check_rarity_atlantic_ants: Identify Ant Rarity Forms (Atlantic Forest)

In AntClassify: Functional Guilds, Invasion Status, Endemism, and Rarity of Ants

Identify Ant Rarity Forms (Atlantic Forest)

Description

Checks a community matrix for ant rarity forms in the Brazilian Atlantic Forest based on Silva et al. (2024).

Usage

check_rarity_atlantic_ants(
  comm,
  verbose = TRUE,
  plot = TRUE,
  plot_type = c("status", "species"),
  validate = TRUE,
  delay = 0.5
)

Arguments

comm	A community matrix where species are columns and samples are rows.
verbose	Logical; if TRUE, displays progress messages.
plot	Logical; if TRUE, displays a plot (type controlled by plot_type).
plot_type	Character; type of plot to display. "status" (default) shows a bar plot of rarity form abundance proportions. "species" shows a bar plot of individual rare species abundances as a proportion of the total community, colored by rarity form.
validate	Logical; if TRUE, validates species names using GBIF before analysis.
delay	Numeric; seconds to wait between GBIF API calls when validate = TRUE.

Value

Invisibly returns a list with two elements:

table	A data frame containing rare species detected, with columns species, rarity_form, abundance, and percentage.
plot	A ggplot2 object.

AntClassify documentation built on Sept. 4, 2026, 1:06 a.m.