tbinenglanddataclean is an R package that contains functions and documentation to reproduce clean and munge available TB data in England.
You can install tbinenglanddataclean from github with:
This package relies on raw data from several sources, these are;
The included vignette contains the code necessary to build all datasets associated with this package. Each function needs to be pointed at the correct raw data. If the default file names/locations are changed then this will also require updating. Contact me if you have any problems.
Other vignettes explore approaches for estimating demographic parameters from the clean and munged datasets.
This packge was developed in a docker container based on the tidyverse docker image. To run the docker image run:
The rstudio client can be found on port
:8787 at your local machines ip. The default username:password is tbinenglanddataclean:tbinenglanddataclean, 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. If running without the accomanying data then remove
To run a plain R terminal use:
To run a plain bash session:
To connect as root: