CGAS (Chloroplast Genome Analysis Suite): An Automated Python Pipeline for Comprehensive Comparative Chloroplast Genomics https://www.biorxiv.org/content/10.64898/2025.12.21.695765v1

Closing out my year with a journal editor shocker 🧵 Checking new manuscripts today I reviewed a paper attributing 2 papers to me I did not write. A daft thing for an author to do of course. But intrigued I web searched up one of the titles and that's when it got real weird...

Stay safe out there y'all

Excited to launch the new improved Reproducible Code guide from @britishecologicalsociety.org @methodsinecoevol.bsky.social FREE online here! www.britishecologicalsociety.org//wp-content/... Amazing work by some very talented ECRs. We hope it’s useful!

The Botanical Society of America is excited to invite nominations for the BSA Emerging Leader Award, and–NEW IN 2026–the BSA Mid-Career Excellence in Research Award! Nomination Deadline: March 15, 2026 To learn more about these and all BSA awards, visit: botany.org/home/awards.... #BSAawards

📣Now Free Access: ‘Out of Africa’ origin of the pantropical staghorn fern genus Platycerium (Polypodiaceae) supported by plastid phylogenomics and biogeographical analysis Get the Paper: doi.org/10.1093/aob/...

🎉 Announcing surveydown v1.0.0! surveydown is an #opensource #rstats package for building surveys with #Quarto & #Shiny. This release improves the survey design experience, including: - Simplified YAML settings - Auto page navigation - Previous buttons! More at surveydown.org/blog/2025-11...

CALL FOR PAPERS 🌿 DEADLINE NOV 30 Submit your proposal for the #AppsPlantSci special issue: “Beyond #phylogenomics: Innovative applications of target capture data” More info at: botany.org/home/publica... @yannickwoudstra.bsky.social @erikarmoore11.bsky.social @emcassey.bsky.social #genomics

testthat 3.3.0 is here! Major updates for #RStats testing include failure messages for easier debugging, 6 new specific expectations, and the SlowReporter to find your bottlenecks. Heads Up: R 4.1+ is now required, and old mocking functions are removed. Read the post: tidyverse.org/blog/2025/11...

Call for abstracts for the first ever @rainbowr.org conference is still open! We're looking for talks that either 🦄 Showcase how our diverse community uses #RStats 🏳️‍🌈 Use LGBTQ+ data Get in your abstracts before December 1st. conference.rainbowr.org/abstracts.html #queerdata #PrideinSTEMDay

After years of working with Quarto, I've refined a set of editor settings that significantly improve document editing efficiency. My latest blog post shares these battle-tested configurations. mickael.canouil.fr/posts/2025-1... #Quarto #VSCode #Positron #Productivity #DataScience

📢 rphylopic 📦 1.6.0 is now on #CRAN! - resolve_phylopic() retries failing API calls 🔄 - geom_phylopic()/add_phylopic() work with ggplot2 4.0.0 🪛 - add_phylopic_tree() wraps add_phylopic() for base R trees 🪾 - get_phylopic() can get og source files from #PhyloPic 👤 rphylopic.palaeoverse.org #Rstats

Developers of the "Geospatial Data Carpentry for Urbanism" lesson, currently in The Carpentries Incubator, are looking for Carpentries community members and Instructors willing to to host and teach beta pilot workshops in 2025 and 2026: carpentries.org/blog/2025/10...

🎉 The magic is real: Quarto Wizard 1.0.0 is LIVE! Wave goodbye to complexity, pure enchantment awaits: 🪄 Magical extension browsing (250+ spells available) ✨ One-click wizardry 🔮 VS Code & Positron enchantment quarto.org/docs/blog/po... #DataScience #Quarto #QuartoPub #VSCode #PositronIDE

I did a workshop today on the pointblank package for R (this workshop: r-consortium.org/webinars/how...) and I thought it was great! Lots of great questions asked, and I did enjoy answering them. ALSO: the package is up to 1000 stars! Really glad to see people liking it :)

The #PolyploidyWebinar series is back for another season! 🧬 Join us for talks at 9AM Pacific on the second Thursday of each month. Are you working on something exciting in polyploidy? We'd love to have you speak! Sign up for open dates at the link below. Looking forward to the great research ahead!

1/13 If the only things you're doing on @bsky.app are scrolling, liking, & posting, then you are still riding a bike with training wheels. Hear me out. There are several simple and free tools out there which let you take advantage of bluesky's secret weapon: its open-source skeleton. A how-to🧵:

Upcoming community sessions next week carpentries.org/community/ev... Events are in UTC Time : 📣 Welcome Session with The Carpentries 07 October 12:00 08 October 14:00 🇦🇺 🇳🇿 AU & NZ Instructors: Pre & post workshop meet up 09 October 00:00

🎉🆕📰🎉: Construction costs and tradeoffs in carnivorous pitcher plant leaves: towards a pitcher leaf economics spectrum doi.org/10.1093/aob/...

Some lab updates, which you should read while listening to 'Zoutelande' by BLØF and Geike Arnaert. www.dannyhaelewaters.com/lab-updates-... 🍄 #LFEE #TeamLaboul

🚀 New Quarto Modal Extension! Create stunning Bootstrap modals in your HTML documents with just a few lines of Markdown! The `quarto-modal` extension makes it dead simple to add interactive pop-ups to your content. #Quarto #QuartoPub #Modal #DataScience #BootStrap github.com/mcanouil/qua...

Hey #Botany2025! The California Botanic Garden is only a 1 hour drive from the convention center and attendees get free admission when showing their badge at the ticket kiosk. It’s a botanists paradise, the perfect side trip while you are here! Don’t miss the buckwheats in bloom!

From digitizing specimens to making biodiversity data accessible for all, iDigBio.org is your hub for advancing natural history research. Thank you to iDigBio for your incredible support as a #Botany2025 sponsor!

#botany2025 if you don’t feel like paying $20 plus tip for an uber to the hotel, the no. 4 bus runs once an hour from in front of the airport and can take you there for $1 cash maps.apple.com/place?coordi...

🌿 Calling all Botanists of Color to join the: BIPOC MIXER 2025! Open to all BIPOC-identifying conference attendees of Botany 2025. 📅 Monday, 9–10 AM 📍 Chino AB Let’s meet and mingle with other plant scientists! We hope to see you there! 💚 #Botany2025 #BIPOCMixer2025

🐘 ellmer 🐘 makes it easy and fun to use LLMs from #rstats, and 0.3.0 is out now. Read about the new streamlined chat() function, improvements to tool specifications, and more at www.tidyverse.org/blog/2025/07....

A little belated but I've started a faculty position at Ecology, Evolution and Marine Biology department at @ucsantabarbara.bsky.social. I'm absolutely stoked! I'll be recruiting at all levels and will be at #Botany2025 Reach out! www.martinezgomezlab.com

Y’all, big news, I found out where they’re keeping them all

Wondering if there might be any other fellow crossover plant / #MTG nerds who would want to play a game of commander at #botany2025... 🤓 🎲 🌱 let me know if so!

A simple rule for better public speaking: If you’re using slides that contain text, you must read it out, word-for-word. clauswilke.substack.com/p/read-out-a...

Step 1: Write R code Step 2: Share it Step 3: Spend 2 hours helping someone install R and troubleshoot their environment OR Step 1: Write R code Step 2: webR sharelink webr.r-wasm.org/latest/?mode... Step 3: Profit ✨ #rstats #webr

Positron Assistant: GitHub Copilot and Claude-Powered Agentic Coding in R blog.stephenturner.us/p/positron-a... #rstats

I need this as my email signature.

Taxonomy is under constant change; species classification is revised continuously, and changes accumulate affecting biodiversity metrics & generating uncertainty that is rarely assessed. Juliana Stropp review how taxonomic changes have changed the observed Amazonian palm richness patterns 👇🧪🌐 #NICED

Recently, my book THEY CALLED US ENEMY was banned – again – in Tennessee. Book bans are out of control. Huge parts of American history are being restricted. To join me in standing up for the freedom to read, go to pen.org/action. @penamerica.bsky.social @topshelfcomix.bsky.social @idwpublishing.com

Study: 97% Of Average American’s Day Spent Retrieving 6-Digit Codes theonion.com/study-9...

We ran a randomized controlled trial to see how much AI coding tools speed up experienced open-source developers. The results surprised us: Developers thought they were 20% faster with AI tools, but they were actually 19% slower when they had access to AI than when they didn't.

#tidyverse purrr 1.1.0 is out - now with parallel processing! Scale your #rstats map operations reliably and efficiently across multiple cores and even distributed systems. Powered by the mirai framework, this unlocks new levels of performance. Read more at: www.tidyverse.org/blog/2025/07...

Can we see — and hear — biodiversity? New research in @peopleandnature.bsky.social shows people can assess forest biodiversity accurately using visual and acoustic clues, like birdsong, colour, and light. @uni-jena.de @unileipzig.bsky.social @ufz.de www.idiv.de/study-shows-...

Still thinking about that bear? 🐻 If you haven't yet, catch @hadley.nz on Ep. 1 of #TheTestSet! He dives into spreadsheets, R's early days, & the tidyverse origin. 🎧 Listen at thetestset.co, on Spotify, or Apple Podcasts #DataScience #RStats #PodcastLaunch

BEAST X for Bayesian phylogenetic, phylogeographic and phylodynamic inference www.nature.com/articles/s41...

Added to template. Ty.

A short Quick Tip video showing how to concatenate and deconcatenate matrices in Mesquite 4. youtu.be/1etP6D3SrdE 🧪 #evolbio @bembidion.bsky.social

Is anyone aware of any publicly available data on individuals who have been SNP chipped AND WGS with short reads? Preferably a diploid. Your girl needs some test data to check her pipeline works before assuming a problem with her input data 🧬 🧪

Here is my checklist summarising a small set of some of the simplest tasks you can do that have high potential to improve the reproducibility of your analysis code. This is based on my year of reproducibility reviews for the J. of Archaeological Science: authors.elsevier.com/a/1lHjN_6yUM... 🧪🏺

Announcing Air 0.7.0! 🎈The super-fast #RStats formatter just got even better. New features include default in Positron, usethis::use_air(), auto-bracing for consistent code, GitHub Actions, and more. Find out more in the Tidyverse blog: www.tidyverse.org/blog/2025/06...

{tidytuesdayR} v1.2.0 is now available on CRAN! Check out our new "Curating a Dataset" vignette (dslc-io.github.io/tidytuesdayR...) + associated functions, and help us prepare data for #TidyTuesday in #RStats! Only tested in RStudio so far, but let us know if you try something else!