ordilattice3d: 3D Trellis (Lattice) Plots for Ordination

In vegan3d: Static and Dynamic 3D and Editable Interactive Plots for the 'vegan' Package

3D Trellis (Lattice) Plots for Ordination

Description

Function ordicloud provides an interface for 3D ordination graphics using Trellis function cloud in package lattice.

Usage

ordilattice3d(x, data = NULL, formula, display = "sites", choices = 1:3,
    panel = "panel.ordi3d", prepanel = "prepanel.ordi3d",  ...)

Arguments

x	An ordination result that vegan function scores knows: any ordination result in vegan and many others.
data	Optional data to amend ordination results. The ordination results are found from x, but you may give here data for other variables needed in plots. Typically these are environmental data.
formula	Formula to define the plots. A default formula will be used if this is omitted. The ordination axes must be called by the same names as in the ordination results (and these names vary among methods).
display	The kind of scores: an argument passed to scores.
choices	The axes selected: an argument passed to scores.
panel, prepanel	The names of the panel and prepanel functions.
...	Arguments passed to scores methods or lattice functions.

Details

The functions provide an interface to the lattice function cloud. All graphical parameters are passed to the lattice functions so that the graphs are configurable.

The argument x must always be an ordination result. The scores are extracted with vegan function scores so that these functions work with all vegan ordinations and many others.

The formula is used to define the models. Function has a default formula which is used if formula is missing. The formula must use the names of ordination scores and names of data.

The ordination scores are found from x, and data is optional. The data should contain other variables than ordination scores to be used in plots. Typically, they are environmental variables (typically factors) to define panels or plot symbols (lattice argument groups).

The proper work is done by the panel function. The layout can be changed by defining own panel functions. See panel.cloud for details and survey of possibilities.

Value

The function return Lattice objects of class "trellis".

Note

Function is still rudimentary. For instance, it cannot display biplot arrows or factor centroids from constrained ordination or envfit.

Author(s)

Jari Oksanen

See Also

For functions used in ordilattice3d see Lattice, cloud, panel.cloud. Function ordiplot3d provides a more mature and flexible alternative which can also handle biplot arrows and factor centroids and adding new graphical elements to the plots.

Examples

data(dune, dune.env)
ord <- cca(dune)

ordilattice3d(ord, form = CA2 ~ CA3*CA1, groups = Manure, data = dune.env,
   scaling="sites")
ordilattice3d(ord, form = CA2 ~ CA3*CA1 | Management, groups = Manure,
   data = dune.env, auto.key = TRUE, type = c("p","h"), scaling = "sites")

vegan3d documentation built on April 12, 2025, 1:44 a.m.