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Plotting functions for fitted MSA model

Source: R/report-int-state.R
plot-MSA-state.Rd

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")

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.

Value

Various base graphics plots

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