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. ...

Methods for Short Term Projections in epidemics

#modelling #ebola #forecasting

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. ...

TB: exploring the case of TB elimination with a simple compartmental model

#tuberculosis

Eliminating tuberculosis (TB) is now a priority in the Global Health agenda. Is it achievable? How and when could this happen? Though still uncertain, it is an ongoing discussion in the field. In this practical, we will illustrate important concepts of TB epidemiology with a simple compartmental model and assess the interventions required to achieve elimination thresholds and End TB goals set by the World Health Organization (WHO). Core concepts The following concepts will be developed during the practical: ...

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. ...