ArraySpeciesBySize_plot_data: The complete plotting data of a species-by-size array

In mizer: Dynamic Multi-Species Size Spectrum Modelling

The complete plotting data of a species-by-size array

Description

Everything a plot of an ArraySpeciesBySize needs, prepared once: the species selection, the background grouping, the masking of sizes outside a species' own range, the weight limits, the conversion of the values and of the size coordinate onto the requested axis, the total line, and the length limits.

Usage

ArraySpeciesBySize_plot_data(
  x,
  species = NULL,
  all.sizes = FALSE,
  wlim = c(NA, NA),
  llim = c(NA, NA),
  total = FALSE,
  background = TRUE,
  size_axis = "w",
  per_log_size = NULL
)

Arguments

x	An ArraySpeciesBySize object.
species	Character vector of species to include, or NULL for all.
all.sizes	If FALSE, values outside a species' size range are removed.
wlim	Numeric vector of length two giving the weight limits.
llim	Numeric vector of length two giving the length limits, applied only on a length axis.
total	Whether to append the total line, see total_contributors().
background	Whether background species are included.
size_axis	Either "w" (weight) or "l" (length).
per_log_size	Whether to express a density per logarithmic size.

Details

All of it uses the array's own params. That matters for the comparison plots, where the two operands may come from different models: a length axis and a density Jacobian are both built from the weight-length relationship of the model the values came from, so preparing the second array with the first one's parameters would put it in the wrong place on the axis. Each operand is therefore prepared here, on its own, and the comparison renderers receive data that is already on the axis it will be drawn against.

Value

A data frame with the size coordinate in its first column, the values in its second, and Species and Legend columns.

mizer documentation built on Aug. 24, 2026, 9:08 a.m.