DAISIE (version 4.5.0)

DAISIE_count_species: 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)

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.

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.

Author

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
)