Description Usage Arguments Details Value Note Author(s) See Also Examples
Functions to add convex hulls, ‘spider’ graphs, ellipses
or cluster dendrogram to ordination diagrams. The ordination
diagrams can be produced by vegan
plot.cca
,
plot.decorana
or ordiplot
.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16  ordihull(ord, groups, display = "sites", draw = c("lines","polygon", "none"),
col = NULL, alpha = 127, show.groups, label = FALSE, ...)
ordiellipse(ord, groups, display="sites", kind = c("sd","se"), conf,
draw = c("lines","polygon", "none"), w = weights(ord, display),
col = NULL, alpha = 127, show.groups, label = FALSE, ...)
ordispider(ord, groups, display="sites", w = weights(ord, display),
spiders = c("centroid", "median"), show.groups,
label = FALSE, ...)
ordicluster(ord, cluster, prune = 0, display = "sites",
w = weights(ord, display), ...)
## S3 method for class 'ordihull'
summary(object, ...)
## S3 method for class 'ordiellipse'
summary(object, ...)
ordiareatest(ord, groups, area = c("hull", "ellipse"), permutations = 999,
parallel = getOption("mc.cores"), ...)

ord 
An ordination object or an 
groups 
Factor giving the groups for which the graphical item is drawn. 
display 
Item to displayed. 
draw 
Use either 
col 
Colour of hull or ellipse lines (if 
alpha 
Transparency of the fill 
show.groups 
Show only given groups. This can be a vector, or

label 
Label the 
w 
Weights used to find the average within group. Weights are
used automatically for 
kind 
Whether standard deviations of points ( 
conf 
Confidence limit for ellipses, e.g. 0.95. If given, the
corresponding 
spiders 
Are centres or spider bodies calculated either as centroids (averages) or spatial medians. 
cluster 
Result of hierarchic cluster analysis, such as

prune 
Number of upper level hierarchies removed from the
dendrogram. If 
object 
A result object from 
area 
Evaluate the area of convex hulls of 
permutations 
a list of control values for the permutations
as returned by the function 
parallel 
Number of parallel processes or a predefined socket
cluster. With 
... 
Parameters passed to graphical functions or to

Function ordihull
draws lines
or
polygon
s for the convex
hulls found by function chull
encircling
the items in the groups.
Function ordiellipse
draws lines
or
polygon
s for dispersion ellipses
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.
An ellipsoid hull can be drawn with function
ellipsoidhull
of package cluster.
Function ordihull
and ordiellipse
return invisibly an
object that has a summary
method that returns the coordinates
of centroids and areas of the hulls or ellipses. Function
ordiareatest
studies the onesided hypothesis that these
areas are smaller than with randomized 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 corresponding
‘LC’ score. If the argument is a (invisible
)
ordihull
object, the function will connect the points of the
hull to their centroid.
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.
Functions ordihull
, ordiellipse
and ordispider
return the invisible
plotting structure.
Function ordispider
return the coordinates to which each
point is connected (centroids or ‘LC’ scores).
Function ordihull
returns a list of coordinates of the hulls
(which can be extracted with scores
), and ordiellipse
returns a list of covariance matrices and scales used in drawing the
ellipses.
These functions add graphical items to ordination graph: You
must draw a graph first. To draw line segments, grids or arrows, see
ordisegments
, ordigrid
andordiarrows
.
Jari Oksanen
The functions pass parameters to basic graphical functions,
and you may wish to change the default values in
lines
, segments
and
polygon
. You can pass parameters to
scores
as well. Underlying function for
ordihull
is chull
.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25  data(dune)
data(dune.env)
mod < cca(dune ~ Management, dune.env)
attach(dune.env)
## pass nongraphical arguments without warnings
plot(mod, type="n", scaling = 3)
## Catch the invisible result of ordihull...
pl < ordihull(mod, Management, scaling = 3, label = TRUE)
## ... and find centres and areas of the hulls
summary(pl)
## use ordispider to label and mark the hull
plot(mod, type = "n")
pl < ordihull(mod, Management, scaling = 3)
ordispider(pl, col="red", lty=3, label = TRUE )
## ordispider to connect WA and LC scores
plot(mod, dis=c("wa","lc"), type="p")
ordispider(mod)
## Other types of plots
plot(mod, type = "p", display="sites")
ordicluster(mod, hclust(vegdist(dune)), prune=3, col = "blue")
plot(mod, type="n", display = "sites")
text(mod, display="sites", labels = as.character(Management))
pl < ordiellipse(mod, Management, kind="se", conf=0.95, lwd=2, draw = "polygon",
col="skyblue", border = "blue")
summary(pl)

Loading required package: permute
Loading required package: lattice
This is vegan 2.43
BF HF NM SF
CCA1 0.2917476 0.36826105 1.3505642 0.2762936
CCA2 0.8632208 0.09419919 0.2681515 0.8139398
Area 0.1951715 0.59943363 1.7398193 1.0144372
BF HF NM SF
CCA1 0.4312652 0.5583211 1.87848340 0.5601499
CCA2 1.3273917 0.6373120 0.05503211 1.3859924
Area 1.4559842 1.3806668 2.73667419 1.5559135
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