R: Vector fitting

vf {ecodist} | R Documentation

## Vector fitting

### Description

Fits ancillary variables to an ordination configuration.

### Usage

    vf(ord, vars, nperm = 100)

### Arguments

`ord` | matrix containing a 2-dimensional ordination result with axes as columns.
`vars` | matrix with ancillary variables as columns.
`nperm` | number of permutation for the significance test. If nperm = 0, the test will be omitted.

### Details

Vector fitting finds the maximum correlation of the individual variables with a configuration of samples in ordination space.

### Value

an object of class vf containing matrix with the first 2 columns containing the scores for every variable in each of the 2 dimensions of the ordination space. r is the maximum correlation of the variable with the ordination space, and pval is the result of the permutation test.

### Author(s)

Sarah Goslee

### References

Jongman, R.H.G., C.J.F. ter Braak and O.F.R. van Tongeren. 1995. Data analysis in community and landscape ecology. Cambridge University Press, New York.

### See Also

`plot.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]