voluModel: a new R package to model species distributions in 3 dimensions

Post provided by Hannah Owens (she/her)

One of the base units of analysis for biogeography and conservation science is the species range map. Once we know where a species is, we can ask questions like “Why is it there?”, “How did it get there?”, or “What can we do to make this place better for it?” Especially these days, I am very interested in mapping marine fish distributions, which, it turns out, is not as simple as mapping terrestrial species.

Ben WhittakerMarch 1, 2023February 21, 20231 Comment

Journal Issues

September 2022 Issue Out Now!

Our September issue is now online! This issue contains 22 articles about the latest methods in ecology and evolution, including methods for using the US National Ecological Observatory Network (NEON), measuring understory vegetation structure, inducing cancer in invertebrates and much more! Read on to find out about this month’s featured articles and the article behind our magical marine cover. National Ecological Observatory Network (NEON) In this … Continue reading September 2022 Issue Out Now!

India StephensonSeptember 5, 2022Leave a comment

Journal Issues

July 2022 Issue Out Now!

Our July Issue is now online! This issue contains 20 articles about the latest methods in ecology and evolution, including methods for characterising soil bacterial biodiversity, identifying fish species in fish markets using eDNA, standarising and cleaning biodiversity data and much more! Plus, read the editorial about our switch to a gold open access model this month. Read on to find out about this month’s featured articles … Continue reading July 2022 Issue Out Now!

India StephensonJuly 4, 2022July 4, 2022Leave a comment

Methods papers, Statistical methods

Revealing the hidden lives of cryptic mountain lions using GPS data and a Moving-Resting Motion model

Post provided by Mark Elbroch, Chaoran Hu, Tom Meyer, Vladimir Pozdnyakov & Jun Yan

Female mountain lion collared in Washington USA in late December 2021.

Information on how and even why terrestrial mammals move through their habitat landscapes is important for forming the foundation of how to manage and conserve species. For elusive mountain lions, GPS data is particularly vital for monitoring these important apex predators in relation to their ecosystems and the people they share the land with. In this blog post, the team discusses their novel motion model, published in Methods in Ecology and Evolution, which helps us understand the movement of mountain lions from GPS location data.

Chloe V. RobinsonJanuary 21, 2022Leave 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.

Chloe V. RobinsonJanuary 10, 2022January 10, 2022Leave a comment

Statistical methods

A Multiple-Part Morphospace

Post provided by Daniel Thomas

Many biologists dedicate their careers to finding out why life has taken the shape it has. Darwinian natural selection gives us the how, but researchers are deeply interested in why we find particular morphologies amongst certain organisms, when these morphologies arose, and what these morphologies mean for the organisms and the communities in which they reside. In this post, Daniel Thomas (Massey University, New Zealand) describes the philosophy behind the new morphoBlocks package for R. The package is presented in a new paper within the ‘Realising the promise of large data and complex models’ Special Feature for Methods in Ecology and Evolution. Researchers interested in exploring the morphoBlocks package are encouraged to try these three vignettes.

Ben WhittakerDecember 16, 2021December 16, 2021Leave a comment

Conservation and management, Statistical methods

Let’s get real: translating species distribution models into conservation practice

Post provided by Veronica F. Frans

Species distribution models (SDMs) are popular methods for identifying important habitats for species, but what does it take to translate SDMs into conservation practice? In this post, Veronica Frans discusses the applications of iSDMdb as featured in the paper, “Integrated SDM database: enhancing the relevance and utility of species distribution models in conservation management”, recently published in Methods in Ecology and Evolution.

Ben WhittakerNovember 10, 2021Leave a comment

Conservation and management, Statistical methods

A new tool to identify important sites for conservation using tracking data

Post provided by Martin Beal, Steffen Oppel, Jonathan Handley, Richard Phillips, Paulo Catry, and Maria Dias.

Identifying areas around the world that can best contribute to the conservation of wild animals is a major challenge. Historically, this required conducting extensive surveys in the field, but with the advent of miniature tracking technology we can now follow animals and allow them to indicate which areas they depend on most. In this collaborative post, international researchers from ISPA – Instituto Universitário in Lisbon, the Royal Society for the Protection of Birds, BirdLife International, and British Antarctic Survey present a new conservation tool as outlined in the paper “track2KBA: An R package for identifying important sites for biodiversity from tracking data” recently published in Methods in Ecology and Evolution.

Ben WhittakerSeptember 28, 2021Leave a comment

Methods papers, Statistical methods

Smart genetic analysis made fast and easy

Post provided by: Salvador Herrando-Pérez

If you use genetics to differentiate populations, the new package smartsnp might be your new best friend. Written in R language and available from GitHub and CRAN, this package performs principal component analysis with control for genetic drift, projects ancient samples onto modern genetic space, and tests for population differences in genotypes. The package can load big datasets and run complex stats in the blink of an eye.

In this post, Salvador Herrando-Pérez discusses the features of this new package which is fully described in the new paper “smartsnp, an R package for fast multivariate analyses of big genomic data” recently published in Methods in Ecology & Evolution.

Ben WhittakerAugust 11, 2021August 11, 2021Leave a comment

Methods papers, Robert May Prize, Statistical methods

A new evolutionary simulation R package sheds light on the metaphor of genomic islands of divergence

Robert May Prize Shortlisted Article

Post provided by Claudio S. Quilodrán and Ashley T. Sendell-Price

Nesting eggs of silvereyes (Zosterops lateralis). Heron Island, Australia. Picture: Erik Sandvik.

Each year Methods in Ecology and Evolution awards the Robert May Prize to the best paper in the journal by an author at the start of their career. Claudio S. Quilodrán has been shortlisted for his article ‘The multiple population genetic and demographic routes to islands of genomic divergence’. In this blog, Claudio and co-author Ashley T. Sendell-Price discuss how their paper came to be and how their individual‐based simulation can be used to explore the dynamics of diverging genomes.

streamdnaApril 12, 2021April 12, 2021Leave a comment

Methods Blog

Tag: R package