vegetarian: Jost Diversity Measures for Community Data

This package computes diversity for community data sets using the methods outlined by Jost (2006, 2007). While there are differing opinions on the ideal way to calculate diversity (e.g. Magurran 2004), this method offers the advantage of providing diversity numbers equivalents, independent alpha and beta diversities, and the ability to incorporate 'order' (q) as a continuous measure of the importance of rare species in the metrics. The functions provided in this package largely correspond with the equations offered by Jost in the cited papers. The package computes alpha diversities, beta diversities, gamma diversities, and similarity indices. Confidence intervals for diversity measures are calculated using a bootstrap method described by Chao et al. (2008). For datasets with many samples (sites, plots), sim.table creates tables of all pairwise comparisons possible, and for grouped samples sim.groups calculates pairwise combinations of within- and between-group comparisons.

Author
Noah Charney, Sydne Record
Date of publication
2012-10-29 08:59:58
Maintainer
Noah Charney <noah@alumni.amherst.edu>
License
GPL-2
Version
1.2

View on CRAN

Man pages

bootstrap
Estimates Uncertainties with Bootstrapping
d
'Numbers Equivalents' for Alpha, Beta and Gamma Diversity...
H
'Standard Diversity Indices' for Alpha, Beta, and Gamma...
M.homog
MacArthur's Homogeneity Measure
normalize.rows
Converts absolute abundances to relative proportions of...
p.q.sum
Sum of proportional abundance of species
Rel.homog
Relative Homogeneity
simesants
Harvard Forest Simes Tract Ant Community Data
sim.groups
Within- and Between-Group Similarities
similarity
Similarity Summary Table
sim.table
Similarity Summary Table
turnover
Turnover Rate per Sample
vegetarian-package
Jost Diversity Measures for Community Data

Files in this package

vegetarian
vegetarian/data
vegetarian/data/simesants.rda
vegetarian/NAMESPACE
vegetarian/man
vegetarian/man/normalize.rows.Rd
vegetarian/man/similarity.Rd
vegetarian/man/p.q.sum.Rd
vegetarian/man/simesants.Rd
vegetarian/man/sim.table.Rd
vegetarian/man/turnover.Rd
vegetarian/man/d.Rd
vegetarian/man/H.Rd
vegetarian/man/M.homog.Rd
vegetarian/man/Rel.homog.Rd
vegetarian/man/bootstrap.Rd
vegetarian/man/vegetarian-package.Rd
vegetarian/man/sim.groups.Rd
vegetarian/DESCRIPTION
vegetarian/MD5
vegetarian/R
vegetarian/R/vegetarian.R