ps_diversity {phylospatial}R Documentation

Calculate spatial phylogenetic diversity and endemism metrics

Description

This function calculates a variety of alpha phylogenetic diversity metrics, including measures of richness, regularity, and divergence. If continuous community data (probabilities or abundances) are provided, they are used in calculations, giving quantitative versions of the classic binary metrics.

Usage

ps_diversity(ps, metric = c("PD", "PE", "CE", "RPE"), spatial = TRUE)

Arguments

ps

phylospatial object (created by phylospatial() or ps_simulate()).

metric

Character vector containing the abbreviation for one or more diversity metrics listed in the details below. Can also specify "all" to calculate all available metrics. A small subset of common measures are selected by default.

spatial

Logical: should the function return a spatial object (TRUE, default) or a matrix (FALSE)?

Details

The function calculates the following metrics. Endemism-weighted versions of most metrics are available. All metrics are weighted by occurrence probability or abundance, if applicable.

Richness measures:

Divergence measures:

Regularity measures:

In the above equations, b indexes all taxa including terminals and larger clades; t indexes terminals only; p_i is the occurrence value (binary, probability, or abundance) of clade/terminal i in a given community; L_b is the length of the phylogenetic branch segment unique to clade b; and r_i is the sum of p_i across all sites. For Shannon and Simpson indices, only nonzero elements of p_b are used, n_b = p_b / \sum_{b}{p_b L_b}, and e_b = p_b / \sum_{b}{p_b L_b r_b^{-1}}.

Value

A matrix, sf data frame, or SpatRaster with a column or layer for each requested diversity metric.

References

Faith, D. P. (1992). Conservation evaluation and phylogenetic diversity. Biological Conservation, 61(1), 1-10.

Laffan, S. W., & Crisp, M. D. (2003). Assessing endemism at multiple spatial scales, with an example from the Australian vascular flora. Journal of Biogeography, 30(4), 511-520.

Rosauer, D. A. N., Laffan, S. W., Crisp, M. D., Donnellan, S. C., & Cook, L. G. (2009). Phylogenetic endemism: a new approach for identifying geographical concentrations of evolutionary history. Molecular Ecology, 18(19), 4061-4072.

Allen, B., Kon, M., & Bar-Yam, Y. (2009). A new phylogenetic diversity measure generalizing the Shannon index and its application to phyllostomid bats. The American Naturalist, 174(2), 236-243.

Chao, A., Chiu, C. H., & Jost, L. (2010). Phylogenetic diversity measures based on Hill numbers. Philosophical Transactions of the Royal Society B: Biological Sciences, 365(1558), 3599-3609.

Mishler, B. D., Knerr, N., González-Orozco, C. E., Thornhill, A. H., Laffan, S. W., & Miller, J. T. (2014). Phylogenetic measures of biodiversity and neo-and paleo-endemism in Australian Acacia. Nature Communications, 5(1), 4473.

Tucker, C. M., Cadotte, M. W., Davies, T. J., et al. (2016) A guide to phylogenetic metrics for conservation, community ecology and macroecology. Biological Reviews, 92(2), 698-715.

Kling, M. M., Mishler, B. D., Thornhill, A. H., Baldwin, B. G., & Ackerly, D. D. (2019). Facets of phylodiversity: evolutionary diversification, divergence and survival as conservation targets. Philosophical Transactions of the Royal Society B, 374(1763), 20170397.

Examples

ps <- ps_simulate()
div <- ps_diversity(ps)
terra::plot(div)


[Package phylospatial version 1.1.1 Index]