April 15

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.
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April 09

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.
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February 25

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.
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January 24

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.
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December 15

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.
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December 13

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
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December 13

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
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December 11

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.
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December 11

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.
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December 04

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.
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December 04

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.
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November 10

Beyond the availability of data and methods, reproducible science requires the traceability of analyses. Whether it is for yourself or for collaborators, as series of tools and good practices can facilitate your work flow, simplify analyses, and prevent the loss of data and results. This lecture provides an introduction to reproducibility using .
Slides Click on the image below to access the slides:
Related packages knitr knitr provides excellent resources for literate programming mixing with LaTeX or markdown.
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November 01

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.
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