https://github.com/seabbs/estzoonotictb
Explore, Visualise and Estimate the Global Zoonotic Tuberculosis Burden
https://github.com/seabbs/estzoonotictb
bovine-tb data estimation package rstats tuberculosis visualisation zoonotic-tb
Last synced: 3 months ago
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Explore, Visualise and Estimate the Global Zoonotic Tuberculosis Burden
- Host: GitHub
- URL: https://github.com/seabbs/estzoonotictb
- Owner: seabbs
- License: gpl-3.0
- Created: 2019-09-18T13:41:41.000Z (over 6 years ago)
- Default Branch: master
- Last Pushed: 2020-01-12T15:35:21.000Z (over 6 years ago)
- Last Synced: 2025-02-16T13:02:40.614Z (over 1 year ago)
- Topics: bovine-tb, data, estimation, package, rstats, tuberculosis, visualisation, zoonotic-tb
- Language: HTML
- Homepage: https://www.samabbott.co.uk/EstZoonoticTB
- Size: 53.5 MB
- Stars: 1
- Watchers: 2
- Forks: 0
- Open Issues: 1
-
Metadata Files:
- Readme: README.Rmd
- Changelog: NEWS.md
- Contributing: .github/CONTRIBUTING.md
- License: LICENSE
- Code of conduct: .github/CODE_OF_CONDUCT.md
- Support: .github/SUPPORT.md
Awesome Lists containing this project
README
---
output: github_document
---
```{r, echo = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/"
)
```
# `{EstZoonoticTB}`: an R package for exploring, visualising and estimating the global zoonotic tuberculosis burden 
[](https://mybinder.org/v2/gh/seabbs/EstZoonoticTB/master?urlpath=rstudio)
[](https://github.com/seabbs/EstZoonoticTB)
[](https://zenodo.org/badge/latestdoi/209318552)
`{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](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4816377/); 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:
```{r gh-installation, eval = FALSE}
# install.packages("remotes")
remotes::install_github("seabbs/EstZoonoticTB")
```
## Documentation
### Overview
[](https://www.samabbott.co.uk/EstZoonoticTB/)
[](https://www.samabbott.co.uk/EstZoonoticTB/dev)
[](https://www.samabbott.co.uk/EstZoonoticTB/reference/index.html)
### Vignettes
[](https://www.samabbott.co.uk/EstZoonoticTB/articles/data-sources.html)
[](https://www.samabbott.co.uk/EstZoonoticTB/articles/data-linkage.html)
[](https://www.samabbott.co.uk/EstZoonoticTB/articles/data-exploration.html)
[](https://www.samabbott.co.uk/EstZoonoticTB/articles/data-mapping.html)
## Testing
[](https://travis-ci.org/seabbs/EstZoonoticTB)
[](https://ci.appveyor.com/project/seabbs/EstZoonoticTB)
[](https://codecov.io/github/seabbs/EstZoonoticTB?branch=master)
## 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,
```{r}
EstZoonoticTB::link_data(verbose = FALSE)
```
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,
```{r run-dash, eval = FALSE}
EstZoonoticTB::dashboard()
```
Or accessed online.
## Contributing
File an issue [here](https://github.com/seabbs/EstZoonoticTB/issues) 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](https://github.com/seabbs/EstZoonoticTB/blob/master/.github/CODE_OF_CONDUCT.md). 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),
```{r}
citation("EstZoonoticTB")
```
## 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),
```{bash, eval = FALSE}
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](https://mybinder.org/v2/gh/seabbs/EstZoonoticTB/master?urlpath=rstudio).