https://github.com/seabbs/intro_to_tb_models
A shiny app recreating the models used in the practicals for the Intro to TB modelling course at the 2017 Union Conference
https://github.com/seabbs/intro_to_tb_models
course docker infectious-diseases modelling shiny tb-models tuberculosis
Last synced: 8 months ago
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A shiny app recreating the models used in the practicals for the Intro to TB modelling course at the 2017 Union Conference
- Host: GitHub
- URL: https://github.com/seabbs/intro_to_tb_models
- Owner: seabbs
- License: mit
- Created: 2017-10-11T21:14:48.000Z (almost 8 years ago)
- Default Branch: master
- Last Pushed: 2018-04-24T18:32:02.000Z (over 7 years ago)
- Last Synced: 2025-02-16T13:02:41.917Z (8 months ago)
- Topics: course, docker, infectious-diseases, modelling, shiny, tb-models, tuberculosis
- Language: R
- Homepage: http://www.seabbs.co.uk/shiny/intro_to_tb_models
- Size: 50.8 MB
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.Rmd
- License: LICENSE
Awesome Lists containing this project
README
---
output: github_document
---
```{r, echo = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "README-"
)
```
# Introduction to TB Models
A shiny app reproducing the models used in the Introduction to Tuberculosis modelling course practicals, run by [TB MAC](http://tb-mac.org/) at the [2017 Union conference](http://guadalajara.worldlunghealth.org/about-us). See the [TB MAC](http://tb-mac.org/) website for course materials and further resources. The models used in this course, and reproduced in this shiny app, were based on one published by [Lin et al.](http://www.who.int/bulletin/volumes/90/10/11-101436.pdf)
## Installing the shiny app locally
## Manual Install
To install and run the shiny app locally on your own computer you will need to first install [R](https://www.r-project.org/), it is also suggested that you install [Rstudio](https://www.rstudio.com/products/rstudio/download/). After downloading the source code from [this repository](https://www.github.com/seabbs/intro_to_tb_models) click on the `intro_to_tb_models.Rprof` file, this will open an Rstudio window. Type the following code into the command line;
```{r, eval = FALSE}
install.packages("shiny")
install.packages("shinydashboard")
install.packages("DT")
install.packages("ggplot2")
install.packages("tidyr")
install.packages("dplyr")
install.packages("tibble")
install.packages("rmarkdown")
install.packages("plotly")
```
To run the app open the `ui.R` file and press run, depending on your computer this may take some time.
### Using Docker
[Docker](https://www.docker.com/what-docker) is a container software that seeks to eliminate "works on my machine" issues. For installation and set up instructions see [here](https://www.docker.com/community-edition).
This docker container is based on the [shiny](https://hub.docker.com/r/rocker/shiny/) docker image, see [here](https://github.com/rocker-org/shiny) for instructions on use. To run the docker image run the following in a bash shell:
```{bash, eval = FALSE}
docker pull seabbs/intro_to_tb_models
docker run --rm -p 3838:3838 seabbs/intro_to_tb_models
```
The shiny app can be found on port `:3838` at your local machines ip (or localhost on windows).