rotate2d: Rotate a 2D ordination.

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

Rotate a 2D ordination.

Description

Rotates a two-dimensional ordination configuration to place the direction indicated along the horizontal axis.

Usage

rotate2d(ord, x)

Arguments

ord	A matrix or data frame with two columns, or a vf object, containing the points of an ordination configuration.
x	The coordinates of a point in the ordination space.

Details

The configuration ord is rotated so that the vector defined by c(0, 0), and x is along the horizontal axis. This can be useful for placing a specific variable, for instance from vf(), in a consistent direction across multiple ordinations. Doing so can facilitate interpretation.

Value

A rotated data frame of coordinates of the same size as ord and in the same order. If ord was produced by vf(), the complete vf object is returned.

Author(s)

Sarah Goslee

See Also

vf, nmds

Examples

# Example of multivariate analysis using built-in iris dataset
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)

# fit the data to the ordination as vectors
### vf() is timeconsuming, so this was generated
### in advance and saved.
### set.seed(1234)
### iris.vf <- vf(iris.nmin, iris[,1:4], nperm=1000)
### save(iris.vf, file="ecodist/data/iris.vf.rda")
data(iris.vf)

plot(iris.nmin, col=as.numeric(iris$Species), pch=as.numeric(iris$Species), main="NMDS")
plot(iris.vf)

# rotate configuration so Sepal Width is along the horizontal axis

iris.nmin.rot <- rotate2d(iris.nmin, iris.vf[2, 1:2])
iris.vf.rot <- rotate2d(iris.vf, iris.vf[2, 1:2])

plot(iris.nmin.rot, col=as.numeric(iris$Species), pch=as.numeric(iris$Species), main="NMDS")
plot(iris.vf.rot)

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