vf: Vector fitting

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

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, which is a data frame 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)

# rotate configuration so Sepal Width is along the horizontal axis

iris.nmin.rot <- rotate2d(iris.nmin, iris.vf[2, 1:2])
iris.vf.rot <- rotate2d(iris.vf, iris.vf[2, 1:2])

plot(iris.nmin.rot, col=as.numeric(iris$Species), pch=as.numeric(iris$Species), main="NMDS")
plot(iris.vf.rot)

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