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Sam Abbott's Curriculum VitaegetTBinR
An R package for accessing and summarising the World Health Organisation Tuberculosis data.idmodelr
Infectious disease model library and utilitiesTweetRstudioCheatsheets
A Twitter bots which tweets a randomly selected Rstudio cheatsheet each daythesis
PhD thesis submitted to the University of Bristol. Title: Modelling BCG vaccination in the UK: What is the impact of changing policy?SpeedyMarkov
Speed up Discrete Markov Model Simulations.exploreidmodels
A shiny app which allows the exploration of the dynamics of a range of simple infectious disease modelsbadtobetter
Better computational practice - Bad to betterblogdown-site
Source code for my old personal websitetidyverse-gpu
Adding in support for GPU acceleration via CUDA to rocker/tidyverseCovidInterventionReview
Adoption and impact of non-pharmaceutical interventions for COVID-19personal-server
Setup for my personal serverDirectEffBCGPolicyChange
Estimating the effect of the 2005 change in BCG policy in England: A retrospective cohort studyprettypublisher
R package to help in formatting R markdown documents into a publishable formatcste-forecasting-workshop
An approachable introduction to estimating the effective reproduction number. It's meant for any and all levels of comfort with writing codeseabbs
Personal repositorybackup
Code to automate local backups of remote codeModelTBBCGEngland
Modelling Tuberculosis, including BCG vaccination, in Englandecdc-weekly-growth-forecasts
COVID-19 cases forecasts for the ECDC Forecast Hubepinowcast-fixed-reporting-example
An example of how to modify epinowcast to work with fixed reporting schedules.cmmid.stan.seir
An example SEIR model implemented in stanStackTweetBot
Tools for quickly and easily creating twitter StackOverflow botsExploreBCGOnOutcomes
Analysis to explore the association of BCG vaccination and TB outcomes.epict
ceplotr
Model agnostic cost effectiveness plottingETSMissing
Explore and evaluate the mechanisms for missing data in the Enhanced Tuberculosis Surveillance system.ShowMePerseus
A shiny app aiming to remove some of the potential friction for users of the rperseus packagecovid-climate-rt
Covid Rt estimates for evaluating the role of climatethepebblegame
The pebble game: A simple game that can be used to understand epidemics and vaccinationpresentations
A repository containing presentations that I have given or that I am in the process of writingtbinenglanddataclean
Cleans and Munges Tuberculosis and Demographic Data for EnglandEstZoonoticTB
Explore, Visualise and Estimate the Global Zoonotic Tuberculosis Burdenregional-secondary
Prototype function for forecasting a secondary observation from a primary observation across multiple regions. An example application of this function can be found here: https://github.com/epiforecasts/covid-german-forecasts/blob/master/rt-forecast/update-death-from-cases.R. See the documentation of EpiNow2 for more details: https://epiforecasts.io/EpiNow2/dev/Love Open Source and this site? Check out how you can help us