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

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New Associate Editor: Edward Codling

Today, we are pleased to be the latest new member of the Methods in Ecology and Evolution Associate Editor Board. Edward Codling joins us from the University of Essex, UK and you can find out a little more about him below.

Edward Codling

“My research is focused on using new mathematical and computational techniques to study problems in biology and ecology. In particular, I’m interested in movement ecology, and specifically the development of theoretical models and empirical analysis tools that give insights into animal movement and behaviour. I am also interested in spatial population dynamics and the application of modelling and analysis tools to marine fisheries and other natural resource management questions.”

Edward is currently working on a range of problems within the rapidly growing field of movement ecology. This includes a recent theoretical study of animal navigation using random walk theory and an empirical study into coral reef fish larval settlement patterns. An ongoing project is exploring how analysis of dairy cow movement and behaviour could be used as part of a farm monitoring and management system to improve cow health and welfare. He is also continuing to work on new tools and methods for the assessment and management of fisheries, particularly in the case where data is limited.

We are thrilled to welcome Edward as a new Associate Editor and we look forward to working with him on the journal.

New Associate Editor: David Soto

Today, we are pleased to be the latest new member of the Methods in Ecology and Evolution Associate Editor Board. David Soto joins us from the University of Leuven in Belgium and you can find out a little more about him below.

David Soto

“I am an isotope ecologist with interests in developing new stable isotope methods and techniques for tracing spatio-temporal changes in food webs, and understanding animal movement and large-scale migration. My current research focus is on aquatic food webs using isotopic tracers such as hydrogen isotopes, and on insect migration patterns predicting natal origins by combining isoscapes and likelihood-based geospatial assignment methods.”

David is currently working on isotopic methodologies to quantify the linkages and support of aquatic and terrestrial primary production sources into Afrotropical aquatic food webs. He recently developed a new method to distinguish dietary sources combining stable isotopes and trace metal accumulation data. Other recent published articles investigated the use of hydrogen isotopes to track fish provenance and to infer butterfly migration movements across the Sahara. He is also collaborating with the IsoriX core team to develop a new method and R package to infer spatial origins of migratory animals using mixed models.

We are thrilled to welcome David as a new Associate Editor and we look forward to working with him on the journal.

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!

Two More New Associate Editors

Today we are welcoming two more Associate Editors to the Methods in Ecology and Evolution who were invited to work with the journal following our open call earlier this year. Jessica Royles joins from the University of Cambridge, UK and Simon Blomberg is coming to us from the University of Queensland, Australia. You can find out more about both of them below.

Simon Blomberg

“I am a statistician who started out as a lizard demographer. I am interested in all applications of statistics in evolutionary biology and systematics. It is my passion to see that good science gets done by everybody, and sound statistical methods are essential to reach that goal. My research involves the application of stochastic process models (predominantly Itoh diffusions) to the macroevolution of quantitative traits. I believe that evolution can be described by beautiful mathematics but theory must be tested with data. I have published widely on phylogenetic comparative methods. I use Bayesian methods, data augmentation, regularisation and other modern and traditional statistical methods. I am interested in how to treat missing data. I still like lizards. Also jazz.”

Simon has been working on stochastic process models for a couple of years. His most recent article ‘Beyond Brownian motion and the Ornstein-Uhlenbeck process: Stochastic diffusion models for the evolution of quantitative characters‘ is now available on BioRxiv and he would welcome comments on it from the Methods community.

Jessica Royles

“I am interested in the impact of climate change on plant physiology and specialise in using stable isotopes as environmental markers. Having worked in Antarctica I have strong interests in polar biology, high latitude peatlands and fieldwork techniques. My current work focusses on  temperate bryophytes and I am interested in using techniques including gas exchange and chlorophyll fluorescence at different spatial scales to link the leaf level to the ecosystem level.”

Jessica’s most recently published article – ‘Widespread Biological Response to Rapid Warming on the Antarctic Peninsula‘ – describes how she and her co-authors used moss cores to study Antarctic warming due to climate change. The article builds on her previous paper ‘Plants and Soil Microbes Respond to Recent Warming on the Antarctic Peninsula‘. Jessica is currently working on a Moss Ecophysiology project which aims to investigate the value of mosses as tools to understand past climate.

We are thrilled to welcome Simon and Jessica to the Associate Editor Board and we look forward to working with them over the coming years.

More New Associate Editors

Today we are welcoming another two Associate Editors to the Methods in Ecology and Evolution. Just like the seven AEs who joined last week, Michael Matschiner (of the University of Basel, Switzerland) and Tiago Bosisio Quental (of the University of São Paulo, Brazil) were both invited to work with the journal following our open call earlier this year. You can find out more about both of them below.

Michael Matschiner

“I am an evolutionary biologist interested in the processes that drive speciation and generate biodiversity. To learn about these processes, I use phylogenetic divergence-time estimation based on genome sequences and the fossil record. Since both of these data sources do not usually conform to expectations in standard phylogenetic workflows (no recombination, no hybridization, no sampling bias), much of my work involves method development to assess the impact of model violations, and to account for them in phylogenetic reconstruction.”

Tiago Bosisio Quental

“I am interested on understanding spatial and temporal patterns of biodiversity and the mechanisms involved in generating species diversity. I have a particular interest in mammals, but my research interests are not limited to a specific taxonomic group but are instead motivated by a range of questions and structured around them. At the moment, I am particularly interested in understanding the role of biotic interactions on biodiversity changes in deep time. The main tools used to approach those questions are molecular phylogenies, fossil record, ecological data and numerical simulation.”

We are thrilled to welcome Michael and Tiago to the Associate Editor Board and we look forward to working with them over the coming years.

New Associate Editors

Today we are welcoming seven new people to the Methods in Ecology and Evolution Associate Editor Board. All of these new Associate Editors were invited to join the Board following our open call for applications a couple of months ago. You can find out more about them below.

Karen Bacon

Karen Bacon

Karen Bacon

“I am a plant ecologist and palaeoecologist with interests that span the present day to the Mesozoic. My particular interests include plant–atmosphere interactions, fossil plant taphonomy, mass extinctions, stable isotope ecology, and Anthropocene ecology. My current work focuses on the development of plant-based proxies to improve interpretations of plant responses to past environmental change and investigating plant functional traits that lead to success across environmental upheaval events in both the fossil record and present day.”

Torbjørn Ergon

Torbjørn Ergon

“I am a population/evolutionary ecologist with wide interests. My research has mostly been focused on variation in life-history traits and demographic rates within populations, and I have a strong interest in statistical modelling in this field. As an associate editor of Methods in Ecology and Evolution, I hope to promote novel papers that pay close attention to ecological/evolutionary theory in addition to study design and statistical modelling.” Continue reading

BES Guide to Reproducible Code: Tips and Tricks Needed

The British Ecological Society is currently working on a Guide to Reproducible Code. This will follow on from our previous Guides to Peer Review, Data Management and Getting Published. All of our Guides are intended to provide Early Career Researchers with a concise and easy to understand introduction to the topic. You can download them for free on our website.

Each Guide includes short pieces of advice provided by academics who are familiar with the topic – and this is where you come in. We’re looking for tips and tricks to help Early Career Researchers looking to make their code reproducible and we would like your help.

We’ve set up a Google form with sections that relate to the broad areas that will be covered in our Guide to Reproducible Code:

  1. Organising Code
  2. Writing Code
  3. Report Writing
  4. Versioning
  5. Archiving Code
  6. Additional Resources

The guide is intended for people who are fairly new to coding, so please don’t be too technical. There are options to enter three pieces of advice in each section (if you’ve got more tips and tricks, feel free to fill in the form multiple times). We’ll choose the best pieces of advice and publish them in the Guide, along with the name and affiliation of the person who provided them.

You can submit your Tips and Tricks for Making Code Reproducible here. Thank you for contributing to our Guide.

New Associate Editors

Today we are welcoming four new Associate Editors to Methods in Ecology and Evolution. Graziella Iossa (University of Lincoln) and Theoni Photopoulou (Nelson Mandela Metropolitan University) are joining as regular Associate Editors and Simon Jarman (Unversity of Porto) and Daniele Silvestro (University of Gothenburg) will be working on Applications articles. You can find out more about all of our new Associate Editors below.

Graziella Iossa

“I am an evolutionary ecologist with broad interests in behavioural and population ecology. My research has explored reproductive strategies and the evolution of male and female reproductive traits in mammals and insects and I have used a range of techniques to study the behaviour and welfare of wildlife. I have just started to explore interdisciplinary approaches with the aim to improve our understanding of the value and role of ecosystem services in human health, specifically for antimicrobial resistance.”

Graziella’s most recent paper – Micropyle number is associated with elevated female promiscuity in Lepidoptera – investigates the evolution of the micropyle, a tiny canal which sperm use to fertilise eggs in insects. This is the first study to show that micropylar variation is driven by female promiscuity – the more micropyles her eggs have, the more choice she is likely to have over which male fathers her offspring. Also, Graziella currently holds a NERC Valuing Nature placement which aims to combine perspectives from evolutionary ecology, microbial ecology, epidemiology, ecosystem science and public health to develop a new, holistic way of understanding antimicrobial resistance

Simon Jarman

“Methods employing epigenetics, environmental DNA analysis or bioinformatics for ecological research are improving rapidly and have clear potential for future development. My research focuses on creating new methods in these areas and using them to study population biology and biodiversity. Epigenetic markers for physiological features such as biological age can be used to determine key features of population biology such as age class distribution. Environmental DNA can be used to measure species distributions; biodiversity in environmental samples; and animal diet composition. I am interested in the molecular biology and computational approaches that are required to implement these methods; as well as how they can be used to study specific ecological questions.”

In November 2016, Simon published an Open Access article in Methods in Ecology and Evolution. ‘Optimised scat collection protocols for dietary DNA metabarcoding in vertebrates‘ explains how to collect scat samples to optimise the detection of food DNA in vertebrate scat samples. More recently, Simon was the last author of ‘KrillDB: A de novo transcriptome database for the Antarctic krill (Euphausia superba)‘ – which introduces the most advanced genetic database on Euphausia superba, KrillDB, and includes comprehensive data sets of former and present transcriptome projects.

Theoni Photopoulou

“I am interested in the way biological and ecological phenomena change in space and over time. My special interest is animal movement ecology and the mechanisms behind the patterns of movement we observe. Most of the time I work on ecological questions about how animals use their environment and the resources in it, using data collected remotely with animal-attached instruments. Marine biology was my first love so I will always have a soft spot for marine systems, especially movement of large marine vertebrates, but I work on all sorts of tracking data and also some non-tracking data.”

Theoni has also recently been published in Methods in Ecology and Evolution. Her article ‘Analysis of animal accelerometer data using hidden Markov model‘ appeared in the February issue of the journal (and provided the cover image). In the paper, the authors provide the details necessary to implement and assess a hidden Markov Model in both the supervised and unsupervised learning contexts and discuss the data requirements of each case. Another of Theoni’s articles has just been accepted for publication in Frontiers in Zoology. ‘Evidence for a postreproductive phase in female false killer whales (Pseudorca crassidens)‘ investigates the evidence for postreproductive lifespan (PRLS) in the false killer whale, using a quantitative measure of PRLS and morphological evidence from reproductive tissue.

Daniele Silvestro

“I am a computational biologist and my research focuses on (macro)evolution and the development of new probabilistic models to better understand it. I am interested in the implementation of Bayesian algorithms to model evolutionary processes such as phenotypic trait evolution and species diversification and extinction. I am also interested in historical biogeography and in particular in the estimation of dispersal rates and biotic connectivity between geographic areas. A lot of my work involves developing new models and algorithms and implementing them in computer programs. I have been using both phylogenetic data and fossil occurrences to infer deep time evolutionary dynamics and I am keen to see an improved integration between paleontological and neontological data in evolutionary research.”

In his most recent article – ‘Bayesian estimation of multiple clade competition from fossil data‘ – Daniele and his co-authors explore the properties of the existing Multiple Clade Diversity Dependence implementation, which is based on Bayesian variable selection, and introduce an alternative parameterisation based on the Horseshoe prior. He was also one of the authors of ‘Mammal body size evolution in North America and Europe over 20 Myr: similar trends generated by different processes‘, published in Proceedings of the Royal Society B earlier this year.

We are thrilled to welcome Simon, Graziella, Theoni and Daniele to the Associate Editor Board and we look forward to working with them over the coming years.

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