Points of Significance: Modeling infectious epidemics

Ottar Bjørnstad¹𝄒², Katriona Shea¹, Martin Krzywinski³, Naomi Altman⁴

1. Department of Biology, The Pennsylvania State University, State College, PA, USA.
2. Department of Entomology, The Pennsylvania State University, State College, PA, USA.
3. Canada’s Michael Smith Genome Sciences Center, Vancouver, British Columbia, Canada.
4. Department of Statistics, The Pennsylvania State University, State College, PA, USA.

Explore interactive figures or download the code accompanying the column.

Getting Started

Access remotely

Online interactive server

Downloading code

GitHub repository

Running locally

Download R Studio and install packages.

install.packages(c("shiny","deSolve","ggplot2","tidyverse","stringr","shinyjs","shinyWidgets"))

Run the app by loading app.R and cliking Run App.

Shiny app authors

• Martin Krzywinski

  Coding

• Ottar Bjørnstad

  Code template and tips

Bugs and comments

Martin Krzywinski

Versions

v1.0.0

Initial release.

v1.0.1

Minor text changes and fixed typos.

v1.0.2

UI tweaks.

v1.0.3

Added link to SEIRS column.

v1.0.4

Added link to uncertainty and management column.

Citation

Bjørnstad, O., Shea, K., Krzywinski, M. & Altman, N. Points of Significance: Modelling infectious epidemics. (2020) Nature Methods 17:455-456. (interactive figures, download code)

Related Columns

Bjørnstad, O., Shea, K., Krzywinski, M. & Altman, N. Points of Significance: The SEIRS model for infectious disease dynamics. (2020) Nature Methods 17:557-558. (interactive figures, download code)

Shea, K., Bjørnstad, O., Krzywinski, M. & Altman, N. Points of Significance: Uncertainty and the management of epidemics. (2020) Nature Methods 17 (in press). (interactive figures, download code)

License

This project is licensed under the https://creativecommons.org/licenses/by-nc/4.0/ - see the LICENSE file for details.