Making YOUR Code Reproducible: Tips and Tricks

When we were putting together the British Ecological Society’s Guide to Reproducible Code we asked the community to send us their advice on how to make code reproducible. We got a lot of excellent responses and we tried to fit as many as we could into the Guide. Unfortunately, we ran out of space and there were a few that we couldn’t include.

Luckily, we have a blog where we can post all of those tips and tricks so that you don’t miss out. A massive thanks to everyone who contributed their tips and tricks for making code reproducible – we really appreciate it. Without further ado, here’s the advice that we were sent about making code reproducible that we couldn’t squeeze into the Guide:

Organising Code

©Leejiah Dorward

“Don’t overwrite data files. If data files change, create a new file. At the top of an analysis file define paths to all data files (even if they are not read in until later in the script).” – Tim Lucas, University of Oxford

“Keep one copy of all code files, and keep this copy under revision management.” – April Wright, Iowa State University

“Learn how to write simple functions – they save your ctrl c & v keys from getting worn out.” – Bob O’Hara, NTNU

For complex figures, it can make sense to pre-compute the items to be plotted as its own intermediate output data structure. The code to do the calculation then only needs to be adjusted if an analysis changes, while the things to be plotted can be reused any number of times while you tweak how the figure looks.” – Hao Ye, UC San Diego Continue reading

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A Guide to Reproducible Code in Ecology and Evolution

Post provided by Natalie Cooper and Pen-Yuan Hsing

Cover image by David J. Bird

The way we do science is changing — data are getting bigger, analyses are getting more complex, and governments, funding agencies and the scientific method itself demand more transparency and accountability in research. One way to deal with these changes is to make our research more reproducible, especially our code.

Although most of us now write code to perform our analyses, it’s often not very reproducible. We’ve all come back to a piece of work we haven’t looked at for a while and had no idea what our code was doing or which of the many “final_analysis” scripts truly was the final analysis! Unfortunately, the number of tools for reproducibility and all the jargon can leave new users feeling overwhelmed, with no idea how to start making their code more reproducible. So, we’ve put together the Guide to Reproducible Code in Ecology and Evolution to help. Continue reading

2016 Robert May Prize Winner: Gabriella Leighton

The Robert May Prize is awarded annually for the best paper published in Methods in Ecology and Evolution by an Early Career Researcher. We’re delighted to announce that the 2016 winner is Gabriella Leighton, for her article ‘Just Google it: assessing the use of Google Images to describe geographical variation in visible traits of organisms.

‘Just Google it’ marks an important step in converting ecology to an armchair science. Many species (e.g. owls, hawks, bears) are difficult, time-consuming, expensive and even dangerous to observe. It would be a lot easier if we didn’t have to spend time, energy and risk lives having to observe organisms in the field! Continue reading

2015 Robert May Prize Winner: Kim Calders

The Robert May Prize is awarded annually for the best paper published in Methods in Ecology and Evolution by an Early Career Researcher. We’re delighted to announce that the 2015 winner is Kim Calders, for his article ‘Nondestructive estimates of above-ground biomass using terrestrial laser scanning.

Kim led the work on this article and had an international team of co-authors. They have developed a way to harness laser technology for use in measurements of vegetation structure of forests. The study is an important development in the monitoring of carbon stocks for worldwide climate policy-making. Continue reading

2014 Robert May Prize Winner: Laure Gallien

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 2014 winner is Laure Gallien, for her article ‘Identifying the signal of environmental filtering and competition in invasion patterns – a contest of approaches from community ecology.

Today, biological invasions are of major concern for maintaining biodiversity. However, understanding what drives the success of invasive species at the scale of the community remains a challenge. Two processes have been described as main drivers of the coexistence between invasive and native species: environmental filtering and competitive interactions. However, recent reviews have shown that competitive interactions are rarely detected, and thus their importance as drivers of invasion success placed under question. But can this be due to pure methodological issues? Using a simulation model of community assembly, Laure and co-authors (Marta Carboni and Tamara Münkemüller) show that the infrequent detection of competition can arise from three important methodological shortcomings, and provide guidelines for future studies of invasion drivers at the scale of the community.

Continue reading

Open Access Week 2014

2014 OA VI - coverOnce more Open Access Week has rolled around.

At MEE we operate a hybrid model: although we are a subscription journal, authors can choose to make their papers open access (for a price – sorry). Over the past year, 21 papers have been published as open access (listed here). They span the range of topics we cover, including citizen science, using cell phones, and asking people nicely to not vandalise your equipment.

There are several models for open access, and the Gold route – making the final version freely available – may not be for everyone. But we also let authors put pre-prints on the web (details here); this is an excellent way of getting more feedback on your manuscripts before a final version (there are other green OA models, but personally I think the preprint version has more advantages).

So, enjoy these papers, and next time you have a paper accepted by MEE – or indeed any other journal with a hybrid model – consider making it open access for all to read. You might be surprised: someone might read it.

Bob, Senior Editor

New Editor on the block…

Jana Vamosi

Jana Vamosi University of Calgary

By Jana Vamosi

How’s it going, eh?

Yeah, that’s right. A Canadian has infiltrated the ranks as a new Senior Editor. I will be joining the esteemed Rob Freckleton and Bob O’Hara in directing manuscripts and developing the journal.

My first challenge will be to master some of these modern communication tools, namely this “social media” fad I keep hearing so much about. A flash in the pan I assume, soon to fall out of favour and disappear. And yet we must attempt to stay current with these fickle fashions. 🙂

OK, I’m not entirely clueless. I’ve mastered the basics. I have a twitter account at @jvamosi, where I mostly retweet on topics related to biodiversity, pollination, phylogenetic comparative methods, and food security. I have the typical Facebook and LinkedIn accounts as well. Feel free to befriend me but I have a tendency towards cheekiness and inappropriate profanity on Facebook (consider yourself forewarned).

I’m new to the whole blogging phenomenon but I’ll happily ramble on when I feel I have something important to say. Generally, I become loquacious when the topic of science communication comes up. I’m a proponent of articles reaching as wide an audience as possible. This idea extends to engaging the non-scientific community. I like to get creative from time to time and believe that approaching problems in an unorthodox way can add new insight. Thus, I’m an ideal sounding board for your zaniest ideas. The zanier, the better! I like crazy.

My formative academic years were spent at the University of British Columbia under the supervision of Sally Otto. Not knowing whether graduate school would be to my liking, I signed up to do a Masters degree but I liked it so much I quickly transferred to the PhD program. Part of what I liked so much was the bohemian style encouraged at UBC and it was there that I developed a love of dabbling in every topic that took my fancy. Somehow that congealed into a fairly coherent thesis on dioecy in flowering plants using an assortment of approaches, ranging from phylogenetic comparative approaches, population genetic modeling, and spatially explicit simulations. I continue to use a range of methods in my research on the macroevolution, macroecology, community ecology, and conservation of biodiversity.

With my varied history, I consider myself a good representative of the target audience for new methods. Frequently bridging different subfields, my current research repeatedly necessitates the adoption of new techniques. I believe my role at Methods will involve handling many of the Applications submissions, so I’ll be working with your newest tools. And while I’m familiar with a certain level of frustration whenever learning a new method, it is likely that if I’m tripping up following your instructions, a good proportion of our readership will too.

As for new directions I’m interested in championing, there are three that have caught my attention presently. The first is the field of metagenomics and its relevance to the medical community. Generally, I’m fascinated by the intersections between disciplines, such as how evolutionary and ecological principles can provide insight into the structure of gut microbial communities, the progression of cancer, and the incidence of schizophrenia and HIV.

Secondly, I’m constantly exercised by questions pertaining to biodiversity, and lately that extends to the degree to which biodiversity influences ecosystem function. I think knowing the contexts and thresholds that influence the biodiversity-function relationship will become an increasingly important question in the coming years.

Finally, I’m excited by big datasets as freely available resources to examine questions in ecology and evolution. Citizen Science initiatives that have borne fruit are especially pertinent and they jointly satisfy my desire to get more humans out appreciating other living species as well as often providing the sort of geographic breadth not possible with only a small handful of researchers.

So there you have it. My three topics of concentration for increased submissions to Methods are: 1) ecology and evolution in medicine; 2) improving our ability to measure the biodiversity-ecosystem function relationship; and 3) making large amounts of data readily available to the scientific community.

If you have any other ideas, be sure to let me know!

Jana
Senoir Editor, Methods in Ecology and Evolution

 

2013 Robert May Prize Winner

YIP 2013 - Will PearseThe 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 IndexiVI cover - YIP 2013ng 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.

Senior Editor vacancy

Methods in Ecology and Evolution (MEE) is seeking a new Senior Editor to strengthen and complement the existing team, and to continue raising the Journal’s profile worldwide. The candidate will join Executive Editor, Professor Rob Freckleton, and Senior Editor, Dr Bob O’Hara, who are supported by an international board of 47 Associate Editors along with an in-house editorial team.

MEE promotes the development of new methods in ecology and evolution, and facilitates their dissemination and uptake by the research community. MEE brings together papers from previously disparate sub-disciplines to provide a single forum for tracking Continue reading

BES Virtual Issue: Pollinator Ecology

pollinator VI adTo celebrate the joint meeting on the impact of pesticides on bee health in January, hosted by the Biochemical Society, the British Ecological Society and the Society for Experimental Biology, the BES has compiled a free virtual issue on Pollinator Ecology. The papers included are drawn from all five BES journals and provide examples of the latest research in pollinator ecology from flower visitation and ecosystem services, to the effects of invasive pollinators, agriculture, pesticides and bee pathogens. Click here to read the virtual issue.