R packages
I’ve been using R since the first few months of my PhD. R is a great language for working with and analysing data, has a vibrant community around it and packages to do just about anything you might want to do with data. During that time I’ve written a few R packages and contributed to some others.
R packages I wrote and maintain
My R packages implement methods commonly used in community ecology, and palaeolimnology and palaeoecology.
- analogue contains functions for analogue methods used in palaeoecology, as well as a variety of techniques useful for analysing sediment core data and fitting transfer functions
- permute implements the full range of restricted permutation designs present in the commercial software Canoco for use in evaluating multivariate ordinations and other techniques common to ecology
- cocorresp is an R implementation of co-correspondence analysis, an ordination technique for finding common patterns of covariance in two community matrices
- gratia provides ggplot2-based plots for GAMs fitted using the mgcv package
- ggvegan provides ggplot2 versions of plotting methods available in the vegan package
- temporalEF generates temporal eigenfunctions through the use of 1-dimensional PCNMs and AEMs
- canadaHCD is an R-based interface to the Government of Canada’s Historical Climate Data website, which provides access to hourly, daily, and monthly weather records for stations throughout Canada.
R packages I contribute to
I contribute code and either maintain or help maintain the following R packages
- vegan is a large package for community ecology with a wide range of multivariate methods including common ordination methods, diversity measures, Null models and much more
- pcurve is an R port of Glenn De’Ath’s pcurve library for S-Plus, which is an implementation of the method of principal curves with a focus on their application in identifying long ecological gradients
I am also the maintainer of the Environmetrics Task View on CRAN.
