specpool {vegan} | R Documentation |
The function estimates the extrapolated species richness in a species pool, or the number of unobserved species.
specpool(x, pool) specpool2vect(X, index = c("Jack.1","Jack.2", "Chao", "Boot", "Species"))
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. |
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 |
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.
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.
Jari Oksanen
Colwell, R.K. & Coddington, J.A. (1994). Estimating terrestrial biodiversity through extrapolation. Phil. Trans. Roy. Soc. London B 345, 101118.
Palmer, M.W. (1990). The estimation of species richness by extrapolation. Ecology 71, 11951198.
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)