Resources

Tree Diversity Analysis

My introduction to using R for microbial community analysis was Tree Diversity Analysis by Roeland Kindt and Richard Coe and available from the World Agroforesty Centre as a free PDF file. It is the companion to the R package BiodiversityR. the third chapter, how to install the package, is out of date. BiodiversityR can now be installed fro CRAN like most other R packages. At least originally there was a GUI version, but I found it choked on the large data sets typical of microbial community analyses and do not use it.

I believe everyone can benefit from reading the first two chapters. The first is on the very important topic of sampling design, so read this chapter even if you are already familiar with other topics in the book. The second chapter is on data preparation, including how to check for errors and missing values. These need to be resolved early, otherwise garbage in garbage out, as the saying goes, and one could be misled by their results.

Subsequent chapters include analysis of species richness and diversity, regression of species counts on variables, presence/absence of species, ecological distance methods, clustering, and ordination (PCA, PCoA, NMDS). These chapters are good introductions to the methods, but if there is a downside, it is that there is not sufficient explanation regarding why to chose one (especially ordination) method over another. My  next recommendation covers that problem (perhaps in overwhelming detail).