prepare_ArrayTimeBySpecies_plot_data: 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
)

Value

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

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.