abundant {vegsoup}R Documentation

Return Abundant Species According to a Threshold Value.

Description

Return species meeting the abundance threshold given by argument treshold applied to constancy(obj) along with median abundance (see quantile).

Usage

## S4 method for signature 'Vegsoup'
abundant(obj, threshold = 75, layers = FALSE, ...)

Arguments

obj

An object inheriting from class VegsoupPartition.

threshold

numeric. Threshold value.

layers

logical. If FALSE do not take layers into account.

...

currently not used.

Value

A data.frame.

Author(s)

Roland Kaiser

See Also

constancy, decode

Examples

require(vegsoup)

data(barmstein)
x <- barmstein

abundant(x) # with default values
abundant(x, treshold = 50) # treshold set to 50% constancy
abundant(x, treshold = 75, layers = TRUE) # include layers

x <- VegsoupPartition(barmstein, k = 2)
abundant(x) # threshold applied over all partitions
abundant(partition(x, 1)) # for a selected partition
abundant(partition(x, 2), layers = TRUE) # for a selected partition with layers

[Package vegsoup version 0.2-9 Index]