R2ucare: An Interview with Olivier Gimenez

At the International Statistical Ecology Conference in St Andrews this July (ISEC 2018) David Warton interviewed Olivier Gimenez about R2ucare. R2ucare is an R package for goodness-of-fit tests for capture-recapture models. The full Methods in Ecology and Evolution article on this package – R2ucare: An r package to perform goodness‐of‐fit tests for capture–recapture models – was published in the July 2018 issue of the journal.

David and Olivier also discuss some tips for creating R packages. They mention that if you’re new to writing R packages, there are some excellent resources online. Here’s one of them: A Quickstart Guide for Building Your First R Package

We’ll have more of David’s interviews from the ISEC coming out over the next few weeks. Keep an eye out for them here and on the Methods in Ecology and Evolution YouTube channel.

You can find David’s first ISEC interview (with Kate Jones) here.

What the Past Can Tell Us About the Future: Notes from Crossing the Palaeontological – Ecological Gap

Post provided by Karen Bacon

I had the pleasure of delivering one of the plenary talks at the first (hopefully of many) Crossing the Palaeontological – Ecological Gap meeting held in the University of Leeds on August 30th and 31st. I’m a geologist and a botanist, so this is a topic that’s close to my heart and my professional interests.

How Palaeoecology Can Help Us Today

©Gail Hampshire

©Gail Hampshire

As we move into an ecologically uncertain future with pressures of climate change, land-use change and resource limitations, the fossil record offers the only truly long-term record of how Earth’s ecosystems respond to major environmental upheaval driven by climate change events. The fossil record is, of course, not without its problems – there are gaps, not everything fossilises in the same way or numbers, and comparisons to today’s ecology are extremely difficult.  It’s these difficulties (and other challenges) that make the uniting of palaeontology and ecology essential to fully address how plants, animals and other organisms have responded to major changes in the past. Perhaps uniting them could give us an idea of what to expect in our near-term future, as carbon dioxide levels return to those not previously experienced on Earth since the Pliocene, over 2 million years ago. Continue reading

Bats, Acoustic Methods and Conservation 4.0: An Interview with Kate Jones

At this year’s International Statistical Ecology Conference (ISEC 2018) David Warton interviewed Kate Jones, Chair in Ecology and Biodiversity at University College, London. Their conversation mainly focused on how to classify bats from acoustic data, with particular reference to ‘Acoustic identification of Mexican bats based on taxonomic and ecological constraints on call design‘ by Veronica Zamora‐Gutierrez et al. They also discuss Conservation 4.0!

We’ll have more of David’s interviews from the ISEC coming out over the next few weeks. Keep an eye out for them here and on the Methods in Ecology and Evolution YouTube channel.

Poles Apart Yet Poles Together

Post provided by Matt Davey

Earlier this summer, I attended a rather unique conference – Polar2018 in Davos, Switzerland. This conference brought together the two major committees that help govern and coordinate Arctic, Alpine and Antarctic research around the globe – the Scientific Committee for Antarctic Research (SCAR) – who also celebrates their 60th Anniversary this year – and the International Arctic Science Committee (IASC).

With nearly 2500 delegates over one week it was impressive how talks and sessions kept to time, posters went up and came down, and coffee (good coffee, served with correctly cooked croissants!) was served. The level of organisation you’d hope to see at all conferences, big or small. The venue for Polar2018 was also home to the G7 world economic forum summits and staff seemed at ease with only having 2500 delegates to deal with…

From day one, there was persistent message throughout the conference. Not only does the rest of the human populated world affect the polar environments, but in response, any change in polar ecosystem and environment functioning (biological and non-biological) has a large knock-on effect on the rest of the world. Continue reading

The Future of Research and Publishing in Evolutionary Biology

Are you coming to the Evolution 2018 in Montpellier? Want to share your views on the future of evolution research? Fancy some beer, wine and snacks on us?

We know the history of research and publications in evolution, but what will the future hold?

We would like to invite you to participate in an exciting focus session centred around what the future research landscape might look like through the eyes of up-and-coming researchers.

When: Tuesday 21 August between 14:00 and 16:00

Where:  Bar Les Loges, Grand Hotel du Midi, Montpellier

We’re looking for active researchers (based in universities, research institutes, government agencies, NGOs or the private sector) within about 10 years of having been awarded a PhD. Experienced PhD students who have published in peer reviewed academic journals are also welcome to join. Continue reading

BES Macroecology 2018: Macroecology and Data

Post provided by Faith Jones

© Matthew Leonard

© Matthew Leonard

The annual BES Macroecology Special Interest Group conference took place on the 10th and 11th of July. This year the meeting was in St Andrews, Scotland. Over 100 delegates came together in this old University town to discuss the latest research and concepts in macroecology and macroevolution.

Remote Sensing, Funky Koalas and a Science Ceilidh

The conference opened with a plenary by Journal of Applied Ecology Senior Editor Nathalie Pettorelli from ZSL. She talked about how remote sensing can be used in ecological and conservation studies. In the other plenary talks, we heard from:

  • Methods in Ecology and Evolution Senior Editor Bob O’Hara from NTNU on, among other things, how useful occupancy models are when “occupancy” is such a broad term
  • Anne Magurran from the University of St Andrews discussing turnover and biodiversity change
  • Brian McGill from the University of Maine talking about the data-driven approach to the “biodiversity orthodoxy” and challenging the conventional wisdom about macroecological change

We also hosted a student plenary speaker, Alex Skeels, who gave a lively talk about diversification and geographical modelling using some pretty funky disco koalas. In addition to these talks, there were 60 short 5 minutes talks and 20 posters. Continue reading

An Interview with Alan Gelfand

David Warton interviews Alan Gelfand, a keynote speaker at the Statistics in Ecology and Environmental Monitoring (SEEM) conference in Queenstown, NZ. Alan is best known for proposing Bayesian estimation of a posterior distribution using Gibbs sampling, in his classic papers ‘Sampling-Based Approaches to Calculating Marginal Densities‘ and ‘Illustration of Bayesian Inference in Normal Data Models Using Gibbs Sampling‘.

David and Alan discuss the origins of the idea that revolutionised Bayesian statistics, Alan’s current research, and his passion for ecology.

Check out David’s other interviews on the Methods in Ecology and Evolution YouTube channel.

An Interview with Tony Ives

David Warton interviews Tony Ives, a Keynote speaker at the Statistics in Ecology and Environmental Monitoring (SEEM) conference in Queenstown, NZ. Tony has published a few papers in Methods in Ecology and Evolution over the last couple of years – first we discuss the exchanges on log-transformation of counts (including a paper co-authored with David Warton).

Tony and David then talk about a recent paper by Daijiang Li with Tony, on the need to check for phylogenetic structure when looking for associations between species trait and the environment.

We’ll have more of David’s interviews from the SEEM Conference coming out over the next couple of months. Keep an eye out for them here and on the Methods in Ecology and Evolution YouTube channel.

Ending the Terror of R Errors

Post provided by Paul Mensink

Last year, I introduced R to petrified first-year biology students in a set of tutorials. I quickly realised that students were getting bogged down in error messages (even on very simple tasks), so most of my time was spent jumping between students like a wayward Markov chain. I would often find a desperate face at the end of a raised hand looking hopelessly towards their R console muttering some version of “What the $%# does this mean?”. I instantly morphed from teacher to translator and our class progress was slower than a for-loop caught in the second Circle.

Error messages are often not very helpful

Error messages are often not very helpful

Fast forward to Ecology Across Borders last December in Ghent, where rOpenSci and special interest groups from the BESGfÖ and NecoV  and Methods in Ecology and Evolution  co-hosted a pre-conference R hackathon. I was elated to see that one of the challenges was focused on translating R error messages into “Plain English” (thanks to @DanMcGlinn for the original suggestion!). Continue reading

Ecology Hackathon at Ecology Across Borders 2017

Post provided by Gergana Daskalova

Brainstorming ideas at the Ecology Hackathon in Ghent.

Brainstorming ideas at the Hackathon.

Imagine an ecologist. Now imagine a programmer. Did you imagine the same person? If you were at the Ecology Hackathon on the day before the Ecology Across Borders (#EAB2017) conference in Ghent, Belgium (a joint conference between the BES, GFÖ, NecoV and EEF), you probably did (or at least we hope you did!).

Ecology is becoming increasingly quantitative and, as a result, we can add one more item on our daily to do lists as scientists:

  • Think of questions
  • Go on fieldwork / run simulations
  • Supervise students
  • Meet with our own supervisors
  • Teach
  • Write articles and review manuscripts
  • Answer emails
  • And now code as well

A Coding Community

Coding doesn’t need to be a lonely activity – one of the areas where it truly shines is collaborative coding. This can take us across borders and bring us together to figure out the best way to answer our research questions. That is exactly what the EAB Ecology Hackathon set out to do. Continue reading