Lectures

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. ...

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 R. Slides Click on the image below to access the slides: Related packages knitr knitr provides excellent resources for literate programming mixing R with LaTeX or markdown. ...

Beyond the availability of data and methods, and the use of good practices for reproducible science, the outbreak response context poses a number of practical challenges for data analysis. In this lecture, we introduce tools which can help address some of these challenges, and create robust, efficient, and more easily deployable data analytics pipelines using R. Slides Click on the image below to access the slides: Alternatively, you can view these slides directly on google slides. ...

This short lecture explores the methodologies to produce short term projections of incidence based on estimated transmissibility of a pathogen. It covers various aspects around projections, forecasting and predictions. 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. ...

Collection of miscellaneous slides This is a collection of short slide decks on various topics, too short to form a lecture, but useful every now and then. Why use R Click on the image below to access the slides: Introduction to R Click on the image below to access the slides: Importing data into R Click on the image below to access the slides: ...

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. ...