Analysis of Ecological and Palaeoecological Data with R

University of Maine, 8th-12th August 2013

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

This is an intensive 4-day course that will provide participants with a training in the theory and practice of analysing ecological and palaeoecological data using the free R software environment. The workshop has been timed to coincide with the North American Diatom Symposium 2013 that will run from 13th-17th August in Bar Harbour, Maine.

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 course will be led by Dr. Steve Juggins. Steve is a co-editor and chapter author of the book “Data Handling and Numerical Techniques in Paleolimnology” to be published by Springer in 2012, and author of 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 8th 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 will be posted in due course.

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 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 limited to 20 participants.  Details of costs and registration can be found here.


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: 12 Jul 2013 © Copyright 2013 Steve Juggins