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Policy on Publishing Code Virtual Issue

Nick Golding, University of Melbourne, Australia
Sarah Goslee, USDA, USA
Tim Poisot, Université de Montréal, Canada
Samantha Price, University of California, Davis, USA
In January 2018, Methods in Ecology and Evolution launched a Policy on Publishing Code. The main objective of this policy is to make sure that high quality code is readily available to our readers. set out four key principles to help achieve this, as well as explaining what code outputs we publish, giving some examples of things that make it easier to review code, and giving some advice on how to store code once it’s been published.


To help people to understand how to meet the guidelines and principles of the new policy, a group of our Applications Associate Editors (Nick Golding, Sarah Goslee, Tim Poisot and Samantha Price) have put together a Virtual Issue of Applications articles published over the past couple of years that have followed at least one aspect of the guidelines particularly well.


In the first article, microPop: Modelling microbial populations and communities in R, Helen Kettle and her co-authors did a great job of setting up public version control, testing, and code archiving (on zenodo) during the review process. rptR: repeatability estimation and variance decomposition by generalized linear mixed-effects models by Martin Stoffe et al. does a very good job with code handling, too. The code is in R, and Open Source, with the package released as GPL. The package is on CRAN, which means it has passed basic quality checks, and the development version is on GitHub, so version control is not only in place, but publicly accessible.


Other articles in the Special Feature highlight specific areas of the new policy. Bromaghin includes some good tests based on manual calculation of expected values in qfasar: quantitative fatty acid signature analysis with R. The R package described in biomass: an r package for estimating above-ground biomass and its uncertainty in tropical forest by Réjou-Mécha et al. is on CRAN, the code is documented, and there are vignettes. The data used in the paper is both cited and included with the package.


In SSDM: an R package to predict distribution of species richness and composition based on stacked species distribution models and FLightR: An R package for reconstructing animal paths from solar geolocation loggers (by Schmitt et al. and Rakhimberdiev et al. respectively) the authors added things like continuous integration, consistent coding styles, and high test coverages during review.


Finally, TreeSimGM: Simulating phylogenetic trees under general Bellman Harris models with lineage-specific shifts of speciation and extinction in R by Hagen et al. and ratematrix: an R package for studying evolutionary integration among several traits on phylogenetic trees by Caetano et al. are good examples of our policy, without entirely fulfilling all aspects of it.

Microbial Ecology

Published:
2 November 2017
Edited by Xavier Harrison
Advances in Next-Generation Sequencing (NGS) technology now allow us to study associations between hosts and their microbial communities in unprecedented detail. However, studies investigating host-microbe interactions in the field of ecology and evolution are dominated by 16S and ITS amplicon sequencing. While amplicon sequencing is a useful tool for describing microbial community composition, it is limited in its ability to quantify the function(s) performed by members of those communities. Characterising function is vital to understanding how microbes and their hosts interact, and consequently whether those interactions are adaptive for, or detrimental to, the host. These papers cover a broad suite of approaches that allow us to study host-microbe and microbe-microbe interactions in novel ways.

Open Data

Published:
23 October 2017
The British Ecological Society journals have long supported making the data associated with papers published in the journals publically available and since January 2014 this has been a requirement for publication. To facilitate the archiving of data the BES journals are integrated with the Dryad Digital Repository and through this integration the BES journals offer a smooth and easy process for authors to archive data, with costs covered by the Society.  To celebrate this integration for Open Access Week 2017 we have compiled this Virtual Issue presenting the papers with the most-downloaded datasets from the Dryad Digital Repository in the five BES journals. Dryad’s mission is to promote the preservation and availability of the data underlying findings in the scientific literature for future research and educational use. Data stored in Dryad can be re-used in many different ways such as exploring new analysis methodologies, re-purposing data for new research questions unanticipated by the original authors, performing synthetic studies such as formal meta-analyses or even as teaching resources. Read the full Virtual Issue here.

Invasive Species

Published:
10 March 2017

Edited by Manuela González-Suárez and Pablo González-Moreno

Invasive species represent a serious conservation and social problem. This virtual issue showcases recent work on invasive species published in the journals of the British Ecological Society. The studies are grouped into three non-exclusive themes that showcase the latest approaches to understand and manage invasive species.

Evolutionary Quantitative Genetics

Published:
14 June 2017
Edited by Michael Morrissey

Evolutionary quantitative genetics provides formal theoretical frameworks for quantitatively linking natural selection, genetic variation, and the rate and direction of adaptive evolution.  This strong theoretical foundation has long been important in guiding empirical work. The articles in this Virtual Issue highlight important work being done to advance this field. They include papers that draw on a range of new ways of characterising changes in the distribution of traits due to selection; address the issue of characterising modularity; look at the ability of typical sample sizes used studies to characterise phenotypic measures of trait covariation; investigate the influence of spatial autocorrelation in fitness on measures of selection; and much more.

This is an area where empirically-, statistically-, and theoretically-minded people could probably continue to come together, and Methods in Ecology and Evolution's strong developing tradition of publishing their works is very encouraging for future progress in evolution evolutionary quantitative genetics and at its intersection with other aspects of ecology and evolution.

BES Early Career Researcher Awards 2016

Published:
28 March 2017
Each year the BES awards a prize for the best paper, in each of its journals, by an author at the start of their research career. This Virtual Issue brings together the winning and highly commended papers selected by the editors from journal issues published in 2016. Read the papers here.

Biogeography

Published:
10 January 2017
Edited by Will Pearse and Pedro Peres-Neto
This Virtual Issue, created to celebrate the International Biogeography Society's 2017 conference in Tuscon, Arizona, shows off new articles in the field from a diverse array of authors.


To truly understand how species' distributions vary through space and time, biogeographers often have to make use of analytical techniques from a wide array of disciplines. As such, these papers cover advances in evolutionary analysis (Weir & Lawson), biodiversity definitions (Pavoine et al.), and species distribution modelling (Brewer et al.). Equally, they reflect the growing understanding that biogeography can include experiments (Borer et al.), and discuss the pitfalls and opportunities of working with remote-sensing data (Pettorelli et al.; Leempoel et al.). Finally, biogeography often has meaningful implications for policy, such as in disease modelling (Verity et al.) and conservation (Boakes et al.).


This selection of papers also highlights the growing number of software packages focused towards biogeography (Rominger et al.; Bocedi et al.). Many of these manuscripts have early-career lead-authors, and one of these papers won our journal's Robert May prize (Gallien et al.).