Sam Abbott
@seabbs.bsky.social
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
Come join me on the epinowcast forum: https://community.epinowcast.org/latest
Pinned
Sam Abbott
@seabbs.bsky.social
· Dec 13
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
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...
epiforecasts.io/posts/2022-0...
Reposted by Sam Abbott
I was recently asked to comment on superspreading for a BBC article. Little did I know, my quote would become the title!
www.bbc.com/future/artic...
www.bbc.com/future/artic...
'Some people have 10 million times more virus than others': Are you a flu superspreader?
A growing body of research suggests that everything from the shape of your lungs to how you enunciate your Ts and Ks could make you a flu superspreader.
www.bbc.com
February 4, 2026 at 5:52 AM
I was recently asked to comment on superspreading for a BBC article. Little did I know, my quote would become the title!
www.bbc.com/future/artic...
www.bbc.com/future/artic...
Tomorrow at 3 pm UK time for the #epinowcast seminar, we have another in our series of informal show-and-tell discussions, rather than a traditional speaker. Please come and share a bit on what you are working on!
See here for more and the links: www.epinowcast.org/seminars/202...
See here for more and the links: www.epinowcast.org/seminars/202...
Community Show and Tell - Recent work and ideas – Epinowcast
Epinowcast community site
www.epinowcast.org
February 3, 2026 at 6:14 PM
Tomorrow at 3 pm UK time for the #epinowcast seminar, we have another in our series of informal show-and-tell discussions, rather than a traditional speaker. Please come and share a bit on what you are working on!
See here for more and the links: www.epinowcast.org/seminars/202...
See here for more and the links: www.epinowcast.org/seminars/202...
New #epinowcast seminar organiser needed: community.epinowcast.org/t/looking-fo...
Looking for new co-organizer for seminars
Dear Epinowcast Community, As my postdoc at Institut Pasteur comes to an end, this month will be my last as co-organizer of the Epinowcast seminars. I started co-organizing the seminars with Sam over...
community.epinowcast.org
February 3, 2026 at 3:04 PM
New #epinowcast seminar organiser needed: community.epinowcast.org/t/looking-fo...
Reposted by Sam Abbott
What if you could see live gas turn-up in England at the same time as wind, gas and battery curtailment in Scotland?
That'd be kinda interesting right?
I suppose it's a good job it's coming to my map, and soon…
That'd be kinda interesting right?
I suppose it's a good job it's coming to my map, and soon…
January 30, 2026 at 9:14 AM
What if you could see live gas turn-up in England at the same time as wind, gas and battery curtailment in Scotland?
That'd be kinda interesting right?
I suppose it's a good job it's coming to my map, and soon…
That'd be kinda interesting right?
I suppose it's a good job it's coming to my map, and soon…
Reposted by Sam Abbott
Very happy to have had the opportunity to contribute to this work. Thanks to Robin Thompson for leading, the amazing team of co-authors and the INI for hosting us.
New paper! "Infectious disease outbreak controllability: biological, social and public health factors" - we provide a modelling-informed discussion of what 'controllability' means for an infectious disease outbreak.
royalsocietypublishing.org/rspb/article...
royalsocietypublishing.org/rspb/article...
Infectious disease outbreak controllability: biological, social and public health factors
Abstract. Early in an infectious disease outbreak, key policy questions include whether and how the outbreak can be brought under control. In the epidemiol
royalsocietypublishing.org
January 29, 2026 at 12:19 AM
Very happy to have had the opportunity to contribute to this work. Thanks to Robin Thompson for leading, the amazing team of co-authors and the INI for hosting us.
It took me an embarrassingly long time to understand why this was called the warehouse. A really cool project with I think some great potential for making packages more discoverable/ surfacing user feedback.
I’ve been thinking about how to find R packages by functionality when you don’t already know the package name.
So over the holidays, Claude Code and I built The Warehouse: a functionality-first R package directory that helps you find packages by what they do.
rwarehouse.netlify.app
#rstats
So over the holidays, Claude Code and I built The Warehouse: a functionality-first R package directory that helps you find packages by what they do.
rwarehouse.netlify.app
#rstats
The Warehouse
rwarehouse.netlify.app
January 27, 2026 at 8:41 PM
It took me an embarrassingly long time to understand why this was called the warehouse. A really cool project with I think some great potential for making packages more discoverable/ surfacing user feedback.
Reposted by Sam Abbott
Bayesian Workflow by
Andrew Gelman, Aki Vehtari, @rmcelreath.bsky.social with @danpsimpson.bsky.social, @charlesm993.bsky.social, @yulingy.bsky.social, Lauren Kennedy, Jonah Gabry, @paulbuerkner.com, @modrakm.bsky.social, @vianeylb.bsky.social
(in production, estimated copy-editing time 6 weeks)
Andrew Gelman, Aki Vehtari, @rmcelreath.bsky.social with @danpsimpson.bsky.social, @charlesm993.bsky.social, @yulingy.bsky.social, Lauren Kennedy, Jonah Gabry, @paulbuerkner.com, @modrakm.bsky.social, @vianeylb.bsky.social
(in production, estimated copy-editing time 6 weeks)
January 26, 2026 at 8:18 AM
Bayesian Workflow by
Andrew Gelman, Aki Vehtari, @rmcelreath.bsky.social with @danpsimpson.bsky.social, @charlesm993.bsky.social, @yulingy.bsky.social, Lauren Kennedy, Jonah Gabry, @paulbuerkner.com, @modrakm.bsky.social, @vianeylb.bsky.social
(in production, estimated copy-editing time 6 weeks)
Andrew Gelman, Aki Vehtari, @rmcelreath.bsky.social with @danpsimpson.bsky.social, @charlesm993.bsky.social, @yulingy.bsky.social, Lauren Kennedy, Jonah Gabry, @paulbuerkner.com, @modrakm.bsky.social, @vianeylb.bsky.social
(in production, estimated copy-editing time 6 weeks)
Reposted by Sam Abbott
A lot of discussion of the loss in research funding, and I get that's bad, but you know what would accelerate a ton of research and cost very little?
Build an open-source hosted solution for academic publishing. Allow anyone to make their own journal with it. Modern tools for interactive web pubs.
Build an open-source hosted solution for academic publishing. Allow anyone to make their own journal with it. Modern tools for interactive web pubs.
a woman in a red jacket is sitting in a chair and says boom .
Alt: a woman in a red jacket is sitting in a chair and says boom .
media.tenor.com
January 23, 2026 at 2:52 PM
A lot of discussion of the loss in research funding, and I get that's bad, but you know what would accelerate a ton of research and cost very little?
Build an open-source hosted solution for academic publishing. Allow anyone to make their own journal with it. Modern tools for interactive web pubs.
Build an open-source hosted solution for academic publishing. Allow anyone to make their own journal with it. Modern tools for interactive web pubs.
Reposted by Sam Abbott
Really neat bit on Rt confidence (also loving the blog write-up, more edible than skimming the full paper)
Is it a problem that common Reproduction number estimators produce overconfident results?
New blog post from Barbora Němcová and Johannes Bracher summarising there recent preprint:
www.epinowcast.org/posts/2026-0...
New blog post from Barbora Němcová and Johannes Bracher summarising there recent preprint:
www.epinowcast.org/posts/2026-0...
Overconfident \(R_t\) estimates from the Poisson renewal equation method – Epinowcast
Epinowcast community site
www.epinowcast.org
January 22, 2026 at 11:53 AM
Really neat bit on Rt confidence (also loving the blog write-up, more edible than skimming the full paper)
Is it a problem that common Reproduction number estimators produce overconfident results?
New blog post from Barbora Němcová and Johannes Bracher summarising there recent preprint:
www.epinowcast.org/posts/2026-0...
New blog post from Barbora Němcová and Johannes Bracher summarising there recent preprint:
www.epinowcast.org/posts/2026-0...
Overconfident \(R_t\) estimates from the Poisson renewal equation method – Epinowcast
Epinowcast community site
www.epinowcast.org
January 21, 2026 at 7:51 PM
Is it a problem that common Reproduction number estimators produce overconfident results?
New blog post from Barbora Němcová and Johannes Bracher summarising there recent preprint:
www.epinowcast.org/posts/2026-0...
New blog post from Barbora Němcová and Johannes Bracher summarising there recent preprint:
www.epinowcast.org/posts/2026-0...
I had a nice time reading the responses to Wood et al.'s piece and think that many of them captured the strengths and limitations
academic.oup.com/jrsssa/issue...
academic.oup.com/jrsssa/issue...
Volume 189 Issue 1 | Journal of the Royal Statistical Society Series A: Statistics in Society | Oxford Academic
Series A looks at how statistical thinking, design and analyses play a vital role in all walks of life and benefit society. Subject matter is not restricted. Official Journal of the Royal Statistical ...
academic.oup.com
January 20, 2026 at 11:19 AM
I had a nice time reading the responses to Wood et al.'s piece and think that many of them captured the strengths and limitations
academic.oup.com/jrsssa/issue...
academic.oup.com/jrsssa/issue...
ESPIDAM 2026 now advertising. Pretty good snacks and lots of ferries. Also infectious disease modelling:
See: community.epinowcast.org/t/sismid-202...
See: community.epinowcast.org/t/sismid-202...
January 19, 2026 at 5:00 PM
ESPIDAM 2026 now advertising. Pretty good snacks and lots of ferries. Also infectious disease modelling:
See: community.epinowcast.org/t/sismid-202...
See: community.epinowcast.org/t/sismid-202...
Reposted by Sam Abbott
Our work about extending contact matrices beyond age, accounting for socio-economic dimensions, is finally published! Here, we analyse social contact data in Switzerland. Happy to see this output from my research period at @ispm.unibe.ch w/ @calthaus.bsky.social
www.nature.com/articles/s43...
www.nature.com/articles/s43...
Individual and neighborhood based socioeconomic factors relevant for contact behaviour and epidemic control - Communications Medicine
Di Domenico et al. develop a method to reconstruct contact matrices fully stratified by age, education level and socioeconomic position. Results show that accounting for contact assortativity with soc...
www.nature.com
January 16, 2026 at 2:37 PM
Our work about extending contact matrices beyond age, accounting for socio-economic dimensions, is finally published! Here, we analyse social contact data in Switzerland. Happy to see this output from my research period at @ispm.unibe.ch w/ @calthaus.bsky.social
www.nature.com/articles/s43...
www.nature.com/articles/s43...
Reposted by Sam Abbott
Thanks to claude code, I wrote my first iphone app:
apps.apple.com/us/app/time-...
It's what I have always wanted for a talk timer (as both a speaker and a chair). It's very minimal, designed to be read from across the room, and make it clear when you're running out of time.
apps.apple.com/us/app/time-...
It's what I have always wanted for a talk timer (as both a speaker and a chair). It's very minimal, designed to be read from across the room, and make it clear when you're running out of time.
Time Will Tell App - App Store
Download Time Will Tell by Hadley Wickham on the App Store. See screenshots, ratings and reviews, user tips, and more games like Time Will Tell.
apps.apple.com
January 14, 2026 at 7:49 PM
Thanks to claude code, I wrote my first iphone app:
apps.apple.com/us/app/time-...
It's what I have always wanted for a talk timer (as both a speaker and a chair). It's very minimal, designed to be read from across the room, and make it clear when you're running out of time.
apps.apple.com/us/app/time-...
It's what I have always wanted for a talk timer (as both a speaker and a chair). It's very minimal, designed to be read from across the room, and make it clear when you're running out of time.
This has been rescheduled for today!
#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...
www.epinowcast.org/seminars/202...
David Hodgson – Epinowcast
Epinowcast community site
www.epinowcast.org
January 14, 2026 at 10:59 AM
This has been rescheduled for today!
Reposted by Sam Abbott
gemini deep research is the most pretentious model out there
January 13, 2026 at 3:25 PM
gemini deep research is the most pretentious model out there
I really thought google's nano banana pro was going to be great for making visual paper abstracts.... several days of screaming at it later I think we aren't quite there...
January 13, 2026 at 2:51 PM
I really thought google's nano banana pro was going to be great for making visual paper abstracts.... several days of screaming at it later I think we aren't quite there...
Reposted by Sam Abbott
Preprints of pandemic potential - new historical piece from me on the history of bioRxiv/medRxiv, their role in the pandemic, and the way forward. 1/n journals.asm.org/doi/10.1128/...
January 12, 2026 at 2:33 PM
Preprints of pandemic potential - new historical piece from me on the history of bioRxiv/medRxiv, their role in the pandemic, and the way forward. 1/n journals.asm.org/doi/10.1128/...
Something I have been "enjoying" recently whilst writing a draft is keeping the letter to the editor in sync as I go.
In the past I have just fired these out just before submission. The benefit to keeping it up to date I am finding is that it is a helpful tool to keep the intended reader in mind.
In the past I have just fired these out just before submission. The benefit to keeping it up to date I am finding is that it is a helpful tool to keep the intended reader in mind.
January 12, 2026 at 12:13 PM
Something I have been "enjoying" recently whilst writing a draft is keeping the letter to the editor in sync as I go.
In the past I have just fired these out just before submission. The benefit to keeping it up to date I am finding is that it is a helpful tool to keep the intended reader in mind.
In the past I have just fired these out just before submission. The benefit to keeping it up to date I am finding is that it is a helpful tool to keep the intended reader in mind.
Starting to think about our teaching for this year's EPISIDAM in Stockholm (advert coming next week!) and looking at the group photos. Two years running, I have managed to stand in essentially the same place wearing the same clothes so fingers crossed for this year.
January 9, 2026 at 4:05 PM
Starting to think about our teaching for this year's EPISIDAM in Stockholm (advert coming next week!) and looking at the group photos. Two years running, I have managed to stand in essentially the same place wearing the same clothes so fingers crossed for this year.
Reposted by Sam Abbott
How can diagnostic tests for infection support public health – and what challenges do we need to overcome to maximize their potential? Kristin Nelson, Tyler Brown, and I have a new article out digging into this exciting, complex issue: www.tandfonline.com/doi/full/10....
Diagnostic testing as a public health intervention: challenges and opportunities
Published in Future Virology (Vol. 20, No. 12, 2025)
www.tandfonline.com
January 6, 2026 at 7:11 PM
How can diagnostic tests for infection support public health – and what challenges do we need to overcome to maximize their potential? Kristin Nelson, Tyler Brown, and I have a new article out digging into this exciting, complex issue: www.tandfonline.com/doi/full/10....
Reposted by Sam Abbott
Rather applaud JOSS's revised approach to deal with AI-based submissions. blog.joss.theoj.org/2026/01/prep... , particularly with 'starting open' and at least 'six months developer history'. More of scholarly pub could benefit from such policies methinks.
Preparing JOSS for a generative AI future: From code to human creativity and design | Journal of Open Source Software Blog
Blog for the Journal of Open Source Software • <a href='https://joss.theoj.org'>https://joss.theoj.org</a>
blog.joss.theoj.org
January 5, 2026 at 11:49 PM
Rather applaud JOSS's revised approach to deal with AI-based submissions. blog.joss.theoj.org/2026/01/prep... , particularly with 'starting open' and at least 'six months developer history'. More of scholarly pub could benefit from such policies methinks.