Practicals

Introduction This tutorial is part of the pre-course materials of a “Short Course on Outbreak Analysis and Modelling for Public Health.” The aim is to introduce students to the very basic concepts of R and R Studio, in order to get some baseline knowledge in R and R programming. Installing R and R Studio R is a free software environment and RStudio is a free and open-source environment for working in R. ...

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 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. ...