plotSpectraRelative: Plot relative difference between abundance spectra

In mizer: Dynamic Multi-Species Size Spectrum Modelling

Plot relative difference between abundance spectra

Description

plotSpectraRelative() plots the difference between the spectra relative to their average. If we denote the number density from the first object as N_1(w) and that from the second object as N_2(w), then this plot shows

2 (N_2(w) - N_1(w)) / (N_2(w) + N_1(w)).

Note that it does not matter whether the relative difference is calculated for number density, biomass density, or biomass density in log weight, because the factors of w by which the densities differ cancel out in the relative difference.

Usage

plotSpectraRelative(
  object1,
  object2,
  species = NULL,
  wlim = c(NA, NA),
  llim = c(NA, NA),
  ylim = c(NA, NA),
  total = FALSE,
  resource = TRUE,
  background = TRUE,
  highlight = NULL,
  log_x = TRUE,
  size_axis = c("w", "l"),
  ...
)

Arguments

object1	First MizerParams or MizerSim object.
object2	Second MizerParams or MizerSim object.
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.
wlim	A numeric vector of length two providing lower and upper limits for the w axis. Use NA for the default: the lower default is min(params@w) / 100 when resource = TRUE (to show some resource below the fish grid) or min(params@w) when resource = FALSE; the upper default is max(params@w_full). Data is filtered to this range and the axis limits are set accordingly.
llim	A numeric vector of length two providing lower and upper limits for the length axis when size_axis = "l". Use NA to auto-scale to the data range. Data is filtered to this range and the axis limits are set accordingly.
ylim	A numeric vector of length two providing lower and upper limits for the y axis (the relative difference). Use NA to refer to the existing minimum or maximum.
total	A boolean value that determines whether the total is plotted as well. The total is the total of everything the object holds — every species and the resource — whatever is drawn, so it does not move when species, resource or background change. Default is FALSE.
resource	A boolean value that determines whether resource is included. Default is TRUE.
background	A boolean value that determines whether background species are included. Ignored if the model does not contain background species. Default is TRUE.
highlight	Name or vector of names of the species to be highlighted by being plotted with thicker lines.
log_x	If TRUE (default), use a log10 x-axis.
size_axis	Whether to plot size as weight ("w", default) or length ("l"), using the allometric weight-length relationship. Spectrum densities and their units are transformed to match the chosen axis.
...	Additional arguments passed to plotSpectra() for preparing the spectra data, for example time_range or geometric_mean for MizerSim objects.

Details

plotlySpectraRelative() is the interactive plotly version.

Value

A ggplot2 object. plotlySpectraRelative() returns a plotly object.

See Also

plotting_functions, plotSpectra(), plotSpectra2()

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

Examples

sim1 <- project(NS_params, t_max = 10, progress_bar = FALSE)
sim2 <- project(NS_params, effort = 0.5, t_max = 10, progress_bar = FALSE)
plotSpectraRelative(sim1, sim2)

mizer documentation built on Aug. 31, 2026, 5:08 p.m.