R: Find minimum stress configuration

min.nmds {ecodist} | R Documentation

## Find minimum stress configuration

### Description

Finds minimum stress configuration from output of nmds()

### Usage

    ## S3 method for class 'nmds'
    min(..., na.rm = FALSE, dims = 2)
    nmds.min(x, dims = 2)

### Arguments

`...` | output from nmds()
`x` | output from nmds()
`dims` | desired dimensionality of result. If dims = 0 then the overall minimum stress configuration is chosen. By default, the best two-dimensional configuration is returned.
`na.rm` | Not used; there should be no NA values in a NMDS configuration.

### Details

For back-compatibility, the `nmds.min` function remains.

### Value

Configuration of minimum stress ordination (dataframe of coordinates). The stress and r^2 for the minimum stress configuration are stored as attributes.

### Author(s)

Sarah Goslee

### 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)

[Package ecodist version 2.0.1 Index]