Joel Nitta
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joelnitta.com
Joel Nitta
@joelnitta.com
300 followers 490 following 91 posts
Associate Prof. at Chiba University, Japan. Father. Pteridologist. Outdoor Activist. Nikkei Yonsei. Posts mine.

https://www.joelnitta.com
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joelnitta.com
Joel Nitta @joelnitta.com · Dec 13
I've created a starter pack of #fern researchers! I am sure there are more of us, suggestions welcome 💚

go.bsky.app/UqHk9kT
Reposted by Joel Nitta
ab604.uk
Based on others work, I've created Claude Code configurations for R: modular skills (tidyverse, rlang, performance, OOP, testing), enforcement rules (security, testing, git workflow), workflow commands (planning, code review, TDD), and context management hooks. #claudecode #rstats
GitHub - ab604/claude-code-r-skills: Claude Code configurations for R development.
Claude Code configurations for R development. Contribute to ab604/claude-code-r-skills development by creating an account on GitHub.
github.com
February 2, 2026 at 12:12 PM
Reposted by Joel Nitta
newphyt.bsky.social
Life phases integration uncovers long‐lived gametophytes mediated reticulate evolution in Haplopteris (Pteridaceae)

Chen et al.

nph.onlinelibrary.wiley.com/share/WRH3JT...
Hypothesis of reticulate evolution of Haplopteris yakushimensis complex.
February 3, 2026 at 10:27 AM
joelnitta.com
After a >1 yr hiatus, the #fern tree of life (FTOL) #phylogeny is back with another update! 🌿 🌏 🧬

For the first time including >1,000 whole plastomes and >6,000 fern species!

Available at fernphy.github.io/downloads.html
Downloads – Fern Tree of Life
Current and past versions of FTOL available for download
fernphy.github.io
February 3, 2026 at 8:20 AM
Reposted by Joel Nitta
eliotmiller.bsky.social
Taxonomy and phylogeny are two sides of the same coin, but that doesn't mean they are always in agreement. I wrote a blog post on why the new Phylogeny Explorer in @birdsoftheworld.bsky.social is such a big deal in that regard, and what's in store next for us.

eliotmiller.weebly.com/blog/birds-o...
Birds of World's new Phylogeny Explorer
It’s been an exciting week. Five years in the making, we’re very excited to release this new, updated, dynamic phylogeny of the world’s birds. By harnessing Open Tree of Life ’s existing...
eliotmiller.weebly.com
January 29, 2026 at 7:03 PM
Reposted by Joel Nitta
physaliacourses.bsky.social
❓ Do you want to level up your #SDM skills?
Learn Bayesian Additive Regression Trees (BART) for SDMs in R. A hands-on course with @jbyoder.org on predictor selection, model training, interpretation & spatial projections using embarcadero and dbarts 🚀

www.physalia-courses.org/courses-work...
#Rstats
Species distribution modeling with Bayesian additive regression tree (BART) methods
Dates 1-3 July 2026
www.physalia-courses.org
January 27, 2026 at 1:29 PM
Reposted by Joel Nitta
sinalana.bsky.social
Machine translation isn't trained on gibberish, so any random string of characters is transformed into sentences. And the user never knows.
Screenshot of a comment made of Japanese characters that, combined, mean nothing. The characters were just chosen because their shapes are similar to each other Machine translation of the comment to English: You must do your best in the evening. One thousand times.
January 27, 2026 at 8:59 AM
Reposted by Joel Nitta
usrbinr.bsky.social
I don't know if there was any one thing that skilled up #rstats skills but for sure learning how to use browser() was key.

Many resources available but @brodriguesco.bsky.social video below helped me the most.
www.youtube.com/watch?v=ATIl...
Debugging your R code with the browser() function and a second pipe operator
YouTube video by Bruno Rodrigues
www.youtube.com
January 26, 2026 at 1:50 PM
Reposted by Joel Nitta
coatless.bsky.social
webRios is live. #rstats on your iPhone and iPad.

I showed native R compilation on #iOS last week. Shipping it is another story (thanks, GPL). This version uses #webR 's #WebAssembly build instead. Different tradeoffs, but this one clears App Review.

apps.apple.com/us/app/webri...
Promotional image for webRios showing the app icon and an iPhone displaying the R console. The console shows example R commands with syntax highlighting: basic arithmetic (1 + 1), a print statement saying 'Hello from iOS!', a warning message in orange reading 'Uh-oh, I'm in the Apple-verse?', an error message in red with the HAL 9000 quote 'I'm sorry, Dave. I'm afraid I can't do that.', and a plot command.
January 27, 2026 at 2:42 AM
joelnitta.com
good to know
Screenshot from program saying "You've been upgraded to Zotero {$version}!"
January 25, 2026 at 4:24 AM
Reposted by Joel Nitta
simon.fedi.simonwillison.net.ap.brid.gy
I had a fascinating conversation with @wilsonzlin about FastRender, the browser rendering engine he built with the help of 2,000+ coding agents over the past few weeks. It's 47m on YouTube or you can read my highlights here: https://simonwillison.net/2026/Jan/23/fastrender/
Wilson Lin on FastRender: a browser built by thousands of parallel agents
Last week Cursor published Scaling long-running autonomous coding, an article describing their research efforts into coordinating large numbers of autonomous coding agents. One of the projects mentioned in the article …
simonwillison.net
January 23, 2026 at 9:53 PM
Reposted by Joel Nitta
ellisjrosen.bsky.social
January 20, 2026 at 7:20 PM
Reposted by Joel Nitta
libbyheeren.bsky.social
DID YOU MISS the very first #DataScienceLab when @isabelizimm.bsky.social and @davisvaughan.bsky.social joined us to talk about some of our favorite #Positron settings? Some folks had asked so I wanted to share!

It's up on YouTube here: youtu.be/QIYyeuZ_ISY

#rstats #python #databs #pydata
Exploring Positron settings | Isabel Zimmerman & Davis Vaughan | Data Science Lab
YouTube video by Posit PBC
youtu.be
January 16, 2026 at 10:49 PM
Reposted by Joel Nitta
ferncurator.bsky.social
Applications for 2026 Botany Travel Awards to support the resident study of collections in the United States National Herbarium are due on 15 February. This year, awards will
be for six weeks, with a stipend of $6,000! For more information, please visit: naturalhistory.si.edu/research/bot...
Opportunities
naturalhistory.si.edu
January 16, 2026 at 1:28 AM
Reposted by Joel Nitta
phypapers.bsky.social
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
December 24, 2025 at 12:16 AM
Reposted by Joel Nitta
benpatrickwill.bsky.social
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...
December 19, 2025 at 5:20 PM
Reposted by Joel Nitta
lauraehall.bsky.social
Stay safe out there y'all
An illustration showing cute fat rabbits piling into an underground burrow. There is text, part of which has been edited. The original text says "There are tunnels underground where bunnies are safe — safe" and the edited text adds "from emails"
December 18, 2025 at 2:53 AM
Reposted by Joel Nitta
nhcooper123.bsky.social
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!
Book cover for Reproducible Code guide. The cover has a red background with a large yellow-bodied black-headed stag beetle.
December 16, 2025 at 3:03 PM
Reposted by Joel Nitta
botsocamerica.bsky.social
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
A green and white graphic titled “BSA Awards.” On the left, the BSA Emerging Leader Award description reads: “Recognizing early-career BSA members whose creative and influential scholarship—and clear promise for future impact across basic research, education, public policy, or service—signals the next generation of leadership in the botanical sciences.” A QR code for more information appears below. On the right, the BSA Mid-Career Excellence in Research Award description reads: “Honoring mid-career BSA members—typically eight to sixteen years post-Ph.D.—whose sustained scholarly achievements, positive impacts in research and education, and significant service and outreach strengthen and advance the botanical community.” The words “NEW AWARD!” appear above the QR code to highlight that this mid-career award is new for 2026. A black banner at the bottom says “Deadline – March 15, 2026.” Botanical illustrations decorate the lower background.
December 9, 2025 at 8:09 PM
Reposted by Joel Nitta
annbot.bsky.social
📣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/...
December 4, 2025 at 7:05 AM
Reposted by Joel Nitta
jhelvy.bsky.social
🎉 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...
Announcing surveydown v1.0.0! – surveydown.org
We are thrilled to announce the v1.0.0 release of surveydown, a stable release with improvements to YAML settings, page navigation, question creation, and a smoother overall developer experience.
surveydown.org
November 25, 2025 at 9:53 PM
Reposted by Joel Nitta
botsocamerica.bsky.social
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
The text at the top reads: “APPS Special Issue Call for Papers: Beyond phylogenomics: Innovative applications of target capture data”. The image beneath the title: On the left side of the image is a large circle divided in two halves: the left side of the circle comprises four images of flowers/herbarium specimens and the right side of the circle contains the text “Target Capture.” Five dotted line arrows point from the large circle to five smaller circles on the right. Smaller circles (clockwise from top): (1) “Off Target”, (2) “Biodiversity assessments”, (3) “Population genomics”, (4) “Evo-Devo”, (5) “Species identification”. The text beneath the image reads: “Proposal deadline November 30, 2025”. The Applications in Plant Sciences logo is in the bottom left corner, and a QR code is in the bottom right corner. Image credit: Yannick Woudstra.
November 24, 2025 at 4:51 PM
Reposted by Joel Nitta
posit.co
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...
testthat hex
November 24, 2025 at 3:34 PM
Reposted by Joel Nitta
statsrhian.bsky.social
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
Abstracts – rainbowR conference
conference.rainbowr.org
November 20, 2025 at 4:59 PM
Reposted by Joel Nitta
mickael.canouil.fr
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
Optimising VS Code and Positron for Quarto: Essential Settings for Better Editing – MCU
Discover the custom settings I use in VS Code and Positron to enhance my Quarto document editing workflow, from improved Git diffs to better visual guides for nested divs.
mickael.canouil.fr
November 20, 2025 at 9:43 AM
Reposted by Joel Nitta
willgearty.bsky.social
📢 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
November 18, 2025 at 3:30 PM