beta.raref: Rarefaction of true beta diversity (Whittaker's...

In zdealveindy/theta: Co-occurrence based measure of species habitat specialization

Description

Calculates true beta diversity rarefied to given number of samples.

Usage

beta.raref(comm, sites, conditioned = TRUE, gamma = "jack1")

Arguments

comm	Community matrix (or data frame) for which rarified beta diversity is calculated.
sites	Number of sites for which rarefied true beta should be calculated.
conditioned	Logical; should the result be conditioned on the provided dataset (comm matrix) or not? Default = TRUE.
gamma	Estimator of gamma diversity used to estimate number of species in the community (in case that conditioned = FALSE). gamma = c('chao', 'jack1', 'jack2', 'boot').

Value

The function returns list with the following items:

• sites: number of sites for which rarefaction is calculated;

• gamma: estimated number of species (gamma diversity) for given number of sites;

• gamma.sd: standard deviation of gamma estimate;

• alpha: mean number of species per sample (alpha diversity);

• beta: true beta diversity, calculated as gamma / alpha;

• beta.sd: standard deviation of true beta diversity, calculated as gamma.sd / alpha (perhaps wrongand better not to use, needs proof!);

Author(s)

David Zeleny ([e-mail]). Heavily builds on the code from function specaccum in package vegan written by Roeland Kindt and Jari Oksanen to construct sample-based rarefaction curves.

Examples

sc <- sample.comm (simul.comm (totS = 100), Np= 100)
beta.raref (comm = sc$a.mat, sites = 10)

# True beta diversity calculated on pair of samples (minus one) 
# is very close to mean pairwise Sorensen:
beta.raref (comm = sc$a.mat, sites = 2)$beta-1
library (vegan)
mean (vegdist (decostand (sc$a.mat, 'pa')))

zdealveindy/theta documentation built on May 4, 2019, 9:13 p.m.