Reproducibility using R

#rmarkdown #data science #reproducibility

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. ...

A primer on statistical outbreak analysis

#epicurve #delays #reproduction number #forecasting

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. ...

Introduction to phylogenetics

#genetics #evolution

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. ...

Outbreak investigation using outbreaker2

#reconstruction #outbreaker2

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

Basic Concepts on Vector Borne Disease Modelling

#vdb #malaria #chagas #zika

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