calcbeta: Compute beta diversity summary statistic via distances from...

In bbolker/betararef: Beta Diversity with Rarefaction

Description

Compute beta diversity summary statistic via distances from centroid

Usage

calcbeta(m, method = "jaccard", distances = c("centroid", "pairwise"),
  trap.errors = TRUE, trans = NULL, ...)

Arguments

m	community matrix
method	diversity measure
distances	calculate average distance to centroid or average pairwise distance? The former is generally recommended, but the latter gives results that are easier to compare across treatments with different numbers of patches/sites/communities.
trap.errors	replace error returns with NA values?
trans	transformation to be used; specifies the method parameter for decostand. A value of NULL indicates the default, which depends on the value of method: "hellinger" for "manhattan", "log" for "gower" or "altGower", and "pa" (presence-absence, i.e. reduce data to binary outcomes) for "jaccard" or "raup". Use "identity" if you want to override the defaults and calculate distances from un-transformed data.
...	additional parameters for raupcrick

Examples

## Not run: 
d1 <- replicate(1000,median(calcbeta(betasim(rand="poiss",p.mix=0.25))))
par(las=1,bty="l")
hist(d1,col="gray",main="",xlab="median Jaccard distance from centroid", freq=FALSE)

## End(Not run)

bbolker/betararef documentation built on Sept. 17, 2021, 8:49 a.m.