vegan (version 1.6-0)

specpool: Extrapolated Species Richness in a Species Pool

Description

The function estimates the extrapolated species richness in a species pool, or the number of unobserved species.

Usage

specpool(x, pool)
specpool2vect(X, index = c("Jack.1","Jack.2", "Chao", "Boot", "Species"))

Arguments

x

Data frame or matrix with species data.

pool

A vector giving a classification for pooling the sites in the species data. If missing, all sites are pooled together.

X

A specpool result object.

index

The selected index of extrapolated richness.

Value

• The function returns a data frame with entries for observed richness and each of the indices for each class in pool vector. The utility function specpool2vect maps the pooled values into a vector giving the value of selected index for each original site.

Details

Many species will always remain unseen or undetected in a collection of sample plots. The function uses some popular ways of estimating the number of these unseen species and adding them to the observed species richness (Palmer 1990, Colwell & Coddington 1994).

In the following, $S_P$ is the extrapolated richness in a pool, $S_0$ is the observed number of species in the collection, $a_1$ and $a_2$ are the number of species occurring only in one or only in two sites in the collection, $p_i$ is the frequency of species $i$, and $N$ is the number of sites in the collection. The variants of extrapolated richness are: ll{ Chao $S_P = S_0 + \frac{a_1^2}{2 a_2}$ First order jackknife $S_P = S_0 + a_1 \frac{N-1}{N}$ Second order jackknife $S_P = S_0 + a_1 \frac{2N - 3}{N} - a_2 \frac{(N-2)^2}{N (N-1)}$ Bootstrap $S_P = S_0 + \sum_{i=1}^{S_0} (1 - p_i)^N$ }

References

Colwell, R.K. & Coddington, J.A. (1994). Estimating terrestrial biodiversity through extrapolation. Phil. Trans. Roy. Soc. London B 345, 101--118.

Palmer, M.W. (1990). The estimation of species richness by extrapolation. Ecology 71, 1195--1198.

See Also

veiledspec, diversity.

Examples

data(dune)
data(dune.env)
attach(dune.env)
pool <- specpool(dune, Management)
pool
op <- par(mfrow=c(1,2))
boxplot(specnumber(dune) ~ Management, col="hotpink", border="cyan3",
 notch=TRUE)
boxplot(specnumber(dune)/specpool2vect(pool) ~ Management, col="hotpink",
 border="cyan3", notch=TRUE)
par(op)