Sam Abbott (@[email protected])

Real-time infectious disease modelling. Developing methods for outbreak response, surveillance, and pandemic preparedness.

[Sam Abbott (@[email protected]) @seabbs]

We started this with the aim to provide both decision-makers and the general public with real-time information on how the epidemic was progressing

So was it useful? Hard to tell.

https://t.co/ScI1H4p0cq

[Sam Abbott (@[email protected]) @seabbs]

@epinowcast @FoxandtheFlu Woops this is next week!

[Epinowcast @epinowcast]

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

https://t.co/ciY7U5yAWD

[Sam Abbott (@[email protected]) @seabbs]

Modelling epidemiological delays being useful

https://t.co/AcWPwgcUKx
Some nice work from folks at the CFA CDC and partners

[Sam Abbott (@[email protected]) @seabbs]

I also enjoyed talking through the last five years of thinking about situational awareness. Slides are here with lots of links out.

https://t.co/KdoPZk2t02

I had some good feedback that people enjoyed the focus on mistakes so planning to keep making plenty more.

[Sam Abbott (@[email protected]) @seabbs]

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]) @seabbs]

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 https://t.co/zZMi0BUi8h or come along to our course next June in Stockholm.

[Epinowcast @epinowcast]

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

https://t.co/GatVB6ewJ4

[Sam Abbott (@[email protected]) @seabbs]

primarycensored #rstats 📦 is now on CRAN and stable.

https://t.co/fNYlEhEIxz

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.

[Sam Abbott (@[email protected]) @seabbs]

@nikosbosse We is doing a lot of work here Nikos…

[Sam Abbott (@[email protected]) @seabbs]

If anyone finds this tooling useful and has ideas about developments models I would love to hear them.

[Sam Abbott (@[email protected]) @seabbs]

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.

[Nikos Bosse @nikosbosse]

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.
https://t.co/sxvygzDdeq

[Sam Abbott (@[email protected]) @seabbs]

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.

[Nikos Bosse @nikosbosse]

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.
https://t.co/sxvygzDdeq

[Sam Abbott (@[email protected]) @seabbs]

This will all soon be supported epidist to allow even more efficient, flexible, and accurate delay estimation at scale

https://t.co/IsRpjscjun

[Sam Abbott (@[email protected]) @seabbs]

Woo! Really good reviews on this have really improved it I think. Check it out if estimating or working with delay distributions in epi.

[Kelly Charniga, PhD MPH @kcharniga]

Publication day for my first perspective piece 🎉 Lucky to have worked with such great collaborators on this project 🤩 Read it here: https://t.co/8Xs4BGNvnL @institutpasteur

[Sam Abbott (@[email protected]) @seabbs]

If you want to implement some of the ideas from this work primarycensored just hit CRAN (Julia to follow soon)

https://t.co/fNYlEhEIxz

[Sam Abbott (@[email protected]) @seabbs]

(though I should probably stop doing all of this and write some grants instead...)

[Sam Abbott (@[email protected]) @seabbs]

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!

[Sam Abbott (@[email protected]) @seabbs]

Okay, I hear you Sam being Bayesian is cool but what if like I just don't want to be right now?

https://t.co/H06b6DzjCB

(fit primary censored and truncated distributions using fitdistrplus)