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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 PDF slides (click the image below) PPTX slides (click the image below) About this document Contributors Pierre Nouvellet: initial version Contributions are welcome via pull requests. ...

This practical aims to illustrate the basics of Ebola modelling using R, with an emphasis on how the method works. We will start with a basic model for Ebola. We will then illustrate how to account for an evolving context, e.g. implementation of control measures. Finally, we will explore basic principle of model fitting. Core Concepts From the previous lecture, we will further develop these concepts: Compartmental models Flow diagrams and writing down a model Natural history of Ebola Control strategies Introduction to model fitting Required packages install. ...

This practical aims to illustrate the basics of phylogenetic reconstruction using R, with an emphasis on how the methods work, how their results can be interpreted, and the relative advantages and limitations of the methods. Three main classes of phylogenetic approaches are introduced, namely distance-based, maximum parsimony, and maximum likelihood methods. We also illustrate how to assess the reliability of individual nodes using bootstrap, and show how a simple linear model can be used to estimate a molecular clock in rooted phylogenies. ...