plotGrowthCurves: Plot growth curves

Description

The growth curves represent the average age of all the living fish of a species as a function of their size. So it would be natural to plot size on the x-axis. But to follow the usual convention from age-based models, we plot size on the y-axis and age on the x-axis.

Usage

plotGrowthCurves(
  object,
  species = NULL,
  max_age = 20,
  percentage = FALSE,
  species_panel = FALSE,
  highlight = NULL,
  size_at_age = NULL,
  return_data = FALSE,
  log_x = FALSE,
  log_y = FALSE,
  log = NULL,
  ...
)

Value

A ggplot2 object

Arguments

object: An object of class MizerSim or MizerParams.
species: The species to be selected. Optional. By default all target species are selected. A vector of species names, or a numeric vector with the species indices, or a logical vector indicating for each species whether it is to be selected (TRUE) or not.
max_age: The age up to which to run the growth curve. Default is 20.
percentage: Boolean value. If TRUE, the size is given as a percentage of the maximal size.
species_panel: If TRUE (default), and percentage = FALSE, display all species as facets. Otherwise puts all species into a single panel.
highlight: Name or vector of names of the species to be highlighted.
size_at_age: A data frame with observed size at age data to be plotted on top of growth curve graphs. Should contain columns species (species name as used in the model), age (in years) and either weight (in grams) or length (in cm). If both weight and length are provided, only weight is used.
return_data: A boolean value that determines whether the formatted data used for the plot is returned instead of the plot itself. Default is FALSE.
log_x: If TRUE, use a log10 x-axis. Default is FALSE.
log_y: If TRUE, use a log10 y-axis. Default is FALSE.
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.
...: Unused.

Details

In each panel for a single species, a horizontal line is included that indicate the maturity size of the species and a vertical line indicating its maturity age.

If size at age data is passed via the size_at_age argument, this is plotted on top of the growth curve. When comparing this to the growth curves, you need to remember that the growth curves should only represent the average age at each size. So a scatter in the x-direction around the curve is to be expected.

If the species parameters contain the variables a and b for length to weight conversion and the von Bertalanffy parameter k_vb, w_inf (and optionally t0), then the von Bertalanffy growth curve is superimposed in black. Note that the von Bertalanffy curve (which approximates the average length at each age) should not be compared directly to the mizer growth curves (which approximate the average age at each length).

Examples

Run this code

# \donttest{
params <-  NS_params
sim <- project(params, effort=1, t_max=20, t_save = 2, progress_bar = FALSE)
plotGrowthCurves(sim, percentage = TRUE)
plotGrowthCurves(sim, species = "Cod", max_age = 24)
plotGrowthCurves(sim, species_panel = TRUE)

# Returning the data frame
fr <- plotGrowthCurves(sim, return_data = TRUE)
str(fr)
# }