Lectures

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 lecture is about Vector Borne Diseases (VBD) modelling. The aim is to gain a general understanding on the role of modelling on the main vector borne diseases, with special enphasis on Malaria, Chagas and Zika. Slides Click on the image below to access the slides: About this document Contributors Zulma Cucunuba & Pierre Nouvellet: initial version Contributions are welcome via pull requests. Legal stuff License: CC-BY Copyright: Zulma Cucunuba & Pierre Nouvellet, 2017

This short lecture gives a primer on how modelling can help inform public health response. It focuses on few examples where modelling has been used to integrate various types of information and help implement control or raise situational awarness. Slides Click on the image below to access the slides: About this document Contributors Pierre Nouvellet: initial version Contributions are welcome via pull requests. The source file can be found here. ...

This short lecture gives a primer in building compartmental models. It covers various aspects around epidemiological modelling such as flow diagrams, writing ordinary differential equations and reproduction number. The example of the dynamics of Ebola is used. Slides Click on the image below to access the slides: About this document Contributors Pierre Nouvellet: initial version Contributions are welcome via pull requests. The source file can be found here. ...

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. ...