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Plot relative difference between two mizer arrays

Source: R/ArraySpeciesBySize-class.R, R/ArrayTimeBySpecies-class.R, R/ArrayTimeBySpeciesBySize-class.R
plotRelative.Rd

plotRelative() plots the difference between two compatible mizer array objects relative to their average. If the values in the first object are \(N_1\) and the values in the second are \(N_2\), it plots $$2 (N_2 - N_1) / (N_1 + N_2).$$

Usage

plotRelative(
  x,
  y,
  species = NULL,
  log_x,
  ylim = c(NA, NA),
  total = FALSE,
  background = TRUE,
  ...
)

Arguments

x

The first of two compatible mizer array objects to compare. Can be an ArraySpeciesBySize, ArrayTimeBySpecies, or ArrayTimeBySpeciesBySize object.

y

The second mizer array object, compatible with x.

species

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

log_x

If TRUE, use a log10 x-axis. Default is TRUE for size spectra and FALSE for time series.

ylim

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

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.

...

Further arguments used by only some of the methods:

For ArraySpeciesBySize and ArrayTimeBySpeciesBySize 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).

For ArrayTimeBySpeciesBySize methods:

time

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

Value

A ggplot2 object.

See also

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

Examples

# \donttest{
params <- NS_params
given_species_params(params)["Cod", "w_mat"] <- 1200
plotRelative(getEGrowth(NS_params), getEGrowth(params),
             wlim = c(500, 2000), log_x = FALSE, species = "Cod")

# }