Skip to contents

Quantitative phylogenetic dissimilarity

ps_dissim.Rd

This function calculates pairwise phylogenetic dissimilarity between communities. It works with both binary and quantitative community data sets. A wide range of phylogentic community dissimilarity metrics are supported, including phylogenetic Sorensen's and Jaccard's distances, turnover and nestedness components of Sorensen's distance (Baselga & Orme, 2012), and phylogenetic versions of all community distance indices provided through the vegan library. The function also includes options to scale the community matrix in order to focus the analysis on endemism and/or on proportional differences in community composition. The results from this function can be visualized using ps_rgb or ps_regions, or used in a variety of statistical analyses.

Usage

ps_dissim(
  ps,
  method = "sorensen",
  fun = c("vegdist", "designdist", "chaodist"),
  endemism = FALSE,
  normalize = FALSE,
  ...
)

Arguments

ps

phylospatial object.

method

Character indicating the dissimilarity index to use:

  • "sorensen": Sorensen's dissimilarity, a.k.a. Bray-Curtis distance (the default)

  • "sorensen_turnover": The turnover component of Sorensen's dissimilarity, a.k.a. Simpson's.

  • "sorensen_nestedness": The nestedness component of Sorensen's dissimilarity.

  • Any other valid method passed to fun. For options, see the documentation for those functions.

fun

Character indicating which general distance function from the vegan library to use: "vegdist" (the default), "designdist", or "chaodist". (While these functions are not explicitly designed to calculate phylogenetic beta diversity, their use here incorporates the phylogenetic components.) This argument is ignored if one of the three "sorensen" methods is selected.

endemism

Logical indicating whether community values should be divided by column totals (taxon range sizes) to derive endemism before computing distances.

normalize

Logical indicating whether community values should be divided by row totals (community sums) before computing distances. If TRUE, dissimilarity is based on proportional community composition. Normalization is applied after endemism.

...

Additional arguments passed to fun.

Value

A pairwise phylogenetic dissimilarity matrix of class dist.

References

Graham, C. H., & Fine, P. V. (2008). Phylogenetic beta diversity: linking ecological and evolutionary processes across space in time. Ecology Letters, 11(12), 1265-1277.

Baselga, A., & Orme, C. D. L. (2012). betapart: an R package for the study of beta diversity. Methods in Ecology and Evolution, 3(5), 808-812.

Pavoine, S. (2016). A guide through a family of phylogenetic dissimilarity measures among sites. Oikos, 125(12), 1719-1732.

See also

ps_add_dissim()

Examples

# example data set:
ps <- ps_simulate(n_tips = 50)

# The default arguments give Sorensen's quantitative dissimilarity index
# (a.k.a. Bray-Curtis distance):
d <- ps_dissim(ps)

# Specifying a custom formula explicitly via `designdist`;
# (this is the Bray-Curtis formula, so it's equivalent to the prior example)
d <- ps_dissim(ps, method = "(b+c)/(2*a+b+c)",
      fun = "designdist", terms = "minimum", abcd = TRUE)

# Alternative arguments can specify a wide range of dissimilarity measures;
# here's endemism-weighted Jaccard's dissimilarity:
d <- ps_dissim(ps, method = "jaccard", endemism = TRUE)