plot.nmds: Plot information about NMDS ordination

In phiala/ecodist: Dissimilarity-Based Functions for Ecological Analysis

Plot information about NMDS ordination

Description

Graphical display of stress and r2 for NMDS ordination along number of dimensions.

Usage

## S3 method for class 'nmds'
plot(x, plot = TRUE, xlab = "Dimensions", ...)

Arguments

x	an object of S3 class nmds, created by nmds()
plot	optional, if TRUE a figure is produced
xlab	optional, label for x axis of graph
...	optional, other graphics parameters

Value

Produces a two-panel plot with stress and r2 for ordination by number of dimensions. Points show the mean value; lines indicate minimum and maximum.

Author(s)

Dean Urban

See Also

nmds

Examples

data(iris)
iris.d <- dist(iris[,1:4])

### nmds() is timeconsuming, so this was generated
### in advance and saved.
### set.seed(1234)
### iris.nmds <- nmds(iris.d, nits=20, mindim=1, maxdim=4)
### save(iris.nmds, file="ecodist/data/iris.nmds.rda")
data(iris.nmds)

# examine fit by number of dimensions
plot(iris.nmds)

# choose the best two-dimensional solution to work with
iris.nmin <- min(iris.nmds, dims=2)

phiala/ecodist documentation built on Nov. 5, 2023, 10:47 a.m.