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Benjamin Hlina, PhD

@benjaminhlina.bsky.social
254 followers 382 following 117 posts

Postdoctoral Fellow @DalhousieU working on spatial ecology and food web dynamics Gulf of St.Lawrence | 🇺🇸🇨🇦 | benjaminhlina.com

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Reposted by Benjamin Hlina, PhD
Gavin Simpson @gsimpson.bsky.social · 06/10/2026
📝 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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Benjamin Hlina, PhD @benjaminhlina.bsky.social · 25/09/2026
Current scientific peer review process: 1. Submit original paper for peer review 2. Get back two reviews with review 1 having submitted your paper to AI and the entire review being AI generated. Review 2 minimal comments. Huh, so I guess that’s what we are doing now.
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Benjamin Hlina, PhD @benjaminhlina.bsky.social · 23/09/2026
Check out {ggview}…this was a game changer for me to solve this. It creates the plot in viewer at the dimensions you give it/would want to save it so you don’t have to export and then check and reconfigure and then reexport. github.com/idmn/ggview
github.com
GitHub - idmn/ggview: Ggplot picture previewer
Ggplot picture previewer. Contribute to idmn/ggview development by creating an account on GitHub.
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Benjamin Hlina, PhD @benjaminhlina.bsky.social · 22/09/2026
At the time I was trying to implement a 3D plot in ggplot, ~2016/2017 and remember stumbling upon a post. I opted to use plotly as ggcube didn’t exist.
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Benjamin Hlina, PhD @benjaminhlina.bsky.social · 22/09/2026
You can often obtain 3 dimensions by using colour, shape, line type ect. Hadley at one point argued that 3D plots were confusing a poor representation of the data (don’t remember the SO but I do remember reading it) hence why it wasn’t implemented until ggcube.
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Reposted by Benjamin Hlina, PhD
Charlie Gao @shikokuchuo.net · 18/09/2026
I'm super glad to report that mori is now part of r-lib. mori.r-lib.org
mori.r-lib.org
Shared Memory for R Objects
Share R objects across processes on the same machine via a single copy in POSIX shared memory (Linux, macOS) or a Win32 file mapping (Windows). Every process reads from the same physical pages through...
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Reposted by Benjamin Hlina, PhD
Katie O'Reilly @drkatfish.bsky.social · 10/09/2026
This year's crop of wild rice/manoomin in Wisconsin has been better than average, due to both stable weather conditions during the growing season and the efforts of tribes to restore and protect wild rice-growing waters www.wpr.org/environment/...
wpr.org
Wisconsin's wild rice harvest is expected to be up this year
Wild rice, or manoomin in the Ojibwe language, is culturally significant to northern Wisconsin tribes, and Wisconsin regulators are anticipating an increased wild rice harvest this year.
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Reposted by Benjamin Hlina, PhD
Barret Schloerke @schloerke.com · 15/09/2026
🎤 Just presented “shinyreact: Building Custom Shiny UI with React” at posit::conf(2026) 🤔 Ever written JS or CSS inside an R string? shinyreact moves your UI to React: two hooks on the client, reactive_output() on the server. 📚 bit.ly/posit-2026-shinyreact #rstats #shiny #reactjs
The shinyreact hex logo — Shiny’s swoosh with a React atom in its tail.
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Benjamin Hlina, PhD @benjaminhlina.bsky.social · 29/08/2026
Would creating a container solve this problem? I have faced the same issue and recently was thinking if I built a container, that once it is built maybe this would not be an issue…I haven’t tried it yet though.
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Reposted by Benjamin Hlina, PhD
Aaron Rupar @atrupar.com · 25/08/2026
"I was not shocked that he helped somebody. My shock is that he was murdered. And no one has given us the complete truth or anyone has been held accountable. And it's been 7 months! ... there was more effort in vilifying him than pursuing justice" -- Alex Pretti's parents
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Reposted by Benjamin Hlina, PhD
Max Woolf @minimaxir.bsky.social · 21/08/2026
actual lol
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Benjamin Hlina, PhD @benjaminhlina.bsky.social · 18/08/2026
Great question but poor lead up, hence why you got a snarky comment. Could plainly state, “Considering transit in Ottawa has been quite inefficient for a while, what would you do differently as mayor to improve the current situation?”.
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Benjamin Hlina, PhD @benjaminhlina.bsky.social · 05/08/2026
This has been like this for years if I’m not mistaken. It would create a pop in the background where I would have to verify once to get zotero to be able recognize that I had access and wasn’t a bot and then it would be fine. Maybe it has changed 🤷‍♂️
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Reposted by Benjamin Hlina, PhD
Phil Swatton @philswatton.bsky.social · 08/07/2026
Two brief thoughts on why I think it's still worth keeping LLM use out of introductory programming for stats/data science: - You need to be a good programmer to get good code out of an LLM - You need to be a good programmer to evaluate the code you get out of an LLM
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Reposted by Benjamin Hlina, PhD
Brian Hayden @drhaydo.bsky.social · 07/07/2026
Training got a refresh at Atomic Ecology recently: new courses, new rates and new ways to learn - www.atomicecology.com/training
atomicecology.com
Training | Atomic Ecology
"From atoms to ecosystems....."
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Reposted by Benjamin Hlina, PhD
Minnesota Aquatic Invasive Species Research Center @maisrc.bsky.social · 07/07/2026
Protecting our waters depends on good information, but valuable data are often scattered across orgs. In this pub, MAISRC researchers highlight an interesting solution: P.I. Charter, a web-based tool that brings decades of aquatic plant survey data together onlinelibrary.wiley.com/doi/10.1002/...
onlinelibrary.wiley.com
P.I. Charter: A Shiny Application for Collecting, Cleaning, Compiling, and Communicating Point‐Intercept Aquatic Plant Data
When ecological data are collected by many entities for different purposes, they can be difficult to locate and integrate; web applications can address this by standardizing submission, automating cl...
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Reposted by Benjamin Hlina, PhD
Jon Pye @jdpye.bsky.social · 02/07/2026
Getting ready to hang out with some fish telemetry folks in a very chill open-floor Zoom environment. Check out our guest speakers for this month, a Q+A with Edward Lavender mid July and a deep dive into the work of the Smithsonian's own Beth Bowers! Join us Thursday afternoons if you're interested!
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Reposted by Benjamin Hlina, PhD
ProfColinBean @profcolinbean.bsky.social · 25/06/2026
The OTN Data Centre: enabling reliable acoustic telemetry data through a global cooperative data exchange. Canadian Journal of Fisheries and Aquatic Sciences. Just-IN doi.org/10.1139/cjfa...
doi.org
The OTN Data Centre: enabling reliable acoustic telemetry data through a global cooperative data exchange
Acoustic telemetry is a powerful tool for aquatic animal movement studies, and to enhance its potential to inform management and conservation, sound data management and quality control structures are ...
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Benjamin Hlina, PhD @benjaminhlina.bsky.social · 06/06/2026
But with that said…I do like the idea of not having to setup nginx, certbot as some of that I found tedious. I really like how streamlined lightbulb is.
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Benjamin Hlina, PhD @benjaminhlina.bsky.social · 06/06/2026
This is correct..it isn’t something that is needed for many Shiny apps but for something where concurrent users occur/uploads ect. It is helpful.
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Benjamin Hlina, PhD @benjaminhlina.bsky.social · 06/06/2026
Thanks for the explanation..this all makes sense and is super helpful in understanding how this works. I found golem when I was much further in development and felt like it provided more overhead than I was willing to do considering I am comfortable with pkg building, docker, and GHA.
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Reposted by Benjamin Hlina, PhD
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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Benjamin Hlina, PhD @benjaminhlina.bsky.social · 06/06/2026
See the following repo, in the readme i detail both the repo stucture and the GHA. github.com/benjaminhlin...
github.com
GitHub - benjaminhlina/glatar-app: {glatar} is an R package that creates a {shiny} app that interfaces with the GLATAR PostgreSQL database that contains energy density, proximate composition, stable i...
{glatar} is an R package that creates a {shiny} app that interfaces with the GLATAR PostgreSQL database that contains energy density, proximate composition, stable isotope, thiamine, fatty acid, me...
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Benjamin Hlina, PhD @benjaminhlina.bsky.social · 06/06/2026
I can hunt what crashed/look at tests and fix but that relies on someone to maintain which you’re trying to avoid which is understandable.
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Benjamin Hlina, PhD @benjaminhlina.bsky.social · 06/06/2026
I have not worked much with powerBI but that might be the way to go if cost , staff time and capacity and internet speed are issues. For a Shiny app I built I used GH actions and renv, with the first GHA having a cron job to run once a week. When it fails because of updates to pkgs it will ping me…
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Benjamin Hlina, PhD @benjaminhlina.bsky.social · 06/06/2026
Have you made an issue on GH?
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Benjamin Hlina, PhD @benjaminhlina.bsky.social · 06/06/2026
Recently in positron even when I disable pop up suggestions from AI which I hate it wouldn’t stop doing it..I eventually figured it out but I would also prefer if it was easier to control ect.
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Reposted by Benjamin Hlina, PhD
Tom Smith @analyst42.bsky.social · 04/06/2026
Sooo #rstats, I built a thing... Deploying R shiny to your own cloud server is still too hard in 2026. Lightbulb.is is my answer - connect to your digital ocean account, click to create a server, and point it at a shiny GitHub repo. That's it - spend the time you save making your customers happy!
lightbulb.is
Lightbulb.is
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Benjamin Hlina, PhD @benjaminhlina.bsky.social · 06/06/2026
github.com/benjaminhlin...
github.com
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Benjamin Hlina, PhD @benjaminhlina.bsky.social · 06/06/2026
When a push to main happens it kicks off R Cmd Check and pkgdown GHA. if R Cmd Check is successful it will tigger building a container that relies on rocker shiny, renv, copy’s app.r, and reinstall the package - this then tiggers a deployment GHA to the droplet. github.com/benjaminhlin...
github.com
GitHub - benjaminhlina/glatar-app: {glatar} is an R package that creates a {shiny} app that interfaces with the GLATAR PostgreSQL database that contains energy density, proximate composition, stable i...
{glatar} is an R package that creates a {shiny} app that interfaces with the GLATAR PostgreSQL database that contains energy density, proximate composition, stable isotope, thiamine, fatty acid, me...
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Benjamin Hlina, PhD @benjaminhlina.bsky.social · 05/06/2026
also GLATAR is now pkg which has R CMD check run beforehand. It won’t run the container and deploy GHA if the R CMD check fails…does lightbulb handle something like this?
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Benjamin Hlina, PhD @benjaminhlina.bsky.social · 05/06/2026
Ultimately deploying on a DO, AWS, GC server gives you full control. Not everything needs that but this is a great tool to help make that easier. I still like my GHA setup lol would love to know how easy it would be to switch over…
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Benjamin Hlina, PhD @benjaminhlina.bsky.social · 05/06/2026
This is awesome @analyst42.bsky.social! How does it handle load balancing?
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Benjamin Hlina, PhD @benjaminhlina.bsky.social · 04/06/2026
There's the article for those that can't actual access it. www.dropbox.com/scl/fi/v1qah...
dropbox.com
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Reposted by Benjamin Hlina, PhD
Eric Pedersen @ericjpedersen.bsky.social · 08/09/2023
Hi #stats folks! Curious about how GAMs work behind the scenes? I've put together a shiny app to demonstrate how changing the coefficients for basis functions for a smooth affects the final fitted smooth and the penalty. Looking for any feedback on the UI! 206.12.100.5/gam-basis-de...
206.12.100.5
Demo: Basis functions, coefficients, and penalties
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Benjamin Hlina, PhD @benjaminhlina.bsky.social · 03/06/2026
Thanks @ericjpedersen.bsky.social ever since you demonstrated this I’ve wanted to share it with others!
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Reposted by Benjamin Hlina, PhD
Katie O'Reilly @drkatfish.bsky.social · 01/06/2026
While Congress ultimately sets budgets, the president's budget request is a signal of priorities - and unfortunately for the #GreatLakes, the current proposal would zero out several critical NOAA programs such as the Great Lakes Observing System (GLOS) www.interlochenpublicradio.org/ipr-news/202...
interlochenpublicradio.org
Great Lakes researchers worry about federal cuts to NOAA
The President’s proposed budget would cut funding to efforts that improve public safety, the maritime economy and health on the Great Lakes, researchers say.
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Benjamin Hlina, PhD @benjaminhlina.bsky.social · 01/06/2026
📣 Check out Great Lakes Aquatic Tissue Analysis Repository (GLATAR) - a repository containing energy density, proximate composition, stable isotope, thiamine, fatty acid, and contaminant data for fish and aquatic inverts in the Great Lakes and North America. Link below: GLATAR.org #ecology #rstats
glatar.org
Great Lakes Aquatic Tissue Analysis Repository (GLATAR)
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Benjamin Hlina, PhD @benjaminhlina.bsky.social · 29/05/2026
📣 the Great Lakes Aquatic Tissue and Analysis Repository (GLATAR) - a data repository containing energy density, proximate composition, stable isotope, thiamine, fatty acid, and contaminant data for fish and aquatic inverts in the Great Lakes and North America. Check it out at GLATAR.org #ecology
glatar.org
Great Lakes Aquatic Tissue Analysis Repository (GLATAR)
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Reposted by Benjamin Hlina, PhD
JD Long @jdlong.cerebralmastication.com · 28/05/2026
A lot of folks aren’t distinguishing clearly between “AI figured X out” and “AI helped write code that enabled us to figure X out”. They are very very different.
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Benjamin Hlina, PhD @benjaminhlina.bsky.social · 12/05/2026
Just walking along Bronson near Carleton and it’s obvious the speed cameras had an effect and were safer. Thank you for diving into the data to back up my own visual observation
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Reposted by Benjamin Hlina, PhD
Jason Gantenberg @jrgant.bsky.social · 08/05/2026
The R install you never knew you needed #rstats
reddit.com
From the rstats community on Reddit: R on a Flip Phone
Explore this post and more from the rstats community
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Benjamin Hlina, PhD @benjaminhlina.bsky.social · 07/05/2026
What about protecting the wild and wolves in the BWCA?!?! That would be more Minnesotan of you.
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Benjamin Hlina, PhD @benjaminhlina.bsky.social · 01/05/2026
What about the BWCA?! Where the Wolves and Wild live ;)
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Reposted by Benjamin Hlina, PhD
Danielle Ferraro @dferraro.bsky.social · 30/04/2026
Did #TidyTuesday this week for the first time in many years 🥹 and posted about it over on @weare.rladies.org!
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Benjamin Hlina, PhD @benjaminhlina.bsky.social · 01/05/2026
Lastly this paper also in the animal tracking/positioning world uses python and might be worth reaching out to. link.springer.com/article/10.1...
link.springer.com
High precision 3-D coordinates for JSATS tagged fish in an acoustically noisy environment - Animal Biotelemetry
Background Acoustic tagging methods have been used to track fish for some time. Multiple systems have been developed, including those that give researchers the ability to position fish in three dimens...
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Benjamin Hlina, PhD @benjaminhlina.bsky.social · 01/05/2026
Should also note the python package resonATe. github.com/ocean-tracki...
github.com
GitHub - ocean-tracking-network/resonATe
Contribute to ocean-tracking-network/resonATe development by creating an account on GitHub.
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Benjamin Hlina, PhD @benjaminhlina.bsky.social · 01/05/2026
Python is used at times in the animal tracking world. See Ed paper on particle filters used in animal tracking. He built patter which is an R package that ports into Julia. I think he was going to also get this to work in python. besjournals.onlinelibrary.wiley.com/doi/10.1111/...
besjournals.onlinelibrary.wiley.com
State‐space models and inference approaches for aquatic animal tracking with passive acoustic telemetry and biologging sensors
Passive acoustic telemetry systems are widely deployed to track animals in aquatic environments. However, investments in integrative methods of data analysis have remained comparatively limited, w...
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Reposted by Benjamin Hlina, PhD
Thomas Lin Pedersen @thomasp85.com · 20/04/2026
I am excited beyond description to lift the veil on what we have been working on in 2026: Please meet ggsql! A new extension of the SQL language for creating visualisations using the grammar of graphics. Read all about it in the blog post or visit the website at ggsql.org
opensource.posit.co
ggsql: A grammar of graphics for SQL
Introducing ggsql, a grammar of graphics for SQL that lets you describe visualizations directly inside SQL queries.
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Benjamin Hlina, PhD @benjaminhlina.bsky.social · 16/04/2026
I have a shiny app that uses fnct that have {cli} outputs. Prior to wrapping the ui, server, and shinyApp() as a fnct, the app would dump {cli} outputs into the console. Once wrapped, all {cli} outputs are logged but not displayed until app process is closed. How do I restore this behaviour? #rstats
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