occARU: Bayesian (multispecies) occupancy models for ARU data using @mc-stan.org. Automated recording units (ARUs) like camera traps produce rich time series which warrant going beyond occupancy and focusing on detection rates. 1/n

mhollanders.github.io/occARU/

New pre-print! I cover a range of open capture-recapture models (single survey/robust design, multistate/multievent, in (Cormack-)Jolly-Seber variants) in Stan, and provide efficient log likelihood functions. I also introduce a method to account for unequal survey intervals in the entry process.

No, copilot. I don't want you to summarise that for me.

Our latest paper from the Urbis project investigating the spatial structuring of bird assemblage in the city of Rome 🐦🏙️

Can scientists really resurrect the dodo? Inside the company that says it can Colossal Biosciences’ CEO says its work follows a ‘moral obligation’ while critics say it’s ‘tech bro’ hype that could undermine conservation

This story is a good example of why it is so difficult to communicate genuine science to the public. Despite every scientist not on the company payroll decrying it as a bogus and unscientific project, the story presents it as some sort of both-sides issue.

www.theguardian.com/us-news/2026...

Eucalypt Australia are pleased to present Professor Patrick Baker with the Bjarne K Dahl Medal for 2026 in recognition of his significant and sustained contribution to the science of eucalypts in the fields of forest ecology and silviculture.

#NationalEucalyptDay2026 #OurEucalyptHome

Principles of experimental design for ecology and evolution Here I argue that we do not discuss experimental design, often until it is too late. This editorial seeks to begin a conversation about how and where to replicate appropriately.

The principles of experimental design in ecology and evolution has 20k downloads, but unfortunately I still have to reject ~20% of papers without review because they lack replication at the right level. More discussion among mentors and mentees please.
onlinelibrary.wiley.com/doi/full/10....

A Typology of Australian Terrestrial Bird Communities Aim Holistic measurement of the response of fauna communities to interventions requires suitable community condition metrics. However, the development of such metrics is hindered by the absence of b...

Thrilled to be part of this new study that aims to derive a meaningful classification of distinct and recognisable Australian terrestrial bird communities. Lead by @martinemaron.bsky.social and Hannah Fraser with many other colleagues check it out here.

onlinelibrary.wiley.com/doi/10.1111/...

New paper out in Biological Invasions! We show that “genetic rescue” can unintentionally boost invasive fallow deer in Australia. Genomic data & simulations reveal how escaped genotypes from farms may increase pop growth & spread → key implications for management. link.springer.com/article/10.1...

Water sparing versus sharing: Depolarising wetland management with novel environment-agriculture policy Land sparing centres on agricultural intensification to increase yields and free land for conservation, while land sharing integrates farming and biod…

Published today in Biological Conservation, we introduce water into the land sparing versus sharing debate, develop novel water sharing policy options for conserving threatened species in the Murray-Darling, and ask people what they think about such amendments.
www.sciencedirect.com/science/arti...

Crabeater seals. Source: https://www.asoc.org/learn/crabeater-seal/

Biorxiv preprint: “We report the first confirmed highly pathogenic avian influenza H5N1 virus infection in an Antarctic ice-dependent seal, the crabeater seal, and document mortality of these seals across the northern Weddell Sea during November-December 2024.” www.biorxiv.org/content/10.6...

Side-by-side comparison of two multi-panel bubble charts faceted by world region. The left column shows the default facet labels placed above each panel (“Africa”, “Americas”, “Asia”, “Europe”, “Oceania”). The right column shows the same charts, but the facet labels are moved inside each panel at the top-left using a negative margin. In the center, there is a title reading “Want to place your facet labels inside each panel?” with an arrow pointing right, followed by a short ggplot2 theme code snippet demonstrating how to move strip text inside the panel.

I ignored the strip.clip argument in #ggplot2 for way too long 😲

Combined with a small negative margin tweak, you can place facet labels inside each panel. A tiny trick that makes small multiples feel so much cleaner.

🔵 no manual coordinates
🔵 inherits theme styling
🔵 scales nicely when resizing

Jay M. Savage, witness to disappearing frogs and builder of tropical science In the late 1980s, something began to go wrong in places that were supposed to be safe. Protected cloud forests, buffered from chainsaws and bulldozers, started losing animals that had persisted…

In the late 1980s, Jay M. Savage showed that amphibian losses in cloud forests signaled a global pattern, not isolated anomalies.

His career blended field science, institution-building, mentorship, treating extinction as evidence — noticed by those who return often enough to see absence.

collinear: Automated Multicollinearity Management Provides a comprehensive and automated workflow for managing multicollinearity in data frames with numeric and/or categorical variables. The package integrates five robust methods into a single functi...

{collinear} 3.0 is now on CRAN (yay! 🥳)

This #rstats package automates multicollinearity management to improve model robustness and interpretability.

You can learn more at blasbenito.github.io/collinear/, but here's a summary of the most exciting new features: 🧵 1/5

HEY! YOU! ggdibbler 0.6.1 is finally up on CRAN!

harriet-mason.github.io/ggdibbler/in...

You can now pass random variables to any aesthetic in any ggplot geom/stat. If you can express it as a distribution, ggdibbler can plot it. It also works with ggplot extensions, like gganimate. #rstats

Earth history and trait innovation drive the global radiation of modern toads Abstract. The distributions of species radiations reflect environmental changes driven by both Earth history (geological processes) and the evolution of bi

True toads (Bufonidae) originated in South America and invaded Africa via the Antarctic in the Cenozoic! (which was temperate/sub-tropical at the time). Super cool.

🐸🐸🐸

royalsocietypublishing.org/rspb/article...

Model is: b3 <- scasm( y ~ s(x0, bs = "bs", k= k) + s(x1, bs = "sc", xt = "m+", k = k) + s(x2, bs = "bs", k = k) + s(x3, bs = "bs", k = k), family=poisson, bs=200 ) The second smooth `s(x1) is a shape constrained smooth with a positive monotonicity constraint (xt = "m+"). The `bs = 200` arguments uses 200 boostrap samples, which generates bootstrap distributions for each coefficient in the model. These bootstrap samples respect the shape constraints, while the usual +/- 2 SE credible intervals may not. The uncertainty in the partial effects is shown by two credible interval bands; a dark blue central band is a 68% Bayesian credible interval, while the lighter blue outer interval is a 95% Bayesian credible interval. The background of each panel is light grey with white grid lines, in a similar style to ggplot2's default theme.

A new release of the mgcv #RStats 📦 is out on CRAN and Simon Wood (U Edinburgh) has added some significant new features despite the small bump in version number:

🌟 scasm() for estimating GAMs with shape constrained smooths. Can be used with any family & smoothness selection is via the EFS method

GitHub - hadley/genzplyr: dplyr but make it bussin fr fr no cap dplyr but make it bussin fr fr no cap. Contribute to hadley/genzplyr development by creating an account on GitHub.

Do you teach #rstats? Do your students complain about how lame and old-fashioned dplyr is? Don't worry: I have the solution for you: github.com/hadley/genzp....

genzplyr is dplyr, but bussin fr fr no cap.

any other Aussies annoyed at the new BoM website? they've made it look like the app, which is good for mobile but terrible information density on desktop, and now it takes extra clicks to get to the forecast rather than today's weather.

RETVRN to compact monospace text weather forecasts!!

Welcome to the world Aevipertidus gracilis - the gracile one from a lost age. 14-19 Mya ancient #NewZealand appears to have had a bowerbird. Check out this amazing research mahi led by Elizabeth Steell (www.tandfonline.com/doi/full/10....). Artwork by Sasha Votyakova/Te Papa CC-BY-SA. 1/9 🧵

And then there were none: Australia’s only shrew declared extinct Australia’s only known shrew has been declared extinct. Its loss emphasises the need for national protection of Australia’s rare and unique wildlife.

Sad news for Australian mammals..Australia's only shrew officially declared #extinct.
theconversation.com/and-then-the...

Google developer #1: "That's it. Our search engine is simple, efficient, and reliable. It's perfect. We're done."

Google developer #2, presumably: "But wouldn't it be *more* perfect if the first search result was always a robot who mansplained your search results to you incorrectly?"

🚀 gratia 0.11.1 is out!
Compatibility with ggplot2 4.0.0 + usability improvements + bug fixes.

#Rstats #mgcv #gam #statistics

Conceptual overview of the deepSSF neural network used to predict animal movement.

📖Published📖

Forrest et al. present deepSSF, an approach to fit and predict animal movement data using deep learning 🐃 🌍 🧪 Read the full article here 👇

buff.ly/BWQ3Oni

An R package for working with generalized additive models Graceful 'ggplot'-based graphics and utility functions for working with generalized additive models (GAMs) fitted using the 'mgcv' package.

🚀 gratia 0.11.0 is out!

Now has a paper in JOSS — please cite 📄 doi.org/10.21105/jos...

Experimental parallel processing ⚡

New assemble() for building plots 🎨

Better support for complex families + new diagnostics 🧪

Lots of bug fixes + polish ✨

👉 gavinsimpson.github.io/gratia/

#Rstats

Article on BBC news. Title: AI designs antibiotics for gonorrhoea and MRSA superbugs Description: Two new potential drugs have been designed by AI to kill drug-resistant bacteria, in a major Massachusetts Institute of Technology study.

I really dislike how science has started calling almost any fancy computational technique AI. 🧪

The framing of this entire article makes it sound like a benevolent AI independently made these drugs.

That is *pure fantasy*.

Instead: a team of scientists made a machine learning model for a study.

I wish to speak with whomever is responsible for the frankly bizarre distribution of the Slender-billed Gull (C. genei). What nonsense is this?!

Grade F level diagram of an ostrich skeleton. The pelvis is labelled as a humerus, and sternum appears to be labeled as the pelvis.

The team of Ph.D. level experts in ChatGPT apparently doesn't include any anatomists.