format_driors: Format data and priors for sraplus

Description Usage Arguments Value

View source: R/format-driors.R

Description

Format data and priors for sraplus

Usage

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format_driors(taxa = "lutjanus griseus", initial_state = 1,
  initial_state_cv = 0.1, terminal_state = NA,
  terminal_state_cv = 0.2, u_v_umsy = NA, u_years = NA, u_cv = 0.2,
  final_u = NA, final_u_cv = NA, catch = NA, years = NA,
  index = NA, effort = NA, b_ref_type = "k", f_ref_type = "fmsy",
  index_years = 1, effort_years = NA, use_heuristics = FALSE,
  use_b_reg = FALSE, growth_rate_prior = NA,
  growth_rate_prior_cv = 0.1, fmi = c(research = NA, management = NA,
  enforcement = NA, socioeconomics = NA), fmi_cv = NA, sar = NA,
  sar_cv = NA, q_slope_prior = 0, q_slope_prior_cv = 0.1, m = NA,
  k_prior = NA, k_prior_cv = 2, sigma_r_prior = 0.05,
  sigma_r_prior_cv = 0.5, shape_prior = 1.01, shape_prior_cv = 0.25,
  q_prior_cv = 1, sigma_obs_prior = 0.05, sigma_obs_prior_cv = 2,
  isscaap_group = NA, prob = 0.9)

Arguments

taxa

the genus and species of the species (case insensitive)

initial_state

reference point in the initial year, units of depletion or B/Bmsy (set ref_type accordingly). when initial_state is 1, implies either B/K = 1 or B/Bmsy = 1

initial_state_cv

CV associated with initial state reference point

terminal_state

reference point in the terminal year, units of depletion or B/Bmsy (set ref_type accordingly). when initial_state is 1, implies either B/K = 1 or B/Bmsy = 1

terminal_state_cv

CV associated with terminal state reference point

u_v_umsy

u/umsy data over time

u_years

years in which u/umsy data are available

u_cv

cv associated with u/umsy data

final_u

vector of priors on u/umsy in the terminal years

final_u_cv

vector of cvs on u/umsy in the terminal years

catch

vector of catches over lifetime of fishery

years

vector of years that the catch data correspond to

index

vector of an abundance index

effort

vector of an effort series

b_ref_type

the units of the initial and final depletion. k means that units are relative to carrying capacity, b bmsy

f_ref_type

the units of the fishing mortality rates. fmsy means F/Fmsy, f means fishing mortality rate f

index_years

the years in which abundance index data are available

effort_years

years in which effort data are available

use_heuristics

logical,TRUE uses catch-msy hueristics for priors, FALSE requires user to pass them

use_b_reg

logical marking whether to use the regression to put priors on biomass as well as fishing mortality

growth_rate_prior

manually pass prior on the growth rate r in the Pella-Tomlinson model

growth_rate_prior_cv

manually pass cv for prior on the growth rate r in the Pella-Tomlinson model

fmi

named vector of fisheries management index scrores

fmi_cv

overwrite posterior predictive cv of FMI derived U/Umsy (NA to use empirical CV)

sar

swept area ratio

sar_cv

overwrite posterior predictive cv of SAR derived U/Umsy (NA to use empirical CV)

q_slope_prior

prior on the slope of catchability q

q_slope_prior_cv

the cv on the prior on q_slope

m

natural mortality

k_prior

prior on carrying capacity

k_prior_cv

CV of prior on carrying capacity

sigma_r_prior

prior on process error

sigma_r_prior_cv

CV of prior on process error

shape_prior

prior on shape parameter of Pella-Tomlinson model

shape_prior_cv

CV of prior on shape parameter of Pella-Tomlinson model

q_prior_cv

CV of prior on q itself (prior on q set in fit_sraplus)

sigma_obs_prior

prior on observation error

sigma_obs_prior_cv

cv of prior on observation error

isscaap_group

the isscaap group of the stock. If NA will try and find

prob

the probability range of the posterior predictive to use in construction of the priors

Value

a list of data and priors


DanOvando/sraplus documentation built on Dec. 1, 2019, 5:15 a.m.