R: Plots fitted vectors onto an ordination diagram

plot.vf {ecodist} | R Documentation

## Plots fitted vectors onto an ordination diagram

### Description

Add vector fitting arrows to an existing ordination plot.

### Usage

    ## S3 method for class 'vf'
    plot(x, pval = 1, cex = 0.8, ascale = 0.9, ...)

### Arguments

`x` | an object of S3 class `vf`, created by `vf()`
`pval` | optional, critical p-value for choosing variables to plot
`cex` | text size
`ascale` | optional, proportion of plot area to use when calculating arrow length
`...` | optional, other graphics parameters

### Value

Adds arrows to an existing ordination plot. Only arrows with a p-value less than pval are added. By default, all variables are shown.

### Author(s)

Sarah Goslee

### See Also

`vf`

### 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)

[Package ecodist version 2.0.7 Index]