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
adams-prize
Code to accompany Adams Prize paper
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
llm-api-scripts
Scripts for interface with common LLM APIs in R
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/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/llm-api-scripts
Scripts for interface with common LLM APIs in R
adamkucharski/sir-multi-population
Simple multi-population SIR model
adamkucharski/adams-prize
Code to accompany Adams Prize paper
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/covid-import-model
Modelling variant importations
adamkucharski/seroshiny
Package for shiny dashboards for serological data
adamkucharski/epiexport
Calculating local epidemic size from exported cases
adamkucharski/epiparameter
R package with library of epidemiological parameters for infectious diseases and functions and classes for working with parameters
adamkucharski/rjmcmc_methods
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/covidm_shiny2
COVID-19 transmission model Shiny app, version 2
adamkucharski/EpiNow2
Estimate Realtime Case Counts and Time-varying Epidemiological Parameters
adamkucharski/epiverse-llm
Concept for LLM interface to Epiverse packages
adamkucharski/mobility_models
Common mobility models
adamkucharski/pl-testing
Accompanying code for: Kucharski AJ, Russell TW, Hellewell J et al. SARS-CoV-2 Dynamics in the Premier League Testing Program, United Kingdom. Emerg Infect Dis. 2024
adamkucharski/proof
TBC
adamkucharski/quickfit
Simple parameter estimation functions
adamkucharski/redirect-index
HTML index page that redirects to a custom blog post
adamkucharski/ringbp
adamkucharski/serogam
Non-parameteric estimation of dynamics from serological data
adamkucharski/simex
Simulating epidemics and interventions
adamkucharski/subcritical_chains
Accompanying code for: Kucharski AJ, Edmunds WJ. PLOS Comput Biol 2015
adamkucharski/test-shiny
Sandbox shiny app
adamkucharski/timedepeff_test