Category: Code and Applications

Code and Applications, Methods papers

Students, software, and soil flux: lessons learned from development of a package to estimate soil carbon flux at National Ecological Observatory Sites across the United States

By Naupaka Zimmerman and John Zobitz We (Naupaka and John) are faculty at primarily undergraduate institutions (PUIs) where our lives are a blend of teaching and scholarship. We’re always looking for projects that impact our teaching, mentoring, and scholarship duties simultaneously—those sweet spots where one effort advances multiple aims. Due to higher teaching loads and institutional missions that focus on undergraduate research, it can be … Continue reading Students, software, and soil flux: lessons learned from development of a package to estimate soil carbon flux at National Ecological Observatory Sites across the United States

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Code and Applications

Studying social transmission using STbayes

Post provided by Michael Chimento. When studying animal culture, it’s important to establish whether novel behaviours or information have spread through social contact, or are rather innovated or personally discovered. Unfortunately, we can’t give animals a survey asking how they learned something! While many methods for studying social transmission have been proposed over the years, network-based diffusion analysis (NBDA), first introduced in Franz and Nunn … Continue reading Studying social transmission using STbayes

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Code and Applications, Uncategorized

Tracking animals in an underwater maze

Post provided by Edward Lavender Skating in the deep A decade ago, the Movement Ecology of Flapper Skate project was established to track flapper skate (Dipturus intermedius) in Scotland. Flapper skate are large, flattened, benthic animals, with pale undersides and mottled, grey-brown colouration above. Growing in excess of two metres long, they roam over the seabed down to depths of 1200 m. It is thought … Continue reading Tracking animals in an underwater maze

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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

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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

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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

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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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