This repository is intended as a place to host any scripts or functions used within automated workflows that generate State of the Ecoystem indicators.

To contribute an indicator workflow to this repo, please follow the steps below:

• Clone this repo
• Switch to dev branch and pull
• Build the package Ctrl + Shift + B
• Create branch off dev for your indicator. Name the branch the same name as your indicator
• Add a main wrapper workflow function in data-raw folder. Name it workflow_<ecodata_dataset_name>.r
  • This function should take only filepaths as arguments and should save the ecodata data set (see examples that already exist in the data-raw folder)
• Add file in the R folder. Name this as <ecodata_dataset_name>.r.
  • This file should contain the set of functions required to calculate the indicator. The format of the indicator should match the format as found in the ecodata package. You may need to look at the ecodata/data-raw/get_<your_indicator> function to see any additional formatting that is required
  • This/these functions should be called from the workflow_<ecodata_dataset_name>.r function
• Use the data-raw/example_test_runs.r script to see how you might set up your functions.
  • All functions should only take file paths as arguments. All data dependencies should be read in by passing a file path to the data.
• Check that there is a create_ecodata_dataset_name.Rd file in the man folder. If not, run devtools::document() to create and commit one.
• Add any packages used to create the indicator in the DESCRIPTION file.
• Add instructions in the tempate_readme.md file (in the root of this repo)
• Final testing should be done inside your Rstudio container. (You'll need to repeat the first few steps; clone, pull, build)
• To test your workflow use the example_test_runs.r as a template.
• To test the R package, please build the package and then run devtools::check(), either from the command line or click the check button under the build tab in Rstudio
  • If any errors arise (you can ignore Notes and warnings), please try to fix them prior to creating a pull request
• When checks pass, create a pull request into the dev branch and assign two people as reviewers

This repository is a scientific product and is not official communication of the National Oceanic and Atmospheric Administration, or the United States Department of Commerce. All NOAA GitHub project code is provided on an ‘as is’ basis and the user assumes responsibility for its use. Any claims against the Department of Commerce or Department of Commerce bureaus stemming from the use of this GitHub project will be governed by all applicable Federal law. Any reference to specific commercial products, processes, or services by service mark, trademark, manufacturer, or otherwise, does not constitute or imply their endorsement, recommendation or favoring by the Department of Commerce. The Department of Commerce seal and logo, or the seal and logo of a DOC bureau, shall not be used in any manner to imply endorsement of any commercial product or activity by DOC or the United States Government.