1. Overview

Here we provide links to the tutorials of the “Analysis of biodiversity and ecosystem functioning in R” class. The tutorials are written as R markdown scripts.

R is a free software environment for statistical computing and graphics. It is the most frequent programming language in ecology.

RStudio is an IDE (Integrated Development Environment) for R. It includes a console, syntax-highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management.

The tutorials contain chunks of code that can be run in R, as well as results and figures produced by R, annotations and excercises. Instructions on how to set up R and RStudio, to start a new project and install R packages will be given on the first day. Please install the latest versions of the following programs and always install the R packages indicated at the beginning of each tutorial before the classes start.

R from http://www.r-project.org/

RStudio from https://posit.co/download/rstudio-desktop/

1.1. Main content

Practical Content
1 Introduction to R
2 Barro Colorado site-species matrix; Species richness; Species frequency
3 Rarefaction curves; Species Richness Estimators
4

Non-parametric indices (Shannon, Simpson, Pielou’s evenness)

Parametric indices (Rank-abundance, Fisher’s alpha)
5 Alpha vs gamma richness; species-area slope; similarity indices
6 Alpine dataset; CA; Interpretation
7 Phylogenetic diversity; Functional diversity

1.2. R packages needed

Extra R packages are needed for some practicals:

  • All practicals: vegan
  • Practical 4:\(~\)\(~\) psych and hillR
  • Practical 6:\(~\)\(~\) ade4
  • Practical 7:\(~\)\(~\) ape, picante, fundiversity and BAT