Analysis of Ecological and Palaeoecological Data with R

University of Cape Town, 4th-7th February 2015

Prof Steve Juggins, School of Geography, Politics & Sociology, Newcastle University.

This is an intensive 4-day course that will provide participants with a training in the theory and practice of analysing palaeoecological data using the R statistical software. The workshop has been timed to coincide with the AfQUA (African Quaternary) Conference that will run from 30th Jan to 4th Feb in Cape Town.

The R statistical language and environment has become increasingly popular in recent years, in part because it is a free, open source application, and because it is incredibly powerful and easily extended via add-on packages. This course is aimed at those with little or no experience in R and will address both the essential numerical understanding and the R skills required to handle, process and analyse palaeoecological data.

The course will be led by Prof Steve Juggins. Steve is a co-editor and chapter author of the book "Data Handling and Numerical Techniques in Paleolimnology" and author of several R packages for analysing palaeolimnological and palaeoenvironmental data. 

Course content

The course will comprise formal lectures and practical computer sessions with time available in the evenings for informal discussion and for students to work on their own data. 

Participants will be expected to bring their own laptops with R installed and we will provide a self-led tutorial to help with this before the course. The first day will cover exploratory data analysis and graphics in R. Day 2 will cover regression, including the use of modern regression methods involving smoothers. On day 3 we will focus on ordination and related methods for analysing multivariate data. Appropriate hypothesis testing using permutations for spatial and temporal data will be emphasised. Finally, we consider palaeoenvironmental reconstruction and developing age models for stratigraphic sequences. Chronological clustering, smoothing, and interpolating stratigraphic data and calculating rates of change will also be covered.  A provisional lecture / practical list is appended below.

Each topic will be presented using a 30-45-minute lecture and 1-hour practical. The lecture will introduce the theory of each set of methods and models, discuss their assumptions, and give participants the knowledge to enable them to identify the type of model appropriate for a particular data analytical problem. The practicals will then reinforce the understanding of the lecture material as you apply the techniques to datasets to address real palaeoecological questions.

You are particularly encouraged to bring your own data to discuss and work on during the course.

The course will be limited to 20 participants 

Provisional timetable

University of Cape Town, 5th to 8th February 2015

Programme based on 30-45 minute lectures and 1-2 hour practicals.

Day 1


1. Introduction and summarising data, graphics and exploratory data analysis (EDA)

EDA practical

2. Data types, data structures and data manipulation

EDA practical


3. Data transformation and outliers

Data transformation practical

4. Data manipulation and R programming

Data manipulation practical

Day 2



5. Regression

Regression practical

6. Multiple regression, model building and variable selection

Model building with R


7. Distance measures and cluster analysis

Cluster analysis practical

Day 3


8. Ordination overview, principal components analysis (PCA)

PCA practical

9. Correspondence analysis (CA), detrended CA, and Non-metric multidimensional scaling

CA, DCA and nMDS practical


10. Constrained ordination (CCA, RDA)

CCA / RDA practical

11. Variable selection, partial ordination, variance partitioning, permutation tests

Ordination model building practical

Day 4

12. Environmental reconstruction, visualising palaeoecological data
13. Age-depth modelling or analysis of stratigraphic data Practical


A full reading list will be included with the course materials. In the meantime we recommend the following two books: Borcard, D., Gillet, F., & Legendre, P. (2011) Numerical Ecology with R Springer.
Zuur, A., Ieno, E., & Meesters, E. (2009) A Beginner's Guide to R Springer.

R may be downloaded from

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Last updated on: 16 Apr 2014  Copyright 2014 Steve Juggins