In this article we explain how to contribute new posts and slidedecks for the website. General workflow for contributing If you’re new to git and GitHub check out this nifty guide. The general workflow would include the following steps: Fork the project from the GitHub RECON learn project: This will create a copy of the project in your own GitHub account. You will need to clone this archive, and make the modifications there. ...

This practical simulates the early assessment and reconstruction of an Ebola Virus Disease (EVD) outbreak. It introduces various aspects of analysis of the early stage of an outbreak, including contact tracing data, epicurves, growth rate estimation from log-linear models, and more refined estimates of transmissibility. A follow-up practical will provide an introduction to transmission chain reconstruction using outbreaker2. A novel EVD outbreak in Ankh, Republic of Morporkia A new EVD outbreak has been notified in the small city of Ankh, located in the Northern, rural district of the Republic of Morporkia. ...

Motivation At which time point during an outbreak of a person-to-person transmitted disease can one declare the outbreak as having ended? Answering this question can be important in order to calm the population, re-attract tourists, stop export bans or reduce alertness status. The current WHO method for answering the above question is as follows: a period of two times the longest possible incubation time needs to pass without observing additional cases, before the outbreak can be declared as being over. ...

This practical is the second part of the response to a simulated Ebola Virus Disease (EVD) outbreak taking place in the city of Ankh, Republic of Morporkia. While the first part focussed on early assessments of transmissibility, this part explores more methodological options for estimating transmissibility, and provides an introduction to outbreak reconstruction using outbreaker2. An update on the EVD outbreak in Ankh, Republic of Morporkia After some rather concerning preliminary results on the new EVD outbreak in the city of Ankh, Republic of Morporkia, Public Health Morporkia (PHM) has sent you updates of the linelists and contact data. ...

This lecture introduces general concepts pertaining to phylogenetic tree reconstruction, as well as the main approaches used for building trees, including distance-based, maximum parsimony, and maximum likelihood methods. It also discusses phylogenetic uncertainty, bootstrap, and some caveats and bad practices. Slides Click on the image below to access the slides: About this document Contributors Thibaut Jombart: initial version Contributions are welcome via pull requests. The source files of this lecture can be found here. ...

This short lecture gives a primer on some methodological aspects of outbreak reconstruction using outbreaker2. Slides Click on the image below to access the slides: About this document Contributors Thibaut Jombart: initial version Finlay Campbell: figure on *outbreaker2*’s contact model Contributions are welcome via pull requests. The source file can be found here. Legal stuff License: CC-BY Copyright: Thibaut Jombart, 2017