Software Review Collaboration with rOpenSci

© The rOpenSci Project, 2017

The role of science journals is to publish papers about scientific research. We need to maintain some quality in what is published, so we use peer review, and ask experts in the subject of a paper to read it and check that it is correct, the arguments make sense etc.

One of the types of paper we publish is Applications, most of which describe software that will help ecologists and evolutionary biologists to do their research. Our focus is on the paper itself, but we also want to be confident that the software is well written, e.g. that it has no obvious bugs, and that it is written so that future versions will not break.

Of course, it takes a lot of time to thoroughly review software, and that is not the primary job of the journal’s peer review process. But we appreciate that this needs to be done, and indeed many of our reviewers and editors put a lot of time into doing just this, something we really appreciate. But can we do this better?

Fortunately, we were approached by the rOpenSci organisation, who wanted to collaborate with us to do this (a huge thanks to Scott Chamberlain for this initial approach and all of his hard work in putting this collaboration together). They are a group of coders, mainly in ecology, who have written a large number of open source R packages for a variety of tasks (e.g. importing data, visualisation). They also want to maintain good quality code, so they have implemented a variety of methods to do this.

One of these is code review. This is another form of peer review, but focused on the code, not the paper. This means the reviewer can concentrate on checking that the code works, that it is well written and documented (so other people can read the code and adapt it), and that it has the right sets of tests, so that if something changes, it is straightforward to check that it still works. Continue reading

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!

Tips for Publishing Methods Papers in Ecological Journals

At the 2015 Eco-Stats Conference at the University of New South Wales there was a Q&A panel discussion of tips for authors publishing methods papers. The panel was chaired by Methods in Ecology and Evolution Associate Editor David Warton. It included Jane Elith (winner of the Methods Recognition of Achievement award), Associate Editor Matt Schofield and former Associate Editor Shinichi Nakagawa. There was also a late appearance, straight off a long haul flight from China, by Doug Yu (another current Associate Editor).

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The Arborist Throw-line Launcher

Collecting leaves or seeds from tall trees is a difficult task that many plant physiologists, ecologists, geneticists and forest managers encounter repeatedly. In a series of videos on the Methods in Ecology and Evolution YouTube channel, Kara N. YoungentobChristina Zdenek and Eva van Gorsel demonstrate how to use the arborist throw-line launcher, which significantly simplifies this task. This new way of collecting seeds and leaves from tall trees is explained in their Applications article ‘A simple and effective method to collect leaves and seeds from tall trees‘. As this is an Applications paper, it is freely available to everyone.

Basic Techniques for the Arborist Throw-line Launcher

The first of the three videos is a basic overview of the method. In this tutorial, the authors teach you how to find the ideal branch, how to use the throw-line launcher and go through some important safety information. Continue reading

New Associate Editor: Sarah Goslee

Today, we are pleased to be welcoming a new member of the Methods in Ecology and Evolution Associate Editor Board. Sarah Goslee joins us from the USDA Agricultural Research Service in the USA and you can find out a little more about her below.

Sarah Goslee

“‘Why is this plant growing here?’ Tackling this question has led me through wetlands, forests, deserts and grasslands. I’ve poked at this question from the scale of plant traits all the way up to satellite imagery. I employ tools that include multivariate analysis, community and landscape diversity metrics, simulation modelling, and spatial classification. My current focus is on agricultural decision support tools for pasture and rangeland.”

Sarah will be handling Applications articles for the journal. Applications papers describe new software, equipment or other practical tools, with the intention of promoting and maximising the uptake of these new approaches. All of our published Applications articles are freely available to everyone.
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