ggvegan2

ggvegan2 provides ggplot2 graphics for some vegan objects. Current versions of vegan have support of ggplot2 compatible scores of many result objects. This package provides functions that can directly access those scores to build graphics using ggplot2 style geom_ functions with full control. The package also provides ggplot2 alternatives for some lattice panel functions.

The package is complementary to ggvegan package which has larger choice of functions and supports a wider range of vegan methods. The ggvegan package is mainly built on fortify to extract data and autoplot to fast and easy graphics.

Currently ggvegan2 contains:

• Flexible and configurable plotting for most vegan ordination objects. These are an alternative with contrasting philosophy to autoplot functions in ggvegan package. The basic function is ordiggplot that only sets up the graphic data frame to which users can add ordination elements with geom_ordipoint, geom_orditext, geom_ordilabel and geom_ordiarrow. It also provides support functions for adding fitted environmental vectors in ordination. Moreover, it provides function ggscores that can be used to pass ordiggplot elements to standard ggplot2 geometries.

• Alternatives to lattice graphics function in vegan using autoplotand fortify. Currently implemented for Rank-Abundance Distributions models (radline, radfit, radfit.frame), permustats diagnostic plots, and Rényi diversities (renyi, renyiaccumand shold also work for similar tsallis functions). The plan is to phase out lattice graphics from vegan in favour of these ggplot2 alternatives.