DAISIE_count_species {DAISIE} | R Documentation |
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
)