Format data and priors for sraplus
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 = 1, 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 = 0.05, 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 )
| 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 | 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_cv | |
| 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