Dynamical Systems Approach to Infectious Disease Epidemiology (Ecology/Evolution)

Description

DSAIDE is an R package containing a set of simulation models (apps) that teach infectious disease epidemiology (ecology/evolution) from a dynamical system perspective.

All models can be explored through a graphical user interface, no reading or writing code is required. Each app comes with documenation and instructions which teach important concepts of infectious disease epidemiology (ecology/evolution) and how to use simulation models to understand such concepts.

It is also possible to go beyond the graphical interface and directly access and modify all simulations to adapt them to your needs.

Getting Started

The best approach to use this package is to install it, load it, and start the main menu, then you are ready to go. These lines of code typed into the R console will get you there:

install.packages('DSAIDE')
library('DSAIDE')
dsaidemenu()

You can also give the package a quick try online, without having to install it. I still recommend you install it like any regular R package should you decide that you want to use it. Note that I only have a free plan for shinyapps.io, where the online version is hosted. If the link fails to work it likely means I reached my maximum monthly allowed capacity. In that case, just go ahead and install the package. It’s only 3 commands to get it up and running!

For a quick introduction to the package, step-by-step instructions on getting started, and more information on the different ways you can use the package see the tutorial (vignette).

Further information

  • I published a paper describing the package. The paper is by now somewhat outdated whith regards to the details of the package, but it describes the overall idea and context well.
  • The package tutorial (vignette) contains up-to-date and detailed instructions on the different ways the package can be used.
  • If you want to take a deeper look at the package, see this Markdown file which provides further information on the details of the package structure. (If you plan to develop new apps, or make other substantial contributions, it is best to get in touch with me first.)
  • A ‘companion’ package to this one, called Dynamical Systems Approaches for Immune Respone Modeling (DSAIRM), focuses on models for analyzing with-host infection dynamics. It has the same structure as DSAIDE. See the DSAIRM site for more information.
  • I have solutions (in progress) to most of the ‘What to do’ tasks for the different apps. If you are an instructor using this package as part of a class, email me if you are interested in having access to these solutions.
  • I heard that DSAIDE doesn’t seem to work quite right using Docker. This is likely irrelevant for almost all users.

Citation and Contributors

If the DSAIDE package does in any way help you with your work such that it warrants citing it in one of your papers, please cite the DSAIDE publication in PLoS Comp Bio.

This R package is developed and maintained by Andreas Handel. A full list of contributors and a Bibtex entry for the citation can be found here.