plot.ArrayTimeBySpecies: Plot method for 'ArrayTimeBySpecies' objects

In mizer: Dynamic Multi-Species Size Spectrum Modelling

Plot method for ArrayTimeBySpecies objects

Description

See plot() for an overview of the mizer plotting system and the arguments shared by all of its methods.

Usage

## S3 method for class 'ArrayTimeBySpecies'
plot(
  x,
  species = NULL,
  tlim = c(NA, NA),
  y_ticks = 6,
  ylim = c(NA, NA),
  total = FALSE,
  background = TRUE,
  highlight = NULL,
  log_x = FALSE,
  log_y = TRUE,
  log = NULL,
  return_data = FALSE,
  ...
)

Arguments

x	An ArrayTimeBySpecies object.
species	Character vector of species to include. NULL (default) means all species.
tlim	A numeric vector of length two providing lower and upper limits for the time axis, e.g. c(1980, 2000). Use NA to apply no limit at that end. Default is c(NA, NA).
y_ticks	The approximate number of ticks desired on the y axis.
ylim	A numeric vector of length two providing lower and upper limits for the value (y) axis. Use NA to refer to the existing minimum or maximum.
total	A boolean value that determines whether the total is plotted as well. The total is the total over every species the array holds, whatever is drawn. Default is FALSE.
background	A boolean value that determines whether background species are included. Ignored if the model does not contain background species. Default is TRUE.
highlight	Name or vector of names of the species to be highlighted.
log_x	If TRUE, use a log10 x-axis. Default is FALSE.
log_y	If TRUE, use a log10 y-axis. Default is TRUE.
log	Character string specifying which axes should use log10 scales, in the same form as the base plot() argument. For example, "x", "y", "xy" or "". If supplied, this overrides log_x and log_y.
return_data	If TRUE, return the data frame instead of the plot.
...	Unused.

Value

A ggplot2 object, unless return_data = TRUE, in which case a data frame is returned.

Examples

plot(getBiomass(NS_sim))
plot(getBiomass(NS_sim), species = c("Cod", "Herring"), total = TRUE)
plot(getYield(NS_sim), species = c("Cod", "Herring"))

mizer documentation built on Aug. 24, 2026, 9:08 a.m.