diversity(x, index = "shannon", MARGIN = 1, base = exp(1))
rarefy(x, sample, MARGIN = 1)shannon, simpson or
invsimpson.base used in shannon. Both variants of Simpson's index are based on $S = \sum p_i^2$. Choice simpson returns $1-S$ and
invsimpson returns $1/S$.
Function rarefy gives the expected species richness in random
subsamples of size sample from the community. The maximum
permissible sample size is $N - \max(n_i)$, where $N$ is the
total number of individuals and $n_i$ are the abundances of
species on site $i$. Please note that rarefaction can be done only with real
counts of individuals: the current function will silently truncate
abundances to integers and give wrong results. The function
rarefy is based on Hurlbert's (1971) formulation.
Better histories can be told about Simpson's index than about Shannon's index, and still more grandiose stories about rarefaction (Hurlbert 1971). However, these indices are all very closely related, and there is no reason to despise one more than others (but if you are a graduate student, don't drag me in, but obey your Professor's orders).
data(varespec)
H <- diversity(varespec)
## Species richness (S) and Pielou's evenness (J):
S <- apply(varespec>0, 1, sum)
J <- H/log(S)Run the code above in your browser using DataLab