Sam Abbott Profile picture
19 Apr, 12 tweets, 7 min read
1/10 Since October @ftargument has been running a crowd forecasting project for #COVID19. First in Germany and Poland and now in all ECDC nations + the United Kingdom.

You can contribute your forecasts here: cmmid-lshtm.shinyapps.io/crowd-forecast/ Image
2/10 We submit an ensemble of these forecasts to the ECDC forecast hub where they are combined with many other models from other forecasters and evaluated.

covid19forecasthub.eu/visualisation Image
3/10 This crowd forecasting method has been found to perform well compared to models submitted by multiple groups and to be one of the only methods to produce useful forecasts at longer time horizons.

medrxiv.org/content/10.110…
4/10 If you submit a forecast you can review your performance vs other forecasters (and several model based forecasts produced by our group) either in a weekly email or in this report.

epiforecasts.io/europe-covid-f… Image
5/10 For example, at the moment I am outperforming the ensemble but forecast deaths less well than cases. Importantly, I outperform @sbfnk and so look set for promotion (😅). Image
6/10 You can also compare the performance of the combined crowd forecast vs all other submissions to the ECDC hub. The crowd forecast (EpiExpert) is currently performing quite well vs other forecasters.

covid19forecasthub.eu/reports Image
7/10 @ftargument is currently working on new methods of crowd forecasting. One of these is an exciting combination of a model based forecast (using #EpiNow2) augmented with crowd opinion. This is a WIP but see more here:

cmmid-lshtm.shinyapps.io/crowd-rt-forec… Image
8/10 If interested in submitting @ftargument has put together this video tutorial.

9/10 This project is implemented in #rstats using #shiny and @mcmc_stan. All the backend code is #OpenSource and available here:

github.com/epiforecasts/e…

All the underlying code is packaged and available for use by other groups. #openscience
10/10 As a modeller I have found participating in this routinely extremely helpful as a way of evaluating my own assumptions about infectious disease transmission. I'm looking forward to building these insights into my next generation of tools.
We are currently writing up our evaluation of the forecasts submitted to German/Poland forecast hub but hope to use these insights to improve our ensembling of crowd forecasts going forwards.

kitmetricslab.github.io/forecasthub/fo…

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More from @seabbs

9 Aug 19
1. PhD thesis 'Modelling BCG vaccination in the UK: What is the impact of changing policy?' submitted and everything is totally normal....

Written with #rstats, #bookdown, and #thesisdown.

Read here: bit.ly/seabbs-thesis

#phdchat #epitwitter #openscience #tuberculosis
2. Thanks to my supervisors @n3113n and @Christensen_H + my funders @HPRU_EI + @PHE_uk for the data.
3. Some results: 'getTBinR: an R package for accessing and summarising the World Health Organisation Tuberculosis data'

Code: github.com/seabbs/getTBinR

Paper: doi.org/10.21105/joss.…

#getTBinR
Read 13 tweets
1 Aug 19
1. First release of {#idmodelr} is now on CRAN. {idmodelr} is a library of #infectiousdisease models and utilities for using them. Use case is exploration/education/research + signposting.

bit.ly/idmodelr

#rstats #epitwitter #dynamics #opensource #openscience
2. Current status is WIP with more features - and additional models - planned. Contributions much appreciated!

Planned features: github.com/seabbs/idmodel…
3. {#idmodelr} has an accompanying #shiny app that demos some of the functionality and can be used as a standalone tool for exploring infectious disease models.

See here: github.com/seabbs/explore…
Read 9 tweets
9 Jul 19
1. New (first) paper now available: Exploring the effects of BCG #vaccination in patients diagnosed with #tuberculosis: Observational study using the Enhanced Tuberculosis Surveillance system

Paper: doi.org/10.1016/j.vacc…
Preprint: doi.org/10.1101/366476

#phdchat #rstats
2. Highlights

Evidence of an association between BCG vaccination and reduced all-cause mortality in TB cases.

Weaker evidence of an association between BCG vaccination and reduced repeat TB episodes in TB cases.

Little evidence of an association with other TB outcomes.
3. Background: Bacillus Calmette–Guérin (BCG) is one of the most widely-used vaccines worldwide. BCG primarily reduces the progression from infection to disease, however, there is evidence that BCG may provide additional benefits.
Read 7 tweets

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