Sam Abbott Profile picture
Research Fellow in real-time modelling @cmmid_lshtm. Member of https://t.co/2qRs8dfVuV.
19 Apr
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…
Read 12 tweets
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