This repository contains code to generate FluSight hospitalization forecast evaluations, and support for updating/publishing the reports via GitHub Pages. These reports are generated on Thursdays.
There are two ways to run the program: as a Docker container (the default, which is run on Amazon Web Services), or manually on a local machine.
Please see docker/README.md.
- Clone/update your copy of https://github.com/cdcepi/FluSight-forecast-hub . Make a note of its location for the next step.
- Temporarily edit
code/score_flusight_forecasts.R
: 1/2) Uncomment the line that setshub_path
, setting it to the location of the repo in the previous step. E.g.,hub_path <- "../FluSight-forecast-hub"
. 2/2) Comment out the lines after that line, starting withargs <- commandArgs(trailingOnly = TRUE)
through the end of theif
statement. - Generate scores: Run
code/score_flusight_forecasts.R
. - Produce reports: Knit
code/Evaluation_flu_hosp.Rmd
. This will create a new .html file in the current directory. - Rename and move the .html file to
reports/YYYY-MM-DD_Evaluation_flu_hosp.html
(where YYYY-MM-DD is current date). E.g.,reports/2024-01-05_Evaluation_flu_hosp.html
. - Update
reports/reports.json
by runningcode/update-reports-json.py
. This file is used byindex.html
to list all reports. - Add, commit, and push the above two files under
reports/
to this repo. This push will initiate rebuilding and publishing the website (it may take a few minutes). - Check https://reichlab.io/flusight-eval/ to verify that it's been updated.