Towards a More Reproducible Ecology

The following post has been provided by Dr Nick Isaac. Nick is organising the OpenData and Reproducibility Workshop at Charles Darwin House, London on 21 April 2015 (more information below). He is also an Associate Editor for Methods in Ecology and Evolution.

Macro_finalThe open science movement has been a major force for change in how research is conducted and communicated. Reproducibility lies at the heart of the open science agenda. It’s a broad topic, covering how data are shared, interpreted and reported.

Reproducibility has been advanced by a coalition of publishers (who have been embarrassed by a series of high-profile retractions), funding agencies keen that data should be re-useable after the life of a grant, and young researchers taking a more collaborative attitude than previous generations.

There is now a vast range of tools and platforms to help scientists share data and other materials (e.g. Dryad, Github, Figshare) and to create efficient and reproducible workflows (e.g. Sweave, Markdown, Git and, of course, R). There’s even a MOOC (Massive Open Online Course) in Reproducible Research, run out of Johns Hopkins University.

Ecology has lagged behind wet-lab biology and other disciplines in the adoption of reproducibility concepts and there are few examples of ecological studies that are truly reproducible. To address this, we’re running a one-day workshop at Charles Darwin House, London on Tuesday 21 April entitled OpenData & Reproducibility Workshop: the Good Scientist in the Open Science era. Continue reading

Understanding and Presenting YOUR Data

A Beginner’s Guide to Data Exploration and Visualisation with R
by Elena N. Ieno and Alain F. Zuur

A Beginner's Guide to Data ExplorationIn 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?”
Audience: “Yes.”
Speaker: “Do you like the statistical part of these manuscripts?”
Audience: “No!”
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

Issue 6.3

Issue 6.3 is now online!

The March issue of Methods is now online!

We have three freely available Applications articles in this issue. Anyone can access these with no subscription required and no charge to download.

TR8: This R package was built to provide plant scientists with a simple tool for retrieving plant functional traits from freely accessible online traitbases.

StereoMorph: A new R package for the rapid and accurate collection of 3D landmarks and curves using two standard digital cameras.

MotionMeerkat: A new standalone program that identifies motion events from a video stream. This tool reduces the time needed to review videos and accommodates a variety of inputs.

This month we have a total of FIVE Open Access articles. That makes eight articles in this issue of Methods in Ecology and Evolution that you can read for free!

Continue reading

My Career in Science (and Elsewhere)

The following is a piece written by Jane Elith, the author highlighted in our first International Women’s Day article. Dr Elith also won the Recognition of Achievement for a Research Paper award for Methods in Ecology and Evolution in 2014 (you can read her full paper here).

 We asked Jane: what drew you to a career in science?

Jane Elith MEE Recognition of Achievement for a Research Paper Award Winner

Dr Jane Elith

I’ve always loved nature, and at school found I was better at science than other subjects. Obvious choices for university would have been Quantitative Ecology or Conservation Biology, but back in the early 1970s such courses didn’t exist in Melbourne. I decided on a Bachelor of Science (Forestry) – science, but focused on trees. However that wasn’t to be – the Head of Forestry advised me that there was no future for women in Forestry. By memory, his reasoning was that there were no facilities for women in the field and entrenched attitudes amongst foresters would make it impossible to get a job. I can’t quite believe, looking back, that I accepted that and changed tracks. But I did.

Continue reading

Senior Editor Profile: JANA VAMOSI

As many of you will already know, Dr Vamosi is the newest (and first female) Senior Editor for Methods in Ecology and Evolution. She joined Rob Freckleton and Bob O’Hara in June of 2014 and has been working on manuscripts ever since. Jana is also organising the Canadian half of our 5th Anniversary Symposium in April (the Early Bird deadline for which is approaching – Friday 20 March). We are also running a Poster Session at this event; if you would be interested in submitting a poster, please contact Jana here.

Jana VamosiThe research in Jana’s lab focuses on the macroevolution, macroecology, community ecology, and conservation biology of plants. Many of their projects require gathering empirical data on the mechanistic underpinnings of plant diversity in specific locales. However, they often incorporate global phylogenetic perspectives as well. You can learn more about the lab’s work here.

Jana’s most recent publications include ‘Species and Phylogenetic Heterogeneity in Visitation Affects Reproductive Success in an Island System’ (along with Lorraine Adderley) which was published in International Journal of Plant Sciences in February and ‘Evolutionary ecology of specialization: insights from phylogenetic analysis’ (along with W Scott Armbruster and Susanne S Renner) first published in October 2014.

As part of our International Women’s Day activities, we wanted to have a short profile on Jana. Luckily, she had recently written one for the 6th International Barcode of Life Conference which will be taking place at the University of Guelph from 18 August to 21 August 2015. Jana will be giving a Plenary session (along with Charles Godfrey and Naomi Pierce) on Ecological Interactions.

The following was originally posted on the International Barcode of Life Conference Continue reading

Our 5th Anniversary Symposium

Charles Darwin House, London, UK: 10:00 – 18:00 (GMT)

Alberta Room, Dining Centre, University of Calgary, Canada: 08:30 – 17:00 (MST)

22 April 2015

Symp ad w_bannerMethods in Ecology and Evolution, the British Ecological Society’s youngest journal, turns five this year. To celebrate we will be holding a joint Symposium – beginning in the UK and concluding in Canada.

We will be hearing what’s in store for the future from young, international researchers including the first winner of the Robert May Young Investigator’s Prize and some of the journal’s Associate Editors. Topics that will be discussed include model selection, data analysis, R and more.

You can find out more about the Symposium, including information on all of the talks on our website. If you have any questions that aren’t answered there, feel free to get in touch (coordinator@methodsinecologyandevolution.org).

If you haven’t registered to attend the Symposium yet, there is still time. Be quick though, our Early Bird prices are coming to an end on Friday 20 March.

You can register for our 5th Anniversary Symposium HERE.

We understand that for a lot of our dedicated readers, it simply won’t be possible to get to either Calgary or London. Therefore, we will be live streaming the whole event. Every speaker’s talk, from the UK and from Canada, will be available LIVE – online and free of charge. We will be releasing more information about the live stream closer to the date, so keep an eye out for it here and on our website (link above).

We hope that you will be able join us, in person or online, to celebrate five wonderful years of Methods in Ecology and Evolution.

 

Flawed Method puts Tiger Rise in Doubt

The following is a press release about the Methods paper ‘An examination of index-calibration experiments: counting tigers at macroecological scales‘ taken from the University of Oxford News and Events page:

Flaws in a method commonly used in censuses of tigers and other rare wildlife put the accuracy of such surveys in doubt, a new study suggests.

A team of scientists from theNH_QT_K2934024 University of Oxford, Indian Statistical Institute, and Wildlife Conservation Society exposes, for the first time, inherent shortcomings in the ‘index-calibration’ method that means it can produce inaccurate results. Amongst recent studies thought to be based on this method is India’s national tiger survey (January 2015) which claimed a surprising but welcome 30 percent rise in tiger numbers in just four years.

The team urges conservation practitioners to guard against these sources of error, which could mislead even the best conservation efforts, and suggests a constructive way forward using alternative methods of counting rare animals that avoid the pitfalls of the index-calibration approach.

A report of the research is published this week in the journal Methods in Ecology and Evolution.

Continue reading

Issue 6.2

Issue 6.2 is now online!

The February issue of Methods is now online!

This month we have two applications articles. Both are free to access, no subscription required.

– NLMpy: A PYTHON software package for the creation of neutral landscape models (there are also two videos associated to this paper on our Youtube channel)

BAT - an R package for the measurement and estimation of alpha and beta taxon, phylogenetic and functional diversity

There are also two OnlineOpen articles in this month’s issue. Power analysis for generalized linear mixed models in ecology and evolution, by Paul C. D. Johnson,Sarah J. E. Barry, Heather M. Ferguson and Pie Müller, focuses on why and how we use power analysis for GLMMs using simulations more than we should.

Our second Open Access article is also the source of our cover image, which shows the ciliate protist Paramecium caudatum (about 0.25 mm long). Protist species like this are commonly found in aquatic habitats and offer a unique study system to test ecological and evolutionary concepts. The protist was isolated from a natural pond and subsequently used for microcosm experiments, which have a long tradition in order to test ecological and evolutionary concepts.

In the accompanying review paper, Florian Altermatt et al. describe a wide range of available techniques to use this and many other protists species to conduct microcosm experiments. The review paper gives detailed protocols of available techniques with a focus on modern, high-frequency and high-throughput measurements, and outlines how such microcosm experiments may be used to address a wide range of questions.

This comprehensive guide to using protist microcosms as a model system in ecology and evolution in ‘Big answers from small worlds‘, which is available free of charge.
Photo © Regula Illi and Florian Altermatt.

To keep up to date with Methods newest content, have a look at our Accepted Articles and Early View articles, which will be included in forthcoming issues.

BES 2015 Annual Symposium: Demography Beyond the Population

Demographic methods and population modeling have been popular tools amongst ecologists for a long time. Recent advances, some of which have been written about in the pages of Methods, have allowed these approaches to be applied to a wide range of questions, helping to integrate population-level processes more broadly into ecological research.

Continue reading

Thank you to our 2014 Reviewers

image.axd2014 was a wonderful year for Methods in Ecology and Evolution. We had a record number of submissions and we published some fantastic articles (if we do say so ourselves). None of this would have been possible though without the work of the people who generously provide reviews for the journal.

Whether you reviewed one paper or twenty, we really appreciate your time and effort. Without the expertise and commitment of our reviewers, Methods would not be the successful journal that it is.

Thank you!

The full list of of 2014 reviewers can be found here.