mizer (version 3.0.0)

addPlot: Add lines to an existing plot

Description

addPlot() adds another set of values to an existing ggplot. The first method supports adding an ArraySpeciesBySize object to a compatible plot, for example to compare the same rate before and after a model change. The method checks whether the existing plot uses a compatible x variable, and warns if the y variable or y-axis units appear to differ.

Usage

addPlot(
  plot,
  x,
  species = NULL,
  total = FALSE,
  background = TRUE,
  colour = NULL,
  linetype = "dashed",
  linewidth = 0.8,
  alpha = 1,
  ...
)

Value

A ggplot2 object.

Arguments

plot

A ggplot2 object to which the new values should be added.

x

An object containing the values to add.

species

Character vector of species to include. NULL (default) means all species.

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.

colour

Optional fixed colour for the added lines. If NULL, the species colours from the existing plot are used.

linetype

Optional fixed line type for the added lines. If NULL, the species line types from the existing plot are used.

linewidth

Width of the added lines.

alpha

Transparency of the added lines.

...

Further arguments used by only some of the methods:

For ArraySpeciesBySize methods:

all.sizes

If FALSE (default), values outside a species' size range (w_min to w_max) are removed.

wlim

A numeric vector of length two providing lower and upper limits for the weight (x) axis. Use NA to refer to the existing minimum or maximum.

llim

A numeric vector of length two providing lower and upper limits for the length (x) axis when size_axis = "l". Use NA to refer to the existing minimum or maximum.

size_axis

Whether to plot size as weight ("w", default) or length ("l"), using the allometric weight-length relationship.

For ArrayTimeBySpecies methods:

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).

ylim

A numeric vector of length two providing lower and upper limits for the value (y) axis.

See Also

Other plotting functions: animate.ArrayTimeBySpeciesBySize(), plot, plot2(), plotBiomass(), plotCDF(), plotCDF2(), plotDiet(), plotFMort(), plotFeedingLevel(), plotGrowthCurves(), plotMizerParams, plotMizerSim, plotPredMort(), plotRelative(), plotSpectra(), plotSpectra2(), plotSpectraRelative(), plotYield(), plotYieldGear(), plotting_functions

Examples

# \donttest{
p <- plot(getEncounter(NS_params), species = "Cod")
addPlot(p, getEncounter(NS_params), species = "Cod")
# }