Description Usage Arguments Value Author(s) Examples
Calculates true beta diversity rarefied to given number of samples.
beta.raref(comm, sites, conditioned = TRUE, gamma = "jack1")
Community matrix (or data frame) for which rarified beta diversity is calculated.
Number of sites for which rarefied true beta should be calculated.
Logical; should the result be conditioned on the provided dataset (
Estimator of gamma diversity used to estimate number of species in the community (in case that
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
gamma.sd: standard deviation of
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!);
David Zeleny (firstname.lastname@example.org). Heavily builds on the code from function
specaccum in package
vegan written by Roeland Kindt and Jari Oksanen to construct sample-based rarefaction curves.
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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')))
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