check_endemic_atlantic_ants: Identify Endemic Ant Species (Atlantic Forest)

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

Identify Endemic Ant Species (Atlantic Forest)

Description

Checks a community matrix for ant species endemic to the Brazilian Atlantic Forest based on Silva et al. (2025).

Usage

check_endemic_atlantic_ants(comm, verbose = TRUE, plot = TRUE)

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 the plot of endemic vs. other species proportions.

Value

Invisibly returns a list with two elements:

table	A data frame containing endemic species detected, with columns species, abundance, and percentage.
plot	A ggplot2 object showing the proportion of endemic vs. other species.

Examples

# Create a small example community matrix
species_list <- c(
  "Camponotus fallatus", "Solenopsis saevissima", "Hypoponera leninei",
  "Pachycondyla striata", "Pheidole megacephala"
)
set.seed(123)
comm_data <- matrix(
  rpois(length(species_list) * 3, lambda = 2),
  nrow = 3,
  ncol = length(species_list),
  dimnames = list(paste0("sample", 1:3), species_list)
)
result <- check_endemic_atlantic_ants(comm_data, verbose = FALSE, plot = FALSE)
head(result$table)

AntClassify documentation built on April 9, 2026, 9:08 a.m.