ordihull: Display Groups or Factor Levels in Ordination Diagrams
In pattakosn/Rworkshop: Community Ecology Package

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.

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),
         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, ...)

`ord`	An ordination object or an `ordiplot` object.
`groups`	Factor giving the groups for which the graphical item is drawn.
`display`	Item to displayed.
`draw`	Use either `lines` or `polygon` to draw the lines. Graphical parameters are passed to both. The main difference is that `polygon`s may be filled and non-transparent. With `none` nothing is drawn, but the function returns the `invisible` plotting data.
`col`	Colour of hull or ellipse lines (if `draw = "lines"`) or their fills (if `draw = "polygon"`) in `ordihull` and `ordiellipse`. When `draw = "polygon"`, the colour of bordering lines can be set with argument `border` of the `polygon` function. For other functions the effect depends on the underlining functions this argument is passed to.
`alpha`	Transparency of the fill `col`our with `draw = "polygon"` in `ordihull` and `ordiellipse`. The argument takes precedence over possible transparency definitions of the colour. The value must be in range 0...255, and low values are more transparent. Transparency is not available in all graphics devices or file formats.
`show.groups`	Show only given groups. This can be a vector, or `TRUE` if you want to show items for which condition is `TRUE`. This argument makes it possible to use different colours and line types for groups. The default is to show all groups.
`label`	Label the `groups` by their names in the centroid of the object. `ordiellipse` and `ordihull` use standard `text`, and others use `ordilabel`.
`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` sets equal weights to all points.
`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.
`object`	A result object from `ordihull` or `ordiellipse`. The result is `invisible`, but it can be saved, and used for summaries (areas etc. of hulls and ellipses).
`...`	Parameters passed to graphical functions or to `scores` to select axes and scaling etc.

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

Function ordiellipse draws lines or polygons 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 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 result objects have a summary method that returns the coordinates of the centres of the ellipses or hulls and their surface areas in user units. With draw = "none" only the result object is returned and nothing is drawn.

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.

data(dune)
data(dune.env)
mod <- cca(dune ~ Management, dune.env)
attach(dune.env)
## pass non-graphical 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)