Ben Bolker
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bbolker.bsky.social
Ben Bolker
@bbolker.bsky.social
2.2K followers 570 following 680 posts
Ecology, evolution, epidemiology, statistics (mixed models). McMaster University, Hamilton, Ontario https://math.mcmaster.ca/bolker
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bbolker.bsky.social
Huh. Surprised you'd imagine it was 2x higher (sorry if your point was hyperbolic for entertainment value ...) CAD hasn't been > $1.10USD since 1950 ... (data from fx.sauder.ubc.ca/etc/CADpages..., © 2024 Prof Antweiler, University of British Columbia) gist.github.com/bbolker/0bf3...
Time series of CAD from 1950 to 2025. Value fluctuated between $0.90 and $1.05 USD from 1950-1975, $0.60 to $0.90 1975-2005, briefly exceeded par around 2010, now back down to about $0.75 USD
November 15, 2025 at 8:29 PM
bbolker.bsky.social
reminded me of this guy en.wikipedia.org/wiki/Keron_T... (there were a lot of jokes about "he took the A train" ...)
Keron Thomas (c. 1975 – July 22, 2013)[2] was primarily known for posing as New York City Subway motorman "Regoberto Sabio" on May 8, 1993, and operating an A train in revenue service for over three hours, when he was sixteen years old.
November 13, 2025 at 2:05 AM
bbolker.bsky.social
Scraped data from the plot ... gist.github.com/bbolker/d6a6... Scraping is imperfect because the plot is a fairly crappy JPG (hard to distinguish overlapping points). Dashed line is 156 particles per liter, nominal normal/superspreader cutoff (points fall on either side due to scraping error)
plot of scraped data from Edwards et al 2021. On a logarithmic y scale, regression slopes are very similar. Red points are superspreaders (nominally > 156), black are 'normal' (nominally < 156)
November 9, 2025 at 5:46 PM
bbolker.bsky.social
Perhaps OP was referring to this (somewhat) famous quotation?

Singer & Pincus. 1998. “Irregular Arrays and Randomization.” PNAS. doi.org/10.1073/pnas....
 ‘What would you do,’ I had asked, ‘if drawing a Latin square at random for an experiment, you happened to draw a Knut-Vik (Knight’s move) square?’ Sir Ronald said he thought he would draw again and that, ideally, a theory explicitly excluding regular squares should be developed.” (L. J. Savage to R. A. Fisher, 1952, p. 88, ref. 21).
November 3, 2025 at 1:59 AM
bbolker.bsky.social
what do you think about these options bsky.app/profile/bbol... ? (Also: etherpad.org Apparently also www.authorea.com (owned by Wiley), although amusingly this was one of the first public documents that came up ...)
the title block of an obviously AI-generated paper on Authorea (although maybe only AI-organized?): Certainly! Apologies for the previous omissions. Below is the complete LaTeX document that includes all the requested sections, arguments, code snippets, and proofs, organized logically into a single cohesive document. “‘latex Diagnosis and Treatment of Foot Fusarium Infection Confirmed by Next-Generation Sequencing Technology: A Case Report and Literature Review dermatology +7 Yulin Wang, Danyue He, Qi Zhao, Jie Hu, Ruyi Wang, Yiyang Hu, Xiangning Li, Jia Cai, Lili Tang, Xing Fan
November 1, 2025 at 11:55 PM
bbolker.bsky.social
there's also this nice recent extension: Gelman, Hullman, & Kennedy. 2024. “Causal Quartets: Different Ways to Attain the Same Average Treatment Effect.” The American Statistician 78 (3): 267–72. doi.org/10.1080/0003... sites.stat.columbia.edu/gelman/resea...
Figure 2: Four graphs showing patterns of causal effects, each with average effect of 0.1, but varying in different ways as a function of a pre-treatment predictor: (e) linear interaction, (f ) no effect then steady increase, (g) plateau, (h) intermediate zone with large effects
October 28, 2025 at 1:35 AM
bbolker.bsky.social
Depends where you live. Favism (glucose-6-phosphate dehydrogenase deficiency) is thought to be associated with malaria tolerance and/or resistance.
a map of the incidence of favism (G6PD deficiency), showing concentrations in sub-Saharan Africa and the middle east, some in India, SE asia, and Brazil
October 24, 2025 at 12:52 AM
bbolker.bsky.social
Unless there are many columns I'm not sure this even counts as "big"/requires special techniques (recently had a student tell me she had cleaned a 166M-row data set directly in R ...) Reading *and* writing a 15M x 10 (numeric) row data set (2.8G on disk) takes 8 seconds on my laptop ...
library(vroom) system.time({ dd <- rnorm(15e6*10) |> matrix(nrow = 15e6) |> as.data.frame() vroom_write(dd, "tmp.csv") dd2 <- vroom("tmp.csv") } ) ## user system elapsed ## 34.995 5.127 8.327
October 15, 2025 at 9:32 PM
bbolker.bsky.social
A web search found this from April 3, 1978 bnl.contentdm.oclc.org/digital/coll... I guess Peter Dalgaard has an encyclopedic knowledge of Peanuts strips?
Lucy (L) and Charlie Brown (R) are standing behind a wall. (Panel 1) CB: "I hate being a nothing! I refuse to go through the rest of my life as a zero!" (2) L: "What would you like to be, Charlie Brown, a five? Or how about a twenty-six? Or a par seventy-two?" (3) L: "I know what you could be, Charlie Brown ... a square root!" (4) L: "I think you'd make a great square root, Charlie Brown ..." CB: "I can't stand it!"
October 14, 2025 at 8:35 PM
bbolker.bsky.social
www.numberworld.org/digits/Euler...
A screenshot of samples of digits of the Euler-Mascheroni constant (go to the URL for text-based version)
October 9, 2025 at 6:51 PM
bbolker.bsky.social
Recently attended a workshop using allisonhorst.github.io/palmerpengui... for examples but it's hard to use for mixed models (3 species/3 islands isn't enough for MMs). With a little help from Claude → Tobias et al doi.org/10.1111/ele.... and extracted the penguins: github.com/bbolker/bbmi...
An image of beak width vs beak depth for a variety of penguin species.
September 3, 2025 at 12:28 AM
bbolker.bsky.social
(2/2) its second answer started with "Based on my search, I cannot find credible medical experts who currently contend that the MMR vaccine should not be given routinely to children." The rest is below ...
Based on my search, I cannot find credible medical experts who currently contend that the MMR vaccine should not be given routinely to children. Here's what I found: Lack of Current Expert Opposition: The medical literature and recent sources don't identify specific credentialed medical experts who oppose routine MMR vaccination based on scientific evidence. Studies show that 93% of surveyed physicians agree with current official vaccination recommendations and would apply them to their own children Measles 2025 | New England Journal of Medicine Historical Context: The most prominent medical figure associated with MMR vaccine opposition was Andrew Wakefield, but as mentioned earlier, his 1998 study was retracted for fraud, and he lost his medical license. His work has been thoroughly debunked. Current Political vs. Medical Opposition: While there are concerns about potential policy changes under Health Secretary Robert F. Kennedy Jr., who has historically been vaccine-skeptical medRxiv, this represents political rather than credentialed medical expert opinion. Notably, RFK Jr. recently endorsed the MMR vaccine, which "stoked fury among his supporters" The Evidence on Vaccines and Autism | Johns Hopkins | Bloomberg School of Public Health in the anti-vaccine community. The Distinction: While there are individuals who call themselves doctors or health practitioners who oppose vaccines, finding credentialed medical experts (licensed physicians with relevant training) who oppose routine MMR vaccination based on scientific evidence is extremely difficult because the scientific consensus is so strong in favor of the vaccine. The overwhelming medical and scientific consensus continues to support routine MMR vaccination for children, with major medical organizations, pediatricians, and public health experts maintaining this position based on extensive safety and efficacy data.
August 24, 2025 at 6:21 PM
bbolker.bsky.social
yes, this terminology is from @jdushoff.bsky.social
Another things that jumps out is that maybe I should drop the early data. First off, there’s lots of reasons to ignore them anyways, since testing infrastructure was so different then, and second off, they make the range of the graph go really low, below minus nine “nels.” So, what is a nel? You’ve probably guessed, it’s called that because it is one Natural Log unit, (one NL; one “nel”). A nel is a big number: 1 nel is over 2.5 times my reference rate, and 2 nels is over 7 times my reference rate. Once I drop the very early data, I might see that a “nel”, like a “bel”, might be an awkwardly sized unit for the kinds of changes I’m most interested in, so we’ll look at “centinels” instead. This is the same idea as changing from a proportion to a percent.
August 21, 2025 at 7:43 PM
bbolker.bsky.social
This is nice. I drew a related picture based on a slide presented by Nathalie Moon at the Statistical Society of Canada conference (tl;dr AI may be good for many things, but we definitely *don't* want students to use it as short-cut to get good marks without learning ...)
a flow chart showing things you can use LLMs for (learning, getting good marks, getting a job, getting into graduate school). Some of these flow downstream (learning stuff gets good marks; good marks get good jobs/grad school entrance; grad school gets good jobs), all of them (except LLMs) may also lead to happiness. There is a red X on the direct path from LLMs to good marks; this is what we want to forbid.
August 15, 2025 at 12:53 AM
bbolker.bsky.social
super-random #rstats/VSCode question. VSCode > hosted Linux virtual machine > Windows remote desktop > Firefox tab > Ubuntu (don't ask ...). Standard extensions AFAICT (R 2.8.6, R Syntax 0.1.3). It is magically converting "<" to ">" on entry ... very frustrating. Anyone seen this?
VSCode installed-extensions tab showing Container Tools, Dev Containers, R, R Syntax
August 6, 2025 at 3:31 PM
bbolker.bsky.social
FWIW Ontario appears to have changed its guidance along these lines in 2008: www.publichealthontario.ca/-/media/docu...
flow chart for assessment of exposure to bats. post-exposure management is only recommended if direct exposure is known to have occurred, or if the bat was in the same room as a person *and* there was evidence of direct contact (i.e. scratch, crying/upset child) with a person who may not be able to give a reliable history (child or cognitively impaired adult)
August 3, 2025 at 9:37 PM
bbolker.bsky.social
www.jstor.org/stable/2332181
Platypus/kangaroo cartoon
August 3, 2025 at 2:31 AM
bbolker.bsky.social
Seems like you can add any package(s) you want in the `Imports:` directive of the module/package DESCRIPTION ... ? e.g. dev.jamovi.org/tuts0106-add...
Adding ggplot2 We’re going to use ggplot2 for plotting, so make sure you have that installed. To use ggplot2 in this package/module, we need to add some entries into the DESCRIPTION and NAMESPACE files. We add ggplot2 to the imports line in the DESCRIPTION, so it reads: Imports: jmvcore, R6, ggplot2 and we’ll add the following line into NAMESPACE: import(ggplot2) These entries are standard for using R code from other packages in a package. More information is available in Writing R Extensions. Now we have ggplot2 ready, we can proceed with using it in our analysis.
July 26, 2025 at 7:46 PM
bbolker.bsky.social
2/2 ... e.g. complaints about www.evolution.reading.ac.uk/BayesTraitsV... , the canonical tool, which does some technically brilliant but (IMO) philosophically questionable stuff ...
BayesTraits, the leading software platform for analyzing the evolution of discrete traits (Pagel and Meade 2006), uses a highly sophisticated algorithm (reversible-jump Markov chain Monte Carlo) to compute BFs, so that researchers can draw conclusions like “a model where the rate of accessory gland gain differs between male-care vs male-care-absent lineages is better supported than one where they are identical (BF ratio >2)”. By convention, a model comparison with a BF factor greater than 2-3 is assumed to be “substantial” evidence in favour of the better (more probable) model. While the computational machinery required to compute BFs in an evolutionary context is technically impressive, the simpler models considered represent biologically impossible scenarios, analogous to the null models used in frequentist testing; no two evolutionary rates are ever truly identical. Rather than consider the relative strength of the hypotheses as “equal” vs “not equal”, researchers will often gain more insight by estimating the relative rates of transitions. In a Bayesian context, we can use the posterior distribution of the rate difference (the contrast in hazard rates as defined in our methods section above) to find a 95% credible interval for the ratio of rates.
July 26, 2025 at 7:28 PM
bbolker.bsky.social
This is great. (Adding a picture, just for eye candy.)
A plot showing forest succession in the model (crown area over time): Fast peaks early, short-lived breeders peak and decline slowly (with wide confidence bounds), long-lived pioneers and slow strategies grow slowly (half-maximum around 250 years). Caption: Patch- level post-gap crown area trajectories in the four-group niche models. Lines correspond to a single run. Highlighted areas around the lines show one standard deviation around the mean of 40 focal patches, each from an independent metacommunity simulation. Standard deviation areas are shown only for positive values.
July 22, 2025 at 3:20 PM
bbolker.bsky.social
What if you express it in Kelvin? (or in Rankine <https://en.wikipedia.org/wiki/Rankine_scale>, although that won't actually get you more numbers, just bigger ones)
illustration of the Mathemagician, from _The Phantom Tollbooth_ (Norton Juster, illustration by Jules Feiffer). A large man in a wizard's robe covered with mathematical symbols, carrying a staff in the form of a pencil. "Yes, please,” said Milo. "Can you show me the biggest number there is? "I'd be delighted,” he replied, opening one of the closet doors. "We keep it right here. It took four miners just to dig it out.” Inside was the biggest [3] Milo had ever seen. It was fully twice as high as the Mathemagician. "No, that’s not what I mean," objected Milo. "Can you show me the longest number there is?” "Surely," said the Mathemagician, opening another door. "Here it is. It took three carts to carry it here." Inside this closet was the longest [8] imaginable. It was just about as wide as the three was high.
July 21, 2025 at 8:46 PM
bbolker.bsky.social
taking yet another opportunity to repost this from @stephenjwild.bsky.social
"American chopper" meme. Frame 1: "YOU SHOULD REPORT MARGINAL EFFECTS". Frame 2: "I REPORTED THE COEFFICIENT VALUES. WHAT MORE DO YOU WANT?" Frame 3: "PEOPLE HAVE A HARD TIME INTERPRETING THOSE VALUES". Frame 4 (throwing chair): "MINUS MEANS LESS AND PLUS MEANS MORE. THAT'S GOOD ENOUGH!" Frame 5: INTERPRETING EFFECTS ON THE SCALE OF INTEREST IS NATURAL AND BENEFICIAL"
July 16, 2025 at 8:23 PM
bbolker.bsky.social
Some possibly interesting/useful refs on socioeconomic barriers to success in academia ... comments welcome.

McClain 2025 doi.org/10.1371/jour...;
Morgan et al. 2022 doi.org/10.1038/s415...; Arbuckle et al 2025 doi.org/10.1111/jzo....; Wanelik et al 2020 doi.org/10.1002/ece3....
Figure 4 from Morgan et al 2022. Average income distribution estimated using faculty members’ childhood zip codes (green), compared with the income distribution across the 1998 US population (black). Two densities overlaid: both are skewed with a long/fat right tail. Black (US pop) peaks around $40K, median around $60K. Green (faculty) peaks at $50K, median around $70K.
July 14, 2025 at 11:44 PM
bbolker.bsky.social
Or "Eastern spotted skunk": I was surprised by the unfamiliar Latin name because there were only *Mephitis mephitis* (striped skunks) where I grew up: upload.wikimedia.org/wikipedia/co... upload.wikimedia.org/wikipedia/co...
range map of the Eastern spotted skunk (central US, parts of southeastern US including most of Florida) range map of Mephitis mephitis; almost all of US and southern Canada, a bit of northern Mexico
July 1, 2025 at 4:07 PM
bbolker.bsky.social
(1/2) Started to write a screed about the effect of 'quality' on getting an appointment at a prestigious institution, deleted it after locating and reading the supp material ... I think I'd still like to have seen these effects incorporated directly in the models ...
Analyzing individual publication counts in the five years before becoming faculty, we find that pre-hire productivity is not significantly correlated with doctoral prestige (p = 0.067, t-test). However, productivity does slightly correlate with the prestige of initial faculty appointments (Figure S3; p < 0.05, t-test). Together, these results suggest that faculty hiring does tend to lightly sort more productive individuals into higher ranked institutions. The sorting, however, is far from strict: for every 10-rank increase in employer prestige, faculty produced on average an additional 0.28 papers over the five-year period (R2 = 0.033). Citation counts correlate significantly but modestly with the prestige of both doctoral institutions and researchers’ initial appointments (p < 0.005, t-test). As with productivity, hiring lightly sorts individuals by prominence. A 10-rank increase in doctoral prestige corresponds to 16.43 additional citations, compared to 18.59 additional citations for each 10-rank increase in appointment prestige (R2 = 0.068). The observations above were largely unaffected by the inclusion of dummy variables corresponding to individuals’ gender and whether they received postdoctoral training. Gen- der’s effect was significant in regressions of both publication and citation counts (p < 0.05, t-test). However, normalizing citation counts by publications eliminated gender’s effect, suggesting that women receive similar numbers of citations per publication as men in our dataset, yet produce fewer papers. Further, we found that postdoctoral experience is significant in predicting publication counts but not citations (normalized or unnormalized). Postdoctoral experience was significantly linked to employment at elite institutions (π < 50; p < 0.05, χ2), yet including it as a dummy variable in regressions for publications and citations does not challenge the only modest sorting effects of faculty placement.
June 24, 2025 at 10:00 PM