Docker container for hubPredEvalsData generation

This docker container is a wrapper around hubPredEvalsData::generate_evals_data() and hosts the in-development code from hubverse-org/hubPredEvalsData, which is used to generate tables of evaluation data from a hub's oracle output.

The image is built and deployed to the GitHub Container Registry (https://ghcr.io). You can find the latest version of the image by using the latest tag:

From the command line:

docker pull ghcr.io/hubverse-org/hubpredevalsdata-docker:latest

Usage

The main usage for this image is a step in the hub dashboard control room that builds evals data if it exists.

The container packages the create-predevals-data.R script, which will display help documentation if you pass --help to it.

docker run --rm -it \
ghcr.io/hubverse-org/hubpredevalsdata-docker:latest \
create-predevals-data.R --help

Calculate eval scores data and a predevals-config.json file

USAGE

   create-predevals-data.R [--help] -h </path/to/hub> -c <cfg> -d <oracle> [-o <dir>]

ARGUMENTS

  --help             print help and exit
  -h </path/to/hub>  path to a local copy of the hub
  -c <cfg>           path or URL of predevals config file
  -d <oracle>        path or URL to oracle output data
  -o <dir>           output directory

EXAMPLE

```bash
prefix="https://raw.githubusercontent.com/elray1/flusight-dashboard/refs/heads"
cfg="${prefix}/main/predevals-config.yml"
oracle="${prefix}/oracle-data/oracle-output.csv"

tmp=$(mktemp -d)
git clone https://github.com/cdcepi/FluSight-forecast-hub.git $tmp

create-predevals-data.R -h $tmp -c $cfg -d $oracle
```

Example

This is an example of running this container with the reichlab/flu-metrocast hub.

# setup --------------------------------------------------------------
git clone https://github.com/reichlab/flu-metrocast.git flu-metrocast
cd flu-metrocast
mkdir -p predevals/data
cfg=https://raw.githubusercontent.com/reichlab/metrocast-dashboard/refs/heads/main/predevals-config.yml

# run the container
docker run --rm -it --platform=linux/amd64 -v "$(pwd)":"/project" \
ghcr.io/hubverse-org/hubpredevalsdata-docker:latest \
create-predevals-data.R -h /project -c $cfg -d /project/target-data/oracle-output.csv -o /project/predevals/data

Updating

Because hubPredEvalsData is constantly improving, this image needs to be rebuilt with the updated version.

Dependency management

This project uses renv with the explicit snapshot type. Dependencies are declared in the DESCRIPTION file, which ensures reproducible and predictable lockfile generation. This approach:

• Captures only the packages actually needed (declared in DESCRIPTION)
• Avoids including unrelated packages from the base R image
• Is the standard R approach for dependency management

Note

If you add a new dependency to any script in this project, you must also add it to the DESCRIPTION file's Imports field for it to be captured in the lockfile.

How to update

The update script must be run inside the Docker container. From the root of this repository:

docker run --rm -it --platform=linux/amd64 \
  -v "$(pwd)/renv.lock":/project/renv.lock \
  -v "$(pwd)/scripts/update.R":/project/scripts/update.R \
  -v "$(pwd)/DESCRIPTION":/project/DESCRIPTION \
  ghcr.io/hubverse-org/hubpredevalsdata-docker:latest \
  Rscript scripts/update.R

This mounts the local renv.lock, DESCRIPTION, and update script into the container, runs the update, and writes the updated lockfile back to your host.

If there are updates, the lockfile will change and you will need to commit it. Once you commit and push, the docker image will be rebuilt automatically.