adamkucharski Goto Github PK

2020-cov-test-frequency

Analysis of screening tests for SARS-CoV-2

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

antigenic-evo

Accompanying code for: Kucharski AJ, Baguelin M. PLOS Path 2017

clauder

An R package for interacting with Anthropic's API

contagion-review

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

covid-import-model

Modelling variant importations

covidhm

covidm_shiny2

COVID-19 transmission model Shiny app, version 2

ebola-cfr

Accompanying code for: Kucharski et al, Lancet, 2014

epiexport

Calculating local epidemic size from exported cases

epinow2

Estimate Realtime Case Counts and Time-varying Epidemiological Parameters

epiparameter

R package with library of epidemiological parameters for infectious diseases and functions and classes for working with parameters

epiverse-llm

Concept for LLM interface to Epiverse packages

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

flu-model

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

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

mobility_models

Common mobility models

ncov-cfr

R code and documentation to estimate case fatality ratio of 2019-nCoV from cases outside China

outbreaks

outbreaks: an R package compiling disease outbreak data

pcr-profile

perceptions

Perceptions of Probability and Numbers

pl-testing

Analysis of testing data

quickfit

Simple parameter estimation functions

real-time

Real-time reproduction number estimation

redirect-index

HTML index page that redirects to a custom blog post

reducing-uncertainty

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

ringbp