/neon4cast-beetles

Primary LanguageR

NEON-community-forecast

  • 01_download.R Download latest NEON data products, storing the raw data in <NEONSTORE_HOME>.
  • 02_targets.R Generate the target prediction variables from the raw data files.
  • 03_forecast.R Run a dummy forecast and write out to csv files.
  • 04_score.R Score the forecast and write out to csv files.

Workflow notes

  • .Renviron

The workflow uses a .Renviron to configure behavior. These are optional parameters that allow the workflow scripts to publish and download data from EFI server. These could easily be configured for a workflow using a different server.

  • NEON_TOKEN Optional, will speed downloading of raw NEON data

  • NEONSTORE_HOME Path to the neonstore, if you need to override the default.

  • AWS_ACCESS_KEY_ID Only needed to publish data to AWS.S3-style server, such as MINIO

  • AWS_SECRET_ACCESS_KEY ditto.

  • AWS_DEFAULT_REGION Set to data to download data from ecoforecast.org automatically.

  • AWS_S3_ENDPOINT Set to "ecoforecast.org" to download data automatically.

  • Running 01_download.R and 02_targets.R wil upldate the resulting latest target data files and publish them to the EFI targets bucket. Some time after challenge entries are submitted, this workflow will thus result in an updated set of targets that contains the true values for the sites and times that the teams were trying to submit.

  • The 04_score.R script will score all .csv.gz forecasts found in the forecasts/ bucket that start with beetle-richness-forecast-<project_id>.csv.gz or beetle-abund-forecast-<project_id>.csv.gz respectively (and conform to the same tabular structure used here: columns of: siteID, month, year, value, rep). These scores will be written out to scores bucket using filenames that correspond to the submission files, replacing forecast with score.

  • 03_forecast.R generates a benchmark forecast based on a simple null model (historical mean and standard deviation). Entry teams will replace this script with their own more involved forecasting mechanisms, generating output forecasts that follow the above filenaming convention. These can be uploaded directly to the challenge server at URL TBD.

  • The Challenge Coordinating Team server will use a cron job to regularly (intervals TBD) run the full workflow scripts, resulting in updated raw data, derived data, benchmark forecast, and scores for any submissions.

Access / Publishing of target, null forecast, and scores

All files are exposed via public buckets on MINIO for now. Automated functions need to be added that will publish the target, benchmark forecast, and possibly benchmark scores in a persistent, version-controlled manner. details TBD