DAISIE_count_species: Count number of species in DAISIE datalist or simulated data.

In DAISIE: Dynamical Assembly of Islands by Speciation, Immigration and Extinction

Count number of species in DAISIE datalist or simulated data.

Description

Calculates various island diversity metrics from island datasets.

Usage

DAISIE_count_species(islands, sort_clade_sizes = TRUE)

Arguments

islands	Island datalist or simulated data in DAISIE datalist format. Can be a single island (empirical data) generated with DAISIE_dataprep or DAISIEprep. Can also be simulated data generated with DAISIE_sim function.
sort_clade_sizes	Default sort_clade_sizes = T outputs clade sizes sorted in ascending order of number of species. sort_clade_sizes=F outputs clade sizes in the same order as they appear in the input datalist.

Value

The output is a list containing the following items:

clade_sizes_sorted	List showing the total number of species in each island clade (including missing species). Each item [[i]] on the list gives the sizes of all clades for a single island. If option sort_clade_sizes = T, the clade sizes for are sorted by increasing number of species. If option sort_clade_sizes = F the clade sizes are given in the same order as in the input datalist.
size_largest_clade	The total number of species in the largest island clade for each island.
mean_clade_size	Mean clade size (average of all island clades)
number_colonisations	The total number of colonisations (clades) on each island.
total_number_species	The total number of species on each island. These are the extant species at present, including missing species; in case of simulations, this is the number of species present on the island at the end of the simulation.

Author(s)

Luis Valente

See Also

DAISIE_dataprep, DAISIE_plot_island

Examples

# Run function with clade sizes in the order they appear in the input data
data("NewZealand_birds_datalist")
species_count <- DAISIE_count_species(NewZealand_birds_datalist)

# Run function with clade sizes in ascending order
species_count_sorted <- DAISIE_count_species(
  NewZealand_birds_datalist,
  sort_clade_sizes = TRUE
)

DAISIE documentation built on Oct. 22, 2023, 1:06 a.m.