Plot method for ArrayTimeBySpecies objects

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 over all selected species is plotted as well. 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

# \donttest{
plot(getBiomass(NS_sim))

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

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

# }