format_driors: Format data and priors for sraplus
In DanOvando/sraplus: Run sraplus Assessments

format_driors

R Documentation

Format data and priors for sraplus

Description

Format data and priors for sraplus

Usage

format_driors(
  taxa = "lutjanus griseus",
  initial_state = 1,
  initial_state_cv = 0.1,
  terminal_state = NA,
  terminal_state_cv = 0.2,
  u = NA,
  u_years = NA,
  u_cv = 0.2,
  terminal_u = NA,
  terminal_u_cv = NA,
  catch = NA,
  years = NA,
  index = NA,
  effort = NA,
  b_ref_type = "k",
  f_ref_type = "fmsy",
  index_years = NA,
  effort_years = NA,
  use_heuristics = FALSE,
  use_b_reg = FALSE,
  growth_rate_prior = NA,
  growth_rate_prior_cv = 0.25,
  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_ratio_prior = 1,
  sigma_ratio_prior_cv = 0.01,
  shape_prior = NA,
  shape_prior_cv = 0.25,
  q_prior = 0.001,
  q_prior_cv = 1,
  sigma_obs_prior = 0.05,
  sigma_obs_prior_cv = 1,
  isscaap_group = NA,
  f_prior_form = 0,
  shape_prior_source = "thorson",
  prob = 0.9,
  use_fmsy_based_r = FALSE,
  use_catch_priors = FALSE
)

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`	u/umsy data over time
`u_years`	years in which u/umsy data are available
`u_cv`	cv associated with u/umsy data
`terminal_u`	vector of priors on u/umsy in the terminal years
`terminal_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_ratio_prior`	prior on the ratio of process to observation error
`sigma_ratio_prior_cv`	cv on prior on the ratio of process to observation 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