Adam Kucharski

2020-ncov. Accompanying code for: Kucharski AJ, Russell TW et al. Early dynamics of transmission and control of COVID-19: a mathematical modelling study. Lancet Infectious Diseases, 2020

pdf2plot. Extract raw underlying data from PDF figures in the browser

scrapR. Extract raw underlying data from PDF figures

rules-of-contagion. Code and data to accompany The Rules of Contagion

2020-cov-tracing. Accompanying code for: Kucharski AJ, Klepac P et al. Effectiveness of isolation, testing, contact tracing, and physical distancing on reducing transmission of SARS-CoV-2 in different settings: a mathematical modelling study. Lancet Infectious Diseases, 2020

llm-api-scripts. Scripts for interface with common LLM APIs in R

CAPphrase. Comparative and Absolute Probability phrase dataset

hit-analysis. Accompanying code for: Hodgson D et al. The potential for vaccination-induced herd immunity against the SARS-CoV-2 B.1.1.7 variant. Eurosurveillance, 2020

sir-multi-population. Simple multi-population SIR model

digital-twin-example. Simulated public opinion survey responses using LLM-generated distributions

ebola-cfr. Accompanying code for: Kucharski et al, Lancet, 2014

adams-prize. Code to accompany Adams Prize paper

contagion-review. Review paper: Contagion dynamics in real-life and digital settings

fiji-denv3-2014. Accompanying code for: Kucharski AJ, Kama M et al. Using paired serology and surveillance data to quantify dengue transmission and control during a large outbreak in Fiji. eLife, 2018

reducing-uncertainty. Accompanying code for: Kucharski AJ, Riley S. Lancet Infect Dis. 2016

seroshiny. Package for shiny dashboards for serological data

covid-import-model. Modelling variant importations

2020-cov-test-frequency. Analysis of screening tests for SARS-CoV-2

proof. Code to accompany Proof: The Uncertain Science of Certainty

flu-model. Accompanying code for: Kucharski AJ et al. Timescales of influenza A/H3N2 antibody dynamics. PLOS Biology, 2018

serogam. Non-parameteric estimation of dynamics from serological data

epiexport. Calculating local epidemic size from exported cases

school-networks-15. Accompanying code for: Kucharski AJ, Wenham C et al. Structure and consistency of self-reported social contact networks in British secondary schools. PLOS ONE, 2018

real-time. Real-time reproduction number estimation

SIRfinalsize. Calculate final epidemic size in a heterogeneously mixing population

redirect-index. HTML index page that redirects to a custom blog post