{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.
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,
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/estzoonotictbThe 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.
