What is vegan3d?

vegan3d is an R package of 3D plotting routines split apart from vegan. It can be used for dynamic plots based on rgl package, and for static 3D plots based on scatterplot3d package.

The package contains the following functions:

• orditkplot: a Tcl/Tk-based 2D editable plot. Function opens a graphic window where labels can be moved with mouse, but points are fixed. It is also possible to edit labels and zoom into graph, and the final plot can be saved in various graphic formats or saved as an R object that can be further manipulated or plotted with standard R graphics commands.

• ordirgl with its support functions orglpoints, orgltext, orglsegments, orglellipse, orglspider, orglcluster and orglspantree. These require rgl package and provide dynamic ordination graphics.

• rgl based support functions rgl.isomap to display isomap results, and rgl.renyiaccum to display renyiaccum results.

• ordiplot3d (based on scatterplot3d) and ordilattice3d (based on lattice) for static 3D ordination diagrams.

• orditree3d and ordirgltree functions to display a coloured dendrogram tree over a 2D plane. The first is a static function based on scatterplot3d and the latter a dynamic spinnable plot based on rgl. The method was initially designed for showing dendrograms over ordination plane but it can use other planes, for instance a map of locations of points.