plot-MSA-state: Plotting functions for fitted MSA model

Description

A set of functions to plot state variables (biomass, recruitment time series, etc.)

Usage

plot_S(fit, by = c("stock", "region"), r, s, prop = FALSE, facet_free = FALSE)
plot_B(fit, by = c("stock", "region"), r, s, prop = FALSE, facet_free = FALSE)
plot_R(fit, s)
plot_SRR(fit, s = 1, phi = TRUE)
plot_Rdev(fit, s = 1, log = TRUE)
plot_Fstock(fit, s, by = c("annual", "season"))
plot_self(fit, f = 1, type = c("length", "age"))
plot_seli(fit, i = 1)
plot_selstock(
  fit,
  s = 1,
  by = c("annual", "season"),
  plot2d = c("contour", "filled.contour"),
  ...
)
plot_N(fit, m = 1, r, s = 1, plot2d = c("contour", "filled.contour"), ...)
plot_V(fit, f = 1, by = c("stock", "region"), prop = FALSE, facet_free = FALSE)
plot_Ffleet(fit, f = 1)
plot_mov(fit, s = 1, y, a, palette = "Peach")
plot_recdist(fit, palette = "Peach")

Value

Various base graphics plots

Arguments

fit: MSAassess object returned by fit_MSA()
by: Character to indicate whether to calculate selectivity from F per year or per season
r: Integer for the corresponding region
s: Integer for the corresponding stock
prop: Logical, whether to plot proportions (TRUE) or absolute numbers
facet_free: Logical, whether to allow the y-axis limits to vary by panel in facetted plots
phi: Logical, whether to plot unfished replacement line
log: Logical, whether to plot the natural logarithm of the response variable
f: Integer for the corresponding fleet
type: For plot_self, indicates whether to plot the selectivity by age or length.
i: Integer for the corresponding survey
plot2d: Character, plotting function for either a contour() or filled.contour() plot
...: Other argument to the base graphics function
m: Integer for the corresponding season
y: Integer, year for plotting the movement matrix (last model year is the default)
a: Integer, corresponding age for plotting the movement matrix (age 1 is the default)
palette: Character, palette name to pass to grDevices::hcl.colors(). See grDevices::hcl.pals() for options.

Details

plot_S plots spawning output by stock or region (either whole numbers or proportions for the latter)

plot_B plots total biomass by stock or region (either whole numbers or proportions for the latter)

plot_R plots recruitment by stock

plot_SRR plots the stock-recruitment relationship and history (realized recruitment) by stock

plot_Rdev plots recruitment deviations by stock

plot_Fstock plots apical instantaneous fishing mortality (per year or per season) by stock

plot_self plots fishery selectivity

plot_seli plots index selectivity

plot_selstock plots the realized selectivity from total catch and total abundance at age

plot_N reports total abundance at age

plot_V plots vulnerable biomass, availability to the fishery

plot_Ffleet plots apical instantaneous fishing mortality (per season) by fleet

plot_mov plots movement matrices and the corresponding equilibrium distribution in multi-area models

plot_recdist plots the distribution of recruitment for each stock