Plot the relative difference between two mizer array objects

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, ...)

# S3 method for class 'ArraySpeciesBySize'
plotRelative(
  x,
  y,
  species = NULL,
  all.sizes = FALSE,
  log_x = TRUE,
  wlim = c(NA, NA),
  ylim = c(NA, NA),
  total = FALSE,
  background = TRUE,
  ...
)

# S3 method for class 'ArrayTimeBySpecies'
plotRelative(
  x,
  y,
  species = NULL,
  start_time = NULL,
  end_time = NULL,
  ylim = c(NA, NA),
  total = FALSE,
  background = TRUE,
  log_x = FALSE,
  ...
)

# S3 method for class 'ArrayTimeBySpeciesBySize'
plotRelative(
  x,
  y,
  species = NULL,
  time = NULL,
  all.sizes = FALSE,
  log_x = TRUE,
  wlim = c(NA, NA),
  ylim = c(NA, NA),
  total = FALSE,
  background = TRUE,
  ...
)

Arguments

x, y

Two compatible mizer array objects of the same class.

...

Further arguments (currently unused).

species

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

all.sizes

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

log_x

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

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. Only applies to ArraySpeciesBySize.

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.

start_time

The first time to be plotted. Default (NULL) is the beginning of the time series. Only applies to ArrayTimeBySpecies.

end_time

The last time to be plotted. Default (NULL) is the end of the time series. Only applies to ArrayTimeBySpecies.

time

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

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{
enc <- getEncounter(NS_params)
plotRelative(enc, enc, species = "Cod")

plotRelative(getBiomass(NS_sim), getBiomass(NS_sim), species = "Cod")

# }