Ensemble - reichlab/covid19-forecast-hub GitHub Wiki

Software Dependencies

You will need Python 3 and R 3.x or 4.x, as well as the packages listed below:

Python packages:

  • pandas and requests. To install, run the following in a terminal:
pip install pandas
pip install requests

R packages:

  • The quantgen package by Ryan Tibshirani. Follow the instructions at https://github.com/ryantibs/quantgen.

  • Other packages: tidyverse, MMWRweek, magrittr, Matrix, NlcOptim, zeallot, googledrive, yaml, here. In an R session, run the following:

install.packages(c("tidyverse", "MMWRweek", "magrittr", "Matrix", "NlcOptim", "zeallot", "googledrive", "yaml", "here"))
  • The covidEnsembles package. Clone the repository and install as an R package. In a terminal, you can run the following commands:
git clone https://github.com/reichlab/covidEnsembles
R CMD INSTALL covidEnsembles
  • The covidData package. Clone the repository. You don't need to install it as an R package immediately; this will be done as part of the automated ensemble build process.
git clone https://github.com/reichlab/covidData

Weekly ensemble build

The following instructions can be used to build the weekly COVID-19 Forecast Hub ensemble.

  1. Clone a version of the covid19-forecast-hub repository on your local machine. This should be either a fork or a temporary branch of the actual repository.
  2. Clone the covidData repository. If you are cloing this repo for the first time on your machine, you will need to manually create a covidData/data-raw/JHU directory and leave it empty.
  3. In a terminal window, navigate to covidData/code/data-processing/ and run the make all command.
  4. Clone the covidEnsembles repository.
  5. Create a tag for the repository for the current week's ensemble build inputs using commands similar to those below with suitable adjustments of the dates:
git pull origin master
git tag -a 2021-04-19-COVIDhub-ensemble -m "2021-04-19-COVIDhub-ensemble build inputs"
git push origin 2021-04-19-COVIDhub-ensemble
  1. In a terminal window, navigate to covidEnsembles/code/application/weekly-ensemble/ and run the make all command.