Epiforecasts

A research group @lshtm working on the real-time modelling and forecasting of infectious disease dynamics.

[Epiforecasts @epiforecasts]

Some reflections on our work estimating effective reproduction numbers daily for the last two years.

[Sebastian Funk (@[email protected]) @sbfnk]

In early 2020 ago we put together a dashboard for tracking SARS-CoV-2 globally. Next week we'll update the estimates for the last time. Here we reflect on their utility, unanticipated challenges, and finally whether we would do it again. With @seabbs. https://t.co/luRA6oM7RG

[Sebastian Funk (@[email protected]) @sbfnk]

And if R programming is your thing you should also consider this Research Software Engineer post https://t.co/llRiytitf2 @RStatsJobsBot @RStatsJobs

[IDDjobs: infectious disease dynamics jobs @IDDjobs]

Postdoc (London, United Kingdom)
Real-time outbreak modelling and forecasting
with @sbfnk
at @epiforecasts @cmmid_lshtm
More details: https://t.co/0nfVtIyhZR

[Sebastian Funk (@[email protected]) @sbfnk]

📢Three jobs available in the @epiforecasts group @cmmid_lshtm @LSHTM, working on broad topics in real-time modelling for decision making in infectious disease outbreaks.
https://t.co/W2lkM2Z4Cu
https://t.co/kqhQjeB5jb

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

{epinowcast} 0.1.0 📦 now live on main. 🎉🥳🍾

In this release, we focus on the user experience and prepare the ground for extensions enabling a range of real-time IDE questions to be answered.

PRs from: Adrian Lison, @sbfnk, and @seabbs

https://t.co/AaMJN8Zqvh

1/n

[Sophie Meakin @SophieMeakin]

🔍👀 Searching for users of the https://t.co/O7PjTxjU3n R package!🎁
Have you used the mapping between local authorities and NHS Trusts that is included in the package? If yes, I would LOVE to hear what you used it for, and if you’re still using it!
https://t.co/4XsoLoIErP 1/3

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

Interested in public health? Want to contribute to #rstats 📦 development?

We are working on {epinowcast} 0.1.0 and have some issues for you.

https://t.co/Q1coL83kdH

[Sophie Meakin @SophieMeakin]

In this week’s @epiforecasts group meeting, @grusonh got us chatting about contributing to #opensource projects on GitHub - why do it, how to contribute, and how we can encourage contributions to our own projects?👩🏻‍💻👨🏼‍💻
My takeaways ⤵️

[Epiforecasts @epiforecasts]

New analysis led by lab member @_akiraendo investigating the hypothesis that network effects might explain why this monkeypox outbreak looks so different from previous ones.

[akiraendo @_akiraendo]

Our monkeypox (MPX) analysis paper now out: https://t.co/Am9Sm06vnJ
Using a math model based on sexual partnership data in UK, we tried to explain the epidemiology of the current outbreak, which has shown a distinct pattern from the past outbreaks.

*Not yet peer-reviewed*

1/8

[Sebastian Funk (@[email protected]) @sbfnk]

It was an honour to present some @epiforecasts work at this event (if sad not to be there in person). Slides at https://t.co/6LH9R3y8SN

[Epiforecasts @epiforecasts]

Check out this #rstats package from lab member @nikosbosse for evaluating forecasts. We have made lots of use of this in the group already so it's exciting to share.

[Nikos Bosse @nikosbosse]

After more than 2 years of work I'm very happy to be able to share this new preprint & the CRAN release of scoringutils version 1.0.0, an R package that aims to make forecast evaluation in R simple and straightforward. 🥳 https://t.co/qZket7sizg 1/

[Sebastian Funk (@[email protected]) @sbfnk]

We’ve been investigating Ct values as a proxy for viral load of symptomatic (pillar 2) Covid-19 cases in England in the last 18 months. Work-in progress report (w/ @seabbs) at https://t.co/tf7OGyyvk9 and a few observations in this thread. 1/9

[Epiforecasts @epiforecasts]

We had a great presentation/discussion on time management systems in our last group meeting led by @Hannah_Choi_

In this thread, Hannah (in her first 🐦) summarises her thoughts on the bullet journal system and contrasts it with other approaches.

A must-read!

[Hannah Choi @Hannah_Choi_]

✏️ Bullet journals: are they a useful task management system for #ECR 👩‍🎓?

Here is a whistle-stop tour through my presentation at last week's @epiforecasts group meeting, where I made the case that ✅ YES, they are a real game-changer! 🧵(1/12)

Slides: https://t.co/ghTehHeop1

[Richard Martin-Nielsen @RMartinNielsen]

Thoughts here from @seabbs & @sbfnk (🧵) on @epiforecasts R(t) estimation dashboards.

I really liked being a small cog in one widget of this larger machine - and recognise the work it takes to manage volunteers. I appreciate that effort - tx also to @kathsherratt @joepgpalmer

[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

[Sebastian Funk (@[email protected]) @sbfnk]

Less than two weeks left to apply for these posts. This is an exciting project and I’d strongly encourage anyone with experience in software engineering (esp. using #rstats) and interested in helping prepare for future epidemics and pandemics to apply. Here's why: 1/8

[Imperial Patient Experience Research Centre (PERC) @Imperial_PERC]

Can humans beat computer models at predicting the spread of COVID-19?

As part of #BSW22 @nikosbosse shares findings from the UK COVID-19 Crowd Forecasting Challenge, a #citizenscience project inviting the public to predict #COVID19 infections & deaths ➡️https://t.co/w3tRsQdCQ8

[Sebastian Funk (@[email protected]) @sbfnk]

Registration now open (and free)

The endemic-epidemic framework is a great way to model infectious diseases, combining statistical and epi approaches. And it's implemented in an R package.

Find out all about it and applications to measles, covid etc in this hybrid workshop. 👇