Compartmental model, example for Ebola

#modelling #ebola #compartmental models

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. ...

VBD: building a simple model for Zika

#zika #compartmental models

This practical aims to illustrate the basics of vector borne disease (VBD) modelling using R, with an emphasis on how the methods work. We will use a basic model for an arboviral infection as an example. In this practical we will begin by gaining some understanding of the components which contribute to R0 and how potential interventions influence transmission. Later in the practical you will construct a model of Zika transmission to look at the effects of several parameters. ...

Ebola: building few models for Ebola

#ebola #compartmental models

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. ...

Phylogenetic tree reconstruction

#genetics #evolution #influenza

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. ...