plot_retro_recruits: Make squid plot of retrospectives of recruitment deviations.

In pacific-hake/hake-assessment: Stock Assessment for Pacific Hake

Make squid plot of retrospectives of recruitment deviations.

Description

Make squid plot of retrospectives of recruitment deviations.

Usage

plot_retro_recruits(
  retroSummary,
  endyrvec,
  cohorts,
  ylim = NULL,
  uncertainty = FALSE,
  labels = c("Recruitment deviation", "Recruitment (billions)",
    "relative to recent estimate", "Age"),
  main = "Retrospective analysis of recruitment deviations",
  mcmcVec = FALSE,
  devs = TRUE,
  relative = FALSE,
  labelyears = TRUE,
  legend = FALSE,
  leg.ncols = 4
)

Arguments

retroSummary	List object created by r4ss::SSsummarize()
endyrvec	Vector of years representing the final year of values to show for each model
cohorts	Which cohorts to show in plot
ylim	Limits of y-axis
uncertainty	Logical. If TRUE, show uncertainty intervals around lines
labels	Vector of plot labels
main	Title for plot
mcmcVec	Either vector of TRUE/FALSE values indicating which models use MCMC. Or single value applied to all models
devs	Plot deviations instead of absolute recruitment values?
relative	Show deviations relative to most recent estimate or relative to 0
labelyears	Label cohorts with text at the end of each line?
legend	Add a legend showing which color goes with which line (as alternative to labelyears).
leg.ncols	Number of columns for the legend.

Details

Based on r4ss::SSplotRetroRecruits() Inspired by Jim Ianelli and named by Sean Cox, the squid plot is a way to examine retrospective patterns in estimation of recruitment deviations.

pacific-hake/hake-assessment documentation built on Nov. 8, 2024, 1:16 p.m.