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README.Rmd
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README.Rmd
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---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# emdash
<!-- badges: start -->
[](https://github.com/asiripanich/emdash/actions)
[](https://github.com/asiripanich/emdash/actions/workflows/publish-docker-image.yaml)
[](https://hub.docker.com/repository/docker/amarins/emdash)
[](https://zenodo.org/badge/latestdoi/280847367)
<!-- badges: end -->
The goal of emdash is to provide a deployer dashboard for an e-mission deployment.
| **Tab** | **Example** |
|--------------------------------------------|---------------------------------------------------------------------------|
| **Dashboard** |  |
| **Tables** (and interactive visualisation) |  |
| **Map** |  |
## Installation
You can install emdash from GitHub:
``` r
install.packages("remotes")
remotes::install_github("asiripanich/emdash")
```
Alternatively, with Docker CLI:
docker pull amarins/emdash
docker run -d -p 80:80 --name emdash amarins/emdash
After that, open your favourite browser and type `localhost` or `http://0.0.0.0:80` in the URL bar to see the dashboard.
## How to use the dashboard
### Run locally
To use the dashboard you must config the port of your e-mission mongoDB in the `emdash::run_app(mongo_url = 'mongodb://localhost:27017')` command. As you can see, the default is `27017`. The easiest way to use this dashboard with your e-mission deployment is to create a SSH tunnel to the e-mission mongo on your e-mission server.
``` ssh
ssh -L {my-local-port}:localhost:{remote-server-port} username@your-server-ip-address-or-domain-name
ssh -L 27017:localhost:27017 ec2-user@123.12.12.1
```
Here is how you launch a e-mission dashboard with emdash.
``` r
library(emdash)
emdash::run_app(mongo_url = 'mongodb://localhost:27017')
```
## Loading test data
This repository contains a test mongodump with entries from the [e-mission unit test real data](https://github.com/e-mission/e-mission-server/tree/master/emission/tests/data/real_examples).
- 2016-07-22
- 2016-07-25
- 2016-07-27
- 2016-08-04
- 2016-08-05
- 2016-08-09
- 2016-08-10
- 2016-08-11
It includes background sensed data (`background/*`), analysis results (`analysis/*`) and the mode and purpose confirm objects from the master branch (`manual/mode_confirm` and `manual/purpose_confirm`).
To load the data into a local mongodb,
$ unzip test-data/2016_jul_aug_test_trips.zip
$ mongorestore
If you would like to load additional data, you can do so through the [e-mission server](https://github.com/e-mission/e-mission-server/#loading-test-data).
For convenience, you may use this `docker_start_test_mongodb.sh` for starting up a Docker container that will run the test database.
### Use with Docker
We provide a Dockerfile to run this dashboard. In the future we may include this as part of an e-mission docker-compose file which will be hosted on [the e-mission-docker github repo](https://github.com/e-mission/e-mission-docker).
Be warned that the emdash Docker image is quite large, around 2.8 GB, and take a while to build. You can use pull from [the emdash docker repository](https://hub.docker.com/r/amarins/emdash) and skip the wait!
## How to customise the dashboard
First you need to know [R](https://www.r-project.org/) and [Shiny](https://shiny.rstudio.com/). I tried to modularise each component as much as possible so that the dashboard is easy to be customised. Any advices to improve the dashboard are welcomed. :)
### Customise query functions
See `R/utils_query_database.R`.
The functions in this script are for querying data from the e-mission mongoDB database.
### Customise data
See `R/utils_tidy_data.R`.
The functions in this script are for cleansing and transforming data queried using the functions in `R/utils_query_database.R`.
# Citation
Use `emdash` in your work? Consider citing the package:
@software{siripanich_amarin_2021_4456315,
author = {Siripanich, Amarin and
Rashidi, Taha Hossein and
Shankari, K and
Allen, Michael and
Yip, Arthur},
title = {asiripanich/emdash: v1.5.0},
month = Jul,
year = 2021,
publisher = {Zenodo},
version = {v1.5.0},
doi = {10.5281/zenodo.5166881},
url = {https://doi.org/10.5281/zenodo.5166881}
}