Multivariate Analysis of Ecological Data with R

Quick notes for a postgraduate course

Preface

These are quick notes on multivariate statistical applications in R for a postgraduate course taught at the Faculty of Biology, University of Barcelona in April-May 2023. They are intended only as teaching materials for the course. They are not comprehensive, might evolve with time and are to be taken “as is”.

Most of the example code uses package vegan (Oksanen et al. 2022). The chapter on cluster analysis will also showcase functions from packages cluster (Maechler et al. 2022) and vegclust (De Caceres, Font, and Oliva 2010). Plots will be done in base graph with examples in ggplot2 (Wickham 2016) as needed. Other packages may be used sparingly and commented on as needed. Code will mostly use base R functions and syntax, with tidyverse (Wickham et al. 2019) exemplified on occasion.

Data sets used in the code come either from example data in the above-cited packages, and Primer example data. Other data, including the authors’ own data, will be referenced on use.

De Caceres, Miquel, Xavier Font, and Francesc Oliva. 2010. “The Management of Vegetation Classifications with Fuzzy Clustering” 21: 1138–51. https://doi.org/10.1111/j.1654-1103.2010.01211.x.

Maechler, Martin, Peter Rousseeuw, Anja Struyf, Mia Hubert, and Kurt Hornik. 2022. “Cluster: Cluster Analysis Basics and Extensions.” https://CRAN.R-project.org/package=cluster.

Oksanen, Jari, Gavin L. Simpson, F. Guillaume Blanchet, Roeland Kindt, Pierre Legendre, Peter R. Minchin, R. B. O’Hara, et al. 2022. “Vegan: Community Ecology Package.” https://CRAN.R-project.org/package=vegan.

Wickham, Hadley. 2016. “Ggplot2: Elegant Graphics for Data Analysis.” https://ggplot2.tidyverse.org.

Wickham, Hadley, Mara Averick, Jennifer Bryan, Winston Chang, Lucy D’Agostino McGowan, Romain François, Garrett Grolemund, et al. 2019. “Welcome to the Tidyverse” 4: 1686. https://doi.org/10.21105/joss.01686.