Skip to content

Conversation

@lucy-dwr
Copy link
Collaborator

@lucy-dwr lucy-dwr commented Sep 23, 2025

Incorporated recently-released EMP data from EDI. Primary changes are:

  • EMP macro data no longer contain amphipods, so tests and the changelog were updated to reflect that
  • EDI object names (and therefore urls) changed and were updated
  • Some column names in EMP files changed to reflect full Latin names (i.e., genus was no longer abbreviated), so downstream code and the taxa crosswalk were updated to incorporate this
  • EMP non-static monitoring station locations and sampling dates were added to the EMPEZ station inventory

@lucy-dwr lucy-dwr requested a review from sbashevkin September 23, 2025 00:39
# "Americorophium_UnID Adult Macro"
# - All other Macro-missing taxa must be amphipod-related
# (any species or higher grouping within Amphipoda).
testthat::expect_true("Americorophium_UnID Adult Macro" %in% macro_missing)
Copy link
Collaborator

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Why is "Americorophium_UnID Adult Macro" treated differently from the rest of the amphipods? Wouldn't it be caught in the next test?

Copy link
Collaborator Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Hi @sbashevkin! Sorry to be tardy in responding. Here is my thinking:

Americorophium isn’t treated differently/uniquely in the data itself—the test here just uses it as a quick sanity check. After EMP Macro dropped amphipods, the list of missing macro taxa can change, so the test can’t rely on an exact list. The next test only checks that anything missing is amphipod‑related, which could still pass even if no amphipod roll‑up showed up at all. Calling out Americorophium makes sure at least one expected amphipod roll‑up is actually present.

Does that make sense? You know the data better than I do, so if that's not actually the desired behavior, we can nix this.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

None yet

Development

Successfully merging this pull request may close these issues.

3 participants