alpha {BAT}

Alpha diversity (Taxon, Phylogenetic or Functional Diversity - TD, PD, FD).

Description

Observed richness with possible rarefaction, multiple sites simultaneously.

Usage

alpha(comm, tree, raref = 0, runs = 100)

Arguments

comm

A sites x species matrix, with either abundance or incidence data.

tree

A phylo or hclust object (used only for PD or FD) or alternatively a species x traits matrix or data.frame to build a functional tree.

raref

An integer specifying the number of individuals for rarefaction (individual based). If raref < 1 no rarefaction is made. If raref = 1 rarefaction is made by the minimum abundance among all sites. If raref > 1 rarefaction is made by the abundance indicated. If not specified, default is 0.

runs

Number of resampling runs for rarefaction. If not specified, default is 100.

Details

TD is equivalent to species richness. Calculations of PD and FD are based on Faith (1992) and Petchey & Gaston (2002, 2006), which measure PD and FD of a community as the total branch length of a tree linking all species represented in such community. PD and FD are calculated based on a tree (hclust or phylo object, no need to be ultrametric). The path to the root of the tree is always included in calculations of PD and FD. The number and order of species in comm must be the same as in tree. The rarefaction option is useful to compare communities with much different numbers of individuals sampled, which might bias diversity comparisons (Gotelli & Colwell 2001)

Value

A matrix of sites x diversity values (either "Richness" OR "Mean, Median, Min, LowerCL, UpperCL and Max").

References

Faith, D.P. (1992) Conservation evaluation and phylogenetic diversity. Biological Conservation, 61, 1-10.

Gotelli, N.J. & Colwell, R.K. (2001) Quantifying biodiversity: procedures and pitfalls in the measurement and comparison of species richness. Ecology Letters, 4, 379-391.

Petchey, O.L. & Gaston, K.J. (2002) Functional diversity (FD), species richness and community composition. Ecology Letters, 5, 402-411.

Petchey, O.L. & Gaston, K.J. (2006) Functional diversity: back to basics and looking forward. Ecology Letters, 9, 741-758.

Examples

comm <- matrix(c(0,0,1,1,0,0,2,1,0,0), nrow = 2, ncol = 5, byrow = TRUE)
trait = 1:5
tree <- tree.build(trait)
plot(tree, "u")
alpha(comm)
alpha(comm, raref = 0)
alpha(comm, tree)
alpha(comm, tree, 2, 100)