A Beginner’s Guide to Data Exploration and Visualisation with R
by Elena N. Ieno and Alain F. Zuur
In 2010 Alain Zuur, Elena Ieno and Chris Elphick published a paper in Methods in Ecology and Evolution entitled ‘A protocol for data exploration to avoid common statistical problems‘ (Volume 1, Issue 1). Little did they know at the time that this paper would become one of the journal’s all-time top downloaded and top cited papers, with a total of 22,472 downloads between 2010 and 2014.
Based on this success they decided to extend the material in the paper into a book.
Zuur and his colleagues at Highland Statistics ltd. give about 25 five-day statistics courses per year. Their typical audience consists of biological scientists at the post-graduate and post-doctoral levels. Early on in each course they have the following conversation with the participants:
Speaker: “Do you review submitted manuscripts for journals?”
Speaker: “Do you like the statistical part of these manuscripts?”
Speaker: “Do you understand the statistical part?”
Audience: “Not always.”
What if there were ways you could make reviewing your paper easier and more enjoyable for reviewers? What if making your manuscript easier to understand and nicer to read would increase the likelihood of your work being published?
A Beginner’s Guide to Data Exploration and Visualisation with R explains how you can do exactly that! Alain Zuur and Elena Ieno use ecological datasets to discuss the data exploration and visualisation tools you can use to make your paper simpler for readers and reviewers to understand. The authors also explain how to visualise the results of statistical models, an important aspect of scientific papers. Continue reading
What links tea bags, glove puppets, vandalism, and cheddar? Or catching birds, bug soup, criminal profiling, snow leopards and jaguars? Methods in Ecology and Evolution, obviously! We have now been publishing new methods for over 4 years, and the sheer variety of papers we have received is quite amazing: field, lab, statistics, simulations and computing. All areas of methodology have been covered, as have all areas of ecology and evolution: evolutionary biology, population genetics, conservation, stable isotopes, plant ecology, simulation modelling…the variety is almost overwhelming! In this Virtual Issue we have collated some of the most popular papers that we have published over the past four years, to showcase their high quality and diversity.
Our applications papers are always free, and all papers are free after 2 years; in addition all papers are completely free for BES members. So if you don’t have access already, why not join the BES, and along with all of the membership benefits you will get free access to MEE as a bonus?
Our editors and I will be attending some of the major ecology and evolution conferences this summer – so look out for us and do say hi!
The Robert May Prize is awarded annually for the best paper published in Methods by a young author at the start of their research career. We’re delighted to announce that the 2013 winner is Will Pearse, for his Application article “phyloGenerator: an automated phylogeny generation tool for ecologists”.
Although ecologists frequently want to make use of phylogenies, they often lack the skills to create detailed phylogenies of their study taxa. phyloGenerator greatly simplifies the process of creating a phylogeny, automating the download of DNA data and the use of modern phylogenetic software to produce a dated, defensible phylogeny. By linking together a number of existing tools into a single command-line interface and providing an extendable Python library, phyloGenerator is also a useful tool for phylogeneticists wishing to use an open, reproducible phylogenetic workflow. The Editors commented that, “this is an exciting idea that makes phylogenies almost immediately accessible to any researcher needing to use them. It is also a terrific example of the power of what we can achieve when data are made open and accessible.”
Will studied Zoology as an undergraduate at the University of Cambridge, then completed an MSc in Ecology, Evolution and Conservation, and later a PhD at Imperial College London supervised by Andy Purvis and David Roy (Centre for Ecology and Hydrology, Wallingford). His PhD focused on how the phylogeny of species in a community can be used to understand the ecological assembly of that community, and how phylogeny informs our understanding of communities undergoing change. Will is now a post-doc in Jeannine Cavender-Bares’ lab at the University of Minnesota, where he studies urban plant communities.
In addition to Will, the following young authors have been highly commended for their innovative articles:
– Emily Dennis from the University of Kent, for her co-authored paper Indexing butterfly abundance whilst accounting for missing counts and variability in seasonal pattern.
– Joost Keuskamp and Bas Dingemans from Utrecht University, for their co-authored paper Tea Bag Index: a novel approach to collect uniform decomposition data across ecosystems. There is also an interview with the Tea Bag Index team to accompany this article.
The above 3 articles are included in a free virtual issue, along with all of the winning and highly commended articles from the other 4 British Ecological Society journals young investigator prizes.
The Robert May Prize is awarded annually to the best paper published in Methods by a young author at the start of their research career. We’re delighted to announce that the 2012 winner is Sarah Papworth from Imperial Collage London, for her article “Movement ecology of human resource users: using net squared displacement, biased random bridges and resource utilization functions to quantify hunter and gatherer behaviour”. Although GPS trackers can rapidly collect vast amounts of data on animal movement, appropriate methods for analysing this data are still being developed. The paper describes a methodological framework for the analysis of GPS track records of foragers which routinely return to a central place after foraging, such as a den or nest. The framework combines three existing methods in a flexible method for the accurate description of resource use and movement in humans and animals. This approach will be particularly useful for our understanding of human resource extraction and conservation planning.
Sarah studied a BA Honours in Anthropology at the University of Durham, which focused on human and primate behaviour. This lead to an interest in field biology in the tropics, and she went on to study blue monkeys in Uganda. She then completed an MSc in Ecology, Evolution and Conservation, and a PhD in Conservation Science, at Imperial College London, supervised by E.J. Milner-Gulland and Katie Slocombe (University of York). Her PhD focused on human and primate behaviour within the context of hunting by the Waorani of Amazonian Ecuador, and involved extensive fieldwork. Data collected for her PhD were used to illustrate the methodological framework developed in the Robert M. May prize-winning paper. She has just moved to Singapore, where she is currently a research fellow focusing on poverty and biodiversity at the National University of Singapore.
In addition to the above winner, the following young authors have been highly commended for their innovative articles:
– Brett Favaro from the Marine Ecology Lab, for his article “TrapCam: an inexpensive camera system for studying deep-water animals“, which is accompanied by a video demonstrating the construction of the TrapCam apparatus.
– David Jacoby from the Marine Biological Association of the United Kingdom, for his article “Developing a deeper understanding of animal movements and spatial dynamics through novel application of network analyses“.
The above 3 articles will be included in a free virtual issue this year, along with all of the winning and short-listed articles from the other 4 British Ecological Society journals young investigator prizes.
Welcome to part 3 of our review of the most highly cited papers published by Methods in Ecology and Evolution in 2011. In case you missed them, here are part 1 and part 2 of this series.
Population monitoring and management
Evolutionary ecology and phylogenomics
Today we look at part 2 of our most cited papers in Methods in Ecology and Evolution in 2011.
Plant monitoring and modelling
Our most cited papers on statistical methods in ecology and evolution, modelling species and the environment, and physiological ecology were covered in part 1 – and finally tomorrow we’ll look at our top papers in population monitoring, climate change, evolutionary ecology and phylogenomics.
Methods in Ecology and Evolution will be receiving its first Impact Factor in summer 2012 and we are very impressed with how well our articles are being cited. For those of you who have been following Methods from the start, you will notice some papers that we have already mentioned last year in our top cited blog posts. These are still going strong! Over the next few days we’ll be highlighting our most cited papers across a broad range of fields – stay tuned on MethodsBlog.
Statistical methods in ecology & evolution
Modelling species and the environment
Tomorrow we will be posting part 2, where we’ll be showcasing our top cited papers in plant monitoring and modelling, stable isotope ecology and community ecology, and come back on Wednesday for part 3, when we’ll be revealing our top papers in population monitoring, climate change, evolutionary ecology and phylogenomics.
How safe is mist netting? Evaluating the risk of injury and mortality to birds remains our most highly accessed article for the second month in a row – just managing to stay ahead of RNCEP: global weather and climate data at your fingertips, which has been receiving fantastic interest since we published it in July of this year. This open source package, written in R, is intended to help ecologists integrate long-term atmospheric data into their research, and the published application note is, of course, free to access.
Other papers making a splash include Holger Schielzeth’s Simple means to improve the interpretability of regression coefficients, which was recently rated a “must read” on F1000, and Comparative interpretation of count, presence–absence and point methods for species distribution models, published at the start of the month, by Geert Aarts, John Fieberg and Jason Matthiopoulos.
Welcome back for the final part of our look at the most highly cited papers published by Methods in Ecology and Evolution so far, as recorded by ISI. (Don’t forget to look back at the first two parts, if you missed them previously!)
- Featuring 10 phenological estimators using simulated data
Jean-Pierre Moussus, Romain Julliard and Frédéric Jiguet
- A framework for assessing threats and benefits to species responding to climate change
Chris D. Thomas, Jane K. Hill, Barbara J. Anderson, Sallie Bailey, Colin M. Beale, Richard B. Bradbury, Caroline R. Bulman, Humphrey Q. P. Crick, Felix Eigenbrod, Hannah M. Griffiths, William E. Kunin, Tom H. Oliver, Clive A. Walmsley, Kevin Watts, Nicholas T. Worsfold and Tim Yardley
Evolutionary ecology and phylogenomics
Here’s part 2 of our look at Methods in Ecology and Evolution’s most highly cited papers to date!
Plant monitoring and modelling
We covered statistical methods in ecology and evolution, modelling species and the environment, and physiological ecology in part 1 of our look at our most popular papers so far – and on Monday we’ll be rounding off with our top papers in population monitoring, climate change, evolutionary ecology and phylogenetics.