Get Plots of Biological Quantities

Generates plots of movement probabilities, natural mortality, weight-at-age, and maturity-at-age across one or more SPoRC model runs. All plots use a user-specified year index; movement plots additionally show all seasons and are returned as a separate plot per population.

Usage

get_biological_plot(data, rep, model_names)

Arguments

data

List of length n_models, where each element is a SPoRC data list. Used to extract WAA, MatAA, ages, n_pop, and do_recruits_move.

rep

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

model_names

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

Value

A list of four elements:

[[1]] move_plot

A list of n_pop ggplot objects, one per population. Each plot shows age-specific movement probabilities for all seasons at year_indx, faceted by Region_To × (Region_From + Season), with lines coloured by model and distinguished by sex linetype. If do_recruits_move = 0, age-1 fish are excluded. Y-axis is fixed to [0, 1].

[[2]] natmort_plot

Natural mortality at age at year_indx, faceted by Region × Sex. Lines coloured by model and distinguished by population linetype.

[[3]] waa_plot

Spawning weight-at-age at year_indx, faceted by Region × (Sex + Season). Lines coloured by model and distinguished by population linetype.

[[4]] mataa_plot

Maturity-at-age at year_indx, faceted by Region × (Sex + Season). Lines coloured by model and distinguished by population linetype.

See also

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

Examples

if (FALSE) { # \dontrun{
  plots <- get_biological_plot(
    data        = list(data1, data2),
    rep         = list(rep1, rep2),
    model_names = c("Base", "Sensitivity"),
    year_indx   = 40
  )

  plots[[1]][[1]]  # movement plot for population 1
  plots[[1]][[2]]  # movement plot for population 2, etc
  plots[[2]]       # natural mortality
  plots[[3]]       # weight-at-age
  plots[[4]]       # maturity-at-age
} # }