similarity: Similarity Summary Table

In vegetarian: Jost Diversity Measures for Community Data

Description

Creates a summary table of community overlap for all possible pairwise combinations of samples (e.g. sites, plots) using the similarity function.

Usage

similarity(abundances, abundances2 = NULL, q = 1, boot = FALSE, boot.arg = list(s.sizes = NULL, num.iter = 100))

Arguments

abundances	Community data as a matrix where columns are individual species and rows are sites. Matrix elements are abundance data (e.g. counts, percent cover estimates). May be given as a vector with abundances2 as a vector for a second community.
abundances2	Community data, a vector of different species within a site. Vector elements are abundance data (e.g. counts, percent cover estimates). If abundances is given a matrix, then abundances2 defaults to a logical FALSE statement.
q	Order of the diversity measure. Defaults to the Shannon case where q = 1.
boot	Logical indicating whether to use bootstrapping to estimate uncertainty.
boot.arg	(optional) List of arguments to pass bootstrapping function: list(s.sizes=number you specify, num.iter=number you specify)

Details

This function calculates pairwise similarity for two or more samples, so the abundance data must be a matrix with two or more rows (samples). Depending on the specification of the order (q), other different similarity indices may be calculated (e.g. Sorenson index when q=0, Horn index when q=1, Morisita-Horn index when q=2) (Jost 2007).

Value

Similarity	A matrix of pairwise similarities showing community overlap calculated using the similarity function.
StdErr	(optional) Standard error of value estimated through bootstrapping.

Author(s)

Noah Charney, Sydne Record

References

Jost, L. 2007. Partitioning diversity into independent alpha and beta components. Ecology 88(10): 2427-2439.

See Also

sim.table, sim.groups, bootstrap

Examples

data(simesants)
hemlock<-subset(simesants,Habitat=="Hemlock")[,-1]
hardwood<-subset(simesants,Habitat=="Hardwood")[,-1]
similarity(rbind(hemlock,hardwood))
similarity(hemlock,abundances2=hardwood)
similarity(hemlock,abundances2=hardwood,boot=TRUE)
similarity(hemlock,abundances2=hardwood,q=2,boot=TRUE,boot.arg=list(num.iter=200))

Example output

[1] 0.8847291
[1] 0.8847291
$Simlarity
[1] 0.8847291

$StdErr
[1] 0.02305693

$Simlarity
[1] 0.9478082

$StdErr
[1] 0.01632159

vegetarian documentation built on May 1, 2019, 8:01 p.m.