WK 14

Advanced Community Data Analysis Using the vegan Package in R

This session is envisioned as a follow-up to the "Introduction to vegan" session offered in an earlier workshop or one for those that already use vegan and want to delve into some of the detail. We will focus on vegan’s more advanced and recently released features, including the use of restricted permutations to test a range of experimental designs. We will focus in particular on when and how to use multivariate methods including constrained ordination (CCA, RDA, Constrained PCoA), as well as between-group tests such as PERMANOVA. We will cover concepts such as design- and model-based permutations and the exchangeability of samples in tests. We will also discuss the use of vegan to go beyond simply fitting a constrained ordination model, to diagnostics, plotting, etc. The workshop will assume that participants have a basic level of familiarity with working in R, including data import and basic indexing and subsetting, with the use of basic functions in vegan, and with community ecology statistics, such as ordination. All participants must bring their own laptop with R and RStudio (available free online for all platforms at rstudio.com) pre-installed. All data files and code for this workshop will be made publicly available on github.com, so participants as well as those unable to attend will have access to them as a resource. The organizers are expert users of R and vegan, and include one of the maintainers of the package.