data(BCI)
H <- diversity(BCI)
simp <- diversity(BCI, "simpson")
invsimp <- diversity(BCI, "inv")
## Unbiased Simpson (Hurlbert 1971, eq. 5) with rarefy:
unbias.simp <- rarefy(BCI, 2) - 1
## Fisher alpha
alpha <- fisher.alpha(BCI)
## Plot all
pairs(cbind(H, simp, invsimp, unbias.simp, alpha), pch="+", col="blue")
## Species richness (S) and Pielou's evenness (J):
S <- specnumber(BCI) ## rowSums(BCI > 0) does the same...
J <- H/log(S)
## beta diversity defined as gamma/alpha - 1:
data(dune)
data(dune.env)
alpha <- with(dune.env, tapply(specnumber(dune), Management, mean))
gamma <- with(dune.env, specnumber(dune, Management))
gamma/alpha - 1
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