seabbs/estzoonotictb repository overview

⁠{EstZoonoticTB}: an R package for exploring, visualising and estimating the global zoonotic tuberculosis burden

{EstZoonoticTB} is an R package containing data relevant to global zoonotic tuberculosis (TB), tools for manipulating and visualising these data, and analysis aiming to improve country level estimates of zoonotic TB. Packaged datasets include: cleaned data from a recent systematic review⁠; data on the country specific epidemiology of TB; demographic data (including data on rural populations); animal demographic data; and data on the presence of zoonotic TB in animal populations (both domesticated and wild). Tooling includes functions for linking the built in datasets (built with the aim of accommodating external data sources), data mapping functions, and convenience functions for manipulating the linked datasets. The long term aim of the package is to provide a suite of data and tools that can be used to iteratively improve the estimation of global zoonotic TB burden. A secondary aim is to provide a user friendly interface to zoonotic TB relevant data in order to help spread awareness of zoonotic TB. See the package vignettes for further details.

⁠Installation

Install the development version from GitHub:

# install.packages("remotes")
remotes::install_github("seabbs/EstZoonoticTB")

⁠Documentation

⁠Overview

⁠Vignettes

⁠Testing

⁠Data

The package comes prepackaged with multiple datasets that can then be linked into a single dataset ready for analysis. This linked dataset can be accessed using the following,

EstZoonoticTB::link_data(verbose = FALSE)
#> # A tibble: 15,061 x 26
#>    country country_code g_whoregion  year tb_cases tb_inc tb_inc_lo
#>    <fct>   <fct>        <fct>       <dbl>    <int>  <dbl>     <dbl>
#>  1 Afghan… AFG          Eastern Me…  2000    38000    190       123
#>  2 Afghan… AFG          Eastern Me…  2001    40000    189       123
#>  3 Afghan… AFG          Eastern Me…  2002    42000    189       122
#>  4 Afghan… AFG          Eastern Me…  2003    44000    189       122
#>  5 Afghan… AFG          Eastern Me…  2004    46000    189       122
#>  6 Afghan… AFG          Eastern Me…  2005    47000    189       122
#>  7 Afghan… AFG          Eastern Me…  2006    49000    189       122
#>  8 Afghan… AFG          Eastern Me…  2007    50000    189       122
#>  9 Afghan… AFG          Eastern Me…  2008    52000    189       122
#> 10 Afghan… AFG          Eastern Me…  2009    53000    189       123
#> # … with 15,051 more rows, and 19 more variables: tb_inc_hi <dbl>,
#> #   prop_tb_ep <dbl>, prop_hiv <dbl>, prop_hiv_lo <dbl>,
#> #   prop_hiv_hi <dbl>, z_tb_dom_animal <fct>, z_tb_wild_animal <fct>,
#> #   z_tb_id <int>, z_tb_geo_coverage <fct>, z_tb_study_pop <fct>,
#> #   z_tb_multi_year_study <fct>, tb_z_prop <dbl>, tb_z_prop_lo <dbl>,
#> #   tb_z_prop_hi <dbl>, tb_z_prop_se <dbl>, population <dbl>,
#> #   prop_rural <dbl>, cattle <int>, cattle_per_head <dbl>

See the package vignettes for details.

⁠Shiny dashboard

Work in progress

To explore the package functionality in an interactive session, or to investigate Zoonotic TB without having to code extensively in R, a shiny dashboard has been built into the package. This can either be used locally using,

EstZoonoticTB::dashboard()

Or accessed online.

⁠Contributing

File an issue here⁠ if there is a feature, or a dataset, that you think is missing from the package, or better yet submit a pull request!

Please note that the EstZoonoticTB project is released with a Contributor Code of Conduct⁠. By contributing to this project, you agree to abide by its terms.

⁠Citing

If using EstZoonoticTB please consider citing the package in the relevant work. Citation information can be generated in R using the following (after installing the package),

citation("EstZoonoticTB")
#> 
#> To cite EstZoonoticTB in publications use:
#> 
#>   Sam Abbott (2019). EstZoonoticTB: an R package for exploring,
#>   visualising and estimating the global zoonotic tuberculosis
#>   burden
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @Article{,
#>     title = {EstZoonoticTB: an R package for exploring, visualising and estimating the global zoonotic tuberculosis burden},
#>     author = {Sam Abbott},
#>     journal = {-},
#>     year = {-},
#>     volume = {-},
#>     number = {-},
#>     pages = {-},
#>     doi = {-},
#>   }

⁠Docker

This package has been developed in docker based on the rocker/geospatial image, to access the development environment enter the following at the command line (with an active docker daemon running),

docker pull seabbs/estzoonotictb
docker run -d -p 8787:8787 -e USER=EstZoonoticTB -e PASSWORD=EstZoonoticTB --name EstZoonoticTB seabbs/estzoonotictb

The rstudio client can be accessed on port 8787 at localhost (or your machines ip). The default username is EstZoonoticTB and the default password is EstZoonoticTB. Alternatively, access the development environment via binder⁠.