specpool {vegan}R Documentation

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.

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, a1 and a2 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:
Chao S_P = S_0 + a1/2/a2
First order jackknife S_P = S_0 + a1*(N-1)/N
Second order jackknife S_P = S_0 + a1*(2*n-3)/n - a2*(n-2)^2/n/(n-1)
Bootstrap S_P = S_0 + Sum (1-p_i)^N

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.

Note

The functions are based on assumption that there is a species pool: The community is closed so that there is a fixed pool size S_P. Such cases may exist, although I have not seen them yet. All indices are biased for open communities.

An approximate ("traditional") variant is used for the Chao index.

The function is still preliminary. I may add variances, although these seem to be biased and confusing.

See http://viceroy.eeb.uconn.edu/EstimateS for a more complete (and positive) discussion and alternative software for some platforms.

Author(s)

Jari Oksanen

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)

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