A primer on statistical outbreak analysis

#epicurve #delays #uncertainty #variability #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. ...

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. ...

Tools for outbreak analytics infrastructures

#rmarkdown #data science #reproducibility #outbreak #response

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. ...

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. ...

Real-time outbreak analysis: Ebola as a case study - part 3

#simulation #response #ebola #epicurve #reproduction number

Introduction This practical is the third (and last) part of a practical which simulates the early assessment and reconstruction of an Ebola Virus Disease (EVD) outbreak. Please make sure you have gone through part 1 and part 2 before starting part 3. In part 3 of the practical, we give an introduction to transmission chain reconstruction using outbreaker2. Note: This practical is derived from earlier practicals called Ebola simulation part 1: early outbreak assessment and Ebola simulation part 2: outbreak reconstruction ...

Real-time outbreak analysis: Ebola as a case study - part 2

#simulation #response #ebola #epicurve #reproduction number

Introduction This practical is the second (out of three) part of a practical which simulates the early assessment and reconstruction of an Ebola Virus Disease (EVD) outbreak. Please make sure you have gone through part 1 before starting part 2. In part 2 of the practical, we introduce various aspects of analysis of the early stage of an outbreak, including growth rate estimation, contact tracing data, delays, and estimates of transmissibility. ...