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Get Time Series Plots

get_ts_plot.Rd

Generates a suite of time series plots for key population dynamics quantities (spawning stock biomass, dynamic unfished SSB, total biomass, recruitment, and fishing mortality) across one or more SPoRC model runs. Optionally overlays approximate 95 sdreport.

Usage

get_ts_plot(rep, sd_rep, model_names, do_ci = TRUE)

Arguments

rep

List of length n_models, where each element is a SPoRC report list (i.e. the output of obj$report() after optimisation).

sd_rep

List of length n_models, where each element is a SPoRC sdreport list (i.e. the output of sdreport(obj)). Used to extract delta-method standard errors on log-scale quantities (log_SSB, log_Dynamic_SSB0, log_Total_Biom, log_Rec).

model_names

Character vector of length n_models giving display names for each model run. Used as legend labels across all plots.

do_ci

Logical. If TRUE (default), approximate 95 ribbons are added to SSB, total biomass, dynamic SSB0, and recruitment plots. Ribbons are computed on the natural scale as exp(log(value) ± 1.96 * se).

Value

A named list of seven ggplot objects:

[[1]] comb_ts_plot

All quantities faceted by Type × Region.

[[2]] f_ts_plot

Fishing mortality by fleet and season, faceted by Region.

[[3]] rec_ts_plot

Recruitment by population, faceted by Region.

[[4]] ssb_ts_plot

Spawning stock biomass by population, faceted by Region. Dynamic SSB0 is excluded from this panel.

[[5]] total_biom_plot

Total biomass by population, faceted by Region.

[[6]] ssb0_plot

Dynamic unfished SSB (B0) by population, faceted by Region.

[[7]] ssb_ssb0_plot

SSB and dynamic SSB0 overlaid on the same panel, distinguished by linetype, faceted by Region. Useful for visualising depletion.

See also

Other Plotting: get_biological_plot(), get_data_fitted_plot(), get_selex_plot(), plot_all_basic(), theme_sablefish()

Examples

if (FALSE) { # \dontrun{
  plots <- get_ts_plot(
    rep        = list(rep1, rep2),
    sd_rep     = list(sdrep1, sdrep2),
    model_names = c("Base", "Sensitivity"),
    do_ci      = TRUE
  )
  plots[[4]] # SSB time series
  plots[[7]] # SSB vs dynamic B0
} # }