iiinova — where your digital self keeps evolving

Reposted by Gavin Simpson

🚨 New CRAN Task View: Package Development and Maintenance #rstats #cran By Lluís Revilla and Heather Turner @heathrturnr.fosstodon.org.ap.brid.gy URL: cran.r-project.org/view=Package...

Screenshot of the CRAN Task View "Package Development and Maintenance" at https://CRAN.R-project.org/view=PackageDevelopment

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Gavin Simpson @gsimpson.bsky.social · 10h

📝 My paper on generalized additive models (GAMs) in animal science is out! Learn nonlinear relationships from data, estimate growth rates and compare treatments, with cows, pigs and quail + reproducible #RStats code. Open access: doi.org/10.1016/j.an... #mgcv #AnimalScience #Statistics 🧪

Eight panels show body mass over 78 days for 57 Japanese quail. Columns represent control, T4, T3 and combined T3–T4 hormone treatments; rows separate females and males. Coloured points are measurements, lines are individual growth curves fitted by a hierarchical generalized additive model, and shading shows 95% credible intervals. Growth slows towards a plateau, with females generally reaching higher body masses than males.

Eighteen panels show individual pig growth curves. Black points mark daily average weight estimates from a depth camera; blue lines show curves fitted by a hierarchical generalized additive model, with shaded 95% credible intervals. Weights generally increase over time, with differences in growth and measurement variability among pigs. Uncertainty widens where measurements are sparse or absent.

Four-panel comparison of models fitted to a cow’s average daily milk fat production. Observations rise to a peak around weeks 8–10, then decline. The first panel shows fitted curves and uncertainty bands for Wood’s model, a Tweedie GLM and a Tweedie GAM. Residual plots show curved patterns for Wood’s model and the GLM, but little remaining pattern for the GAM.

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Gavin Simpson @gsimpson.bsky.social · 25/09/2026

Thanks! Not yet — still scrambling to get the nth+1 class done, but I will hopefully by next week have the workshop materials cleaned up and posted on the course website

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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 · 09/09/2026

Sheepish look 😳 I left all my copies in Canada for my students when I moved back to Europe so this didn’t occur to me. Reminds me I should pick up a copy of the the new edition!

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Gavin Simpson @gsimpson.bsky.social · 08/09/2026

Missed opportunity 🤦‍♂️

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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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Reposted by Gavin Simpson

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

Today was the wrong day to mess with me over this kind of gatekeeper crap. I’m this close to going torched earth over this.

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Gavin Simpson @gsimpson.bsky.social · 08/09/2026

That would be fantastic Tom; thank you. My work address is gavin AT anivet.au.dk

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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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Gavin Simpson @gsimpson.bsky.social · 06/09/2026

Huh, I haven’t noticed that reversion-to-tidyverse behaviour and I was editing in an older codebase with Emacs+ESS opinions recently. Haven’t tried the Format code thing, but I’d expect that to Air-ify my code if I used it

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Gavin Simpson @gsimpson.bsky.social · 06/09/2026

I haven’t noticed any issues using older opinionated codebases in positron where the opinions deviated markedly from Posit/tidyverse style

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Reposted by Gavin Simpson

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

Furthermore; if you were wearing a balaclava at a “left” cause protest the far right and Conservative and Reform politicians would be calling you all sorts of name ms up to and including being a terrorist.

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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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Reposted by Gavin Simpson

MapQuest @mapquest.com · 27/08/2026

We’re not changing it.

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Reposted by Gavin Simpson

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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Reposted by Gavin Simpson

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 · 09/08/2026

⭕ = 29 doesn't work if the column sums are a thing(?)

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Gavin Simpson @gsimpson.bsky.social · 30/07/2026

Though some more googling has me thinking that Pandora was the route cause of the change here; for over a decade they’ve been working on requiring longtable for any table in LaTeX output and this has now landed in the released version

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Gavin Simpson @gsimpson.bsky.social · 30/07/2026

During my journey through the realms of the dead, I came across a Discussions post you made on the Quarto GH repo, about the issues you were having re indexed, so I got a little snippet of a preview 🍿

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Gavin Simpson @gsimpson.bsky.social · 30/07/2026

And the ability to spell, it would appear 🙄

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Gavin Simpson @gsimpson.bsky.social · 29/07/2026

I’ve used Typst a bit from Quarto, but until journals start accepting typst sources it isn’t something that I’ll be able to use professionally

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Gavin Simpson @gsimpson.bsky.social · 29/07/2026

Think you are right; I was outputting md tables and pandora was using longtable. That narrows down where the change that broke my endfloat usage came from…

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Gavin Simpson @gsimpson.bsky.social · 29/07/2026

I mean't further upstream in **Pandoc**

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Gavin Simpson @gsimpson.bsky.social · 29/07/2026

Are the details of those GAM fits available somewhere? I didn't see anything on these models in the Methods.

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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

Doubt it's anything to do with quarto; knitr uses longtable by default

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Gavin Simpson @gsimpson.bsky.social · 29/07/2026

🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬🤬

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Gavin Simpson @gsimpson.bsky.social · 29/07/2026

I finally fix this and can now render the PDF again, just like I could a couple of months ago and I've lost most of my day. So you'll forgive me if I give a massive 🖕 to: LaTeX (specifically endfloat & longtable) + Pandoc + Quarto + knitr::kable() + stupid Word-using journal

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Gavin Simpson @gsimpson.bsky.social · 29/07/2026

Then I realise that for some reason, some combination of `format = "latex"` and `longtable = FALSE` means that the tables render the LaTeX math markup in the table verbatim

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Gavin Simpson @gsimpson.bsky.social · 29/07/2026

But to give credit to the journal they're willing to try with my LaTeX sources, though I hold out little hope this will work and an preemptively trying to get my beautifully typeset math to render in a docx in the near expectation that I'll have to submit a docx file eventually

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Gavin Simpson @gsimpson.bsky.social · 29/07/2026

Once I figure that out, I need to conditionally set the format to "latex" only when rendering to PDF because the journal I chose — despite being an Elsevier one* — doesn't accept LaTeX sources even if you use elsarticle 🤬 * don't, just don't start on that

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Gavin Simpson @gsimpson.bsky.social · 29/07/2026

I give up and try to stop kable() using longtable. AI says use longtable = FALSE but the help for kable() is quite deficient and longtable isn't an argument to kable(), but is passed on to some internal function *onlY* if `format = "latex"`

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Gavin Simpson @gsimpson.bsky.social · 29/07/2026

So now I'm 4 hours deep in LaTeX and loosing the will to live...

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Gavin Simpson @gsimpson.bsky.social · 29/07/2026

But that just lead to the dreaded ! File ended while scanning use of \efloat@xfloat. <inserted text> \par error. Which is how endfloat fails if you don't have the \begin{} / \end{} on their own lines and at the start of the line 🤬

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Gavin Simpson @gsimpson.bsky.social · 29/07/2026

I try fixing this in the .tex file and I get it to at least stop throwing that particular hissy fit by removing white space around the { } that everything got wrapped in. So now things looked like this: {\begin{longtable} ... stuff ... \end{longtable}}

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Gavin Simpson @gsimpson.bsky.social · 29/07/2026

And that just broke LaTeX as it just threw a hissy fit an emitted the dreaded: Extra }, or forgotten \endgroup. error! Cue 2 hours narrowing down where this was coming from so I could even being understanding what was causing this to fail.

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Gavin Simpson @gsimpson.bsky.social · 29/07/2026

But before that issue even rears it's head, the LaTeX now produced by Quarto + Pandoc + knitr::kable() wasn't even parsing properly as it wrapped everythintg in { }: { \begin{longtable} ... stuff ... \end{longtable} }

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Gavin Simpson @gsimpson.bsky.social · 29/07/2026

endfloat is known to be picky; \begin{longtable} & \end{longtable} must be on their own lines at col 1.

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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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Reposted by Gavin Simpson

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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Reposted by Gavin Simpson

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

Surprised Argentina held out that long after the sending off

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