Analysing Palaeolimnological Data with R

University Marine Biological Station Millport, Isle of Cumbrae, Scotland
16th – 20th August 2012

This course is now full for normal registration.  Please email Steve Juggins if you want to be placed on a waiting list in case of cancellations.  Places are still available for PAGES funding (see below).

Dr Steve Juggins, School of Geography, Politics & Sociology, Newcastle University, Newcastle upon Tyne, NE3 4LP.

Dr Gavin Simpson
, Department of Geography, University College London, Gower Street, London  WC1E 6BT.

Analysing Palaeoenvironmental Data with R is an intensive 4-day course that will provide participants with a training in the theory and practice of analysing palaeolimnological data using the free R software environment. The workshop has been timed to coincide with the 12th International Paleolimnology Symposium, 20-24th August 2012, which will be held in Glasgow, to reduce the expense of attendance for those who will be attending the symposium.

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 palaeolimnological data.

The workshop will be led by Dr. Steve Juggins and Dr. Gavin Simpson. Steve is a co-editor and both are chapter authors in the forthcoming handbook on “Data Handling and Numerical Techniques in Paleolimnology” to be published by Springer in 2012, and both have authored several R packages for analysing palaeolimnological and palaeoenvironmental data. 

Course content

The couse will comprise lectures and computer sessions with time available in the evenings for students to work on their own data and for discussions with the course leaders. 

The workshop will begin on the evening of the 16th August with a welcome and an introduction to R to revise basic understanding. 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 following day we will cover exploratory data analysis and graphics in R. Next we discuss regression, including the use of modern regression methods involving smoothers. We will consider how the temporal nature of palaeo data can be accommodated by relaxation of the assumption of independence. On day 3 we will focus on cluster analysis and ordination, techniques widely used to summarise patterns in stratigraphic data. Appropriate hypothesis testing using permutations for temporal data will be emphasised. Next 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 more detailed lecture / practical list can be found here.

Each topic will be presented using a 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 following practical will reinforce the understanding of the lecture material as you apply the techniques to datasets to adress real palaeolimnological questions.

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

Logistics and cost

The course will be held at the University Marine Biological Station Millport, on the Isle of Cumbrae in the Clyde Estuary (  The station is an excellent location for the course with easy travel links to Glasgow and convenient for those also attending the 12th IPS.

The course will be limited to c. 30 participants, with accommodation in shared (twin rooms).  The total cost of the course is £300 + VAT, which includes food, accommodation and course materials. (Note: there may be limited accommodation in single rooms available at extra cost.  Please let us know if you are interested in this option).

The course has generous financial support from PAGES ( to cover  travel and course costs (up to £1100) for five young researchers from developing countries.  If you would like to apply for PAGES financial support please send a CV and short covering letter outlining your research interests and why the course will benefit you to both Gavin and Steve.

Although convenient for those attending the International Paleolimnology Symposium the course is open to people wanting an introduction to R and not attending the IPS.

The deadline for registration is 31/06/2012 (15/05/2012 for those applying for PAGES financial support).  To register please complete this form and return to and submit payment using the Newcastle University online payment system to secure your place.


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

More details and full lecture / practical list

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Last updated on: 12 Jul 2013 © Copyright 2013 Steve Juggins