Thibaut Jombart

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

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. ...

This short lecture gives a primer on some methodological aspects of outbreak analysis. It includes content on the estimation of key delays (e.g. incubation period, serial interval) and the characterisation of the underlying distributions, the estimation of growth rates, doubling times, of the basic reproduction number and simple short-term forecasting. Slides Click on the image below to access the slides: About this document Contributors Thibaut Jombart: initial version Contributions are welcome via pull requests. ...

Beyond the availability of data and methods, reproducible science requires the traceability of analyses. Whether it is for yourself or for collaborators, as series of tools and good practices can facilitate your work flow, simplify analyses, and prevent the loss of data and results. This lecture provides an introduction to reproducibility using . Slides Click on the image below to access the slides: Related packages knitr knitr provides excellent resources for literate programming mixing with LaTeX or markdown. ...