"An old dog learning new tricks."
If you installed R from the Ubuntu repository with
sudo apt-get install r-baseyou most likely got an out of date version. In February 2018, that method still gave me R version 3.2.3 (2015-12-10). To get the latest versions of R and its packages, you need to add CRAN to the apt-get repositories. Do this with the code below. Enter one line at a time. Cut and paste to prevent errors. Continue reading “Update R in Ubuntu”
The R package vegan includes the function ordiplot for making ordination plots using R’s base graphics. Additionally vegan provides several functions for enhancing the plots with spiders, hulls, and ellipses. It is even possible to overlay an ordination plot with a cluster diagram. (See my package ggordiplots on GitHub for making the same kinds of plots with ggplot graphics.) Vegan’s functions for adding these layers begin with “ordi”: ordispider, ordihull, ordiellipse, ordicluster. Earlier this year I discovered the package vegan3d. It makes use of rgl graphics which means that the plots it generates can be scaled and rotated with the mouse. This is not just fun – it allows you to see how well separated treatment groups are in the ordination space.