Vector fitting

Description

Fits environmental variables to an ordination configuration.

Usage

1
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, Sarah.Goslee@ars.usda.gov

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

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## Not run: 
# Example of multivariate analysis using built-in iris dataset
data(iris)
iris <- iris[seq(1, 150, by=3),]
iris.md <- distance(iris[,1:4], "mahal")

# Minimum-stress 2-dimensional nonmetric multidimensional scaling configuration
# Uses small number of separate ordinations (5) to increase speed of example.
# Use more for final analysis.
iris.nmds <- nmds(iris.md, mindim=2, maxdim=2, nits=3)
iris.nmin <- nmds.min(iris.nmds)

# Plot NMDS result with symbols denoting species
plot(iris.nmin, pch=as.numeric(iris[,5]))

# Fit vectors for the main variables to the NMDS configuration
iris.vf <- vf(iris.nmin, iris[,1:4], nperm=10)
plot(iris.vf, col="blue")

## End(Not run)