plot-MSA-data: Plotting functions for data in MSA model

Description

A set of functions to plot data variables and predicted values (catch, age composition, etc.)

Usage

plot_catch(fit, f = 1, by = c("region", "stock"), prop = FALSE, annual = FALSE)
plot_index(fit, i = 1, zoom = FALSE)
plot_CAA(fit, f = 1, r = 1, do_mean = FALSE)
plot_CAL(fit, f = 1, r = 1, do_mean = FALSE)
plot_IAA(fit, i = 1, do_mean = FALSE)
plot_IAL(fit, i = 1, do_mean = FALSE)
plot_SC(fit, ff = 1, aa = 1, r = 1, prop = FALSE)
plot_tagmov(fit, s = 1, yy = 1, aa = 1)

Value

Various base graphics plots

Arguments

fit: MSAassess object returned by fit_MSA()
f: Integer, indexes the fleet
by: Character to indicate dimension for multivariate plots
prop: Logical, whether to plot proportions (TRUE) or absolute numbers
annual: Logical, whether to plot annual values (summed over seasons)
i: Integer, indexes the survey
zoom: Logical, for plot_index(). If TRUE, plots a subset of years with observed data points. Otherwise, plots predicted values over all model years.
r: Integer, indexes the region
do_mean: Logical, whether to plot full compositions or time series of mean length or mean age
ff: Integer, indexes the aggregate fleet (for stock composition data)
aa: Integer, indexes the aggregate age class (for stock composition and tag data)
s: Integer, indexes the stock
yy: Integer, indexes the aggregate years (for the tag data)

Details

plot_catch plots the fishery catch by stock or region (either whole numbers or proportions)

plot_index plots indices of abundance

plot_CAA plots the fishery catch at age

plot_CAL plots the catch at length

plot_IAA plots the index age composition

plot_IAL plots the index length composition

plot_SC plots the stock composition

plot_tagmov plots the tag movements