Update the Add Data Templates

Updating the Add Data Template

This will rarely need to be done as additions / removals to ecological groups and trophic groups are uncommon

Associated Reference Data

The instructions in the upload data template need to be updated when changes to the reference data sheets occur. When the following files are updated according to the Developer Instructions, those changes may trigger necessary updates to the Add Data templates and instrutions:

  • trophic-groups.csv
    • Update trophic_group and ecological_group column instructions if new groups are added or groups are removed.
      • ie if Plant is removed as a trophic group or Salmonid is removed as an ecological group.
      • Since the groups (Plant, Bacteria, Amphibian, etc) have been written into the instruction tab this is why updates to the instructions are needed if new categories are added.
    • The validation of the values is done from the trophic-groups.csv which means it is possible for the instructions to get out of sync with the allowed values.
    • Adding new species to the trophic-groups.csv does not trigger a change to the instructions.
  • lifestage-codes.csv
    • Update simple_lifestage column instructions if new simple life stages categories are added or removed.
      • ie if els is removed as a simple life stage.
    • The validation is done off the lifestage-codes.csv which means it is possible for the instructions to get out of sync with the allowed values.
  • concentration-endpoints.csv
    • Update endpoint column instructions if endpoints are added or removed.
    • The list of endpoints are generated by the script scripts/concentration-endpoints.R.
    • The validation is done off of the concentration-endpoints.csv so it is possible for the instructions to get out of sync with the allowed values.

To update the template

  1. Make any required changes to the trophic groups, life stage codes or concentration endpoints reference data.
  2. Edit the inst/template/template-data-data.csv and inst/template/template-data-instructions.csv files.
    • Do not edit the file inst/template/template-data.xlsx.
  3. To regenerate the template run the script data-raw/template.R.
  4. Review the inst/template/template-data.xlsx to confirm the edits came through and the template looks as expected.
    • Do not edit the file inst/template/template-data.xlsx.

Push and install the pacakge

Finally, after all of the all of the updates are completed, push them to GitHub. Install the updated package with devtools::install_github("bcgov/wqbench").