Case study walk-through

Please click onward to the case study. The case study contain the following pages:

Case study overview

Summary of the case study scenario, dataset downloads, and links to publications.

Template setup

Opening a template, overview of structure, and the intial setup code chunk.

Import linelist

Choosing the appropriate methods to import your linelist.

Clean variable names

Data dictionaries, cleaning variable names, and mapping to variable names expected by the template.

Import population and lab data

If applicable, import separate datasets giving region- or age-specific population figures and laboratory testing data.

Browse data

Data exploration.

Clean data

A variety of data cleaning steps and techniques.

Person analyses

Descriptive analyses of demographic and clinical variables.

Time analyses

Descriptive analyses (including “epidemic curves”) of temporal trends in incidence, attack and mortality rates and other characteristics.

Place analyses

Maps and tables showing the spatial distribution of incidence, attack and mortality rates, and other characteristics.

Knitting the report

Using RMarkdown in RStudio to produce a polished Microsoft Word report.