Category: Code and Applications

Code and Applications, Field Methods

Teaching Models to Listen to Bats: The Story Behind BSG-BATS

Post provided by Katarina Meramo Bats are extraordinary animals. They fly, echolocate, and navigate in absolute darkness, and produce some of the most complex acoustic signals in the mammalian world. They pollinate, disperse seeds, control insect populations, and quietly hold ecosystems together. Yet, despite their importance, monitoring bats – particularly across large spatial and temporal scales – remains remarkably challenging. Over the past decade, bioacoustic … Continue reading Teaching Models to Listen to Bats: The Story Behind BSG-BATS

Unknown's avatarHarriet RhodesLeave a comment
Code and Applications

An easy-to-manage tool for forest ecosystem modeling—The pnetr R package

Post provided by Xiaojie Gao I am a remote sensing ecologist currently working as a postdoctoral researcher at Harvard Forest department of Harvard University. My research focuses on mapping and understanding the impacts of climate change and human activities on the terrestrial vegetation ecosystems. The development of the pnetr R package for forest ecosystem modeling was inspired by my own research interest in understanding how … Continue reading An easy-to-manage tool for forest ecosystem modeling—The pnetr R package

Unknown's avatarHarriet RhodesLeave a comment
Code and Applications, Ecology

Tracking animals with particles

Post provided by Edward Lavender, Andreas Scheidegger, Carlo Albert, Stanisław W. Biber, Janine Illian, James Thorburn, Sophie Smout, Helen Moor. It’s morning on Scotland’s west coast. In the Firth of Lorn, the deep-blue water sparkles in the early sunlight. Heading south, I glance back across the sea, taking in the snow-speckled mountains beyond. Two hundred metres below, I know the seascape is just as rugged. … Continue reading Tracking animals with particles

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Code and Applications, Ecology, Statistical methods

Into the Swarm-Verse: quantifying collective motion across species and contexts

Post provided by Marina Papadopoulou Authors We are three researchers interested in collective animal behaviour. Marina Papadopoulou is a postdoctoral researcher at Tuscia University in Italy, Simon Garnier is a Professor at the New Jersey Institute of Technology (USA), and Andrew King is an Associate Professor at Swansea University (UK). As a Greek-French-Welsh team with empirical, mathematical, and computational backgrounds in different study systems, we … Continue reading Into the Swarm-Verse: quantifying collective motion across species and contexts

Unknown's avatarplydtanthera1 Comment
Code and Applications, Statistical methods

It is only by understanding what causes sampling bias that we can correct it

Post provided by Rob J. Boyd Colleagues and I recently published a paper in MEE, and its title might induce a bit of head scratching: “Using causal diagrams … to correct geographic sampling biases in biodiversity monitoring data” (Boyd et al., 2025). If you’re familiar with causal inference, you might be wondering, “What have causal diagrams got to do with sampling biases?” And if you’re … Continue reading It is only by understanding what causes sampling bias that we can correct it

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Code and Applications, Phylogenetic analysis, Robert May Prize

Early career research: Increasing access, reproducibility and transparency in phylogenetic analyses with Cristian Román-Palacios

I was born in the Colombian Andes (Armenia, Quindío) back in the 90s. I received my bachelor’s degree in Biology from Universidad del Valle, in Cali, Colombia, in 2015. I moved to the US in 2016 to pursue a Ph.D. in Ecology and Evolutionary Biology at the University of Arizona – a degree that I completed in Fall of 2020. Although my research interests seem … Continue reading Early career research: Increasing access, reproducibility and transparency in phylogenetic analyses with Cristian Román-Palacios

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Code and Applications, Ecology

ToxTrac: A free and user-friendly animal tracking software

Post provided by Magnus Andersson Animal tracking software no longer has to be costly or require advanced computational science skills to operate. Over the last decade, a significant number of free animal tracking software options have been released. However, many of these options suffer from infrequent updates and demand considerable computational expertise to utilize effectively. To address this issue, the creators of ToxTrac launched the … Continue reading ToxTrac: A free and user-friendly animal tracking software

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Code and Applications

How to write clean code

Alessandro Filazzola & Christopher Lortie tell us about their new article ‘A call for clean code to effectively communicate science‘, which provides a series of recommendations and a suite of tools that can be used to help support scientists to produce cleaner code. Can you clearly understand the code that you have written? What about if you gave it to a colleague? Or a reviewer? … Continue reading How to write clean code

Unknown's avatarIndia Stephenson2 Comments
Code and Applications, Ecology

Visualising the flow of matter within ecosystems

Post provided by Mateusz Iskrzyński Would you like to quickly get a clear picture of the food web you are modelling or analysing? Have you thought about including its visualisation in your paper? Or maybe you wanted to show your students or general audience how interconnected food webs are in real ecosystems? Or just wondered how matter flows through an ecosystem? To help you with … Continue reading Visualising the flow of matter within ecosystems

Unknown's avatarChloe V. RobinsonLeave a comment
Code and Applications, Methods papers, Statistical methods

plantR: Managing species records from biological collections

Post provided by Renato Lima

Many biodiversity studies, covering a wide range of goals, need species records. These records are becoming readily available online, however there is minimal standardisation for these records at this stage, therefore requiring final users to spend a significant amount of time formatting records prior to using data. To overcome this, Renato Lima et al. have created plantR – an open-source package that provides a comprehensive toolbox to manage species records from biological collections. In this blog post, Renato discusses the workflow of the package and describes how this package can help researchers better assess data quality and avoid data leakage.

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Unknown's avatarChloe V. RobinsonLeave a comment