Utility functions for the COVID-19 forecast hub

Installation

The covidHubUtils package relies on a small number of packages, including many from the tidyverse and, importantly, the zoltr package that is used to access the Zoltar API for downloading forecasts. Please install zoltr from GitHub, as this development version often has important features not yet on the CRAN version:

devtools::install_github("reichlab/zoltr")

Some additional functionalities in covidHubUtils also rely on covidData. Because there are daily data updates in covidData, please install the latest version of it before using related functions in covidHubUtils:

devtools::install_github("reichlab/covidData")

The covidHubUtils package currently is only available on GitHub, and it may be installed using the devtools package:

devtools::install_github("reichlab/covidHubUtils")

Getting Started

For those starting out we recommend you begin with the Getting Started vignette.

Features

Currently available:

Reading Forecast Data

Reading Observed “Truth” Data

Scoring Forecasts

Download and pre-process “Truth” Data

Calculating Forecast Similarities

Contributing Guidelines

If you would like to contribute your work, please follow this list to create a pull request:

  • New functions should come with unit tests, or a promise of a new unit test in the form of an issue if getting the functionality merged in is urgent.
  • If you added a new .R file with unit tests, add the tests to .github/workflows/pr_unittest.yaml.
  • Small/quick fixes don’t need to be tested, necessarily.
  • Update NEWS.md by adding a short summary of your changes under “Changes since last release.”
  • Update README.md if you created a new function or add a new parameter to existing functions.
  • Update DESCRIPTION when you are using a new dependency in your script.
  • Add yourself as a contributor in DESCRIPTION.
  • Optional: You could also run devtools::check() or devtools::test() locally. Some tests require covidData. To get accurate test results, please make sure to install the latest daily updates from covidData by using devtools::install_github("reichlab/covidData").
  • Make sure your pull request passes all checks in Github Action.