vegan (version 1.6-0)

ordihull: Add Graphical Items to Ordination Diagrams

Description

Functions to add convex hulls, arrows, line segments, regular grids of points, `spider' graphs, ellipses, cluster dendrogram or spanning trees to ordination diagrams. The ordination diagrams can be produced by vegan plot.cca, plot.decorana or ordiplot.

Usage

ordihull(ord, groups, display = "sites", draw = c("lines","polygon"), ...)
ordiarrows(ord, groups, levels, replicates, display = "sites", ...)
ordisegments(ord, groups, levels, replicates, display = "sites", ...)
ordigrid(ord, levels, replicates, display = "sites",  ...)
ordispider(ord, groups, display="sites", w = weights(ord, display), ...)
ordiellipse(ord, groups, display="sites", kind = c("sd","se"), conf,
            draw = c("lines","polygon"), w = weights(ord, display), ...)
ordicluster(ord, cluster, prune = 0, display = "sites",
            w = weights(ord, display), ...)
ordispantree(ord, tree, display = "sites", ...)

Arguments

ord

An ordination object or an ordiplot object.

groups

Factor giving the groups for which the graphical item is drawn.

levels, replicates

Alternatively, regular groups can be defined with arguments levels and replicates, where levels gives the number of groups, and replicates the number of successive items at the same group

display

Item to displayed.

draw

Use either lines or polygon to draw the line. Graphical parameters are passed to both. The main difference is that polygons may be fil

w

Weights used to find the average within group. Weights are used automatically for cca and decorana results, unless undone by the user. w=NULL<

kind

Whether standard deviations of points (sd) or standard deviations of their (weighted) averages (se) are used.

conf

Confidence limit for ellipses, e.g. 0.95. If given, the corresponding sd or se is multiplied with the corresponding value found from the Chi-squared distribution with 2df.

cluster

Result of hierarchic cluster analysis, such as hclust or agnes.

prune

Number of upper level hierarchies removed from the dendrogram. If prune $>0$, dendrogram will be disconnected.

tree

Structure defining a spanning tree. This can be a result of spantree or a vector giving the child node of each parent omitting the first point. Values NA means that there is no lin

...

Parameters passed to graphical functions such as lines, segments, arrows,

Details

Function ordihull draws lines or polygons for the convex hulls found by function chull encircling the items in the groups.

Function ordiarrows draws arrows and ordisegments draws line segments between successive items in the groups. Function ordigrid draws line segments both within the groups and for the corresponding items among the groups.

Function ordispider draws a `spider' diagram where each point is connected to the group centroid with segments. Weighted centroids are used in the correspondence analysis methods cca and decorana or if the user gives the weights in the call. If ordispider is called with cca or rda result without groups argument, the function connects each `WA' scores to the correspoding `LC' score.

Function ordiellipse draws lines or polygons for dispersion ellipse using either standard deviation of point scores or standard error of the (weighted) average of scores, and the (weighted) correlation defines the direction of the principal axis of the ellipse. The function requires library ellipse. An ellipsoid hull can be drawn with function ellipsoidhull of package cluster.

Function ordicluster overlays a cluster dendrogram onto ordination. It needs the result from a hierarchic clustering such as hclust or agnes, or other with a similar structure. Function ordicluster connects cluster centroids to each other with line segments. Function uses centroids of all points in the clusters, and is therefore similar to average linkage methods.

Function ordispantree overlays a (minimum) spanning tree onto ordination. It needs a result from spantree or a vector listing children of each parent, starting from second (i.e., omitting the first: the number of links is one less number of points). Missing links are denoted as NA. For an example, see spantree.

See Also

The function pass parameters to basic graphical functions, and you may wish to change the default values in arrows, lines, segments and polygon. You can pass parameters to scores as well. Other underlying functions are chull and ellipse.

Examples

data(dune)
data(dune.env)
mod <- cca(dune ~ Moisture, dune.env)
attach(dune.env)
plot(mod, type="n")
ordihull(mod, Moisture)
ordispider(mod, col="red")
plot(mod, type = "p", display="sites")
ordicluster(mod, hclust(vegdist(dune)), prune=3, col = "blue")
# The following is not executed automatically because it needs
# a non-standard library `ellipse'. 
ordiellipse(mod, Moisture, kind="se", level=0.95, lwd=2, col="blue")