Description Usage Arguments Value

View source: R/format-driors.R

Format data and priors for sraplus

1 2 3 4 5 6 7 8 9 10 11 12 13 14 | ```
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)
``` |

`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_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 |

`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 |

`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 |

a list of data and priors

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