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Plotting functions for fitted MARS model

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

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

Usage

plot_S(fit, by = c("total", "stock", "region"), r, s, prop = FALSE)

plot_B(fit, by = c("total", "stock", "region"), r, s, prop = 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)

plot_Ffleet(fit, f = 1)

plot_mov(fit, s = 1, y, a)

plot_recdist(fit)

Arguments

fit

MARSassess object returned by fit_MARS()

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

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

a

Integer, corresponding age for plotting the movement matrix

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