace_approximation_calculator::default_calculations(), laplace_approximation_calculator::default_calculations_check_derivatives(), do_gauss_hermite_block_diagonal(), do_gauss_hermite_block_diagonal_multi(), laplace_approximation_calculator::get_fx_fu(), laplace_approximation_calculator::get_hessian_from_components_lme(), function_minimizer::hess_inv(), function_minimizer::hess_routine_noparallel_random_effects(), function_minimizer::hess_routine_slave_random_effects(), function_minimizer::likeprof_routine(), function_minimizer::limited_memory_quasi_newton_block(), function_minimizer::minimize(), function_minimizer::prof_minimize_re(), function_minimizer::quasi_newton_block(), and laplace_approximation_calculator::test_trust_region_method().

void initial_params::set_inactive_random_effects ( void  )

static

Definition at line 288 of file model.cpp.

Referenced by function_minimizer::depvars_routine(), laplace_approximation_calculator::get_gradient_lme_hp(), function_minimizer::hybrid_mcmc_routine(), function_minimizer::limited_memory_quasi_newton_block(), function_minimizer::mcmc_routine(), function_minimizer::minimize(), function_minimizer::nuts_mcmc_routine(), function_minimizer::prof_minimize_re(), function_minimizer::quasi_newton_block(), function_minimizer::rwm_mcmc_routine(), function_minimizer::shmc_mcmc_routine(), and function_minimizer::trust_region_update().

void initial_params::set_initial_value

(

double

x

)

Definition at line 90 of file model.cpp.

Referenced by param_init_vector_vector::allocate(), param_init_bounded_vector_vector::allocate(), param_init_matrix_vector::allocate(), param_init_bounded_matrix_vector::allocate(), param_init_number_vector::allocate(), param_init_bounded_number_vector::allocate(), and param_init_bounded_number::param_init_bounded_number().

void initial_params::set_only_random_effects_active ( void  )

virtual

Reimplemented in random_effects_bounded_matrix, random_effects_matrix, random_effects_bounded_vector, random_effects_vector, random_effects_bounded_number, and random_effects_number.

Definition at line 1280 of file model.cpp.

Referenced by set_active_only_random_effects().

void initial_params::set_only_random_effects_inactive ( void  )

virtual

Reimplemented in random_effects_bounded_matrix, random_effects_matrix, random_effects_bounded_vector, random_effects_vector, random_effects_bounded_number, and random_effects_number.

Definition at line 1286 of file model.cpp.

Referenced by set_inactive_only_random_effects().

void initial_params::set_phase_start

(

int

x

)

Definition at line 101 of file model.cpp.

void initial_params::set_random_effects_active ( void  )

virtual

Reimplemented in random_effects_bounded_matrix, random_effects_matrix, random_effects_bounded_vector, random_effects_vector, random_effects_bounded_number, and random_effects_number.

Definition at line 1290 of file model.cpp.

Referenced by set_active_random_effects().

void initial_params::set_random_effects_inactive ( void  )

virtual

Reimplemented in random_effects_bounded_matrix, random_effects_matrix, random_effects_bounded_vector, random_effects_vector, random_effects_bounded_number, and random_effects_number.

Definition at line 1292 of file model.cpp.

Referenced by set_inactive_random_effects().

void initial_params::set_scalefactor

(

const double

sf

)

Definition at line 34 of file model.cpp.

virtual void initial_params::set_simulation_bounds ( const dmatrix &  symbds, const int &  ii  )

pure virtual

Implemented in param_init_d3array, param_init_bounded_matrix, param_init_matrix, param_init_bounded_number, param_init_number, param_init_bounded_vector, and param_init_vector.

Referenced by set_all_simulation_bounds().

virtual void initial_params::set_value ( const dvar_vector &  , const int &  , const dvariable &  pen  )

pure virtual

Implemented in param_init_d3array, param_init_bounded_matrix, param_init_matrix, param_init_bounded_number, param_init_number, param_init_bounded_dev_vector, param_init_bounded_vector, and param_init_vector.

Referenced by reset(), reset1(), and reset_all().

virtual void initial_params::set_value_inv ( const dvector &  , const int &    )

pure virtual

Implemented in param_init_d3array, param_init_bounded_matrix, param_init_matrix, param_init_bounded_number, param_init_number, param_init_bounded_vector, and param_init_vector.

Referenced by xinit(), xinit1(), and xinit_all().

void initial_params::setshare ( const index_type &  sf, const index_type &  af  )

virtual

Reimplemented in param_init_d3array, param_init_matrix, and param_init_vector.

Definition at line 173 of file shared.cpp.

void initial_params::shared_set_value ( const dvar_vector &  x, const int &  ii, const dvariable &  pen  )

virtual

Reimplemented in param_init_d3array, param_init_bounded_matrix, param_init_matrix, and param_init_vector.

Definition at line 23 of file shared.cpp.

Referenced by reset().

void initial_params::shared_set_value_inv ( const dvector &  x, const int &  ii  )

virtual

Reimplemented in param_init_d3array, param_init_bounded_matrix, param_init_matrix, and param_init_vector.

Definition at line 31 of file shared.cpp.

Referenced by xinit().

int initial_params::shared_size_count ( void  )

virtual

Reimplemented in param_init_d3array, param_init_matrix, and param_init_vector.

Definition at line 15 of file shared.cpp.

Referenced by nvarcalc().

virtual unsigned int initial_params::size_count ( ) const

pure virtual

Implemented in param_init_d3array, param_init_matrix, param_init_number, param_init_bounded_vector, and param_init_vector.

Referenced by check_for_params_on_bounds(), get_param_names(), nvarcalc(), and nvarcalc_all().

int initial_params::stddev_curvscale ( const dvector &  d, const dvector &  x  )

static

Definition at line 214 of file model.cpp.

Referenced by laplace_approximation_calculator::block_diagonal_calculations().

int initial_params::stddev_scale ( const dvector &  d, const dvector &  x  )

static

Definition at line 202 of file model.cpp.

Referenced by laplace_approximation_calculator::banded_calculations(), laplace_approximation_calculator::block_diagonal_calculations(), laplace_approximation_calculator::default_calculations(), laplace_approximation_calculator::default_calculations_check_derivatives(), function_minimizer::dep_hess_routine(), function_minimizer::hess_routine_noparallel(), function_minimizer::hess_routine_noparallel_random_effects(), function_minimizer::hybrid_mcmc_routine(), function_minimizer::likeprof_routine(), function_minimizer::mcmc_routine(), function_minimizer::monte_carlo_routine(), function_minimizer::nuts_mcmc_routine(), function_minimizer::rwm_mcmc_routine(), function_minimizer::sd_routine(), and function_minimizer::shmc_mcmc_routine().

int initial_params::stddev_vscale ( const dvar_vector &  d, const dvar_vector &  x  )

static

Definition at line 191 of file model.cpp.

Referenced by calculate_importance_sample(), calculate_importance_sample_funnel(), calculate_importance_sample_shess(), calculate_laplace_approximation(), function_minimizer::get_hybrid_monte_carlo_value(), and function_minimizer::nuts_mcmc_routine().

void initial_params::xinit ( const dvector &  x )

static

Definition at line 226 of file model.cpp.

Referenced by laplace_approximation_calculator::banded_calculations(), calculate_importance_sample(), calculate_importance_sample_block_diagonal(), calculate_importance_sample_block_diagonal_funnel(), calculate_importance_sample_block_diagonal_option2(), calculate_importance_sample_block_diagonal_option_antithetical(), calculate_importance_sample_funnel(), calculate_importance_sample_shess(), calculate_laplace_approximation(), laplace_approximation_calculator::default_calculations_check_derivatives(), function_minimizer::dep_hess_routine(), function_minimizer::depvars_routine(), do_gauss_hermite_block_diagonal(), do_gauss_hermite_block_diagonal_multi(), fmmt1::fmin2(), laplace_approximation_calculator::get_fx_fu(), laplace_approximation_calculator::get_gradient_lme(), laplace_approximation_calculator::get_gradient_lme_hp(), laplace_approximation_calculator::get_hessian_from_components_lme(), function_minimizer::get_particular_grad(), laplace_approximation_calculator::get_uhat_lm_newton(), laplace_approximation_calculator::get_uhat_lm_newton2(), laplace_approximation_calculator::get_uhat_quasi_newton(), laplace_approximation_calculator::get_uhat_quasi_newton_block_diagonal(), laplace_approximation_calculator::get_uhat_quasi_newton_qd(), function_minimizer::hess_inv(), function_minimizer::hess_routine_and_constraint(), function_minimizer::hess_routine_noparallel(), function_minimizer::hess_routine_noparallel_random_effects(), function_minimizer::hess_routine_slave_random_effects(), function_minimizer::hess_step(), function_minimizer::hybrid_mcmc_routine(), function_minimizer::likeprof_routine(), function_minimizer::mcmc_eval(), function_minimizer::mcmc_routine(), function_minimizer::minimize(), function_minimizer::monte_carlo_routine(), function_minimizer::nuts_mcmc_routine(), function_minimizer::prof_minimize(), function_minimizer::prof_minimize_re(), function_minimizer::rwm_mcmc_routine(), function_minimizer::sd_routine(), and function_minimizer::shmc_mcmc_routine().

void initial_params::xinit1 ( const dvector &  x, const dvector &  g  )

static

Definition at line 296 of file model.cpp.

void initial_params::xinit_all ( const dvector &  _x )

static

Description not yet available.

Parameters

Definition at line 31 of file nvarcall.cpp.

Referenced by laplace_approximation_calculator::get_hessian_components_banded_lme(), function_minimizer::limited_memory_quasi_newton_block(), function_minimizer::prof_minimize_re(), function_minimizer::quasi_newton_block(), and function_minimizer::trust_region_update().

Friends And Related Function Documentation

int active ( const initial_params &  ip )

friend

Definition at line 437 of file model.cpp.

friend class function_minimizer

friend

Definition at line 954 of file admodel.h.

Member Data Documentation

int initial_params::active_flag

protected

Definition at line 821 of file admodel.h.

Referenced by active(), initial_params(), set_active_flag(), and set_inactive_flag().

int initial_params::current_phase =1

static

Definition at line 842 of file admodel.h.

Referenced by add_random_vector(), check_for_params_on_bounds(), function_minimizer::computations1(), copy_all_values(), correct_for_dev_objects(), fmm::fmin(), get_jacobian_value(), get_param_names(), get_reportfile_name(), function_minimizer::hess_step(), initial_params(), function_minimizer::likeprof_routine(), function_minimizer::limited_memory_quasi_newton(), function_minimizer::limited_memory_quasi_newton_block(), function_minimizer::mcmc_eval(), function_minimizer::minimize(), montecarlo_scale(), num_active_calc(), nvarcalc(), function_minimizer::prof_minimize(), function_minimizer::prof_minimize_re(), function_minimizer::quasi_newton_block(), function_minimizer::random_effects_maximization(), reset(), reset1(), restore_all_values(), save(), save_all(), function_minimizer::sd_routine(), set_all_simulation_bounds(), param_init_vector::setshare(), param_init_matrix::setshare(), param_init_vector::shared_set_value(), param_init_matrix::shared_set_value(), param_init_bounded_matrix::shared_set_value(), param_init_vector::shared_size_count(), param_init_matrix::shared_size_count(), param_init_d3array::shared_size_count(), stddev_curvscale(), stddev_scale(), stddev_vscale(), function_minimizer::trust_region_update(), xinit(), and xinit1().

bool initial_params::in_hessian_phase = false

static

Definition at line 845 of file admodel.h.

Referenced by function_minimizer::hess_routine().

double initial_params::initial_value

protected

Definition at line 823 of file admodel.h.

Referenced by param_init_vector::allocate(), param_init_bounded_vector::allocate(), param_init_number::allocate(), param_init_bounded_number::allocate(), param_init_matrix::allocate(), param_init_bounded_matrix::allocate(), param_init_d3array::allocate(), get_initial_value(), initial_params(), and set_initial_value().

int initial_params::initial_value_flag

protected

Definition at line 822 of file admodel.h.

Referenced by param_init_bounded_vector::allocate(), param_init_bounded_number::allocate(), param_init_bounded_matrix::allocate(), initial_params(), and set_initial_value().

int initial_params::max_num_initial_params = 0

static

Definition at line 837 of file admodel.h.

Referenced by function_minimizer::function_minimizer().

int initial_params::max_number_phases =1

static

Definition at line 841 of file admodel.h.

Referenced by allocate(), function_minimizer::computations1(), fmm::fmin(), get_reportfile_name(), function_minimizer::hess_step(), function_minimizer::likeprof_routine(), function_minimizer::mcmc_eval(), function_minimizer::minimize(), function_minimizer::prof_minimize(), function_minimizer::prof_minimize_re(), and save().

int initial_params::mc_phase =0

static

Definition at line 846 of file admodel.h.

Referenced by ad_make_code_reentrant(), laplace_approximation_calculator::banded_calculations(), laplace_approximation_calculator::do_newton_raphson_banded(), laplace_approximation_calculator::do_newton_raphson_state_space(), evaluate_function(), laplace_approximation_calculator::get_uhat_lm_newton(), function_minimizer::hybrid_mcmc_routine(), function_minimizer::mcmc_routine(), function_minimizer::monte_carlo_routine(), function_minimizer::nuts_mcmc_routine(), function_minimizer::rwm_mcmc_routine(), param_init_bounded_vector::sd_scale(), param_init_bounded_number::sd_scale(), df1b2_init_bounded_number::sd_scale(), df1b2_init_bounded_vector::sd_scale(), param_init_bounded_vector::set_value(), param_init_bounded_dev_vector::set_value(), df1b2_init_bounded_vector::set_value(), param_init_bounded_vector::set_value_inv(), and function_minimizer::shmc_mcmc_routine().

int initial_params::mceval_phase =0

static

Definition at line 847 of file admodel.h.

Referenced by ad_make_code_reentrant(), and function_minimizer::computations().

int initial_params::num_active_initial_params

static

Definition at line 840 of file admodel.h.

int initial_params::num_initial_params = 0

static

Definition at line 836 of file admodel.h.

Referenced by ad_make_code_reentrant(), add_random_vector(), add_to_list(), check_for_params_on_bounds(), copy_all_values(), correct_for_dev_objects(), fmm::fmin(), get_jacobian_value(), get_maxparname(), get_param_names(), laplace_approximation_calculator::get_uhat_quasi_newton_qd(), montecarlo_scale(), num_active_calc(), nvarcalc(), nvarcalc_all(), reset(), reset1(), reset_all(), restore(), restore_all_values(), restore_start_phase(), save(), save_all(), function_minimizer::sd_routine(), set_active_only_random_effects(), set_active_random_effects(), set_all_simulation_bounds(), set_inactive_only_random_effects(), set_inactive_random_effects(), stddev_curvscale(), stddev_scale(), stddev_vscale(), xinit(), xinit1(), xinit_all(), and ~initial_params().

int initial_params::phase_save

Definition at line 849 of file admodel.h.

Referenced by allocate(), initial_params(), restore_phase_start(), random_effects_number::set_only_random_effects_active(), random_effects_bounded_number::set_only_random_effects_active(), random_effects_vector::set_only_random_effects_active(), random_effects_bounded_vector::set_only_random_effects_active(), random_effects_matrix::set_only_random_effects_active(), random_effects_bounded_matrix::set_only_random_effects_active(), set_only_random_effects_inactive(), set_phase_start(), random_effects_number::set_random_effects_active(), random_effects_bounded_number::set_random_effects_active(), random_effects_vector::set_random_effects_active(), random_effects_bounded_vector::set_random_effects_active(), random_effects_matrix::set_random_effects_active(), and random_effects_bounded_matrix::set_random_effects_active().

int initial_params::phase_start

Definition at line 848 of file admodel.h.

Referenced by add_random_vector(), allocate(), check_for_params_on_bounds(), copy_all_values(), correct_for_dev_objects(), get_jacobian_value(), get_param_names(), get_phase_start(), initial_params(), montecarlo_scale(), num_active_calc(), nvarcalc(), reset(), reset1(), restore_all_values(), restore_phase_start(), save_all(), set_all_simulation_bounds(), random_effects_number::set_only_random_effects_active(), random_effects_bounded_number::set_only_random_effects_active(), random_effects_vector::set_only_random_effects_active(), random_effects_bounded_vector::set_only_random_effects_active(), random_effects_matrix::set_only_random_effects_active(), random_effects_bounded_matrix::set_only_random_effects_active(), set_only_random_effects_active(), random_effects_number::set_only_random_effects_inactive(), random_effects_bounded_number::set_only_random_effects_inactive(), random_effects_vector::set_only_random_effects_inactive(), random_effects_bounded_vector::set_only_random_effects_inactive(), random_effects_matrix::set_only_random_effects_inactive(), random_effects_bounded_matrix::set_only_random_effects_inactive(), set_only_random_effects_inactive(), set_phase_start(), random_effects_number::set_random_effects_active(), random_effects_bounded_number::set_random_effects_active(), random_effects_vector::set_random_effects_active(), random_effects_bounded_vector::set_random_effects_active(), random_effects_matrix::set_random_effects_active(), random_effects_bounded_matrix::set_random_effects_active(), random_effects_number::set_random_effects_inactive(), random_effects_bounded_number::set_random_effects_inactive(), random_effects_vector::set_random_effects_inactive(), random_effects_bounded_vector::set_random_effects_inactive(), random_effects_matrix::set_random_effects_inactive(), random_effects_bounded_matrix::set_random_effects_inactive(), stddev_curvscale(), stddev_scale(), stddev_vscale(), xinit(), and xinit1().

int initial_params::phase_stop

Definition at line 850 of file admodel.h.

int initial_params::restart_phase =0

static

Definition at line 843 of file admodel.h.

Referenced by function_minimizer::minimize().

double initial_params::scalefactor

protected

Definition at line 824 of file admodel.h.

Referenced by get_scalefactor(), initial_params(), param_init_vector::sd_scale(), param_init_bounded_vector::sd_scale(), param_init_number::sd_scale(), param_init_bounded_number::sd_scale(), param_init_matrix::sd_scale(), param_init_bounded_matrix::sd_scale(), set_scalefactor(), param_init_vector::set_value(), param_init_bounded_vector::set_value(), param_init_number::set_value(), param_init_bounded_number::set_value(), param_init_matrix::set_value(), param_init_bounded_matrix::set_value(), param_init_vector::set_value_inv(), param_init_bounded_vector::set_value_inv(), param_init_number::set_value_inv(), param_init_bounded_number::set_value_inv(), param_init_matrix::set_value_inv(), and param_init_bounded_matrix::set_value_inv().

int initial_params::sd_phase =0

static

Definition at line 844 of file admodel.h.

Referenced by ad_make_code_reentrant(), and function_minimizer::computations1().

shareinfo* initial_params::share_flags

protected

Definition at line 818 of file admodel.h.

Referenced by param_init_vector::get_share_flags(), initial_params(), nvarcalc(), reset(), param_init_vector::set_value_inv(), param_init_vector::setshare(), param_init_matrix::setshare(), param_init_vector::shared_set_value(), param_init_matrix::shared_set_value(), param_init_bounded_matrix::shared_set_value(), param_init_d3array::shared_set_value(), param_init_vector::shared_set_value_inv(), param_init_matrix::shared_set_value_inv(), param_init_vector::shared_size_count(), param_init_matrix::shared_size_count(), param_init_d3array::shared_size_count(), xinit(), and ~initial_params().

int initial_params::straight_through_flag =0

static

Definition at line 839 of file admodel.h.

Referenced by laplace_approximation_calculator::banded_calculations(), laplace_approximation_calculator::block_diagonal_calculations(), laplace_approximation_calculator::default_calculations(), laplace_approximation_calculator::default_calculations_check_derivatives(), get_second_ders(), funnel_init_df1b2variable::set_value(), funnel_init_bounded_df1b2vector::set_value(), random_effects_bounded_vector_info::set_value(), re_df1b2_init_bounded_vector::set_value(), and set_value().

adlist_ptr initial_params::varsptr

static

Definition at line 838 of file admodel.h.

Referenced by add_random_vector(), add_to_list(), check_for_params_on_bounds(), copy_all_values(), correct_for_dev_objects(), function_minimizer::function_minimizer(), get_jacobian_value(), get_param_names(), laplace_approximation_calculator::get_uhat_quasi_newton_qd(), montecarlo_scale(), num_active_calc(), nvarcalc(), nvarcalc_all(), reset(), reset1(), reset_all(), restore(), restore_all_values(), restore_start_phase(), save(), save_all(), function_minimizer::sd_routine(), set_active_only_random_effects(), set_active_random_effects(), set_all_simulation_bounds(), set_inactive_only_random_effects(), set_inactive_random_effects(), stddev_curvscale(), stddev_scale(), stddev_vscale(), xinit(), xinit1(), and xinit_all().

---

The documentation for this class was generated from the following files:

• admodel.h (Last Changed on May 13, 2022 for git-revision 4aafc7ceeb108263fdf90577fb213d3829bc3084.)
• adglobl.cpp (Last Changed on August 03, 2022 for git-revision f8640678bd7af83c55e23f39d73768d9c698f51a.)
• mc_scale.cpp (Last Changed on April 05, 2018 for git-revision d973ebba3bce19abddbc095f97cad763cea4cca2.)
• mod_hess.cpp (Last Changed on August 06, 2022 for git-revision 808780089317c67198079de06b64df009a4a6543.)
• mod_mc1.cpp (Last Changed on July 20, 2022 for git-revision bd28a66207f41224474ff575abe83a0ba117fb05.)
• mod_mc3.cpp (Last Changed on July 20, 2022 for git-revision 8fb7bcb3ad22c515294a98c3a2cc4bb904b95e49.)
• model.cpp (Last Changed on June 29, 2022 for git-revision be1526a357a87937cf302cae3cdbcf78712362c7.)
• model12.cpp (Last Changed on May 25, 2017 for git-revision 85d4eda92133b5514c892358e5e8f61681b1b43d.)
• model13.cpp (Last Changed on April 22, 2014 for git-revision 219a09ff06fd9cee4c006dd85abbefca00beea03.)
• model3.cpp (Last Changed on July 18, 2022 for git-revision d963619c1b384bec88930e89fe8e139f0b075620.)
• montebds.cpp (Last Changed on July 20, 2022 for git-revision bd28a66207f41224474ff575abe83a0ba117fb05.)
• shared.cpp (Last Changed on March 28, 2021 for git-revision 43e32eda42716324c871f54bfc4212d26a295614.)
• nvarcall.cpp (Last Changed on April 30, 2014 for git-revision 491e0b7f08411701935b75c632268de1d5560d41.)