# ordihull: Display Groups or Factor Levels in Ordination Diagrams In vegan: Community Ecology Package

## Description

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`.

## Usage

 ``` 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"), ...) ```

## Arguments

 `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. `spiders` Are centres or spider bodies calculated either as centroids (averages) or spatial medians. `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). `area` Evaluate the area of convex hulls of `ordihull`, or of ellipses of `ordiellipse`. `permutations` a list of control values for the permutations as returned by the function `how`, or the number of permutations required, or a permutation matrix where each row gives the permuted indices. `parallel` Number of parallel processes or a predefined socket cluster. With `parallel = 1` uses ordinary, non-parallel processing. The parallel processing is done with parallel package. `...` Parameters passed to graphical functions 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 `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 one-sided 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.

## Value

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.

## Note

These functions add graphical items to ordination graph: You must draw a graph first. To draw line segments, grids or arrows, see `ordisegments`, `ordigrid` and`ordiarrows`.

## Author(s)

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`.

## Examples

 ``` 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 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) ```

### Example output     ```Loading required package: permute
This is vegan 2.4-3
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
```

vegan documentation built on May 2, 2019, 5:51 p.m.