R: Example for vector fitting on rotated ordination

iris.vfrot {ecodist} | R Documentation

## 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)

[Package ecodist version 2.0.1 Index]