ordihull {vegan} | R Documentation

## Add Graphical Items to Ordination Diagrams

### Description

Functions to add convex hulls, arrows, line segments, regular grids of points, `spider' graphs, ellipses or cluster dendrogram 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"),
             show.groups, ...)
    ordiarrows(ord, groups, levels, replicates, display = "sites",
             show.groups, startmark, ...)
    ordisegments(ord, groups, levels, replicates, display = "sites",
             show.groups, ...)
    ordigrid(ord, levels, replicates, display = "sites",  ...)
    ordispider(ord, groups, display="sites", w = weights(ord, display),
             show.groups, ...)
    ordiellipse(ord, groups, display="sites", kind = c("sd","se"), conf,
             draw = c("lines","polygon"), w = weights(ord, display),
             show.groups, ...)
    ordicluster(ord, cluster, prune = 0, display = "sites",
             w = weights(ord, display), ...)

### 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 `polygon`s may be filled and non-transparent.
`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.
`startmark` | plotting characer used to mark the first item. The default is to use no mark, and for instance, `startmark = 1` will draw a circle. For other plotting characters, see `pch` in `points`.
`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.
`...` | Parameters passed to graphical functions such as `lines`, `segments`, `arrows`, `polygon` or to `scores` to select axes and scaling etc.

### Details

Function `ordihull` draws `lines` or `polygon`s 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 `polygon`s 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 package 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.

### Note

These functions add graphical items to ordination graph: You must draw a graph first.

### Author(s)

Jari Oksanen

### See Also

The functions 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'.
    ## Not run:
    ordiellipse(mod, Moisture, kind="se", conf=0.95, lwd=2, col="blue")
    ## End(Not run)

[Package vegan version 1.8-8 Index]