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.

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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

Ecology, do we have a problem?

Last week many of us were at the Ecology Across Borders meeting in Ghent, catching up with friends, making new friends, and listening to talks about the latest ecological science. Many of us, of course, were also following social media. On the statistics social media scene a lot of attention was being paid to a post on Medium by Kristian Lum: Statistics, we have a problem. In it she recounts being harassed by two senior statisticians (both of whom have subsequently been publicly identified). The events she describes are appalling, and she has my sympathy, and my admiration for having the courage to speak out.

Kristian’s story is not an isolated incident in science. Over the last few years there has been a drip, drip, drip of stories of bad behaviour and abuse in academia (some of which are summarised here, for example), in the office, when doing field work, and at conferences. But it seems likely that this is only the tip of the iceberg: a lot of women do not report having been harassed, for a variety of reasons. Much of the harassment and bad behavior that is reported is by men towards more junior women, which exacerbates the emotional pressures by adding a fear of retaliation. Even when a report is taken seriously and a perpetrator found guilty, the punishment is often wrapped in a flurry of non-disclosure agreements.

All these stories make me worry about ecology, as a discipline. Whilst I am not aware of any accusations of harassment at our meetings, I can’t see why ecology should be different from other disciplines. My own experience of ecology meetings has been positive, but I have been lucky, and to a large extent this is probably a result of me being male. It seems unlikely that all ecologists are saints. What worries me is that there stories of harassment in ecology, but they haven’t been made public yet. Does this mean that there are issues that we, as a community, will have to face when we find out that some of our biggest names shouldn’t be a part of a scientific discipline that wants to encourage diversity?

At the end of her post, Kristian has a call to arms:

We need to start holding prominent individuals accountable for how their inappropriate behavior negatively impacts the careers of their junior colleagues. I’m saying this publicly because whenever I have shared these stories privately with my colleagues, both men and women, they are appalled. It is time for us to be publicly and openly appalled, not just attempting to tactfully deflect inappropriate advances and privately warning other women. We need to remove the power of the “open secret” that these people use to take advantage of their respected positions in our field. We know who these people are, and we should stop tolerating this culture of harassment, or else we become complicit in it.

I agree: we should be publicly and openly appalled. But we also need to go beyond being appalled. We have to make it clear that this sort of behaviour should not be tolerated. We have to actively support people who come forward with allegations of harassment and make sure that they are heard and taken seriously. We also have to make it clear to people when they have crossed the line.

Now, though, ecological societies are starting to act. The British Ecological Society does have a Code of Conduct for events, and if anyone wants to report harassment or other unacceptable behaviour, they can report it to Amy Everard. The ESA has their own Code of Conduct, and an email address to report misconduct during or following an ESA event. I am confident that both organisations will take any complaints seriously (I know the BES will, having discussed this with them).

So here we are – I feel that we need people to speak out. But the whole problem is one where it is difficult to do this – there are feelings of guilt, shame and fear, and many of the people who need to be talked about have power. But it cannot be the fault of the person who has been harassed, and most people will be supportive.

Solving YOUR Ecology Challenges with R: Ecology Hackathon in Ghent

©2016 The R Foundation

Scientific software is an increasingly important part of scientific research, and ecologists have been at the forefront of developing open source tools for ecological research. Much of this software is distributed via R packages – there are over 200 R packages for ecology and evolution on CRAN alone. Methods regularly publishes Application articles introducing R packages (and other software) that enable ecological research, and we’re always looking for new ways to enable even more and better ecological software.

This December, we will be teaming up with rOpenSci and special interest groups from BES, GfÖ and NecoV to hold our first Ecology Hackathon at the Ecology Across Borders conference in Ghent. The hackathon will be held as a one-day pre-conference workshop on Monday 11th December. Together, the attendees will identify some challenges for ecological research, and team up to build R packages that help solve them.

We’ve started compiling potential topics for new R packages in a collaborative document, but we need more. Are you having any difficulties in your research that could be solved with an R package? Is there a package that you wish existed but have never been able to find? If so, WE WANT TO HEAR FROM YOU!

Please take a look at our current list of challenges and add your suggestions!

RSS Meeting on Model Averaging: Elephants, Oscars and Spiky Data

Post provided by Dr Eleni Matechou

Eleni is a Lecturer in Statistics and a member of the Statistical Ecology @ Kent (SE@K) group at the University of Kent. She develops statistical models motivated by ecological applications to study populations of birds, insects and, more recently, humans.

On September 15th 2016, a half-day meeting on Model Averaging – organised by the Environmental Statistics section and the East Kent local group of the Royal Statistical Society (RSS) – took place at the University of Kent in Canterbury .

There were three invited speakers: Professor Richard Chandler, from University College London, Professor Jonty Rougier, from the University of Bristol and Dr Kate Searle, from the Centre for Ecology and Hydrology, who presented via Skype.

All three talks included interesting motivating data, clever modelling and great insight.

Taming the Pachyderm

elephant-in-the-roomProfessor Richard Chandler presented joint work with Marianna Demetriou on “The interpretation of climate model ensembles”. Projecting future global temperatures is clearly a timely topic and Richard’s talk highlighted the challenges of doing this reliably. And they’re certainly not minor challenges, in his own words, this is a problem he has spent 10 years thinking about! Continue reading

Achieving Reproducibility in Research

Earlier this month Leila Walker attended a panel discussion imparting ‘Practical Tips for Reproducible Research’, as part of the Annual Meeting of the Macroecology Special Interest Group (for an overview of the meeting as a whole check out this Storify). The session and subsequent drinks reception was sponsored by Methods in Ecology and Evolution. Here, Leila reports back on the advice offered by the panel members.

For anyone interested in viewing further resources from the session, please see here. Also, you may like to consider attending the best practice for code archiving workshop at the 2016 BES Annual Meeting. Do you have any tips for making your research reproducible? Comment on this post or email us and let us know!

This year’s Annual Meeting of the Macroecology SIG was the biggest yet, with around 75 attendees and even representation across the PhD, post-doc and faculty spectrum. The panel discussion aimed to consider what reproducibility means to different people, identify the reproducibility issues people struggle with, and ultimately provide practical tips and tools for how to achieve reproducible research. Each of the participants delivered a short piece offering their perspective on reproducibility, with plenty of opportunity for discussion during the session itself and in the poster and wine reception that followed.

Attendees enjoy a wine reception (sponsored by MEE) whilst viewing posters and reflecting on the Reproducible Research panel discussion. Photo credit: Leila Walker

Attendees enjoy a wine reception (sponsored by MEE) whilst viewing posters and reflecting on the Reproducible Research panel discussion. Photo credit: Leila Walker

Continue reading

Meet the Team at ESA 2016

Post provided by EMILIE AIMÉ, Managing Editor, Methods in Ecology and Evolution

This year’s annual ESA meeting is fast approaching. It’s in Fort Lauderdale, Florida and I’ll be heading across the pond, along with Catherine Hill, our Head of Publications, and Hazel Norman, our Executive Director, to chat to delegates about Methods in Ecology and Evolution, as well as our other journals and the British Ecological Society as a whole.

I’m also looking forward to meeting a few of our very hard working Associate Editors and thanking them for all their help towards making MEE the success it is.

If you’re attending ESA and are thinking of submitting to MEE – maybe you’re giving a talk that you think might make a great Methods paper – or if you’re a reader of the journal and want to make suggestions for improvements you’d like to see or content you think we should be publishing come and find me, Catherine or Hazel at the BES stand for a chat. We’ll be at stand number 202-204.

If you’re interesting in finding out about the great work the BES does to communicate and promote ecological knowledge around the world come and meet our amazing President Sue Hartley at our stand on Tuesday 9 August between 4.30pm and 6.30pm.

When we’re not at the stand you’ll mainly find us outside enjoying the only sun we’re likely to get this year, before heading back to grey old London..

See you in Florida!

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Sunny Fort Lauderdale!

RPANDA: A Time Machine for Evolutionary Biologists

Post provided by HÉLÈNE MORLON

Yesterday saw the start of this year’s annual Evolution meeting and to celebrate Hélène Morlon has written a blog post discussing the amazingly versatile RPANDA package that she is developing with her research group. A description of RPANDA was published in the journal earlier this year and, like all our Applications papers, is freely available to read in full.

If you are attending Evolution, as well as attending the fabulous talks mentioned by Hélène below, do stop by booth 125 to see our BES colleague Simon Hoggart. Simon is the Assistant Editor of Journal of Animal Ecology and would be happy to answer your questions about any of our journals or any of the other work we do here at the BES.

RPANDA: a time machine for evolutionary biologists

Imagine “Doc”, Marty’s friend in Back to the Future, trying to travel back millions of years in an attempt to understand the history of life. Instead of building a time machine from a DeLorean sports car powered by plutonium, he could dig fossils, or more likely, he would use molecular phylogenies.

Molecular phylogenies are family trees of species that can be built from data collected today: the genes (molecules) of present-day species (Fig 1). They are often thought of as trees, in reference to Darwin’s tree of life. The leaves represent the present: species that can be found on Earth today. The branches represent the past: ancestral species, which from time to time split, giving rise to two independent species. The structure of the tree tells us which species descend from which ancestors, and when their divergence happened.

birds_phylog

Fig 1: The phylogenetic tree of all birds (adapted from Jetz et al. 2012). Each bird order is represented by a single bird silloutter and a specific colour (the most abundant order of Passeriformes, for example is represented in dark orange). Each terminal leaf represents a present-day bird species, while internal branches represent the evolutionary relationships among these species.

Continue reading