Utility Functions for Infectious Disease Modelling
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README.md

idmodelr

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idmodelr is an R package that contains utility functions for infectious disease modelling. It's main functionality is to facilitate the use of other available modelling packages such as pomp. Although, it does offer some basic modelling functionality itself.

Installation

You can install idmodelr from github with:

# install.packages("devtools")
devtools::install_github("seabbs/idmodelr")

Docker

This packge was developed in a docker container based on the tidyverse docker image. To run the docker image run:

docker run -d -p 8787:8787 --name idmodelr -e USER=seabbs -e PASSWORD=seabbs seabbs/idmodelr

The rstudio client can be found on port :8787 at your local machines ip. The default username:password is seabbs:seabbs, set the user with -e USER=username, and the password with - e PASSWORD=newpasswordhere. The default is to save the analysis files into the user directory.

To run a plain R terminal use:

docker run --rm -it --user seabbs idmodelr /usr/bin/R

To run a plain bash session:

docker run --rm -it --user seabbs idmodelr /bin/bash