Description Usage Arguments Value Author(s) Examples
Calculates true beta diversity rarefied to given number of samples.
1  beta.raref(comm, sites, conditioned = TRUE, gamma = "jack1")

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 ( 
gamma 
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 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!);
David Zeleny (zeleny.david@gmail.com). Heavily builds on the code from function specaccum
in package vegan
written by Roeland Kindt and Jari Oksanen to construct samplebased rarefaction curves.
1 2 3 4 5 6 7 8  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)$beta1
library (vegan)
mean (vegdist (decostand (sc$a.mat, 'pa')))

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