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COVID Staffing Project

Staff Skill Projection

The COVID staffing projection tool can be used to calculate your hospital’s staffing needs over time, based on your projected patient census. Please visit covidstaffing.org for more information on our staffing tools.

Table of Contents

Getting Started

These instructions will get you a copy of the project up and running on your local machine for development and testing purposes. See contributing for more information on how you can help us build the COVID staffing tool. See deployment for notes on how to deploy the project on a live system.

Prerequisites

This application is written in R and uses Shiny to build and deploy the web application. We assume you have basic knowledge of both.

Development Environment

This should detail how to setup a local environment that enables developers to keep all packages version segregated from their local machine. This will make it easy to setup and avoid conflicts due to dependency version miss-matches between development environments.

Running

Using Packrat

To restore the current project you can run the following from within the R console:

install.packages("devtools")
devtools::install_github("rstudio/packrat")
packrat::restore()

If you need to add packages to this project, always run packrat::snapshot() before committing and see Styling. This will add any new dependencies to the packrat.lock file.

Using RStudio

To run the application locally, you can install the packages above in RStudio, and use the function runApp() to start.

Note: You may need to install devtools and tidyext from the console manually:

install.package("devtools")
devtools::install_github('m-clark/tidyext')

Using shinyServer

Instructions on how to run the application on a shiny server.

Styling

This project includes the styler package to maintain consistent styles throughout the codebase. Before making any PRs please be sure to run the styler on your newly written code.

Run the following in the R console:

source("tools/styler.R")

If you add new files or directories please include them in tools/styler.R and tools/lintr.R scripts. By default, the styler script includes everything under /function directory. The syntax used is:

wd = Current working directory

Linter lintr::lint(file.path(wd, "folder1", "folder2", "file"))

Styler style_file(file.path(wd, "file"))

File Structure

ShinyApp searches for the following in the root folder:

  • server.R
    • Contains shinyServer function
  • ui.R
    • Contains shinyUI function
  • styles.css
    • Used for class based global CSS styling
  • staff_projection.Rproj
    • Rstudio project
  • functions/
    • user defined functions that used in serve.R and UI.R
  • data/
    • default datasets, e.g default staffing ratios table, were used in the app
  • packrat/
    • used for project package management
  • www/
    • Accessible to the users web browser (for assets).

Further Information

The COVID-19 pandemic poses an unprecedented challenge to health care systems and their staff In response, our multi-institutional collaborative is developing tools to support your hospital in:

    1. Projecting your frontline workforce needs;
    1. Redeploying your clinical teams; and
    1. Protecting the health and well-being of your providers.

We are software developers, administrators, engineers, big data analysts, social scientists, and clinicians dedicated to supporting hospitals and front line providers during the COVID-19 crisis.

Our goal is not to duplicate work that others have already begun, but rather to combine our work with that of others. We welcome your feedback and suggestions as we navigate this difficult time together.

If you are also working in this domain and interested in collaborating, please contact us.

License

This project is licensed under the MIT license.