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
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
🌟 scasm() for estimating GAMs with shape constrained smooths. Can be used with any family & smoothness selection is via the EFS method
November 12, 2025 at 11:28 AM
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
🌟 scasm() for estimating GAMs with shape constrained smooths. Can be used with any family & smoothness selection is via the EFS method
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...
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
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...
Nice paper here by Rob Sunnucks et al. www.medrxiv.org/content/10.1...
Reposted by Sam Abbott
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
Ten Simple Rules for AI-Assisted Coding in Science arxiv.org/abs/2510.22254 - our latest, led by @ericwbridgeford.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!
@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
📁 https://tidytues.day/2025/2025-11-11
📰 https://samabbott.co.uk/getTBinR/index.html
#RStats #PyData #JuliaLang #DataViz #tidyverse #r4ds
November 11, 2025 at 10:34 AM
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!
Reposted by Sam Abbott
@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
📁 https://tidytues.day/2025/2025-11-11
📰 https://samabbott.co.uk/getTBinR/index.html
#RStats #PyData #JuliaLang #DataViz #tidyverse #r4ds
November 10, 2025 at 1:48 PM
@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
📁 https://tidytues.day/2025/2025-11-11
📰 https://samabbott.co.uk/getTBinR/index.html
#RStats #PyData #JuliaLang #DataViz #tidyverse #r4ds
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
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.
This is today at 3pm UK time
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...
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
This is today at 3pm UK time
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...
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
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...
Why heterogeneity in mosquito exposure is necessary to forecast chikungunya outbreaks in Reunion Island.
www.epinowcast.org/seminars/202...
Reposted by Sam Abbott
Now I'm also looking for a research software engineer to implement a pile of research results to R packages loo, posterior, bayesplot, projpred, priorsense, brms or/and Python packages ArviZ, Bambi and Kulprit. Apply by email with no specific deadline (see contact info at users.aalto.fi/~ave/)
I'm now also looking for a postdoc with strong Bayesian background and interest in developing Bayesian cross-validation theory, methods and software. Apply by email with no specific deadline (see contact information at users.aalto.fi/~ave/).
Others, please share
Others, please share
I'm looking for a doctoral student with Bayesian background to work on Bayesian workflow and cross-validation (see my publication list users.aalto.fi/~ave/publica... for my recent work) at Aalto University.
Apply through the ELLIS PhD program (dl October 31) ellis.eu/news/ellis-p...
Apply through the ELLIS PhD program (dl October 31) ellis.eu/news/ellis-p...
November 3, 2025 at 11:13 AM
Now I'm also looking for a research software engineer to implement a pile of research results to R packages loo, posterior, bayesplot, projpred, priorsense, brms or/and Python packages ArviZ, Bambi and Kulprit. Apply by email with no specific deadline (see contact info at users.aalto.fi/~ave/)
Reposted by Sam Abbott
Can you take a quarter cup of composite sewage, simply ask ‘what’s in there?’, and find out all of the pathogens circulating in that community?
That is the question we asked in our latest pre-print.
Turns out you can.
1/
www.medrxiv.org/content/10.1...
That is the question we asked in our latest pre-print.
Turns out you can.
1/
www.medrxiv.org/content/10.1...
Untargeted longitudinal ultra deep metagenomic sequencing of wastewater provides a comprehensive readout of expected and unexpected viral pathogens
Wastewater surveillance has become a powerful tool to monitor circulating viruses at a community level. Currently, most wastewater surveillance efforts use target-based approaches such as quantitative...
www.medrxiv.org
October 31, 2025 at 12:19 PM
Can you take a quarter cup of composite sewage, simply ask ‘what’s in there?’, and find out all of the pathogens circulating in that community?
That is the question we asked in our latest pre-print.
Turns out you can.
1/
www.medrxiv.org/content/10.1...
That is the question we asked in our latest pre-print.
Turns out you can.
1/
www.medrxiv.org/content/10.1...
Spoke to a colleague last night about what works and doesn't in academic publishing. They were making a case that most work is done by the first and last author and so aside from network effects usually little cost shedding the rest of the list.
October 31, 2025 at 10:19 AM
Spoke to a colleague last night about what works and doesn't in academic publishing. They were making a case that most work is done by the first and last author and so aside from network effects usually little cost shedding the rest of the list.
Today I learnt about: # nolint next:
very handy
very handy
October 30, 2025 at 10:12 AM
Today I learnt about: # nolint next:
very handy
very handy
Reposted by Sam Abbott
I'm now also looking for a postdoc with strong Bayesian background and interest in developing Bayesian cross-validation theory, methods and software. Apply by email with no specific deadline (see contact information at users.aalto.fi/~ave/).
Others, please share
Others, please share
I'm looking for a doctoral student with Bayesian background to work on Bayesian workflow and cross-validation (see my publication list users.aalto.fi/~ave/publica... for my recent work) at Aalto University.
Apply through the ELLIS PhD program (dl October 31) ellis.eu/news/ellis-p...
Apply through the ELLIS PhD program (dl October 31) ellis.eu/news/ellis-p...
ELLIS PhD Program: Call for Applications 2025
The ELLIS mission is to create a diverse European network that promotes research excellence and advances breakthroughs in AI, as well as a pan-European PhD program to educate the next generation of AI...
ellis.eu
October 29, 2025 at 2:37 PM
I'm now also looking for a postdoc with strong Bayesian background and interest in developing Bayesian cross-validation theory, methods and software. Apply by email with no specific deadline (see contact information at users.aalto.fi/~ave/).
Others, please share
Others, please share
Reposted by Sam Abbott
in my post-academic era i have become extremely scathing of the way academia considers papers to the primary outcome of intellectual work, and refuses to give credit to academics who write software or build other tooling. in industry we very rarely read your papers; but we always use your software
October 28, 2025 at 2:15 AM
in my post-academic era i have become extremely scathing of the way academia considers papers to the primary outcome of intellectual work, and refuses to give credit to academics who write software or build other tooling. in industry we very rarely read your papers; but we always use your software
Reposted by Sam Abbott
From @torstenseemann.bsky.social at @pha4ge.bsky.social Conference; "We are stealing from research money to support public health."
We need dedicated funding for maintaining & supporting public health infrastructure & pipelines. Not just startup, not just in pandemics.
We need dedicated funding for maintaining & supporting public health infrastructure & pipelines. Not just startup, not just in pandemics.
October 28, 2025 at 8:52 AM
From @torstenseemann.bsky.social at @pha4ge.bsky.social Conference; "We are stealing from research money to support public health."
We need dedicated funding for maintaining & supporting public health infrastructure & pipelines. Not just startup, not just in pandemics.
We need dedicated funding for maintaining & supporting public health infrastructure & pipelines. Not just startup, not just in pandemics.
Reposted by Sam Abbott
In the past 2 weeks several European countries have reported locally acquired cases of #mpox clade Ib.
This is new. There had been patients before but those infections likely happened elsewhere.
Now it looks like mpox Ib is spreading here in the sexual networks of men who have sex with men.
#IDsky
This is new. There had been patients before but those infections likely happened elsewhere.
Now it looks like mpox Ib is spreading here in the sexual networks of men who have sex with men.
#IDsky
October 24, 2025 at 12:21 PM
This was making me think if anyone has a favourite paper on resource use to write grants / resource from getting the grant.
Here where the timelines and amounts are small but the numbers applying are quite large I wonder how close it works out.
Here where the timelines and amounts are small but the numbers applying are quite large I wonder how close it works out.
For context SSI had 10-20 more post screening applications than it could fund: A
www.software.ac.uk/news/researc...
www.software.ac.uk/news/researc...
Research Software Maintenance Fund: Expressions of Interest Outcomes and Next Steps | Software Sustainability Institute
A total of 360 applications were received for Round 1 of the RSMF, of which 172 were for the large awards and 188 were for small awards.
www.software.ac.uk
October 24, 2025 at 10:07 AM
This was making me think if anyone has a favourite paper on resource use to write grants / resource from getting the grant.
Here where the timelines and amounts are small but the numbers applying are quite large I wonder how close it works out.
Here where the timelines and amounts are small but the numbers applying are quite large I wonder how close it works out.
Apart from the recent SSI grant call in the UK and the essential software grants from CZ (which I think have now paused been redirected to AI) what other mechanisms do people use to support ongoing software development/maintence?
October 24, 2025 at 9:56 AM
Apart from the recent SSI grant call in the UK and the essential software grants from CZ (which I think have now paused been redirected to AI) what other mechanisms do people use to support ongoing software development/maintence?
Reposted by Sam Abbott
Anyone with a lower h-index than me is ineffectual, while anyone with a higher h-index is just better at playing the game and cutting corners. I'm sorry, that's just how numbers work!
I am completely against the use of citation metrics to evaluate scientists. But if your h-index is less than mine, you kinda have do what I say. I don't make the rules.
October 24, 2025 at 8:23 AM
Anyone with a lower h-index than me is ineffectual, while anyone with a higher h-index is just better at playing the game and cutting corners. I'm sorry, that's just how numbers work!
Reposted by Sam Abbott
Opportunity for UK based PhD students to spend 3 months in the Infectious Disease modelling team at UKHSA. It's a great chance to see how modelling is used in public health decision making. If your interested see below for more details:
gateway.newton.ac.uk/media/news/u...
gateway.newton.ac.uk/media/news/u...
UKHSA PhD Student Internships - Newton Gateway to Mathematics
gateway.newton.ac.uk
October 20, 2025 at 10:18 AM
Opportunity for UK based PhD students to spend 3 months in the Infectious Disease modelling team at UKHSA. It's a great chance to see how modelling is used in public health decision making. If your interested see below for more details:
gateway.newton.ac.uk/media/news/u...
gateway.newton.ac.uk/media/news/u...
#epinowcast 0.4.0 is out! This release has been a long time coming and contains work from many contributors. It includdes new features, better better and clearer documentation.
package.epinowcast.org/news/index.h...
package.epinowcast.org/news/index.h...
Changelog
package.epinowcast.org
October 17, 2025 at 3:10 PM
#epinowcast 0.4.0 is out! This release has been a long time coming and contains work from many contributors. It includdes new features, better better and clearer documentation.
package.epinowcast.org/news/index.h...
package.epinowcast.org/news/index.h...
Reposted by Sam Abbott
sensational energy here
October 17, 2025 at 9:21 AM
sensational energy here
Great times today listening to Aphex Twin and running 8 claude code agents in parallel across different tasks. Did I get more work done? Likely no. Did I feel like I was living in the future? Maybe except they apparently spell very badly in the future.
October 10, 2025 at 4:27 PM
Great times today listening to Aphex Twin and running 8 claude code agents in parallel across different tasks. Did I get more work done? Likely no. Did I feel like I was living in the future? Maybe except they apparently spell very badly in the future.
Reposted by Sam Abbott
A nice thread highlighting key findings from our new paper estimating parameters of #HPAI in subsequent outbreaks in common terns. We developed a Bayesian inference approach to infer parameters from just carcass counts. #seabirds #statisticalecology #diseaseecology
doi.org/10.1111/1365...
doi.org/10.1111/1365...
October 9, 2025 at 10:35 AM
A nice thread highlighting key findings from our new paper estimating parameters of #HPAI in subsequent outbreaks in common terns. We developed a Bayesian inference approach to infer parameters from just carcass counts. #seabirds #statisticalecology #diseaseecology
doi.org/10.1111/1365...
doi.org/10.1111/1365...
Reposted by Sam Abbott
We're really excited to announce the first awardees of the new JUNIPER fellowship scheme focused on supporting ECRS: @kathsherratt.bsky.social @joebhilton.bsky.social & @emiliefinch.bsky.social . Find out more about our new fellows here: maths.org/juniper/arti...
JUNIPER welcomes first awardees of new fellowship scheme focused on supporting early career researchers | Juniper
Three promising early career researchers from the JUNIPER partnership have been awarded fellowships as part of a new scheme recognising their role in our network and their potential to make a signific...
maths.org
October 9, 2025 at 9:53 AM
We're really excited to announce the first awardees of the new JUNIPER fellowship scheme focused on supporting ECRS: @kathsherratt.bsky.social @joebhilton.bsky.social & @emiliefinch.bsky.social . Find out more about our new fellows here: maths.org/juniper/arti...