Ebola simulation part 1: early outbreak assessment

#simulation #response #ebola #epicurve #reproduction number

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. ...

Ebola simulation part 2: outbreak reconstruction

#genetics #simulation #response #outbreaker2 #epicurve #reproduction number #ebola

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. ...

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. ...

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. ...