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. In general, the orglXXXX functions are similar as 2D ordiXXXX functions in vegan.

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

• ordiplot3d for static 3D ordination diagrams. This requires scatterplot3d package.

• 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.

Special plotting functions based on lattice and tcltk packages are still in vegan. ggplot2-based functions are in ggvegan and ggvegan2 packages.

Released version

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