mizer (version 3.4.0)

addPlot: Add lines to an existing plot

Description

addPlot() adds another set of values to an existing ggplot, for example to compare the same rate before and after a model change. There are methods for all the mizer array classes. Each 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. Can be an ArraySpeciesBySize, ArrayTimeBySpecies, ArrayTimeBySpeciesBySize, ArrayResourceBySize or ArrayTimeByResourceBySize object.

species

Character vector of species to include. NULL (default) means all species. A resource array holds a single spectrum, so this argument is not used by the resource methods, which warn if it is set.

total

A boolean value that determines whether the total is plotted as well. The total is the total of everything the array holds, every species and every size, whatever is drawn. Default is FALSE. Not used by the resource methods, which warn if it is set.

background

A boolean value that determines whether background species are included. Ignored if the model does not contain background species. Default is TRUE. Not used by the resource methods, which warn if it is set.

colour

Optional fixed colour for the added lines. If NULL, the species colours from the existing plot are used. Because a resource array is a single line whose "Resource" level may be missing from the existing plot's colour scale, the resource methods instead default to the fixed resource colour from getColours().

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 the ArraySpeciesBySize, ArrayTimeBySpeciesBySize, ArrayResourceBySize and ArrayTimeByResourceBySize methods:

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.

For the ArraySpeciesBySize and ArrayTimeBySpeciesBySize methods:

all.sizes

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

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 of each species, or of the resource, see resource_params().

per_log_size

For an array that holds a density, whether to plot it per logarithmic size (TRUE) rather than per size (FALSE). The default, NULL, plots the density as it stands. Unlike size_axis this needs no weight-length relationship, so it is available for the resource classes too. An error for an array that does not hold a density.

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.

For the ArrayTimeBySpeciesBySize and ArrayTimeByResourceBySize methods:

time

The time to display. Default (NULL) is the final time step.

See Also

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

Examples

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

pr <- plot(getResourceMort(NS_params))
addPlot(pr, getResourceMort(NS_params))
# }