Plots fitted vectors onto an ordination diagram

Description

Add vector fitting arrows to an existing ordination plot.

Usage

1
2
## 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, Sarah.Goslee@ars.usda.gov

See Also

vf

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
## 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)