quantile: Sample Quantiles for a Community Matrix

In vegsoup: Classes and Methods for Phytosociology

Description

Returns sample quantiles corresponding to the given probabilities for each species in each partition or for the whole data set.

Usage

## S4 method for signature 'VegsoupPartition'
quantile(x, probs = seq(0, 1, 0.25), na.rm = FALSE, names = TRUE, type = 7,
		  coverscale = FALSE, ...)
## S4 method for signature 'Vegsoup'
quantile(x, probs = seq(0, 1, 0.25), na.rm = FALSE, names = TRUE, type = 7,
		  coverscale = FALSE, ...)

Arguments

x	A VegsoupPartition object.
probs	numeric vector of probabilities. See quantile.
na.rm	Not used. A community matrix in vegsoup is not allowd to have NAs!
names	Not used.
type	Selecting one of the nine quantile algorithms. See quantile.
coverscale	Recode abundances and return orginal scale. Only applies if is.ordinal(x) evaluates to TRUE.
...	Not used.

Details

If the input object has layers the summary statistics are calculated for each layer. If abundances are ordinal as.numeric(obj) is used to obtain numeric values for calculation. If coverscale = TRUE results are back converted to ordinal scale (e.g. Braun-Blanquet scale), otherwise will be returned as class midpoints as defiuned in coverscale(x). Note, suppling presence/absence data is supported, however, results may be meaningless.

For Vegsoup objects values for the whole (unpartitioned) data set are returned.

Value

An array with as many dimensions as length(probs) containing the summary information of quantile for a species by cluster matrix.

Author(s)

Roland Kaiser

See Also

boxplot.stats, fivenum, Coverscale, Latex.

Examples

require(vegsoup)

data(barmstein)
x <- VegsoupPartition(barmstein, k = 2)

x1 <- quantile(x, probs = seq(0, 1, 0.25))
x1[ , , 3]

x2 <- quantile(x, probs = c(0, 0.5, 1), coverscale = TRUE)

x2[ , , 2] # probs[2]

vegsoup documentation built on Feb. 24, 2021, 3 a.m.