model_parameters Class Reference

Inheritance diagram for model_parameters:

List of all members.

Public Member Functions
	~model_parameters ()
void	preliminary_calculations (void)
void	set_runtime (void)
virtual void *	mycast (void)
virtual void	userfunction (void)
virtual void	report (void)
virtual void	final_calcs (void)
	model_parameters (int sz, int argc, char *argv[])
virtual void	initializationfunction (void)
void	get_growth2 (void)
void	get_selectivity (void)
void	get_initial_conditions (void)
void	get_time_series (void)
void	evaluate_the_objective_function (void)
void	get_posteriors (void)
void	get_MSY_forecast (void)
void	between_phases_calculations (void)
void	write_summaryoutput (void)
void	write_rebuilder_output (void)
void	write_nudata (void)
void	write_nucontrol (void)
void	Do_Equil_Calc (void)
void	Make_AgeLength_Key (void)
void	Make_FishSelex (void)
void	write_bigoutput (void)
Static Public Member Functions
static int	mc_phase (void)
static int	mceval_phase (void)
static int	sd_phase (void)
static int	current_phase (void)
static int	last_phase (void)
Private Attributes
ivector	integer_control_flags
dvector	double_control_flags
param_init_bounded_number	dummy_parm
param_init_bounded_number_vector	MGparm
param_init_bounded_matrix	MGparm_dev
param_3array	natM
param_vector	natM1
param_vector	natM2
param_4array	surv1
param_4array	surv2
param_vector	CVLmin
param_vector	CVLmax
param_matrix	mgp_yr
param_matrix	Cohort_Growth
param_3array	wt_len
param_matrix	wt_len2
param_matrix	mat_len
param_matrix	mat_len_w
param_matrix	mat_age
param_4array	ALK
param_4array	Sd_Size_w
param_4array	Ave_Size
param_4array	Use_Ave_Size
param_4array	Save_Ave_Size
param_matrix	save_Lmin
param_vector	AL
param_matrix	CV_G
param_3array	Wt_Age
param_matrix	save_G_parm
param_3array	natage_temp
param_4array	migrrate
param_4array	recrdist
param_init_bounded_number_vector	SR_parm
param_init_bounded_dev_vector	rec_dev1
param_init_bounded_vector	rec_dev2
param_vector	rec_dev
param_number	SpawnBio
param_number	spb_vir_LH
param_vector	S1
param_matrix	Spbio
param_vector	Spbio_area
param_number	Recruits
param_number	R_base
param_number	S_base
param_number	steepness
param_matrix	Recr
param_vector	exp_rec
param_vector	pred_rec
param_vector	use_rec
param_matrix	Nmid
param_matrix	Nsurv
param_number	ave_age
param_init_bounded_number_vector	init_F
param_vector	est_equ_catch
param_vector	equ_catch
param_vector	equ_catch_enc
param_vector	equ_catch_ret
param_4array	natage
param_4array	catage
param_4array	equ_catage
param_4array	equ_numbers
param_matrix	catage_tot
param_matrix	Hrate
param_matrix	tot_catch_enc
param_matrix	tot_catch_dead
param_matrix	tot_catch_ret
param_matrix	fec
param_matrix	virg_fec
param_number	fish_bio
param_number	fish_bio_r
param_number	fish_bio_e
param_number	fish_num
param_number	fish_num_r
param_number	vbio
param_number	vbio1
param_number	Ave_Size_w
param_number	harvest_rate
param_matrix	exp_AL
param_4array	Z_rate
param_matrix	Zrate2
param_3array	catch_seas_area
param_matrix	totcatch_byarea
param_init_bounded_number_vector	F_rate
param_matrix	SPRage
param_vector	Nmigr
param_number	Nsurvive
param_number	YPR_tgt_enc
param_number	YPR_tgt_dead
param_number	YPR_tgt_N_dead
param_number	YPR_tgt_ret
param_number	YPR_spr
param_number	Vbio_spr
param_number	Vbio1_spr
param_number	SPR_actual
param_number	MSY_Fmult
param_number	SPR_Fmult
param_number	Btgt_Fmult
param_number	YPR_Btgt_enc
param_number	YPR_Btgt_dead
param_number	YPR_Btgt_N_dead
param_number	YPR_Btgt_ret
param_number	YPR_Btgt
param_number	Vbio_Btgt
param_number	Vbio1_Btgt
param_number	Btgt
param_number	Btgttgt
param_number	SPR_Btgt
param_number	Btgt_Rec
param_number	Bspr
param_number	Bspr_rec
param_number	YPR
param_number	MSY
param_number	Bmsy
param_number	Recr_msy
param_number	YPR_msy_enc
param_number	YPR_msy_dead
param_number	YPR_msy_N_dead
param_number	YPR_msy_ret
param_number	YPR_enc
param_number	YPR_dead
param_number	YPR_N_dead
param_number	YPR_ret
param_number	caa
param_number	Fmult
param_number	F_forecast
param_number	Fchange
param_number	last_calc
param_matrix	ForeRatePattern
param_number	alpha
param_number	beta
param_number	SPR
param_number	GenTime
param_vector	cumF
param_vector	maxF
param_number	Yield
param_number	Adj4010
param_3array	forecat
param_init_bounded_number_vector	Q_parm
param_matrix	log_q_cr
param_matrix	sd_cr
param_matrix	exp_cr
param_vector	surv_like
param_matrix	Q_dev_like
param_vector	disc_like
param_number	mnwt_like
param_matrix	exp_disc
param_3array	retain
param_vector	retain_M
param_3array	discmort
param_vector	discmort_M
param_vector	exp_mnwt
param_init_bounded_number_vector	selparm
param_init_bounded_matrix	selparm_dev
param_4array	sel_l
param_4array	sel_l_r
param_4array	discmort2
param_4array	sel_a
param_vector	sel
param_4array	fish_body_wt
param_4array	sel_al_1
param_4array	sel_al_2
param_4array	sel_al_3
param_4array	sel_al_4
param_4array	deadfish
param_4array	deadfish_B
param_3array	save_sp_len
param_3array	save_sp_age
param_3array	exp_l
param_matrix	neff_l
param_vector	exp_l_temp
param_vector	exp_l_temp_ret
param_vector	offset_l
param_vector	length_like
param_3array	exp_a
param_vector	exp_a_temp
param_vector	tempvec
param_matrix	neff_a
param_vector	offset_a
param_vector	age_like
param_vector	sizeage_like
param_3array	exp_ms
param_3array	exp_ms_sq
param_init_bounded_vector	fore_recruitments
param_number	equ_catch_like
param_number	catch_like
param_number	prior_rec
param_number	prior_fore_rec
param_number	parm_like
param_number	parm_dev_like
param_number	CrashPen
param_number	Equ_penalty
param_number	F_ballpark_like
param_number	F_ballpark_lambda
param_number	R1
param_number	R1_exp
param_number	t1
param_number	t2
param_number	temp
param_number	temp1
param_number	temp2
param_number	join1
param_number	join2
param_number	join3
param_number	upselex
param_number	downselex
param_number	peak
param_number	peak2
param_number	point1
param_number	point2
param_number	point3
param_number	point4
param_number	timing
param_matrix	smry
param_matrix	env_data
param_number	equ_Recr
param_stddev_number	R0
param_stddev_number	S0
param_stddev_vector	spbio_std
param_stddev_vector	recr_std
param_stddev_vector	depletion
param_vector	MGparm_Like
param_vector	init_F_Like
param_vector	Q_parm_Like
param_vector	selparm_Like
param_vector	SR_parm_Like
objective_function_value	obj_fun
param_vector	phase_output

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Constructor & Destructor Documentation

model_parameters::~model_parameters

(

)

model_parameters::model_parameters	(	int	sz,
		int	argc,
		char *	argv[]
	)

---

Member Function Documentation

void model_parameters::between_phases_calculations

(

void

)

static int model_parameters::current_phase

(

void

)

[inline, static]

void model_parameters::Do_Equil_Calc

(

void

)

void model_parameters::evaluate_the_objective_function

(

void

)

void model_parameters::final_calcs

(

void

)

[virtual]

void model_parameters::get_growth2

(

void

)

void model_parameters::get_initial_conditions

(

void

)

void model_parameters::get_MSY_forecast

(

void

)

void model_parameters::get_posteriors

(

void

)

void model_parameters::get_selectivity

(

void

)

void model_parameters::get_time_series

(

void

)

void model_parameters::initializationfunction

(

void

)

[virtual]

static int model_parameters::last_phase

(

void

)

[inline, static]

void model_parameters::Make_AgeLength_Key

(

void

)

void model_parameters::Make_FishSelex

(

void

)

static int model_parameters::mc_phase

(

void

)

[inline, static]

static int model_parameters::mceval_phase

(

void

)

[inline, static]

virtual void* model_parameters::mycast

(

void

)

[inline, virtual]

void model_parameters::preliminary_calculations

(

void

)

void model_parameters::report

(

void

)

[virtual]

static int model_parameters::sd_phase

(

void

)

[inline, static]

void model_parameters::set_runtime

(

void

)

void model_parameters::userfunction

(

void

)

[virtual]

void model_parameters::write_bigoutput

(

void

)

void model_parameters::write_nucontrol

(

void

)

void model_parameters::write_nudata

(

void

)

void model_parameters::write_rebuilder_output

(

void

)

void model_parameters::write_summaryoutput

(

void

)

---

Member Data Documentation

param_number model_parameters::Adj4010 [private]

param_vector model_parameters::age_like [private]

param_vector model_parameters::AL [private]

param_4array model_parameters::ALK [private]

param_number model_parameters::alpha [private]

param_number model_parameters::ave_age [private]

param_4array model_parameters::Ave_Size [private]

param_number model_parameters::Ave_Size_w [private]

param_number model_parameters::beta [private]

param_number model_parameters::Bmsy [private]

param_number model_parameters::Bspr [private]

param_number model_parameters::Bspr_rec [private]

param_number model_parameters::Btgt [private]

param_number model_parameters::Btgt_Fmult [private]

param_number model_parameters::Btgt_Rec [private]

param_number model_parameters::Btgttgt [private]

param_number model_parameters::caa [private]

param_4array model_parameters::catage [private]

param_matrix model_parameters::catage_tot [private]

param_number model_parameters::catch_like [private]

param_3array model_parameters::catch_seas_area [private]

param_matrix model_parameters::Cohort_Growth [private]

param_number model_parameters::CrashPen [private]

param_vector model_parameters::cumF [private]

param_matrix model_parameters::CV_G [private]

param_vector model_parameters::CVLmax [private]

param_vector model_parameters::CVLmin [private]

param_4array model_parameters::deadfish [private]

param_4array model_parameters::deadfish_B [private]

param_stddev_vector model_parameters::depletion [private]

param_vector model_parameters::disc_like [private]

param_3array model_parameters::discmort [private]

param_4array model_parameters::discmort2 [private]

param_vector model_parameters::discmort_M [private]

dvector model_parameters::double_control_flags [private]

param_number model_parameters::downselex [private]

param_init_bounded_number model_parameters::dummy_parm [private]

param_matrix model_parameters::env_data [private]

param_4array model_parameters::equ_catage [private]

param_vector model_parameters::equ_catch [private]

param_vector model_parameters::equ_catch_enc [private]

param_number model_parameters::equ_catch_like [private]

param_vector model_parameters::equ_catch_ret [private]

param_4array model_parameters::equ_numbers [private]

param_number model_parameters::Equ_penalty [private]

param_number model_parameters::equ_Recr [private]

param_vector model_parameters::est_equ_catch [private]

param_3array model_parameters::exp_a [private]

param_vector model_parameters::exp_a_temp [private]

param_matrix model_parameters::exp_AL [private]

param_matrix model_parameters::exp_cr [private]

param_matrix model_parameters::exp_disc [private]

param_3array model_parameters::exp_l [private]

param_vector model_parameters::exp_l_temp [private]

param_vector model_parameters::exp_l_temp_ret [private]

param_vector model_parameters::exp_mnwt [private]

param_3array model_parameters::exp_ms [private]

param_3array model_parameters::exp_ms_sq [private]

param_vector model_parameters::exp_rec [private]

param_number model_parameters::F_ballpark_lambda [private]

param_number model_parameters::F_ballpark_like [private]

param_number model_parameters::F_forecast [private]

param_init_bounded_number_vector model_parameters::F_rate [private]

param_number model_parameters::Fchange [private]

param_matrix model_parameters::fec [private]

param_number model_parameters::fish_bio [private]

param_number model_parameters::fish_bio_e [private]

param_number model_parameters::fish_bio_r [private]

param_4array model_parameters::fish_body_wt [private]

param_number model_parameters::fish_num [private]

param_number model_parameters::fish_num_r [private]

param_number model_parameters::Fmult [private]

param_init_bounded_vector model_parameters::fore_recruitments [private]

param_3array model_parameters::forecat [private]

param_matrix model_parameters::ForeRatePattern [private]

param_number model_parameters::GenTime [private]

param_number model_parameters::harvest_rate [private]

param_matrix model_parameters::Hrate [private]

param_init_bounded_number_vector model_parameters::init_F [private]

param_vector model_parameters::init_F_Like [private]

ivector model_parameters::integer_control_flags [private]

param_number model_parameters::join1 [private]

param_number model_parameters::join2 [private]

param_number model_parameters::join3 [private]

param_number model_parameters::last_calc [private]

param_vector model_parameters::length_like [private]

param_matrix model_parameters::log_q_cr [private]

param_matrix model_parameters::mat_age [private]

param_matrix model_parameters::mat_len [private]

param_matrix model_parameters::mat_len_w [private]

param_vector model_parameters::maxF [private]

param_matrix model_parameters::mgp_yr [private]

param_init_bounded_number_vector model_parameters::MGparm [private]

param_init_bounded_matrix model_parameters::MGparm_dev [private]

param_vector model_parameters::MGparm_Like [private]

param_4array model_parameters::migrrate [private]

param_number model_parameters::mnwt_like [private]

param_number model_parameters::MSY [private]

param_number model_parameters::MSY_Fmult [private]

param_4array model_parameters::natage [private]

param_3array model_parameters::natage_temp [private]

param_3array model_parameters::natM [private]

param_vector model_parameters::natM1 [private]

param_vector model_parameters::natM2 [private]

param_matrix model_parameters::neff_a [private]

param_matrix model_parameters::neff_l [private]

param_matrix model_parameters::Nmid [private]

param_vector model_parameters::Nmigr [private]

param_matrix model_parameters::Nsurv [private]

param_number model_parameters::Nsurvive [private]

objective_function_value model_parameters::obj_fun [private]

param_vector model_parameters::offset_a [private]

param_vector model_parameters::offset_l [private]

param_number model_parameters::parm_dev_like [private]

param_number model_parameters::parm_like [private]

param_number model_parameters::peak [private]

param_number model_parameters::peak2 [private]

param_vector model_parameters::phase_output [private]

param_number model_parameters::point1 [private]

param_number model_parameters::point2 [private]

param_number model_parameters::point3 [private]

param_number model_parameters::point4 [private]

param_vector model_parameters::pred_rec [private]

param_number model_parameters::prior_fore_rec [private]

param_number model_parameters::prior_rec [private]

param_matrix model_parameters::Q_dev_like [private]

param_init_bounded_number_vector model_parameters::Q_parm [private]

param_vector model_parameters::Q_parm_Like [private]

param_stddev_number model_parameters::R0 [private]

param_number model_parameters::R1 [private]

param_number model_parameters::R1_exp [private]

param_number model_parameters::R_base [private]

param_vector model_parameters::rec_dev [private]

param_init_bounded_dev_vector model_parameters::rec_dev1 [private]

param_init_bounded_vector model_parameters::rec_dev2 [private]

param_matrix model_parameters::Recr [private]

param_number model_parameters::Recr_msy [private]

param_stddev_vector model_parameters::recr_std [private]

param_4array model_parameters::recrdist [private]

param_number model_parameters::Recruits [private]

param_3array model_parameters::retain [private]

param_vector model_parameters::retain_M [private]

param_stddev_number model_parameters::S0 [private]

param_vector model_parameters::S1 [private]

param_number model_parameters::S_base [private]

param_4array model_parameters::Save_Ave_Size [private]

param_matrix model_parameters::save_G_parm [private]

param_matrix model_parameters::save_Lmin [private]

param_3array model_parameters::save_sp_age [private]

param_3array model_parameters::save_sp_len [private]

param_matrix model_parameters::sd_cr [private]

param_4array model_parameters::Sd_Size_w [private]

param_vector model_parameters::sel [private]

param_4array model_parameters::sel_a [private]

param_4array model_parameters::sel_al_1 [private]

param_4array model_parameters::sel_al_2 [private]

param_4array model_parameters::sel_al_3 [private]

param_4array model_parameters::sel_al_4 [private]

param_4array model_parameters::sel_l [private]

param_4array model_parameters::sel_l_r [private]

param_init_bounded_number_vector model_parameters::selparm [private]

param_init_bounded_matrix model_parameters::selparm_dev [private]

param_vector model_parameters::selparm_Like [private]

param_vector model_parameters::sizeage_like [private]

param_matrix model_parameters::smry [private]

param_number model_parameters::SpawnBio [private]

param_number model_parameters::spb_vir_LH [private]

param_matrix model_parameters::Spbio [private]

param_vector model_parameters::Spbio_area [private]

param_stddev_vector model_parameters::spbio_std [private]

param_number model_parameters::SPR [private]

param_number model_parameters::SPR_actual [private]

param_number model_parameters::SPR_Btgt [private]

param_number model_parameters::SPR_Fmult [private]

param_matrix model_parameters::SPRage [private]

param_init_bounded_number_vector model_parameters::SR_parm [private]

param_vector model_parameters::SR_parm_Like [private]

param_number model_parameters::steepness [private]

param_4array model_parameters::surv1 [private]

param_4array model_parameters::surv2 [private]

param_vector model_parameters::surv_like [private]

param_number model_parameters::t1 [private]

param_number model_parameters::t2 [private]

param_number model_parameters::temp [private]

Reimplemented from model_data.

param_number model_parameters::temp1 [private]

param_number model_parameters::temp2 [private]

param_vector model_parameters::tempvec [private]

param_number model_parameters::timing [private]

param_matrix model_parameters::tot_catch_dead [private]

param_matrix model_parameters::tot_catch_enc [private]

param_matrix model_parameters::tot_catch_ret [private]

param_matrix model_parameters::totcatch_byarea [private]

param_number model_parameters::upselex [private]

param_4array model_parameters::Use_Ave_Size [private]

param_vector model_parameters::use_rec [private]

param_number model_parameters::vbio [private]

param_number model_parameters::vbio1 [private]

param_number model_parameters::Vbio1_Btgt [private]

param_number model_parameters::Vbio1_spr [private]

param_number model_parameters::Vbio_Btgt [private]

param_number model_parameters::Vbio_spr [private]

param_matrix model_parameters::virg_fec [private]

param_3array model_parameters::Wt_Age [private]

param_3array model_parameters::wt_len [private]

param_matrix model_parameters::wt_len2 [private]

param_number model_parameters::Yield [private]

param_number model_parameters::YPR [private]

param_number model_parameters::YPR_Btgt [private]

param_number model_parameters::YPR_Btgt_dead [private]

param_number model_parameters::YPR_Btgt_enc [private]

param_number model_parameters::YPR_Btgt_N_dead [private]

param_number model_parameters::YPR_Btgt_ret [private]

param_number model_parameters::YPR_dead [private]

param_number model_parameters::YPR_enc [private]

param_number model_parameters::YPR_msy_dead [private]

param_number model_parameters::YPR_msy_enc [private]

param_number model_parameters::YPR_msy_N_dead [private]

param_number model_parameters::YPR_msy_ret [private]

param_number model_parameters::YPR_N_dead [private]

param_number model_parameters::YPR_ret [private]

param_number model_parameters::YPR_spr [private]

param_number model_parameters::YPR_tgt_dead [private]

param_number model_parameters::YPR_tgt_enc [private]

param_number model_parameters::YPR_tgt_N_dead [private]

param_number model_parameters::YPR_tgt_ret [private]

param_4array model_parameters::Z_rate [private]

param_matrix model_parameters::Zrate2 [private]

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

• ss2.htp
• ss2.cpp

---