ordihull {vegan} | R Documentation |

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`

.

ordihull(ord, groups, display = "sites", draw = c("lines","polygon", "none"), show.groups, label = FALSE, ...) ordiellipse(ord, groups, display="sites", kind = c("sd","se"), conf, draw = c("lines","polygon", "none"), w = weights(ord, display), show.groups, label = FALSE, ...) ordispider(ord, groups, display="sites", w = weights(ord, display), 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", ...) ordicluster(ord, cluster, prune = 0, display = "sites", w = weights(ord, display), ...)

`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. With `none`
nothing is drawn, but the function returns the `invisible`
plotting data. |

`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 centre of the points in hull or the ellipse with the group name. |

`startmark` |
plotting character 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. |

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 `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.
An ellipsoid hull can be drawn with function
`ellipsoidhull`

of package cluster.

Functions `ordihull`

and `ordiellipse`

return the
`invisible`

plotting structure. In `ordihull`

this
is a list of coordinates of the hull and in `ordiellipse`

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. The centres of the hulls may differ
from the location of the `label`

which is the centre of the
points instead of the centre of the polygon. With `draw = "none"`

only the result object is returned and nothing is drawn.

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 corresponding `LC' score.

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.

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

Jari Oksanen

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. 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) ordispider(mod, col="red", scaling = 3) 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, col="blue") summary(pl)

[Package *vegan* version 1.16-32 Index]