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seabbs.bsky.social
Sam Abbott
@seabbs.bsky.social
1.4K followers 700 following 700 posts
Real-time infectious disease modelling. Developing methods for outbreak response, surveillance, and pandemic preparedness. samabbott.co.uk
Come join me on the epinowcast forum: https://community.epinowcast.org/latest
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seabbs.bsky.social
Sam Abbott @seabbs.bsky.social · Dec 13
In 2022 @sbfnk.bsky.social and I wrote this blog on what it was like estimating the effective reproduction number daily for 2 years and if it was helpful

epiforecasts.io/posts/2022-0...
Reflections on two years estimating effective reproduction numbers – EpiForecasts
Over the last two years we have estimated reproduction numbers daily for several thousand locations, presented these estimates as a curated data set and visualised them at epiforecasts.io/covid. In th...
epiforecasts.io
seabbs.bsky.social
I applied for funding from this and was sad not to get it but hard to argue when it is going to projects like this!
rconsortium.bsky.social R Consortium @rconsortium.bsky.social · 15d
Fantastic! $650k awarded via the Research Software Maintenance Fund for “Enabling the Next Generation of Contributors to R”—mentoring new contributors, modernizing R’s dev infrastructure, and strengthening the R Foundation.

r-consortium.org/posts/650K-f...

#rstats
R Consortium - Enabling the Next Generation of Contributors to R
The Software Sustainability Institute (UK) has awarded a grant of USD $650,000 under the Research Software Maintenance Fund, to the project Enabling the Next Generation of Contributors to R.
r-consortium.org
December 19, 2025 at 12:41 PM
Reposted by Sam Abbott
kylieainslie.bsky.social
All of the tools created as part of the @ec.europa.eu funded ESCAPE project on pandemic preparedness in one place (including {mitey}) 😁

www.escapepandemics.com/digitaltoolkit

#EpiSky #IDSky #rstats #AcademicSky
Digital toolkit | Escape Pandemics
Discover the tools created within the ESCAPE team for pathogen archetypes, estimation of key epidemiological variables, reference models for comparison and projecting epidemic outcomes and tools to re...
www.escapepandemics.com
December 18, 2025 at 8:02 PM
Reposted by Sam Abbott
jdushoff.bsky.social
This is a really cool project, I was lucky to have the opportunity to participate.

news.mcmaster.ca/mcmaster-res...
McMaster research team digitizes more than 100 years of Canadian infectious disease data
The new, publicly accessible database contains more than a million infectious disease incidence counts dating back to 1903.
news.mcmaster.ca
December 18, 2025 at 5:41 PM
Reposted by Sam Abbott
meganodris.bsky.social
The final piece of my PhD work is now published in Science Translational Medicine! We present a new framework to jointly infer epidemiological and antigenic parameters from multi-pathogen population serological studies🦠

www.science.org/stoken/autho...
December 18, 2025 at 10:04 AM
seabbs.bsky.social
This is amazing. Sad but not unexpected finding support has taken so long.
rogierk.bsky.social rogier kievit @rogierk.bsky.social · 16d
I've used Lavaan almost every (work)day for 15 years, but this open source labour of love has never received proper institutional support. I'm delighted to be a small part of an 1.5M OpenScienceNL award, led by Jorgensen, to completely revamp and futureproof Lavaan www.openscience.nl/en/news/45-p...
December 18, 2025 at 8:31 AM
Reposted by Sam Abbott
jessbutler.bsky.social
"It must not be overlooked that junior researchers DO NOT TRUST US. We, the directors, are a big part of the problem. We made this system, we remake it every year, and we benefit from it. What can we do to credibly signal our commitment to reform a corrupt research culture?"
rmcelreath.bsky.social Richard McElreath 🐈‍⬛ @rmcelreath.bsky.social · 17d
The Max Planck Society has begun an exploratory round table for open science. We are drafting some recommendations to leadership. Still a long way to go! But here are my notes on the most recent draft, just so you all know how I am trying to steer things.
Richard McElreath: It must not be overlooked that junior researchers DO NOT TRUST US. We, the directors, are a big part of the problem. We made this system, we remake it every year, and we benefit from it. What can we do to credibly signal our commitment to reform a corrupt research culture? My conversations with junior scientists in the society has taught me that directors are too often either indifferent or hostile to science reform. We cannot hope to convince our prize winning colleagues. Their egos are immune. But we can replace retirements with researchers who care more about integrity than their own prestige. This is important both for earning the trust of the junior researchers who really do the research in the MPG and for attracting excellent future directors and starting to earn the trust of the public. So I suggest two strong signals to our junior researchers (and the public): (1) we will reform recruitment and promotion at all levels to eliminate proxies like citation counts and journal brands in favor of reliability and sustainability; (2) we will make open science skills a core part of scientific training, through the graduate schools at a minimum, as conditions for the central funding. The most ambitious thing we could do, as hinted at in item 5 above, is to meaningfully invest in metascientific research. As the largest basic research organization in the world, the MPG is uniquely suited to studying research and its products from a broad perspective that includes the humanities, the sciences, and policy. Governments are already involved in science reform. Someone should study it in an organized and sustained way.
December 17, 2025 at 11:58 AM
Reposted by Sam Abbott
sbfnk.bsky.social
Two more fully funded PhDs in real-time infectious disease modelling & forecasting — developing methods for operational use by @ukhsa.bsky.social and others in outbreak response. UK home students, starting April or September 2026.

www.lshtm.ac.uk/study/fees-a...
PhD Studentships in Health Analytics and Modelling | LSHTM
The London School of Hygiene & Tropical Medicine (LSHTM), Imperial College London and the UK Health Security Agency (UKHSA) are pleased to invite applications for two PhD studentships in real-time
www.lshtm.ac.uk
December 17, 2025 at 10:27 AM
Reposted by Sam Abbott
adamhowes.bsky.social
I've also looked into this and reached the a similar conclusion. Here are some additional links/thoughts:
December 11, 2025 at 11:12 AM
Reposted by Sam Abbott
stuartmcdaniel.bsky.social
UF Biology is searching for an Asst Prof in Evolution, Ecology of Infectious Disease - spread the word! @ufresearch.bsky.social @ufgeog.bsky.social @sse-evolution.bsky.social

explore.jobs.ufl.edu/en-us/job/53...
University of Florida - Details - Assistant Professor in Ecology and Evolution of Infectious Disease
explore.jobs.ufl.edu
December 10, 2025 at 5:04 PM
seabbs.bsky.social
Having some fun trying to understand how Givewell evidences its giving/recommendations. So much text....
December 10, 2025 at 3:31 PM
seabbs.bsky.social
A really nice paper with a very interestingly complicated dataset. Lots of modelling details to dig into in the SI.
December 9, 2025 at 1:36 PM
seabbs.bsky.social
Really nice paper on Universal differential equations in systems biology with some nice looking #julialang code.

www.nature.com/articles/s41...
Current state and open problems in universal differential equations for systems biology - npj Systems Biology and Applications
npj Systems Biology and Applications - Current state and open problems in universal differential equations for systems biology
www.nature.com
December 8, 2025 at 5:33 PM
seabbs.bsky.social
Oo this is fun!
December 5, 2025 at 11:59 AM
Reposted by Sam Abbott
avehtari.bsky.social
In March 2024 I was reading R docs and learned 🧵

1. doc for NaN and is.nan() says: "‘NaN’ means ‘Not a Number’" and "NA, ‘_Not Available_’ which is not a number as well"

-> so neither is "a number".
December 3, 2025 at 9:19 AM
seabbs.bsky.social
#epinowcast seminar tomorrow at 3pm UK time/10am US East time: David Hodgson talking about Serological data and the seroanalytics suite of tools

www.epinowcast.org/seminars/202...
David Hodgson – Epinowcast
Epinowcast community site
www.epinowcast.org
December 2, 2025 at 5:46 PM
seabbs.bsky.social
This is a nice piece and makes some good points. Something it mentions is that work is being done to make the tools we need but ...
December 2, 2025 at 3:15 PM
Reposted by Sam Abbott
jameshay.bsky.social
H3N2 preprint: there are concerns of a severe incoming influenza season due to the drifted H3N2 K clade. We at @psioxford.bsky.social analysed epi data and ran scenario models to see what we could discern about K clade transmission dynamics: zenodo.org/records/1770....

(1/18)
Evaluation of the epidemiological outlook of the influenza A/H3N2 clade K in England during the 2025-26 season
Key findings England is currently experiencing a high growth rate of infections caused by the influenza A/H3N2 K clade. Antigenic change from the previously dominant clade, a rapid selective sweep evi...
zenodo.org
November 25, 2025 at 1:51 PM
Reposted by Sam Abbott
gsimpson.bsky.social
A new release of the mgcv #RStats 📦 is out on CRAN and Simon Wood (U Edinburgh) has added some significant new features despite the small bump in version number:

🌟 scasm() for estimating GAMs with shape constrained smooths. Can be used with any family & smoothness selection is via the EFS method
Model is: b3 <- scasm( y ~ s(x0, bs = "bs", k= k) + s(x1, bs = "sc", xt = "m+", k = k) + s(x2, bs = "bs", k = k) + s(x3, bs = "bs", k = k), family=poisson, bs=200 ) The second smooth `s(x1) is a shape constrained smooth with a positive monotonicity constraint (xt = "m+"). The `bs = 200` arguments uses 200 boostrap samples, which generates bootstrap distributions for each coefficient in the model. These bootstrap samples respect the shape constraints, while the usual +/- 2 SE credible intervals may not. The uncertainty in the partial effects is shown by two credible interval bands; a dark blue central band is a 68% Bayesian credible interval, while the lighter blue outer interval is a 95% Bayesian credible interval. The background of each panel is light grey with white grid lines, in a similar style to ggplot2's default theme.
November 12, 2025 at 11:28 AM
seabbs.bsky.social
Always a pleasure when you see a package or some scratch work being used as part of a longer form piece of work.

Nice paper here by Rob Sunnucks et al. www.medrxiv.org/content/10.1...
Methods for Reproducible Comparison of Strategies in Stochastic Modelling
Stochastic simulations are often used to model real-world phenomena such as infectious disease dynamics. In this modelling, differing strategies are often compared to one another by comparing the mode...
www.medrxiv.org
November 12, 2025 at 2:07 PM
Reposted by Sam Abbott
russpoldrack.org
Ten Simple Rules for AI-Assisted Coding in Science arxiv.org/abs/2510.22254 - our latest, led by @ericwbridgeford.bsky.social
Ten Simple Rules for AI-Assisted Coding in Science
While AI coding tools have demonstrated potential to accelerate software development, their use in scientific computing raises critical questions about code quality and scientific validity. In this pa...
arxiv.org
October 28, 2025 at 1:12 PM
seabbs.bsky.social
Really nice to see this being used - a real blast from the past. If anyone is keen to help get this back on CRAN or do other work on it that would be amazing!
jonthegeek.com Jon Harmon (he/him/his) @jonthegeek.com · Nov 10
@dslc.io welcomes you to week 45 of #TidyTuesday! We're exploring WHO TB Burden Data: Incidence, Mortality, and Population!

📁 https://tidytues.day/2025/2025-11-11
📰 https://samabbott.co.uk/getTBinR/index.html

#RStats #PyData #JuliaLang #DataViz #tidyverse #r4ds
Logo for the #TidyTuesday Project. The words TidyTuesday, A weekly data project from the Data Science Learning Community (dslc.io) overlaying a black paint splash. TidyTuesday is a weekly social data project. All are welcome to participate! Please remember to share the code used to generate your results! TidyTuesday is organized by the Data Science Learning Community. Join our Slack for free online help with R and other data-related topics, or to participate in a data-related book club! How to Participate Data is posted to social media every Monday morning. Follow the instructions in the new post for how to download the data. Explore the data, watching out for interesting relationships. We would like to emphasize that you should not draw conclusions about causation in the data. Create a visualization, a model, a shiny app, or some other piece of data-science-related output, using R or another programming language. Share your output and the code used to generate it on social media with the #TidyTuesday hashtag. World map showing estimated TB incidence rates per 100,000 population. Countries range from light green (low incidence) to dark purple (high incidence), with highest rates in Sub-Saharan Africa and South/Southeast Asia. Map sourced from WHO and rendered using getTBinR::map_tb_burden() in R.
November 11, 2025 at 10:34 AM
Reposted by Sam Abbott
jonthegeek.com
@dslc.io welcomes you to week 45 of #TidyTuesday! We're exploring WHO TB Burden Data: Incidence, Mortality, and Population!

📁 https://tidytues.day/2025/2025-11-11
📰 https://samabbott.co.uk/getTBinR/index.html

#RStats #PyData #JuliaLang #DataViz #tidyverse #r4ds
Logo for the #TidyTuesday Project. The words TidyTuesday, A weekly data project from the Data Science Learning Community (dslc.io) overlaying a black paint splash. TidyTuesday is a weekly social data project. All are welcome to participate! Please remember to share the code used to generate your results! TidyTuesday is organized by the Data Science Learning Community. Join our Slack for free online help with R and other data-related topics, or to participate in a data-related book club! How to Participate Data is posted to social media every Monday morning. Follow the instructions in the new post for how to download the data. Explore the data, watching out for interesting relationships. We would like to emphasize that you should not draw conclusions about causation in the data. Create a visualization, a model, a shiny app, or some other piece of data-science-related output, using R or another programming language. Share your output and the code used to generate it on social media with the #TidyTuesday hashtag. World map showing estimated TB incidence rates per 100,000 population. Countries range from light green (low incidence) to dark purple (high incidence), with highest rates in Sub-Saharan Africa and South/Southeast Asia. Map sourced from WHO and rendered using getTBinR::map_tb_burden() in R.
November 10, 2025 at 1:48 PM
seabbs.bsky.social
I spend a lot of my day interacting with LLMs and reviewing LLM generated content (mostly all via Claude Code). I'd really like it to communicate in a way that is more clearly not human as I find sometimes that when I talk to actual people I might not have switched communication style.
November 6, 2025 at 2:11 PM
seabbs.bsky.social
This is today at 3pm UK time
seabbs.bsky.social Sam Abbott @seabbs.bsky.social · Nov 4
For this week’s #epinowcast seminar (as ever the first Wednesday of the month at 3pm UK time) we have Lina Cristancho Fajardo talking about:

Why heterogeneity in mosquito exposure is necessary to forecast chikungunya outbreaks in Reunion Island.

www.epinowcast.org/seminars/202...
Lina Cristancho Fajardo - Accounting for heterogeneity in mosquito exposure is necessary to forecast chikungunya outbreaks in Reunion Island – Epinowcast
Epinowcast community site
www.epinowcast.org
November 5, 2025 at 12:11 PM
seabbs.bsky.social
For this week’s #epinowcast seminar (as ever the first Wednesday of the month at 3pm UK time) we have Lina Cristancho Fajardo talking about:

Why heterogeneity in mosquito exposure is necessary to forecast chikungunya outbreaks in Reunion Island.

www.epinowcast.org/seminars/202...
Lina Cristancho Fajardo - Accounting for heterogeneity in mosquito exposure is necessary to forecast chikungunya outbreaks in Reunion Island – Epinowcast
Epinowcast community site
www.epinowcast.org
November 4, 2025 at 10:51 AM