jrcpulliam

reinfections

SARS-CoV-2 reinfection trends in South Africa: analysis of routine surveillance data (Pulliam et al. 2021)

AEID

Scripts for use in Applied Ecology of Infectious Diseases (ZOO 4926/6927)

covid19za

COVID 19 Data and Dashboard for South Africa

dataviz

A book covering the fundamentals of data visualization

EbolaVaccPowerSL

Repository for Bellan et al. (2015). The statistical power and validity of Ebola vaccine trials in Sierra Leone: A simulation study of trial design and analysis. Lancet Infectious Diseases.

EbolaVaccSim

epitrix

Small Helpers and Tricks for Epidemics Analysis

epuRate

A clean R Markdown template for your reports

flexiweeks

R packages for

Folder-Structure-Conventions

Folder / directory structure options and naming conventions for software projects

github-for-developers-7

github-for-developers-8

github-workflow-13

godata

Public repo for sharing API and data cleaning/analysis scripts

helloworldpkg

Hello world package (SEAMS Day 3 practical)

HH_Transmission_Model

Codes for analysing household data from an RSV outbreak in rural coastal Kenya.

hostjumps

Code repository for Pulliam & Dushoff 2009 JID

incidence

☣:chart_with_upwards_trend::chart_with_downwards_trend:☣ Compute and visualise incidence

LLsim

Line list simulator for use in testing and practicing outbreak analysis

minimal

Minimal is a Jekyll theme for GitHub Pages

ncov-cfr

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

notebook

ogrants

Open grants list

outbreaks

outbreaks: an R package compiling disease outbreak data

reconhub.github.io

Official website for RECON - The R Epidemics CONsortium

recontools

Tools to develop RECON packages

scratch

ShinyDeveloperConference

Materials collected from the First Shiny Developer Conference Palo Alto, CA January 30-31 2016

SIR_model_family

spilloverIntervention

Ecological interventions to prevent and manage pathogen spillover (Sokolow et al.)