Plot M1 or M2 at age — plot_mortality • Rceattle

Mortality-at-age over the hindcast for one model: predation mortality (M2, the default) or residual natural mortality (M1). One component at a time, never their sum, plot_m_at_age() draws total M (M1 + M2) as a time series.

Usage

plot_mortality(
  Rceattle,
  file = NULL,
  incl_proj = FALSE,
  zlim = NULL,
  type = "lines",
  width = 8,
  height = 5.5,
  title = NULL,
  log = FALSE,
  minyr = NULL,
  theta = 155,
  species = NULL,
  maxage = NULL,
  title_cex = 10,
  M2 = TRUE
)

Arguments

Rceattle: A single fit_mod() object. A list of more than one is an error; call it per model.
file: Path/prefix for the saved figure. NULL (default) draws without saving.
incl_proj: Include the projection years (TRUE/FALSE)
zlim: Ignored. Base-graphics leftover: the fill range of the tile plot. Use p + ggplot2::scale_fill_viridis_c(limits = ...).
type: "lines" (default) draws M-at-age with one line per year; "heatmap" (or 0) draws the same series as an age-by-year tile plot. Any other value gives the lines.
width: Plot width when saved "inches"
height: Plot height when saved "inches"
title: Additional title to add. Will also add species names if not NULL
log: TRUE/FALSE plot the series on a log scale
minyr: First year to plot
theta: Ignored. Base-graphics leftover: viewing angle of a persp surface, which is no longer drawn.
species: Species to plot. Plots all if null.
maxage: Oldest age to draw, on the species' own age scale rather than as a count of age bins. NULL draws every age.
title_cex: Ignored. Base-graphics leftover: title font size. Use p + ggplot2::theme(plot.title = ggplot2::element_text(size = ...)).
M2: Draw predation mortality M2 (TRUE, the default) or residual natural mortality M1 (FALSE). Neither is the sum of the two.

Value

A ggplot.