Extract common population estimates

Return a ready-to-plot table of spawning biomass, recruitment or mortality, without navigating the nested tidy output. These functions select the same estimates, uncertainty and units used in tidy_tam() and the dashboard.

Usage

get_ssb(..., model_list = NULL, interval = 0.95)

get_recruitment(..., model_list = NULL, interval = 0.95)

get_fbar(..., model_list = NULL, interval = 0.95)

get_mbar(..., model_list = NULL, interval = 0.95)

get_f(..., model_list = NULL, interval = 0.95)

get_m(..., model_list = NULL, interval = 0.95)

Arguments

...

One or more fitted tam_fit models or tam_ref reporting references, or one named list of these objects.

model_list

A named list of models, instead of ....

interval

Confidence level in (0, 1), default 0.95. Fitted summaries are rebuilt when their cached interval differs. Reference uncertainty is retained as supplied, because it cannot be recalculated from a reporting reference.

Value

A data frame retaining available keys, est, confidence limits, se, se_scale, unit and is_proj. Available metadata, such as SSB timing, is retained. Annual summaries have year; surfaces also have age.

Details

get_ssb() and get_recruitment() return annual estimates. get_fbar() and get_mbar() return the model's abundance-weighted means over the ages chosen by F_settings$mean_ages and M_settings$mean_ages, respectively. get_f() and get_m() return year-by-age surfaces; F is total fishing mortality, summed over fleets. They do not return process deviations.

A single fit returns its table without a model column. Multiple fits and named-list inputs add model, using the supplied names. Missing reference quantities are omitted rather than reconstructed. Explicit reference comparison_scales follow tidy_tam()'s conversion rules; otherwise known incompatible units must be converted before combining models.

These are lightweight selectors. They never refit models or calculate observation OSA residuals or joint-sample process diagnostics. Supplied objects are not modified.

See also

tidy_pop(), tidy_tam(), plot_trend(), plot_matrix()

Examples

if (FALSE) { # \dontrun{
get_ssb(fit)
get_recruitment(fit, interval = 0.8)
get_fbar(Base = fit, Alternative = other_fit)
get_f(model_list = list(Base = fit, Alternative = other_fit))
} # }