Tag: modelling

Methods papers

From pattern to process: estimating species interactions and driver-species relationships from count data

Post provided by Quinn Asena Uncovering signals from the past Understanding interactions among organisms, and between organisms and their environment, has been a cornerstone of ecology as long as we have been busying ourselves with the lives of other species. How do plants and animals facilitate or compete with each other? How do they respond to the continuous challenge of changing climates or new neighbors? … Continue reading From pattern to process: estimating species interactions and driver-species relationships from count data

Unknown's avatarHarriet RhodesLeave a comment
Ecology, Statistical methods, Theoretical methods

Hybrid Forest Models: integrating mechanistic knowledge and data

Post provided by Yannek Käber and Maximilian Pichler We met at YOMOS, a workshop for early-career researchers and young modelers in ecology supported by the German Society for Ecology, and we came at modeling from opposite ends. Yannek builds dynamic forest models, which are mechanistic models that integrate decades of ecological reasoning about how trees grow, compete, and die. Max builds machine learning models for … Continue reading Hybrid Forest Models: integrating mechanistic knowledge and data

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Statistical methods

Modelling approaches in meta-analysis: from sandwich estimators to correlated hierarchical models

Post provided by Coralie Williams Conducting a meta-analysis involves a series of decisions, from choosing what data to extract to selecting the outcome measure. But then comes the model specification – how should it be formulated? At its simplest, a meta-analysis can be expressed as a simple linear regression model where the outcome is an effect size (yi), which is a quantitative measure derived from … Continue reading Modelling approaches in meta-analysis: from sandwich estimators to correlated hierarchical models

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Robert May Prize

Grace Ridder: Generating spatially realistic environmental null models with the shift-&-rotate approach helps evaluate false positives in species distribution modelling

Throughout March and April, we are featuring articles shortlisted for the 2024 Robert May Prize. The Robert May Prize is awarded by the British Ecological Society each year for the best paper in Methods in Ecology and Evolution written by an early career author. Grace Ridder’s article ‘Generating spatially realistic environmental null models with the shift-&-rotate approach helps evaluate false positives in species distribution modelling‘ is one … Continue reading Grace Ridder: Generating spatially realistic environmental null models with the shift-&-rotate approach helps evaluate false positives in species distribution modelling

Unknown's avatarHarriet RhodesLeave a comment
Ecology

Avoiding Confusion: Modelling Image Identification Surveys with Classification Errors

Post provided by Jon Barry We are a group comprised of statisticians, ecologists and a computer scientist. Back in 2021 when this work started, we were all employed at the Centre for Environment, Fisheries and Aquacultural Science (Cefas) at Lowestoft, U.K. Since then, Robert, our computer scientist, has ‘jumped ship’ (no pun intended) to the Alan Turing Institute. We were aware that AI image recognition … Continue reading Avoiding Confusion: Modelling Image Identification Surveys with Classification Errors

Unknown's avatarHarriet RhodesLeave a comment
Prize winner

Discovering population dynamics and community interactions of migratory birds by individual-based model

It has been a few weeks since the 15th Chinese Symposium on Biodiversity Science and Conservation, where the first “Seminar on Methods in Ecology and Evolution in China” was held. In these blog posts, we hear from some of the winners of the “Outstanding Young Scholar Award in Ecological and Evolutionary Methodology in China”. Here, winner Jin Liu discusses the background behind their research. Post … Continue reading Discovering population dynamics and community interactions of migratory birds by individual-based model

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Theoretical methods

Hidden Markov models have pitfalls…

…but also opportunities! Hidden Markov models (HMMs) and their extensions are attractive methods for analysing ecological data. In recent years, a variety of extensions of the basic model have been proposed, yielding great opportunities for ecological inference. Yet, as these models become more complex and challenging to understand, it is important to consider what pitfalls these methods have and what opportunities there are for future … Continue reading Hidden Markov models have pitfalls…

Unknown's avatarIndia StephensonLeave a comment
Code and Applications, Methods papers, Statistical methods

An Ecologist and a Programmer Walk Into a Bar…

Post provided by Daniel Vedder, Markus Ankenbrand, and Juliano Sarmento Cabral

Five years ago, a new institute opened its doors at the University of Würzburg: the Center for Computational and Theoretical Biology (CCTB). The idea was simple. Take six computational research groups, covering topics from image analysis to genomics and ecological modelling, put them in a building together, and see what happens.

Despite our disparate areas of expertise, this “experiment” has worked really well. It soon turned out that one of our greatest strengths as an institute lay in the cumulative computer know-how we have, or have acquired together. In our experience, many biologists are still somewhat wary of computational techniques, and struggle with them even when they use them. Part of the reason for this unease, we believe, is that few biologists are thoroughly trained in computer science.

Continue reading “An Ecologist and a Programmer Walk Into a Bar…”
Unknown's avatarChloe V. RobinsonLeave a comment
Code and Applications, Methods papers, Statistical methods

Reliably Predicting Pollinator Abundance with Process-Based Ecological Models

Post provided by Emma Gardner and Tom Breeze

Bumblebee. Picture credit: Tom Breeze.

Pollination underpins >£600 million of British crop production and wild insects provide a substantial contribution to the productivity of many crops. There is mounting evidence that our wild pollinators are struggling and that pollinator populations may be declining. Reliably modelling pollinator populations is important to target conservation efforts and to identify areas at risk of pollination service deficits. In our study, ‘Reliably predicting pollinator abundance: Challenges of calibrating process-based ecological models’, we aimed to develop the first fully validated pollinator model, capable of reliably predicting pollinator abundance across Great Britain.

Continue reading “Reliably Predicting Pollinator Abundance with Process-Based Ecological Models”
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Code and Applications, Ecology, Methods papers, Theoretical methods

Creating a package to infer species coexistence

Post provided by Ignasi Bartomeus, David García-Callejas, and Oscar Godoy

Ignasi Bartomeus and colleagues share the story behind their recent Methods article ‘cxr: A toolbox for modelling species coexistence in R’.

This post recalls the journey on how we ended up developing cxr (acronym for CoeXistence relationships in R), an R package for quantifying interactions among species and their coexistence relationships. In other words, it provides tools for telling apart the situations in which different species can persist together in a community from the cases in which one species completely overcomes another.

Continue reading “Creating a package to infer species coexistence”

Unknown's avatarDaniel Caetano1 Comment