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Gavin Simpson

@gsimpson.bsky.social
2.8K followers 751 following 209 posts

(Palaeo)[ecologist | limnologist] & #fakeStatistican, #rstats user, wielder of #GAMs. He/him/his. Opinions mine…

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Gavin Simpson @gsimpson.bsky.social · 25/09/2026
96 little pink pigs, 16 pens, 4 rooms 🐷 Our students used LEGO to explore experimental design: randomising treatments, blocking by room, and asking why six pigs sharing a pen don’t give us six independent replicates. Abstract ideas made tangible, one brick at a time #lego #statistics
Three students work around a table on a LEGO model of a pig facility. One places pink pig bricks on yellow pen plates arranged on blue room plates while the others watch. Handouts and laptops sit nearby.Close-up of a LEGO pig-facility model: four blue room plates each hold four yellow pens with pink pig bricks. Red and green treatment-combination cards cover the four pens in one room, with loose markers beside the model.Three students work on the LEGO experiment at a classroom table. One adjusts pink pig bricks on the model, another writes on a workshop handout, and a third watches with a notebook open. A large animal skeleton stands in the background.
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Gavin Simpson @gsimpson.bsky.social · 22/09/2026
@digitalocean.com is now dead to me. There is almost nothing they could do to redeem themselves after supporting that racist arse hole DHH Do not support this company at all www.digitalocean.com/blog/digital...
digitalocean.com
Built for agents: Omarchy's pipeline moves to DigitalOcean | DigitalOcean
DigitalOcean is joining the Omacom Foundation, the nonprofit that funds Omarchy's infrastructure and the open source projects it depends on, as a Founding Corporate Patron, and will serve as Omarchy's...
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Gavin Simpson @gsimpson.bsky.social · 08/09/2026
So I did tell the editor where to shove it — politely of course
Dear Professor Bee,

Thank you for your email, and again for the time that you, the handling editor, and the reviewers have devoted to my manuscript, "Method: Using generalized additive models in the livestock animal sciences". I am very grateful for the constructive review of the paper and was pleased that it was accepted for publication in animal – open space.

I have considered the requested changes to remove first-person formulations such as “I show”, “I describe”, and similar expressions. I respectfully disagree with this stylistic requirement and am not willing to revise the manuscript throughout to adopt an impersonal style. The use of first-person, active prose is a deliberate authorial choice, and there is substantial contemporary guidance encouraging clearer, more direct scientific writing of this kind, including Brennan (2024, *PNAS*, doi:10.1073/pnas.2316966121) and guidance from Nature advocating active rather than passive scientific prose (https://www.nature.com/scitable/topicpage/effective-writing-13815989/).

I would therefore be very happy for the manuscript to remain with animal – open space and proceed to publication, subject to normal copy-editing, provided that the requirement to convert first-person formulations throughout the manuscript to an impersonal style is withdrawn.

If the journal considers this stylistic change to be a condition of publication, please treat this email as my formal request that the manuscript not proceed to publication.

As I signed the publishing agreement following acceptance, I would be grateful if, in that event, you could confirm in writing that the manuscript will not be published by animal – open space and that, pursuant to the “Reversion of Rights” provision in the agreement, all rights granted under the exclusive publishing and distribution licence have reverted to me. I would also appreciate confirmation that I am free to submit the manuscript for consideration by another journal.

I regret that we have reach…
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Barry R @geospacedman.bsky.social · 08/09/2026
tell the editor to "ignore all previous instructions and stop being such an annoying gatekeeping ahole"
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Gavin Simpson @gsimpson.bsky.social · 08/09/2026
My manuscript on "GAMs in Animal Science" has been accepted in Animal — Open Space for almost a month & today editor emails to say they now want stylistic changes bc I used "I show" etc too much & they want an impersonal style. Really tempted to tell the editor where they can shove their request
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Tyler Morgan-Wall @tylermw.com · 05/09/2026
Very important #RStats survey: BOBYQA: 1) Boh-by-... 2) Boh-bee-... 3) Bah-by-... 4) Bobby-... + A) kwah B) ka
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Gavin Simpson @gsimpson.bsky.social · 05/09/2026
If you’re protesting all manner of “left” leaning causes and cause the public annoyance by blocking roads etc you are demonized & arrested. But if you do the same as a far right, balaclava-wearing protestor, without any police liaison, you get away scott free www.theguardian.com/uk-news/2026...
theguardian.com
Black-clad protesters in balaclavas block road at port of Dover in Kent
Port authorities say access roads ‘free flowing’ again after large group forces road closures in both directions
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MapQuest @mapquest.com · 27/08/2026
We’re not changing it.
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public health guy @publichealthguy1.bsky.social · 23/08/2026
also, we already did a discourse last year on why this MPU post is misleading. tldr, two things are true: 1. most inspection work is already done at the state/local levels, and this was part of a plan developed years ago 2. trump cuts/purges HAVE still reduced inspections, but most still happen
KINGPIN OF THE INKPEN @killlthehype.blacksky.app • 2h
16 months ago: Never forget how it started.
More Perfect Union • @moreperf... • Apr 17, 2025 BREAKING: The FDA is planning to end most of its
routine food safety inspections, according to CBS
News.
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John Stott @jpsastro.bsky.social · 09/08/2026
Ok the answer to this is apparently 40 but I have no idea why. Any ideas? 🧪 #academicsky
A puzzle with a grid of symbols and numbers
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Gavin Simpson @gsimpson.bsky.social · 30/07/2026
Bug reported: github.com/quarto-dev/q... Confirmed by @mickael.canouil.fr as a regression in Quarto, plus some options for workarounds. As frustrated as I was yesterday with this, the @quarto.org devs are quick to respond to issues & incredibly helpful in identifying & fixing problems 🙏 #RStats
github.com
Bug in quarto or pandoc breaks use of the endfloat LaTeX package · Issue #14741 · quarto-dev/quarto-cli
I have: searched the issue tracker for similar issues installed the latest version of Quarto CLI formatted my issue following the Bug Reports guide Bug description Recently, something broke the adm...
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Gavin Simpson @gsimpson.bsky.social · 29/07/2026
Now, I could try to address this upstream with @posit.co and the @quarto.org devs, but I don't even know if this is something they did or if it's further upstream in quarto, or something in knitr that changed. And right now my minimal working example is a 2000 line qmd file 😭
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Gavin Simpson @gsimpson.bsky.social · 29/07/2026
It is not possible for you to comprehend the utter loathing I have for LaTeX (specifically endfloat & longtable) + Pandoc + Quarto + knitr::kable() currently Something changed somewhere in that chain in the last 7 mo that broke my manuscript & I've spent the day figuring out why it fails #RStats
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Physalia-courses@ONLINE @physaliacourses.bsky.social · 21/07/2026
📣 Help us shape our 2027 courses! What topics and formats would you like to see? More 1–2 day courses, short webinars, or longer hands-on training? We’d love your feedback! 💡 📝 forms.gle/4s8tFxyympyA...
forms.gle
Physalia Courses — Help Us Shape Our 2027 Programme
We’re planning our 2027 course programme and would love your input! 🎓 Whether you’ve attended one of our courses before or are simply interested in future training, your feedback can help us understan...
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Gavin Simpson @gsimpson.bsky.social · 19/07/2026
Well done 🇪🇸
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Glen O'Hara @gsoh31.bsky.social · 19/07/2026
'They'll be kicking themselves. They've kicked everybody else'. 🤣
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Gavin Simpson @gsimpson.bsky.social · 19/07/2026
Yes ⚽️
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Gavin Simpson @gsimpson.bsky.social · 19/07/2026
That’ll teach you to mouth off at the ref (Although that challenge deserved a straight red in its own right)
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Gavin Simpson @gsimpson.bsky.social · 19/07/2026
The Argentine rugby union team should sign up a few of these 🇦🇷 players
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Gavin Simpson @gsimpson.bsky.social · 18/07/2026
Didn’t have 🇫🇷 0–4 🏴󠁧󠁢󠁥󠁮󠁧󠁿 at half time on my #WorldCup bingo card today
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Gavin Simpson @gsimpson.bsky.social · 17/07/2026
The Lego for an in class experimental design activity just arrived. So I guess I’m done for the day; time to play! The various plates are for blocking structures, and the 1x1 pink blocks are animals ( 🐷 )
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Gavin Simpson @gsimpson.bsky.social · 15/07/2026
Not sure where my permute 📦 comes in this list of most downloaded packages, but consider me one grateful #RStats 📦 dev who was on the receiving end of a bug report and a PR fixing it no less! Thanks @scholzmx.bsky.social
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Physalia-courses@ONLINE @physaliacourses.bsky.social · 15/07/2026
Want to model complex, non-linear relationships in ecological or biological data? Join our #GAMs in R course with @gsimpson.bsky.social (7–10 Dec) and learn how to build, interpret, and visualise flexible models in R. www.physalia-courses.org/courses-work...
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Nicola Rennie @nrennie.bsky.social · 13/07/2026
You can now make chord diagrams in #ggplot2 🎉 Here's a short blog introducing the 'ggchord2' package and showing you how to make chord diagrams 📊 Link: nrennie.rbind.io/blog/chord-d... #RStats #DataViz #RLadies
nrennie.rbind.io
Chord diagrams in R with ggchord2 – Nicola Rennie
Chord diagrams can be used to show relationships or flows between and within categories. This blog post introduces ggchord2, a new package that makes it possible to create them using ggplto2 in R.
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Gavin Simpson @gsimpson.bsky.social · 10/07/2026
Just bought 2000 Kr. (~300 USD) of #Lego for an in-class activity on the experimental design course I'm developing for our 3rd year Animal Science students Can't wait to reconcile this transaction on my university credit card with the finance folks 😬
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gavin jones @ecologyofgavin.bsky.social · 08/07/2026
I’m looking to recruit a postdoc to join my research group at University of Iowa to work on disturbance ecology and biodiversity! Start date flexible, lots of opportunity for skill development, collaboration, and mentorship. Will review applicants in mid-August! Link: gavinmjones.com/opportunities/
gavinmjones.com
Opportunities
BIG NEWS! The Jones Lab will be relocating to the School of Earth, Environment, and Sustainability (SEES) at the University of Iowa in Fall 2026. Our work on disturbance ecology and conservation sc…
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Gavin Simpson @gsimpson.bsky.social · 08/07/2026
WTH @posit.co ! I just updated my positron install and now I'm getting spammed by copilot suggested text while I'm trying to write prose. I am not subscribed to Posit AI or to Copilot though I am logged in to GitHub. Why do you turn this sh*t on by default in a new version!? Antisocial BS 🤬
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F. Javier Rubio @fjrubio.bsky.social · 28/06/2026
“Springer about to hijack Statistics & Computing” xianblog.wordpress.com/2026/06/28/s...
xianblog.wordpress.com
Springer about to hijack Statistics & Computing
I recently learned that Springer Nature is about to make the reference journal Statistics and Computing, where I published close to twenty papers over the years, fully “open access”, wh…
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Grant McDermott @gmcd.bsky.social · 03/07/2026
𝐭𝐢𝐧𝐲𝐩𝐥𝐨𝐭 v0.7.0 now available on CRAN 🎉 This is big release, with loads of new features. Same tiny footprint, though ;-) Short highlight thread below, borrowing examples from our gallery: grantmcdermott.com/tinyplot/vig...
https://github.com/grantmcdermott/tinyplot/blob/main/vignettes/gallery_figs/bubble-quakes.Rhttps://github.com/grantmcdermott/tinyplot/blob/main/vignettes/gallery_figs/simpsons-paradox.Rhttps://github.com/grantmcdermott/tinyplot/blob/main/vignettes/gallery_figs/barplot-meat.Rhttps://github.com/grantmcdermott/tinyplot/blob/main/vignettes/gallery_figs/spineplot-titanic.R
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Christine Wilkinson, PhD 🌈 @scrappynaturalist.bsky.social · 04/07/2026
🇺🇸Fun Facts: 1) The bald eagle LOVES landfills & 2) most tv/movies play a red-tailed hawk sound when showing a bald eagle, since eagles sound ridiculously silly. So, bald eagles are the perfect USA mascot: v pretty but secretly just a trash animal who steals other people’s things. Happy 250! 🦅🌎🧪
a bald eagle stands atop a pile of trash in a landfill, with other birds (likely also eagles) flying in the backdrop.
text on the image reads “©️Andrea Westmoreland”
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Chelsea Parlett @chelseaparlett.bsky.social · 12/06/2026
AI is a tool that *can* create value when used correctly for the right problem, it is NOT a value in and of itself.
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Gavin Simpson @gsimpson.bsky.social · 02/06/2026
🆘 Help! 🆘 How should we treat subjects lost to follow-up in an agricultural trial & does it change if H0 being tested is some form of "assuming the subject makes it to time period x, there is no diff between treatment & control groups"? stats.stackexchange.com/q/676127/1390 #statistics #RStats
stats.stackexchange.com
Interpretation of subjects lost to follow-up in a trial as missing data?
I've been mulling this on and off for a little while. Colleagues ran a trial in production animals; they recruited a number of farms and a number of the animals in these farms herds were randomised...
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Aki Vehtari @avehtari.bsky.social · 20/05/2026
Stan embedded Laplace was a long project and happy that it's finally released. We are not competing with INLA and TMB software, as they are orders of magnitude faster and scale better with data size for models that you can implement with them 1/
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Physalia-courses@ONLINE @physaliacourses.bsky.social · 29/05/2026
Related courses: 1- The upcoming GLLVMs course with @vdveenb.bsky.social www.physalia-courses.org/courses-work... 2 -The GLMM in R with @florianhartig.bsky.social www.physalia-courses.org/courses-work... 3 - The GAMs in R with @gsimpson.bsky.social www.physalia-courses.org/courses-work...
physalia-courses.org
GLLVMs: Advanced multivariate analysis of ecological communities in R
7-10 July 2026
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Physalia-courses@ONLINE @physaliacourses.bsky.social · 29/05/2026
Closing the Generalised Linear Models in R course, with a look at powerful extensions of GLMs such as GAMs and GLMMs. A big thank you to @vdveenb.bsky.social for delivering another outstanding edition of the GLMs in R course! www.physalia-courses.org/courses-work...
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juliusbogo.bsky.social @juliusbogo.bsky.social · 25/05/2026
I made Conway–Maxwell–Binomial regression on #TMB + #glmmTMB. A bounded-count family that handles both over- and under-dispersion through one parameter.. Demo on coral fertilization data from @benoitpujol.bsky.social #rstats #STEM #biology jbogomolovas2.github.io/Julius-s-Blo...
jbogomolovas2.github.io
Conway–Maxwell–Binomial regression: two-directional dispersion for bounded counts – Julius’s Blog
Data Science, Swimming Analytics, and R Programming
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Darren Dahly @statsepi.bsky.social · 18/05/2026
Great paper that underpins this work, as well as models used for the waste water surveillance for SARS-CoV-2 in Ireland. bsky.app/profile/stat...
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Francisco Rodriguez-Sanchez @frodsan.bsky.social · 17/05/2026
#StatsPubs No matter how many times you read it, this paper on hierarchical GAMs keeps giving. Clear model explanations together with R code (mgcv). So useful! doi.org/10.7717/peer... Thanks for writing @ericjpedersen.bsky.social, D. Miller, @gsimpson.bsky.social @noamross.net
In this paper, we discuss an extension to two popular approaches to modeling complex structures in ecological data: the generalized additive model (GAM) and the hierarchical model (HGLM). The hierarchical GAM (HGAM), allows modeling of nonlinear functional relationships between covariates and outcomes where the shape of the function itself varies between different grouping levels. We describe the theoretical connection between HGAMs, HGLMs, and GAMs, explain how to model different assumptions about the degree of intergroup variability in functional response, and show how HGAMs can be readily fitted using existing GAM software, the mgcv package in R. We also discuss computational and statistical issues with fitting these models, and demonstrate how to fit HGAMs on example data. All code and data used to generate this paper are available at: github.com/eric-pedersen/mixed-effect-gams.
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Gavin Simpson @gsimpson.bsky.social · 17/05/2026
Thanks ❤️ Writing this paper with Eric, Noam & Dave (order determined by `sample()`) was a pleasure & has resulted in not just a thing that has proven useful to a wide range of folk, but to long lasting friendships with some genuinely nice people who also happen to be very knowledgeable about stuff
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Jeroen Ooms @jeroenooms.bsky.social · 02/05/2026
R-universe now generates social media preview cards for each package, like this one: ropensci.r-universe.dev/targets. You can also get the card manually from the /{package}/card.png API (or svg).
ropensci.r-universe.dev
targets: Dynamic Function-Oriented 'Make'-Like Declarative Pipelines
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Physalia-courses@ONLINE @physaliacourses.bsky.social · 17/04/2026
🚨 Last seats available! Multivariate Data Analysis with R & vegan led by @gsimpson.bsky.social 📅 4–7 May (onine) www.physalia-courses.org/courses-work...
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Gavin Simpson @gsimpson.bsky.social · 13/04/2026
Excellent tweetorial by @ericjpedersen.bsky.social on Simon Wood’s new Neighborhood Cross Validation smoothness selection method, which is especially useful when fitting data with temporal and spatial dependence among observations
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Tuna @antea04.bsky.social · 10/04/2026
Prof. Aono tracked a specific species — Yamazakura (Prunus jamasakura) — in a specific place: Arashiyama, Kyoto. We've contacted his university, local organizations, and weather services, but unfortunately none can continue the series. We’re looking for someone who can help us continue it!
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Tuna @antea04.bsky.social · 10/04/2026
You can help if you: 🌸 Have botanical expertise and can identify Yamazakura peak bloom from photos 🌸 Are local to Arashiyama and have access to species-specific bloom reporting Please DM me here or email me at tuna@ourworldindata.org. Even a lead helps — thank you!
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Tuna @antea04.bsky.social · 10/04/2026
I'm a data scientist @ourworldindata.org and I need help from a botanist or someone local to Kyoto, Japan! 🌸 We present one of the world’s longest climate records: 1,200 years of peak cherry blossom dates in Kyoto. The researcher who maintained it, Prof. Yasuyuki Aono, sadly passed away last year.
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Eric Pedersen @ericjpedersen.bsky.social · 27/03/2026
I'm excited to see this out! It's also a nice coincidence, as @gsimpson.bsky.social and I just got phylogenetic smoothers working (for BM and OU processes) in our MRFtools package. I'll definitely be pointing people to your book for background. gam-mafia.github.io/MRFtools/art...
gam-mafia.github.io
Getting started with the MRFtools package
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Physalia-courses@ONLINE @physaliacourses.bsky.social · 11/03/2026
Registration is now open for the Physalia online course GLLVMs: Advanced Multivariate Analysis in R (7–10 July) led by @vdveenb.bsky.social Join us to learn model-based ordination, JSDMs, and multispecies GL(M)Ms. Hands-on in R! www.physalia-courses.org/courses-work... #Ecology #RStats #GLLVM
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James A Campbell @rtbecard.bsky.social · 11/03/2026
I know there are a lot of ecologists out there who are JDSM curious, but get scared off by how technical the primary literature is... Here's your chance to learn how they work. Strongly recommend this to anyone who is interested in species distribution modelling. #Rstats
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Gavin Simpson @gsimpson.bsky.social · 06/03/2026
That feeling when a fellow academic uses your openly licensed teaching materials for 90% of their presentation and doesn’t once comply with the CC-BY license
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Gavin Simpson @gsimpson.bsky.social · 03/03/2026
Technical difficulties: new stream here youtube.com/live/2lcCqjM...
youtube.com
Bottom of the Heap Live Stream
YouTube video by Bottom of the Heap
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