Sam Abbott (@[email protected]) @seabbs
Real-time infectious disease modelling. Developing methods for outbreak response, surveillance, and pandemic preparedness. https://t.co/qIESZxy6rY samabbott.co.uk Bristol, England Joined October 2015-
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@epinowcast @FoxandtheFlu Woops this is next week!
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Sam Abbott (@[email protected]) retweeted
For this weeks #epinowcast seminar (Weds at 3pm UK time (10 am ET)) we have @foxandtheflu.bsky.social talking about Optimizing disease outbreak forecast ensembles and the use of microHubs epinowcast.org/seminars/2024-…
Modelling epidemiological delays being useful cdc.gov/mmwr/volumes/7… Some nice work from folks at the CFA CDC and partners
I also enjoyed talking through the last five years of thinking about situational awareness. Slides are here with lots of links out. samabbott.co.uk/presentations/… I had some good feedback that people enjoyed the focus on mistakes so planning to keep making plenty more.
We had a massive turn out at our understanding and evaluating forecasting workshop which was great and left me with some things to think about on the flight home. If you missed it the material is here nfidd.github.io/ueifid/ or come along to our course next June in Stockholm.
Really enjoyed the first IDM conference in Thailand! Some great talks and a great way to meet a whole lot of new folks at once.
Sam Abbott (@[email protected]) retweeted
Seminar today at 3pm UK time with Matthew Shin talking about: Quantifying regularity of COVID-19 epidemic waves in France to assess predictability of future waves and improve forecasting epinowcast.org/seminars/2024-…
primarycensored #rstats 📦 is now on CRAN and stable. primarycensored.epinowcast.org If you want to use or estimate delay (think incubation periods, reporting delays, etc.) distributions in epi it might be worth checking out. A #julia version is in development.
@nikosbosse We is doing a lot of work here Nikos…
If anyone finds this tooling useful and has ideas about developments models I would love to hear them.
This sort of work is really badly incentivised in academia especially the long term maintenance. Very little change appears to be happening on that. It’s also not really possible in places like public health agencies despite ongoing efforts to change this.
An absolutely huge amount of work from @nikosbosse on this starting before his PhD and continuing completely through it to now as a side project to his full time ai startup gig. Great job handling inputs from lots of people whilst learning on the job.
Happy to share that we FINALLY published version 2.0.0 of scoringutils on CRAN. scoringutils is an R package designed to facilitate the evaluation of forecasts. It operates on data.table, is very slick and has a lot of visualisations and extra features. epiforecasts.io/scoringutils/
Sam Abbott (@[email protected]) retweeted
Happy to share that we FINALLY published version 2.0.0 of scoringutils on CRAN. scoringutils is an R package designed to facilitate the evaluation of forecasts. It operates on data.table, is very slick and has a lot of visualisations and extra features. epiforecasts.io/scoringutils/
This will all soon be supported epidist to allow even more efficient, flexible, and accurate delay estimation at scale epidist.epinowcast.org/articles/epidi…
If you want to implement some of the ideas from this work primarycensored just hit CRAN (Julia to follow soon) primarycensored.epinowcast.org
Woo! Really good reviews on this have really improved it I think. Check it out if estimating or working with delay distributions in epi.
Publication day for my first perspective piece 🎉 Lucky to have worked with such great collaborators on this project 🤩 Read it here: journals.plos.org/ploscompbiol/a… @institutpasteur
(though I should probably stop doing all of this and write some grants instead...)
Woke up today and realised I had a big backlog of PRs to take a look at. Made me reflect and I've realised over the last few years that I've nearly moved away from writing code as my main form of software dev... feels weird!
Okay, I hear you Sam being Bayesian is cool but what if like I just don't want to be right now? primarycensored.epinowcast.org/articles/fitti… (fit primary censored and truncated distributions using fitdistrplus)
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