Will Gearty

Join us later today for Dr Hagen’s talk! An additional reminder, double-check the time if your clocks have recently changed (this will be at 4pm CET) 🕰️

Save the Museum of the Earth – Secure Its Future! In these challenging times, places like the Paleontological Research Institution (PRI) stand as beacons of hope, fostering understanding of the natural world and inspiring action for a sustainable fut...

Loosing the PRI would devastate US science. Any level donation, spreading the word helps. #FossilFriday #SaveScience

priweb.donorsupport.co/page/FUNWALK...

Last week the @palaeoverse.bsky.social team published our new paper outlining steps for cleaning palaeobiological occurrence data. I'm really proud of this one; we even have a step-by-step run-through of data cleaning and an accompanying vignette. Thanks to the fantastic team! ⭐

Yeah, I've definitely run into some issues with {shinymeta}, but I'm hoping I can get through them with enough tinkering. I'll have to check out {shinyscholar}!

Definitely looks like there's some overlap in design and intention, but I think paleopal is at a slightly lower level with individual workflow steps compared to entire modules in {wallace}.

I'll take a look, thanks!

The official home of the Python Programming Language

TLDR; The PSF has made the decision to put our community and our shared diversity, equity, and inclusion values ahead of seeking $1.5M in new revenue. Please read and share. pyfound.blogspot.com/2025/10/NSF-...
🧵

Series of plots and graphs illustrating the five different evolution model configurations studied. They correspond to a range of simple to (moving down the page) increasingly complex and parameter-rich models of morphological evolution.

Assessing the impact of character evolution models on phylogenetic and macroevolutionary inferences from fossil data onlinelibrary.wiley.com/doi/10.1111/... @daveyfwright.bsky.social @datadryad.bsky.social

Reposting this today to give it some more attention. Working on this paper with other @palaeoverse.bsky.social folks was a great experience 😄. Hopefully this will serve as a great resource for paleontologists in the future!

It even comes with R code that you can copy/paste: tenrules.palaeoverse.org

Glad you enjoyed it! And we totally agree this is important! While not called out by name in the paper, palaeoverse::tax_check() and fossilbrush::check_taxonomy() can be really useful for flagging misspellings of taxa like you describe here.

Hit me up if you're interested in getting involved! I'm also happy to chat your ear off about paleopal and other #opensource and #openscience initiatives I've got going on in paleontology.

I'm building a new webapp that enables users to build 100% reproducible workflows for paleontological data science with zero technical experience. It's still a work-in-progress, but I'm hoping to work with potential users and other computational paleontologists to make it as useful as possible.

YouTube video by useR! Conference paleopal: A Shiny app for building data science workflows in paleontology - William Gearty

I've had such a great time talking about some of my recent #opensource and #openscience work at #useR2025, #USRSE25, and #GSAConnects2025 over the last few months!

If you missed it, you can watch the recording of my #useR2025 talk on YouTube.

#reproducibility #paleontology #datascience #Rstats

Currently looking for a postdoctoral position and interested in this kind of research? 👀
Dr Hagen currently has an open position in his new Computational Integrative Biodiversity group at Goethe University Frankfurt, for more details see: www.uni-frankfurt.de/48794987/Zen...

A flyer for the next instalment of the Palaeoverse Lecture Series. The flyer features a cartoon landscape with a river and trees, overlying a grid showing how the system might be simulated across space. There is also a picture of Dr Oskar Hagen, wearing a white shirt and navy suit jacket, smiling into the camera.

🚨Palaeoverse Lecture Series🚨
🗓️30th October 2025, 15:00 UTC🗓️

Join us next week to hear from Dr Oskar Hagen, on “Mechanistic biodiversity modelling with gen3sis: population-based simulations across regional and global domains to deep and shallow time” 🌐

Register here: bit.ly/palaeoverse-...

Graphic summary of the proposed ten rules and steps to follow when cleaning occurrence data for palaeobiological analysis. The rules are grouped within their respective theme: project setup (Rules 1–3; blue); data exploration and cleaning (Rules 4–8; red); and reporting and archiving (Rules 9 and 10; green).

Ten simple rules to follow when cleaning occurrence data in palaeobiology onlinelibrary.wiley.com/doi/10.1111/... @lewisajones.bsky.social @es-ucl.bsky.social @paleodb.bsky.social #FossilFriday

Ten simple rules to follow when cleaning occurrence data in palaeobiology Large datasets of fossil occurrences, often downloaded from online community-maintained databases, are a vital resource for understanding broad-scale evolutionary patterns, such as how biodiversity h...

Just in time for #FossilFriday! Our paper is out today in Palaeontology @thepalass.bsky.social

Ten simple rules to follow when cleaning occurrence data in palaeobiology 🧹🦕

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

Another great @palaeoverse.bsky.social team effort to offer a community resource!

A schematic showing “Ten simple rules to follow when cleaning occurrence data im palaeobiology”, each illustrated with a cartoon and arranged around three key processes, in circles. The first stage is Project setup. Here we have: 1. Choose the right data for your question, with a cartoon of an arrow in a bullseye 2. Keep raw data raw, with a cartoon of a hand next to a small ‘no entry’ sign 3. Document your workflow, next to a cartoon of two stacked papers with writing on The second stage is Data exploration & cleaning, which can be performed iteratively: 4. Explore your data, with a cartoon of a magnifying glass over a normal distribution 5. Identify and handle incomplete data records, with a cartoon showing four squares in a larger square, all filled except the one in the bottom right, which is outlined 6. Identify and handle outliers, with a cartoon showing four squares in a larger square, where the one in the bottom right is larger and extends beyond the others 7. Identify and handle inconsistencies, with a cartoon showing three squares in a larger square, with the bottom right quadrant instead featuring a triangle 8. Identify and handle duplicates, with a cartoon showing an opaque square stacked over a transparent (edge only) square The final stage is Reporting and archiving: 9. Report your data and cleaning efforts, with a cartoon of a loudspeaker 10. Deposit your data and workflow, with a cartoon of a safe

🎉 This #FossilFriday we’re happy to share our new paper! 🎉

We take readers through 10 key steps for cleaning palaeontological data ready for computational analyses 🦕🧽

There’s also an R vignette showing you how to put these steps into practice! 💻

Check it out: doi.org/10.1111/pala...

SORTEE The Society for Open, Reliable, and Transparent Ecology and Evolutionary Biology (SORTEE) is a service organization which brings together researchers working to improve reliability and transparency…

#SORTEE2025 Conference is over but you can (re)watch @ www.youtube.com/@SORTEcoEvo/...
- Introductory & closing remarks by @eivimeycook.bsky.social
- Plenary 1 by Dr. Israel Borokini
- Plenary 2 by Prof. Simine Vazire

The cover of the Cleaning Biodiversity Data in R book. It has an illustration of an Pacific Cleaner Shrimp in the middle of a navy background. The shrimp has a bright red-orange shell, pale-yellow body and white whiskers.

Still want to make cleaning biodiversity data shrimp-ler? 🦐

Good news: We just updated our Cleaning Biodiversity Data in R book, so you still can! We've updated data for 2025, added new content & fixed lots of silly typos 😀

Live the shrimp-le life:
cleaning-data-r.ala.org.au

#rstats #ecology 🧪🌏

We are honoured and excited to be running the 2025 @paleosoc.bsky.social Short Course at #GSAConnects2025 this Saturday! Come and join us (it’s 100% free) if you will be around! 😎

Super excited for GSA this week!

I am especially hyped to teach members of @paleosoc.bsky.social some open science best practices 🔓, help folks with the data at the GSA Data Help Desk 📓, and see lots of great talks about comp paleo 🦴 and geoinformatics 🌐!

#GSAConnects

Happy Indigenous Peoples' Day!

We are opening the last call for workshop proposals in 2025! Deadline is December 15, 2025. Visit the website with the necessary information before preparing a proposal. Questions? Contact Danijela Dimitrijevic (science) or Barbara Seuß (logistics) Info: www.paleosynthesis.nat.fau.de/index.php/sc...

I'll be presenting a poster at USRSE'25 next week and a talk at GSA later in October, both about paleopal and its development! Come check it out!

#USRSE25 #GSAConnects2025

Open Source, Open Science: New App Leads Data Reproducibility Open-source app "Paleopal" facilitates replication and sharing of information among researchers using data science tools to create workflows.

@syracuseu.bsky.social News just published a short piece about a new Shiny-based open-source webapp that I'm working on that is called paleopal!

It's still very much a work-in-progress, but you can check out a working prototype here: williamgearty.com/paleopal/.

news.syr.edu/2025/10/02/o...

Same thing goes for job applications! I recently read a job app for a paid intern position in my office where the applicant claimed they had already developed the entirety of a software package that matched the exact software package we had described in the job ad. What a waste of my time 🫩

Comic. PERSON 1 to person with white hat: I finished all the gen-ed back in 2010, and I’m up to the 400-level courses in most departments. But now one of my advisors is saying I “can’t have more than 20 majors” and “need to graduate next year.” It’s outrageous! [caption] My university is making it really hard to finish a 100% all achievements speedrun.

100% All Achievements

xkcd.com/3148/

Slide Title for September CURIOSS Deep Dive: Opening Skills & Solutions - Experiential leaning at Saint Louis University Speaker: Daniel Shown, Open Source with SLU

Our September Deep Dive with Daniel Shown of @slu-official.bsky.social is a must watch❗

Open Source with SLU's Opening Skills & Solutions program has demonstrated success with $500K+ in development value delivered and 80+ professionals trained annually.

📺https://bit.ly/4o3Ox0Z

#AcademicOSPO #OSS

NSF unexpectedly changed (at the last minute) who is eligible to apply for the Grad Research Fellowship, dropping 2nd year students. We started a petition to reverse this unfair change, Sign here:
laurenkuehne.github.io/grfpChanges/
and please spread the word!!!!