prepare_ArrayTimeBySpecies_plot_data: The complete plotting data of a time-by-species array

In mizer: Dynamic Multi-Species Size Spectrum Modelling

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

Description

The species selection and the background grouping are done in a single pass, so that no species can be both selected under its own name and appended again under the "Background" legend — which is what a separate appending step used to do to every background species whenever species was left at its default of all of them.

Usage

prepare_ArrayTimeBySpecies_plot_data(
  x,
  species = NULL,
  tlim = c(NA, NA),
  ylim = c(NA, NA),
  total = FALSE,
  background = TRUE,
  log_y = TRUE
)

Arguments

x	An ArrayTimeBySpecies object.
species	Character vector of species to include, or NULL for all.
tlim	Numeric vector of length two giving the time limits.
ylim	Numeric vector of length two giving the value limits. Values outside them are dropped, as they cannot be seen anyway.
total	Whether to append the total, which is the total over every species the array holds, whatever is drawn.
background	Whether background species are included.
log_y	Whether the values will be drawn on a logarithmic axis. Only then are non-positive values dropped: they have no place on a log axis, but on a linear one they are data like any other, and a quantity that can go negative — a rate of change, a difference between two models — would otherwise lose exactly the part of it that is interesting.

Value

A data frame with Year, value, Species and Legend columns.

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