A research group @lshtm working on the real-time modelling and forecasting of infectious disease dynamics.
London
Joined January 2022
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Some reflections on our work estimating effective reproduction numbers daily for the last two years.
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. epiforecasts.io/posts/2022-0…
Epiforecasts retweeted
And if R programming is your thing you should also consider this Research Software Engineer post jobs.lshtm.ac.uk/Vacancy.asp… @RStatsJobsBot @RStatsJobs
5 more days to apply for a postdoc in my group. Short duration but potentially with opportunities for follow-up funding. Details at jobs.lshtm.ac.uk/Vacancy.asp…
Epiforecasts retweeted
Postdoc (London, United Kingdom)
Real-time outbreak modelling and forecasting
with @sbfnk
at @epiforecasts @cmmid_lshtm
More details: iddjobs.org/jobs/research-fe…
Epiforecasts retweeted
📢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.
jobs.lshtm.ac.uk/Vacancy.asp…
jobs.lshtm.ac.uk/Vacancy.asp…
Epiforecasts retweeted
{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
epiforecasts.io/epinowcast/n…
1/n
Epiforecasts retweeted
🔍👀 Searching for users of the covid19.nhs.data 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!
epiforecasts.io/covid19.nhs.… 1/3
Epiforecasts retweeted
Interested in public health? Want to contribute to #rstats 📦 development?
We are working on {epinowcast} 0.1.0 and have some issues for you.
github.com/epiforecasts/epin…
Epiforecasts retweeted
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 ⤵️
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.
Our monkeypox (MPX) analysis paper now out: medrxiv.org/content/10.1101/…
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
Epiforecasts retweeted
It was an honour to present some @epiforecasts work at this event (if sad not to be there in person). Slides at epiforecasts.io/talks/birs_2…
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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.
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. 🥳 arxiv.org/abs/2205.07090 1/
Epiforecasts retweeted
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 epiforecasts.io/covid19_ct_p… and a few observations in this thread. 1/9
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!
✏️ 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: tinyurl.com/bujo-for-ecr
Epiforecasts retweeted
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
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.
epiforecasts.io/posts/2022-0…
Epiforecasts retweeted
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.
epiforecasts.io/posts/2022-0…
Epiforecasts retweeted
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
📢Join our team!💫
We're recruiting 4 Research Software Engineers to develop open-source software for #epidemic preparedness & response as part of the #Epiverse initiative w @mrcunitgambia @DataDotOrg jobs.lshtm.ac.uk/vacancy.asp…
@rozeggo @sbfnk @AdamJKucharski @TeebzR @cmmid_lshtm
Epiforecasts retweeted
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 ➡️bit.ly/3i7tzhu
Epiforecasts retweeted
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. 👇
📣 Save the date!
@cmmid_lshtm are hosting a one-day workshop on the Endemic-Epidemic framework for infectious disease modelling.
📆 23 March
🗣️ @bastistician | @ClaudioFronterr | @johannesbracher | @cici_mydogisQQ | @AlastairMunro | @HeldLeonhard
🔗 bit.ly/34cHbon