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Jonathan Kitt

@jonathankitt.bsky.social
197 followers 237 following 187 posts

🧬 Wheat genomics 📊 Data analysis & visualisation 🖥️ Computational biology jonathankitt.netlify.app/blog

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Reposted by Jonathan Kitt
Peter Ellis @freerangestats.info · 16/09/2026
Inspired by a @f2harrell.bsky.social comment, I did some #rstats simulations about how big a sample needs to be for the central limit theorem to kick in and the sample mean be normally distributed for inference purposes. Yes, with skewed data the answer is "lots". freerangestats.info/blog/2026/09...
Scatter plot with 8 facets, each showing a different distribution, and the actual coverage of a 95% confidence interval for the mean at different sample sizes. Most values are well below 95%.
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Simon P. Couch @simonpcouch.com · 15/09/2026
We're excited to share commons, an R and Python package that helps data scientists build trustworthy data agents for their organizations! Read more on the @posit.co open source blog: opensource.posit.co/blog/2026-09...
A screenshot of the blog post announcing commons. The hero image shows the hex sticker, a common kingfisher on a park bench.
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Tom Mock @themockup.blog · 14/09/2026
R-based virtual envs!
Screenshot of rig R project commands
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Mattan S. Ben-Shachar @mattansb.msbstats.info · 14/09/2026
Upgrading my "hedghog-cake as an estimand" slide with some more hedgehog cakes from hell. #statsmeme
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Stephen Turner @stephenturner.us · 08/09/2026
One of the absolute best newsletters for deep reporting and essays in biology is back www.asimov.press/p/back
asimov.press
Asimov Press is Back
We are returning with a renewed focus on original reporting, investigations, and thesis-driven philanthropy.
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Solomon Kurz @solomonkurz.bsky.social · 04/07/2026
At a basic level, I think this depends on what you care about. If you want quick pubs for a grade or a promotion, just do t-tests. If you are interested in your data, learn how to fit and interpret ordinal models.
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Aki Vehtari @avehtari.bsky.social · 13/08/2026
All four books I've co-authored are freely available online for non-commercial use: - Bayesian Workflow at avehtari.github.io/Bayesian-Wor... Links to other three books are in the quoted post 👇 (too many books to fit in one post!)
avehtari.github.io
Bayesian Workflow book: Website – Bayesian Workflow book
Website for the Bayesian Workflow book by Gelman, Vehtari, McElreath, et al. — case studies, code, and exercises in R and Stan.
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Mickaël CANOUIL, Ph.D. @mickael.canouil.fr · 07/09/2026
So much easier to draft and tweak Typst figure (using Gribouille) for TidyTuesday, when working in a Quarto document. #Typst #Quarto #grammarOfGraphics #TidyTuesday
VSCode window showing a Quarto document on the left panel that shows Typst code cell importing a _plot.typ file and the preview of that file on the right panel
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Hadley Wickham @hadley.nz · 05/09/2026
I wrote up the talk I gave for userR! 2025: tidydesign.substack.com/p/a-no-bulls.... A lot has changed in the last 12 months, but the bulk of this talk still resonates with me.
tidydesign.substack.com
A no bullshit guide to LLMs
A talk from useR! 2025
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Solomon Kurz @solomonkurz.bsky.social · 02/09/2026
Completely astonishing
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Gale Sinatra @galesinatra.bsky.social · 02/09/2026
It was melting permafrost. Even worse than melting glaciers. Deadly Landslide in Nepal Most Likely Caused by Weakened Bedrock www.nytimes.com/interactive/...
nytimes.com
Deadly Flash Floods in Nepal Most Likely Caused by Weakened Bedrock
As the planet warms, glacier meltwater and a thawing permafrost could have contributed to destabilizing the rock.
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Code for Thought / Peter Schmidt @code4thought.bsky.social · 25/08/2026
A new season of #code4thought - the #podcast for researchers who code & digital research professionals - starts today. Listen to the short trailer to find out what's in store between now and the end of 2026. codeforthought.buzzsprout.com/1326658/epis...
codeforthought.buzzsprout.com
[EN] Welcome to Season 12 - Trailer - Code for Thought
English Edition: welcome back from your summer holidays. And what a summer this has been! In this short trailer you'll find out what's in store between now and the end of this year. I hope you find so...
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R for the Rest of Us @rfortherestofus.com · 24/08/2026
This week on What's New in R: ✅ Nicola Rennie introduces {ggchord2} ✅ A package that lets you play Doom in R ✅ Kylie Ainslie’s The Warehouse for easy discovery of R packages Read the issue: ​​https://rfortherestofus.com/2026/08/whats-new-in-r-august-24-2026 #rstats
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Darren Dahly @statsepi.bsky.social · 04/08/2026
Stop trying to explain what a p-value is in a single sentence (ICYMI) statsepi.substack.com/p/no-you-can...
statsepi.substack.com
No, you can't explain what a p-value is with one sentence (Parts I, II)
But I'm going to try and do it in as few as possible. #fml
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Libby Heeren @libbyheeren.bsky.social · 27/07/2026
What up, slide nerds?! Wait, are you NOT a slide nerd? Do... do you want to be? Join the nerd side. We have #Quarto slide themes 🤓 And we have EMIL, which might be even better! Come hang out with us tomorrow on the Labbbb! #rstats
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David Asboth @davidasboth.com · 26/07/2026
New episode! How will we learn things in an age of AI? Recorded it a while ago, but luckily the topics haven't been made obsolete by recent developments in AI (always a risk). open.spotify.com/episode/3Ch2... #databs #datasky
open.spotify.com
S05E03 - How will we learn things?
Half Stack Data Science · Episode
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Tyler Morgan-Wall @tylermw.com · 23/07/2026
oh yeeeaaaahhh that's the good stuff 3D roads generated from #OpenStreetMap data in #RStats with #rayshader and rendered with #rayrender
3d render of highway overpass3d render of highway overpass
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Vincent Arel-Bundock @vincentab.bsky.social · 21/07/2026
Here's a useful page with a **ton** of common tasks in #RStats, done with parallel syntax for tidyverse vs. data.table vs. base. arelbundock.com/posts/dt_tb_... #rdatatable #tidyverse
arelbundock.com
data.table vs. base vs. dplyr | Vincent Arel-Bundock
Academic website and blog of Vincent Arel-Bundock.
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Etienne Bacher @etiennebacher.bsky.social · 07/07/2026
#rstats tidypolars 0.19.0 is available! tidypolars provides the tidyverse syntax while using polars for better performance. In this release: - support more functions, incl. the new %notin% operator - better consistency with tidyverse - bug fixes Changelog: www.tidypolars.etiennebacher.com/news/
tidypolars.etiennebacher.com
Changelog
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Martin Huber @causalhuber.bsky.social · 01/07/2026
📖 News about my book #CausalAnalysis! Many empirical examples are now also available in #Stata - in addition to #R and #Python. You can find the data and code files at 🔗 www.unifr.ch/appecon/en/r... A big thank you to Sarina Oberhänsli for translating the code from R to Stata! 🙏
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Emil Hvitfeldt @emilhvitfeldt.bsky.social · 15/06/2026
I'm excited to announce a long overdue update to {tidyclust}! This release brings support for 3 new model types: DBSCAN, Gaussian mixture, and mean shift models. We also now support parallel processing with {future} and {mirai} opensource.posit.co/blog/2026-06... #rstats #tidymodels #dataBS
opensource.posit.co
tidyclust 0.3.0
tidyclust 0.3.0 is now on CRAN. This release adds support for DBSCAN, Gaussian Mixtures, and Mean Shift Models, plus closer alignment with the tidymodels framework.
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David Pierce @davidpierce.xyz · 15/06/2026
Today’s Vergecast: # The **epic** story of Markdown. Markdown is a system for writing that makes it readable to both humans and computers. It’s all about the symbols. You use – to make a list, * for emphasis, ** for even... www.theverge.com/podcast/950082/mar…
youtube.com
Today’s Vergecast: # The **epic** story of Markdown.
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Jonathan Kitt @jonathankitt.bsky.social · 15/06/2026
À Nantes pour les Rencontres R 2026 qui débutent demain! rr2026.sciencesconf.org Hâte d'y être et de - peut-être - vous y croiser ! #Rstats #RR2026 #RencontresR
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Georgios Karamanis @karaman.is · 14/06/2026
This week's #TidyTuesday is about films based on video games Built as a Quarto reveal.js presentation using the timeline extension by @emilhvitfeldt.bsky.social Interactive version at karaman.is/blog/2026/06... Code: github.com/gkaramanis/t... #RStats #QuartoPub #dataviz
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Eloise Newman @eloisenewman.bsky.social · 12/06/2026
This looks so cool and useful!
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Palaeoverse @palaeoverse.bsky.social · 11/06/2026
Highlights include: ✨ New tax_certainty() function 📊 Grouping support in tax_range_time()/strat() 📏 axis_geo() gains title & autofitting 🔧 Lots of under-the-hood improvements Website: palaeoverse.palaeoverse.org #rstats #palaeobiology #openscience
palaeoverse.palaeoverse.org
Prepare and Explore Data for Palaeobiological Analyses
Provides functionality to support data preparation and exploration for palaeobiological analyses, improving code reproducibility and accessibility. The wider aim of palaeoverse is to bring the palaeob...
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Reposted by Jonathan Kitt
CRAN Updates @cranupdates.bsky.social · 11/06/2026
New on CRAN: tutorizeR (0.4.5). View at CRAN.R-project.org/package=tutorizeR
cran.r-project.org
tutorizeR: Convert R Markdown or Quarto Content into Interactive Tutorials
Helps teachers convert existing '.Rmd' and '.qmd' teaching material into interactive tutorials for 'learnr' or 'quarto-live'. Conversion preserves narrative text, setup chunks, and major chunk options, supports teacher tags, and provides explicit validation and conversion reports. Output conventions follow 'learnr' as described by Aden-Buie et al. (2025) &lt;<a href="https://doi.org/10.32614%2FCRAN.package.learnr" target="_top">doi:10.32614/CRAN.package.learnr</a>&gt;, 'quarto-live' as described by Stagg (2024) &lt;<a href="https://tidyverse.org/blog/2024/10/quarto-live-0-1-1/" target="_top">https://tidyverse.org/blog/2024/10/quarto-live-0-1-1/</a>&gt;, and R Markdown as described by Xie, Allaire and Grolemund (2018, ISBN:9781138359338).
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Jonathan Kitt @jonathankitt.bsky.social · 11/06/2026
My blog is up and running, with a first post about the #30DayChartChallenge. benchmarkdown.netlify.app/posts/2026-0... #blog #RStats #datavis
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Dr Di Cook @visnut.bsky.social · 11/05/2026
Super excited to get this at my door today! Ursula Laa and my book on exploring high-d data and models is in print! Book website is www.routledge.com/Interactivel... if interested I think my 30% discount code might work for you - msg me. Time to update dicook.github.io/mulgar_book/ too! #rstats
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Daniel Gutierrez @ddgutierrez.bsky.social · 28/05/2026
HERE is the textbook I use for my Intro to Data Science class at UCLA. Takes you quickly from 0 knowledge to solving real data science problems with R. Beginners welcome! www.amazon.com/Machine-Lear... #RStats #DataScience #MachineLearning #AI
amazon.com
Machine Learning and Data Science, 2nd Edition: An Introduction to Statistical Learning Methods with R
Machine Learning and Data Science, 2nd Edition: An Introduction to Statistical Learning Methods with R [Gutierrez, Daniel] on Amazon.com. *FREE* shipping on qualifying offers. Machine Learning and Data Science, 2nd Edition: An Introduction to Statistical Learning Methods with R
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Barret Schloerke @schloerke.com · 25/05/2026
See y’all tomorrow!!
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Nicola Rennie @nrennie.bsky.social · 20/05/2026
Regular reminder that there are alternatives to Google Search and Google Chrome. Some European alternatives are listed here: european-alternatives.eu/alternative-... (where you can also find alternatives for other tech products should you be looking for them)
european-alternatives.eu
European alternatives to Google Search | European Alternatives
Google is the biggest search engine in the world, from the USA-based company Alphabet.
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Stephen Turner @stephenturner.us · 17/05/2026
LLM hallucinations in the wild: Large-scale evidence from non-existent citations arxiv.org/abs/2605.07723
arxiv.org
LLM hallucinations in the wild: Large-scale evidence from non-existent citations
Large language models (LLMs) are known to generate plausible but false information across a wide range of contexts, yet the real-world magnitude and consequences of this hallucination problem remain…
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Reposted by Jonathan Kitt
Mickaël CANOUIL, Ph.D. @mickael.canouil.fr · 14/05/2026
One Quarto source. A deck and a report. Quarto Cascade repeats the heading chain on every `---` (including `---` nested inside a Div). github.com/mcanouil/quarto-revealjs-cascade #Quarto #QuartoPub #Slidecrafting #RevealJS
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Alex Selby-Boothroyd @alexselbyb.bsky.social · 07/05/2026
Happy World Password Day, everyone. May your PIN forever be dark on a data-breach heatmap
Heatmap showing every permutation of four-digit PINs. There are many patterns, particularly around pairs of numbers and dates of birth
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Nicola Rennie @nrennie.bsky.social · 07/05/2026
You can find the resources from yesterday's "No more copy and paste! Parameterized plots and reports with #RStats and #Quarto" R/Medicine workshop online! Link: nrennie.rbind.io/r-medicine-2... @rconsortium.bsky.social
nrennie.rbind.io
Welcome! – No more copy and paste! Parameterized plots and reports with R and Quarto
Workshop materials for the 2026 R/Medicine conference workshop on parameterized plots and reports with R and Quarto.
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Stephen Turner @stephenturner.us · 07/05/2026
Five Things: May 7, 2026: BioMysteryBench, the Mythos vetting U-turn, USC’s $200M AI bet, Yihui Xie on AI coding, NIH Highlighted Topics doi.org/10.59350/vs6...
doi.org
Five Things: May 7, 2026
BioMysteryBench, the Mythos vetting U-turn, USC’s $200M AI bet, Yihui Xie on AI coding, NIH Highlighted Topics
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Jonathan Kitt @jonathankitt.bsky.social · 15/04/2026
🎉 This week's RWeekly issue, curated by @batoolmm.bsky.social , includes the following highlights: ➡️ Interactive Pivot Tables and Charts from R (Eli Eydlin) ➡️ Orchestrate multiple LLM agents into coordinated workflows (Arnold Kakas) rweekly.org/2026-W16.html #RStats #newsletter #reading #learning
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Jonathan Kitt @jonathankitt.bsky.social · 03/04/2026
For today's #30DayChartChallenge, I used the {marimekko} package 📦. Day 0️⃣3️⃣ | Comparisons | Mosaic Code available here: github.com/KittJonathan... #RStats #tidyverse #code #datavis
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Phil Ewels @ewels.bsky.social · 02/04/2026
I'm both excited and a little terrified. It feels like a wave of AI-assisted tool rewrites is coming to bioinformatics whether we like it or not. We figured that the best we can do is to try to get ahead of it, so we wrote down some principles for doing it responsibly: rewrites.bio
rewrites.bio
rewrites.bio - A manifesto for bioinformatics
Principles for responsible AI-assisted rewriting of bioinformatics tools.
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Jonathan Kitt @jonathankitt.bsky.social · 02/04/2026
Second day of the 2026 #30DayChartChallenge, tried the {ggpop} package. Day 0️⃣2️⃣ | Comparisons | Pictogram Code available here : github.com/KittJonathan... #RStats #tidyverse #code #datavis
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Jonathan Kitt @jonathankitt.bsky.social · 01/04/2026
The 2026 #30DayChartChallenge kicks off today! For this year's challenge, I'll use the Palmer Penguins dataset as often as possible. Day 0️⃣1️⃣ | Comparisons | Part-to-whole Code available here : github.com/KittJonathan... #RStats #tidyverse #code #datavis
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Stephen Turner @stephenturner.us · 27/03/2026
Weekly Recap (March 27, 2026): NSF AI readiness, AGI forecasts, White House AI policy framework, NIH genomics technology, statistical rethinking, context anchoring, #Rstats + Quarto, NOFO graveyard & grant terminations, organ sacks, YYiki. blog.stephenturner.us/p/weekly-rec...
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Stephen Turner @stephenturner.us · 26/03/2026
LLM agents for biological intelligence across genomics, proteomics, spatial biology, and biomedicine academic.oup.com/bib/article/... 🧬💻🧪
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Jonathan Kitt @jonathankitt.bsky.social · 23/03/2026
The latest RWeekly issue is out! This week's highlights include @ivelasq3.bsky.social 's @rladiesrome.bsky.social tutorial showing the new features in {dplyr} v1.2.0, and @tylermw.com 's post on Atmospheric Simulation in #RStats. rweekly.org/2026-W13.html
rweekly.org
R Weekly 2026-W13 What’s new in dplyr, Atmospheric simulation
Weekly news in the R community
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Páll Melsted @pmelsted.bsky.social · 06/03/2026
Excited to share this preprint that describes my latest work on using GPUs to accelerate processing of RNA-seq data. The title says it all: "RNA-seq analysis in seconds using GPUs" now on biorxiv www.biorxiv.org/content/10.6... and github github.com/pachterlab/k... Figure 1 shows they key result
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Prof Andy Field @profandyfield.com · 06/03/2026
I've just made live the updated website that accompanies my R book (www.discovr.rocks) - it's mostly finished: almost all of the chapter solutions/task solutions are done, data are live, updated info about the `discovr` package of interactive tutorials, and it's had a face lift.
discovr.rocks
discovr
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Bruno Rodrigues @brodriguesco.bsky.social · 04/03/2026
rix, my package that leverages #Nix to provide reproducible data science environments for #RStats (and #python and #julia) is in the top 10 starred ropensci packages! that’s pretty cool
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Jumping Rivers @jumpingrivers.com · 04/03/2026
The recordings from Shiny in Production 2025 are now available. Talks from speakers around the world on how they use Shiny in R and Python to solve real-world data problems. Watch the sessions: youtube.com/playlist?lis...
youtube.com
Shiny in Production 2025 - YouTube
Shiny in Production 2025 showcases real world lessons from teams deploying and maintaining Shiny applications at scale. Topics include infrastructure, DevOps...
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Jonathan Kitt @jonathankitt.bsky.social · 24/02/2026
Just received Josh Starmer's latest book. Great way to dig deeper into some of his videos' concepts! #Stats
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