Epidemic curves made easy using the R package incidence

Area of Science:

• Epidemiology
• Biostatistics
• Computational Biology

Background:

• Epidemiological curves (epicurves) are crucial for understanding infectious disease dynamics.
• Existing tools for generating epicurves may lack user-friendliness or specific functionalities for raw data.
• There is a need for robust and accessible software for outbreak analysis.

Purpose of the Study:

• To introduce the free, open-source R package 'incidence'.
• To enable easy computation, handling, and visualization of epicurves from unaggregated linelist data.
• To provide a reliable tool for infectious disease outbreak analysis and modeling.

Main Methods:

• Development of the 'incidence' package for the R programming language.
• Adherence to R Epidemics Consortium (RECON) development guidelines.
• Implementation of automated testing, comprehensive documentation, and good coding practices.

Main Results:

• The 'incidence' package allows users to efficiently generate and visualize epicurves.
• It processes unaggregated linelist data, filling a gap in R's outbreak analytics toolkit.
• The package is built for robustness and reliability.

Conclusions:

• The 'incidence' R package is a valuable, free, and open-source tool for epidemiologists.
• It facilitates the analysis of infectious disease epidemic dynamics.
• It serves as a foundation for advanced infectious disease modeling research.