spencerdh / dsairm

R Package - Dynamical Systems Approach to Immune Response Modeling

DSAIRM

Dynamical Systems Approach to Immune Response Modeling

Description

This R package consists of a set of Shiny Apps to learn within-host infection dynamics and immune response modeling from a dynamical system perspective. By manipulating the models through the Shiny UI interface and working through the instructions provided within the Shiny UI, you can learn about some important concepts of within-host and immmune response modeling.

Installation

1. Install the CRAN release in the usual way with install.packages('DSAIRM').
2. The latest development version (potentially buggy) can be installed from github, using the devtools package. If you don't have it, install the devtools package. Then, install DSAIRM through devtools. The following commands should get you up and running:

install.packages('devtools')
library('devtools')
install_github('ahgroup/DSAIRM', build_vignettes = TRUE)

The extra build_vignettes ensures you get the vignette (tutorial) for the package installed/created.

Basic Use

After install (which you need to do only once), load the package by runing library('DSAIRM'). You should receive a short greeting. Now you can open the DSAIRM main menu by running dsairmmenu(). From the main menu, choose the different apps corresponding to different modeling topics and scenarios. Each app contains a description of the model and scenario that is implemented. Each app also contains a list of recommeded tasks to work through in order to learn about a specific topic. Once done exploring the apps, close the main menu to exit back to the R console.

Alternative Use

If you don't want to use the main menu, there is another way to run each app: Run the function dsairmapps() to get a list of all available apps. Run the same function specifying an app (with quotation marks), e.g. dsairmapps('BasicBacteria') to run that specific app. Once you close the app, you'll be back at the R console, then use the same function to run a different app.

Advanced Use

You can call the underlying simulation functions directly from the R console. You can also access all functions and modify them to your own needs. To find the folder on your computer where the simulator functions are stored, use the following command:

system.file("simulatorfunctions", package = "DSAIRM")

See the package vignette for more details on the different ways to use the package. You can also get to the vignette by typing vignette('DSAIRM') at the R console.

Contributing to the package

The package is built in a way that makes it (hopefully) easy for others to contribute new simulations/apps. To that end, the package contains a subfolder called docsfordevelopers, which provides information on how the apps are structured and how to add new ones. This Markdown file, documentation.md, provides further information. The information provided is meant to be detailed and complete enough to allow fairly easy development and contribution of new apps (or other enhancements) to the package. If you plan to develop new apps, or for any further questions, feel free to get in touch via email or github.

Further information

• The vignette provides details about the different ways the package can be used.
• The `documentation.md' file described above contains more information about the package structure.
• For feedback, bug reports etc., file a github issue.
• A 'companion' package to this one, called Dynamical Systems Approaches for Infectious Disease Epidemiology (DSAIDE), focuses on models for infectious disease epidemiology (the population level). It has the same structure as DSAIRM. See the DSAIDE site for more information.

Contributors

This R package is developed and maintained by Andreas Handel. The following individuals have made contributions to this package: Spencer Hall, Sina Solaimanpour, Henok Woldu.