Get Retrospective Plot

Generates three retrospective diagnostic plots from a set of peeled model runs: a relative-difference plot with Mohn's rho, an absolute-scale trajectory plot, and a cohort-tracking squid plot for recruitment. Together these plots diagnose systematic retrospective patterns in SSB and recruitment estimates across sequential data removals.

Usage

get_retrospective_plot(retro_output, Rec_Age)

Arguments

retro_output

Data frame produced by do_retrospective, containing columns Year, value, peel, Type (e.g. "SSB", "Recruitment"), Pop, and Region. Rows with peel = 0 represent the full-data terminal run; rows with peel > 0 represent sequential data removals. Rows with value = 0 are excluded before plotting.

Rec_Age

Integer giving the age at recruitment (e.g. 2 for age-2 recruitment). Used to convert model year to cohort year in the squid plot (cohort = Year - Rec_Age).

Value

A list of three ggplot objects:

[[1]] retro_plot

Relative-difference plot. Each line shows the proportional deviation of a peeled run from the terminal-year estimate at each year, computed via get_retrospective_relative_difference. Terminal-year points (where peel = max(Year) - Year) are highlighted. Mohn's rho (mean relative difference across terminal-year points) is annotated on each facet panel. Faceted by Region × (Type + Population); lines and points coloured by peel year on a continuous viridis scale.

[[2]] abs_retro_plot

Absolute-scale trajectory plot. Peeled runs (peel > 0) are drawn as solid lines coloured by peel; the full-data run (peel = 0) is overlaid as a dashed black line. Faceted by Region × (Type + Population) with free y-scales.

[[3]] squid_plot

Cohort-tracking (squid) plot for recruitment. Restricted to the 10 most recent cohorts. X-axis shows years since the cohort was last estimated (terminal - Year - 1), y-axis shows recruitment value, and lines are grouped and coloured by cohort year. Faceted by Population × Region with free y-scales.

See also

Other Model Diagnostics: do_jitter(), do_likelihood_profile(), do_retrospective(), do_runs_test(), get_catch_fits_plot(), get_comp_prop(), get_idx_fits(), get_idx_fits_plot(), get_model_rep_from_mcmc(), get_nLL_plot(), get_osa(), get_retrospective_relative_difference(), plot_resids()

Examples

if (FALSE) { # \dontrun{
  retro <- do_retrospective(
    n_retro        = 7,
    data           = data,
    parameters     = parameters,
    mapping        = mapping,
    random         = NULL,
    do_par         = TRUE,
    n_cores        = 7,
    do_francis     = FALSE,
    n_francis_iter = NULL
  )
  plots <- get_retrospective_plot(retro, Rec_Age = 2)
  plots[[1]]  # relative difference + Mohn's rho
  plots[[2]]  # absolute trajectories
  plots[[3]]  # squid plot
} # }