outlier_multi: Multivariate outliers

In phytomosaic/ecole: ecole: School of Ecology Package

Description

Find extreme values in ecological community data

Usage

outlier_multi(
  x,
  mult = 3,
  method = "bray",
  metric = "SD",
  plot = TRUE,
  perc = NULL,
  pick = NULL,
  ...
)

Arguments

x	array of species data
mult	SD threshold for 'outliers' = the number of SD's away from the mean distance at which an outlier is defined; default is 3 times the SD
method	distance measure; follows vegdist
metric	defaults to 'SD'; only other alternative is 'MAD'
plot	logical, should a histogram of distances be drawn?
perc	numeric, returns outlier values beyond the specified percentile
pick	numeric, returns this number of most extreme outliers
...	further arguments passed to other methods

Details

Outlier analysis based on community distances. Emulates PC-ORD, but see also McCune and Grace (2002).

Value

A data frame with plot identifiers, calculated distances, and standard deviations from the mean distance, either with or without a histogram.

References

McCune, B., and J. B. Grace. 2002. Analysis of Ecological Communities. MjM Software, Gleneden Beach, Oregon, USA. 304 pp.

See Also

outlier_uni for univariate analog.

Other outlier functions: outlier_uni()

Examples

require(vegan)
data(dune)
set.seed(19)
spe <- rbind(dune, runif(ncol(dune),0,1000)) # add an outlier row
outlier_multi(spe, mult=3, plot=FALSE)
outlier_multi(spe, mult=3)
outlier_multi(spe, perc=5)
outlier_multi(spe, pick=5)

phytomosaic/ecole documentation built on Jan. 2, 2022, 11:24 p.m.