Pinned Repositories
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
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
contagion-review
Review paper: Contagion dynamics in real-life and digital settings
ebola-cfr
Accompanying code for: Kucharski et al, Lancet, 2014
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
rules-of-contagion
Code and data to accompany The Rules of Contagion
scrapR
Extract raw underlying data from PDF figures
sir-multi-population
Simple multi-population SIR model
epiparameter
R package with library of epidemiological parameters for infectious diseases and functions and classes for working with parameters
serosolver
Inference framework for serological data
adamkucharski's Repositories
adamkucharski/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
adamkucharski/scrapR
Extract raw underlying data from PDF figures
adamkucharski/rules-of-contagion
Code and data to accompany The Rules of Contagion
adamkucharski/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
adamkucharski/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
adamkucharski/sir-multi-population
Simple multi-population SIR model
adamkucharski/contagion-review
Review paper: Contagion dynamics in real-life and digital settings
adamkucharski/ebola-cfr
Accompanying code for: Kucharski et al, Lancet, 2014
adamkucharski/2020-cov-test-frequency
Analysis of screening tests for SARS-CoV-2
adamkucharski/covid-import-model
Modelling variant importations
adamkucharski/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
adamkucharski/epiexport
Calculating local epidemic size from exported cases
adamkucharski/flu-model
Accompanying code for: Kucharski AJ et al. Timescales of influenza A/H3N2 antibody dynamics. PLOS Biology, 2018
adamkucharski/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
adamkucharski/SIRfinalsize
Calculate final epidemic size in a heterogeneously mixing population
adamkucharski/claudeR
An R package for interacting with Anthropic's API
adamkucharski/covidhm
adamkucharski/EpiNow2
Estimate Realtime Case Counts and Time-varying Epidemiological Parameters
adamkucharski/epiverse-llm
Concept for LLM interface to Epiverse packages
adamkucharski/ncov-cfr
R code and documentation to estimate case fatality ratio of 2019-nCoV from cases outside China
adamkucharski/outbreaks
outbreaks: an R package compiling disease outbreak data
adamkucharski/pcr-profile
adamkucharski/perceptions
Perceptions of Probability and Numbers
adamkucharski/quickfit
Simple parameter estimation functions
adamkucharski/ringbp
adamkucharski/Rsero
A R package to estimate the annual force of infection using serological data
adamkucharski/subcritical_chains
Accompanying code for: Kucharski AJ, Edmunds WJ. PLOS Comput Biol 2015
adamkucharski/test-shiny
Sandbox shiny app
adamkucharski/timedepeff_test
adamkucharski/tti-explorer
Simulation software for exploring test, trace and isolate strategies