knitr::opts_chunk$set( collapse = TRUE, comment = "#>", fig.path = "README-" )
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tbinenglanddataclean
is an R package that contains functions and documentation to reproduce clean and munge available TB data in England.
You can install tbinenglanddataclean from github with:
# install.packages("devtools") devtools::install_github("seabbs/tbinenglanddataclean")
This package relies on raw data from several sources, these are;
The included vignette contains the code necessary to build all datasets associated with this package. Each function needs to be pointed at the correct raw data. If the default file names/locations are changed then this will also require updating. Contact me if you have any problems.
Other vignettes explore approaches for estimating demographic parameters from the clean and munged datasets.
This packge was developed in a docker container based on the tidyverse docker image. To run the docker image run:
```{bash, eval = FALSE} docker run -d -p 8787:8787 --name tbinenglanddataclean --mount type=bind,source=$(pwd)/data/tb_data,target=/home/rstudio/tbinenglanddataclean/data/tb_data -e USER=tbinenglanddataclean -e PASSWORD=tbinenglanddataclean seabbs/tbinenglanddataclean
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 `--mount type=bind,source=$(pwd)/data/tb_data,target=/home/rstudio/tbinenglanddataclean/data/tb_data`. To run a plain R terminal use: ```{bash, eval = FALSE} docker run --rm -it --user seabbs tbinenglanddataclean /usr/bin/R
To run a plain bash session:
```{bash, eval = FALSE} docker run --rm -it --user seabbs tbinenglanddataclean /bin/bash
To connect as root: ```{bash, eval = FALSE} docker exec -ti -u root tbinenglanddataclean bash
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