Description of Model Parameters
b_model_parameters.Rmd
The following table describes all elements contained within
input_list$pars
, which are generated using the
SPoRC::Setup_x
functions. Note that when
n_sexes > 1
, the first dimension will always be females
and the second dimension will always be males.
Parameter | Dimension | Component | Description |
---|---|---|---|
ln_sigmaC |
n_regions, n_fish_fleets |
Fishery Removals | SD for catch fit |
ln_sigmaF |
n_regions, n_fish_fleets |
Fishery Removals | SD for fishing mortality process error |
ln_sigmaF_agg |
n_fish_fleets |
Fishery Removals | SD for aggregated fishing mortality process error |
ln_F_mean |
n_regions, n_fish_fleets |
Fishery Removals | Log mean fishing mortality |
ln_F_devs |
n_regions, n_years, n_fish_fleets |
Fishery Removals | Log deviations in fishing mortality |
ln_F_devs_AggCatch |
n_Catch_Type_years, n_fish_fleets |
Fishery Removals | Region-aggregated log fishing mortality deviations |
ln_F_mean_AggCatch |
n_fish_fleets |
Fishery Removals | Region-aggregated log mean fishing mortality |
fishsel_pe_pars |
n_regions, 4, n_sexes, n_fish_fleets |
Fishery Selectivity | Time-varying selectivity process error parameters |
ln_fishsel_devs |
n_regions, n_years, n_bins, n_sexes, n_fish_fleets |
Fishery Selectivity | Log selectivity deviations (n_bins depends on whether
selectivity is age or length-based) |
ln_fish_fixed_sel_pars |
n_regions, max_fish_pars, max_fishsel_blks, n_sexes, n_fish_fleets |
Fishery Selectivity | Log selectivity function parameters |
ln_fish_q |
n_regions, max_fishq_blks, n_fish_fleets |
Fishery Index | Log fishery catchability |
srvsel_pe_pars |
n_regions, 4, n_sexes, n_srv_fleets |
Survey Selectivity | Time-varying selectivity process error parameters |
ln_srvsel_devs |
n_regions, n_years, n_bins, n_sexes, n_srv_fleets |
Survey Selectivity | Log selectivity deviations (n_bins depends on whether
selectivity is age or length-based) |
ln_srv_fixed_sel_pars |
n_regions, max_srv_pars, max_srv_blks, n_sexes, n_srv_fleets |
Survey Selectivity | Log survey selectivity function parameters |
ln_srv_q |
n_regions, max_srvq_blks, n_fish_fleets |
Survey Index | Log survey catchability |
ln_M |
1 |
Natural Mortality | Log natural mortality |
M_offset |
1 |
Natural Mortality | Offset for M |
ln_global_R0 |
1 |
Recruitment | Log virgin/mean recruitment |
R0_prop |
n_regions – 1 |
Recruitment | Proportions for R0 |
steepness_h |
n_regions |
Recruitment | Steepness parameters (bounded logit space) |
ln_InitDevs |
n_regions, n_ages - 2 |
Recruitment | Log initial age deviations |
ln_RecDevs |
n_regions, n_recdev_years |
Recruitment | Log recruitment deviations |
ln_sigmaR |
2 |
Recruitment | SD for initial and recruitment deviations |
ln_FishAge_theta |
n_regions, n_fish_fleets, n_sexes |
Fishery Compositions | Log overdispersion (fishery age comp) |
ln_FishLen_theta |
n_regions, n_fish_fleets, n_sexes |
Fishery Compositions | Log overdispersion (fishery length comp) |
ln_SrvAge_theta |
n_regions, n_srv_fleets, n_sexes |
Survey Compositions | Log overdispersion (survey age comp) |
ln_SrvLen_theta |
n_regions, n_srv_fleets, n_sexes |
Survey Compositions | Log overdispersion (survey length comp) |
move_pars |
n_regions, n_regions – 1, n_years, n_ages, n_sexes |
Movement | Movement logit parameters |
logit_move_devs |
n_regions , n_regions – 1 ,
n_years , n_ages , n_sexes
|
Movement | Logit movement deviations |
move_pe_pars |
n_regions , n_ages ,
n_sexes
|
Movement | Log process error parameters |
ln_Init_Tag_Mort |
1 |
Tagging | Log tag mortality |
ln_Tag_Shed |
1 |
Tagging | Log chronic tag shedding |
Tag_Reporting_Pars |
n_regions, n_years |
Tagging | Logit tag reporting rate parameters |
ln_tag_theta |
1 |
Tagging | Log overdispersion for tagging |