iris.vfrot: Example for vector fitting on rotated ordination

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

Example for vector fitting on rotated ordination

Description

An object of class vf for use in the examples for nmds and vf. Many of the functions in ecodist take a long time to run, so prepared examples have been included.

Usage

data(iris.vfrot)

Format

See vf for current format specification.

Author(s)

Sarah Goslee

See Also

nmds, vf

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)

# rotate the configuration to maximize variance
iris.rot <- princomp(iris.nmin)$scores

# rotation preserves distance apart in ordination space
cor(dist(iris.nmin), dist(iris.rot))

# 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)

# repeat for the rotated ordination
### vf() is timeconsuming, so this was generated
### in advance and saved.
### set.seed(1234)
### iris.vfrot <- vf(iris.rot, iris[,1:4], nperm=1000)
### save(iris.vfrot, file="ecodist/data/iris.vfrot.rda")
data(iris.vfrot)

par(mfrow=c(1,2))
plot(iris.nmin, col=as.numeric(iris$Species), pch=as.numeric(iris$Species), main="NMDS")
plot(iris.vf)
plot(iris.rot, col=as.numeric(iris$Species), pch=as.numeric(iris$Species), main="Rotated NMDS")
plot(iris.vfrot)

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