https://github.com/ctsit/covid19_reporting

https://github.com/ctsit/covid19_reporting

fr-covid

Last synced: 1 day ago
JSON representation

• Host: GitHub
• URL: https://github.com/ctsit/covid19_reporting
• Owner: ctsit
• Created: 2020-04-22T14:41:11.000Z (over 4 years ago)
• Default Branch: master
• Last Pushed: 2021-01-04T21:51:20.000Z (about 4 years ago)
• Last Synced: 2024-11-11T22:23:31.944Z (2 months ago)
• Topics: fr-covid
• Language: R
• Size: 101 KB
• Stars: 0
• Watchers: 5
• Forks: 3
• Open Issues: 2
• Metadata Files:
  • Readme: README.md
  • Changelog: CHANGELOG.md

Awesome Lists containing this project

README

        
# First Responder Covid-19 Reporting Tools

This repository provides reporting, data cleaning, and export tools in support of the First Responder COVID-19 Testing projects at the University of Florida. This repo provides a Dockerfile to run some of the RMarkdown scripts via a Docker container.

## Prerequisites

This project uses R and these R packages:

    tidyverse

    dotenv

    REDCapR

    lubridate

    sendmailR

    kableExtra

    rmarkdown

To build the Docker container, you will need only Docker. Additionally, this project uses the REDCap API to download the data from REDCap. The API must be enabled on the REDCap project and the host where this script runs will need to have access to it.

## Setup and Configuration

This script is configured entirely via the environment. An example `.env` file is provided as [`example.env`](example.env). To use this file, copy it to the name `.env` and customize according to your project needs. Follow these steps to build the required components and configure the script's `.env` file.

## The Scripts

- `results_summary_by_agency.Rmd` - A person-centric report about the study participants who have received or are still waiting for a result. It summarizes test results by agency.

- `render_report.R` - A script runner that runs and sends the FR COVID reports via email.

- `set_send_survey_invites_field.R` - A script that sets send_survey_invites_field at baseline for study participants.

- `survey_report.Rmd` - A basic data summary and data export script.

## Report renderer

The primary script used to run the RMarkdown reports is [`render_report.R`](render_report.R). `render_report.R` mails out report results to a list of recipients defined in the .env file. At this time, `render_report.R` runs these scripts:

    results_summary_by_agency.Rmd

    survey_report.Rmd

## Release and Deployment

This project uses the Git Flow workflow for releases. Every release should be versioned and have a ChangeLog entry that describes the new features and bug fixes. Every release should also be accompanied by an updated `VERSION` file to allow image builds to be tagged as they are built by the `build.sh`

To deploy a new release on tools4, execute this series of commands or an equivalent from your home directory:

```

git clone https://github.com/ctsit/covid19_reporting.git

cd covid19_reporting

git pull

sudo ./build.sh

```