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. ...

An outbreak of gastroenteritis in Stegen, Germany, June 1998 (part 3)

Univariable and stratified analysis This practical is a continuation of the analysis concerning the outbreak of gastroenteritis after a high school graduation dinner in Stegen, Germany. The introduction to this case is presented in part 1, which focussed on initial data inspection and cleaning. Part 2 focussed on descriptive statistics. This practical will focus on univariable and stratified analysis. To identify (the) potential vehicle(s) in the outbreak, proceed with an analytical study where you use statistical tests to investigate the associations of some suspicious food items with the disease. ...

An outbreak of gastroenteritis in Stegen, Germany, June 1998 (part 2)

Descriptive analysis in R This practical is a continuation of the analysis concerning the outbreak of gastroenteritis after a high school graduation dinner in Stegen, Germany. The introduction to this case is presented in part 1, which focussed on initial data inspection and cleaning. This practical will focus on descriptive stats including 2x2 tables and epicurves. If you get stuck with any of the tasks in this practical, additional information for each task can be found in the Help section ...

An outbreak of gastroenteritis in Stegen, Germany, June 1998 (part 1)

Introduction On 26 June 1998, the St Sebastian High School in Stegen (school A), Germany, celebrated a graduation party, where 250 to 350 participants were expected. Attendants included graduates from that school, their families and friends, teachers, 12th grade students and some graduates from a nearby school (school B). A self-service party buffet was supplied by a commercial caterer in Freiburg. Food was prepared the day of the party and transported in a refrigerated van to the school. ...

Outbreak of gastroenteritis after a high school dinner in Copenhagen, Denmark,November 2006 (part 4)

Stratified analysis This practical is a continuation of the analysis concerning the outbreak of gastroenteritis after a high school dinner in Copenhagen, Denmark. The introduction to this case is presented in part 1, which focussed on initial data inspection and cleaning. Part 2 focussed on descriptive statistics. From the univariate analysis conducted in part 3, you can see that those eating pasta or veal as well as drinking champagne have the highest risk of becoming ill. ...

Outbreak of gastroenteritis after a high school dinner in Copenhagen, Denmark,November 2006 (part 3)

Univariable analysis (Cohort and case control) This practical is a continuation of the analysis concerning the outbreak of gastroenteritis after a high school dinner in Copenhagen, Denmark. The introduction to this case is presented in part 1, which focussed on initial data inspection and cleaning. Part 2 focussed on descriptive statistics. This practical will focus on univariable analysis. To identify (the) potential vehicle(s) in the outbreak, proceed with an analytical study where you use statistical tests to investigate the associations of some suspicious food items with the disease. ...