habs-proxies-forecast-chl

Collection of code from the HABs Proxies group to forecast chl-a for Ecological Forecasting Challenge 2022.

How to work in this repository

NOTE: A lot of the details on standardized environment and automation come from https://github.com/eco4cast/neon4cast-example

Setup the correct environment on your local machine

1) Run install.packages("renv") in R. https://rstudio.github.io/renv/index.html 2) After the installation of renv finishes, run renv::activate() and renv::restore(). renv uses the renv.lock file committed to this repository to download and install the necessary packages to run this pipeline. renv installs the packages to a project-specific location (i.e. it doesn't update R packages installed elsewhere on your machine). NOTE: this might take a while to install all the necessary packages for this project. We also use renv in GitHub to automatically run the pipeline using GitHub actions. 3) If you make changes to the pipeline, especially if you're using a new package not already in use (or updating an existing package to a new version), run renv::snapshot() to update the renv.lock file with any new packages that you have added.
4) Commit and push any changes to your forked version of the repository and open a pull request.

Ready to submit a forecast automatically?

1) Uncomment the p6_submit target. 2) Uncomment the schedule: and - cron: "0 20 * * *" lines in the .github/workflows/do_prediction.yml file. This cron job will run the forecast in this repository daily at 20:00 UTC, and the execution of the forecast occurs on GitHub's servers, so your local computer does not need to be turned on. You can update this to run on a different schedule based on timing codes found in https://crontab.guru 3) Commit and push the changes to Github.

Running the pipeline in GitHub actions manually

1) Under the actions tab, click on ".github/workflows/do_prediction.yml" on the left side. 2) Click Run workflow, and then the green Run workflow button.

Disclaimer

This software is preliminary or provisional and is subject to revision. It is being provided to meet the need for timely best science. The software has not received final approval by the U.S. Geological Survey (USGS). No warranty, expressed or implied, is made by the USGS or the U.S. Government as to the functionality of the software and related material nor shall the fact of release constitute any such warranty. The software is provided on the condition that neither the USGS nor the U.S. Government shall be held liable for any damages resulting from the authorized or unauthorized use of the software.