954 create helper function to auto populate the saltfresh column in tada criteria and methodologies template for users

[hillarymarler]

Closes #954

Adds TADA_SaltFreshIndicator which populates the TADA.SaltFreshIndicator column to support mod 2 workflow and provide salt/fresh info for criteria in Mod 3.

This function will be added to an expanded Mod 2 vignette update in the near future.

This PR adds:

1. TADA_SaltFreshIndicator function
2. tests for the new function2
3. Csv files in extdata to support crosswalking of salt/fresh indicator to ATTAINS.WaterType and TADA.MonitoringLocationIdentifierTypeName

Reviewing the reference table I added to crosswalk to the saltfresh indicator by water type as well as the funciton itself would be helpful. I really was not sure what to to with estuaries - should they get their own indicator value?

Pull Request Checklist (convert PR to draft if in progress)

Required

• Update your branch from the latest develop and resolve any merge conflicts

• Run devtools::test(), devtools::check(), and devtools::document() locally; ensure tests pass and fix any errors, warnings, or notes. Add new dependencies to DESCRIPTION and document appropriately

• Add/update vignettes for corresponding changes in functionality, list these under articles in _pkgdown.yml, and ensure added/updated vignettes run and build with proper formatting locally

• Request review from at least one developer team member (convert PR to ready for review if it was designated as in progress)

Best practices

• Include a summary of the changes made and relevant context/motivation

• Link issues to auto-close on merge (use Development sidebar or include "Closes #" in the PR)

• Refresh inline/block comments for clarity

• Update roxygen docs and include examples; review help pages

• Add/update tests in tests/testthat; review the bot's coverage report from test-coverage and confirm all changes are covered

Conditional

• If there is a bot spelling comment, run spelling::spell_check_package() locally and fix any misspellings; add approved project terms to WORDLIST with spelling::update_wordlist()

• If tests fail suggesting internal reference files need a refresh, run .TADA_UpdateRefFiles() and .TADA_UpdateExampleData() locally via MaintenanceScheduled.R or trigger the Component File Update GitHub Action

• If new example data files were added, document them in ExampleData.R and include them in MaintenanceScheduled.R for regular refresh

• If columns were added/updated, update RequiredCols.R

• If changes affect other package or the shiny app functions, update those impacted functions accordingly

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  WORD                 FOUND IN
SaltFreshIndicator   TADA_SaltFreshIndicator.Rd:28

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SaltFreshIndicator   TADA_SaltFreshIndicator.Rd:28

[github-actions]

coverage-report

File	Coverage		Missing
All files	66%	✅
R/ATTAINSCrosswalks.R	52%	✅	32-876 1102-1106 1111-1116 1121-1124 1129-1160 1166-1169 1175-1178 1192-1195 1206-1221 1267-1270 1514-1515 1522-1523 1528-1529 1556-1563 1694 2018-2021 2026 2055-2059 2071-2074 2082 2091-2098 2113-2122 2127-2135 2141-2164 2184-2199 2204-2207 2212-2243 2256-2259 2331-2335 2430-2439 2655-2656 2725 2896-2902 3123-3705 3884-3887 3895-3900 3906-3926 3934-3938 3951-3955 3986-4095 4147-4302 4307-4310 4371-4372 4408 4484-4490 4609 4686-4688 4692-4694 4730-4775 4832-4834 5138 5142

Minimum allowed coverage is 20%

Generated by 🐒 cobertura-action against 34e69b5

[wokenny13]

if ATTAINS.WaterType hasn't been assigned to a data frame yet, I noticed that if you accidentally made a typo ex I accidentally typed AU' instead of AU, the function will run with the default as ML. Should there be an error if the arg input is not one of AU or ML?

I notice also that when using location_col = "ML" the data frame grows a significant amount (ex. Data_Nutrients_UT would result in 6.6M rows). Is this expected? Are there one to many matches occuring in the WQPMonLocTypeToSaltFresh.csv?

[hillarymarler]

if ATTAINS.WaterType hasn't been assigned to a data frame yet, I noticed that if you accidentally made a typo ex I accidentally typed AU' instead of AU, the function will run with the default as ML. Should there be an error if the arg input is not one of AU or ML?

I notice also that when using location_col = "ML" the data frame grows a significant amount (ex. Data_Nutrients_UT would result in 6.6M rows). Is this expected? Are there one to many matches occuring in the WQPMonLocTypeToSaltFresh.csv?

Thanks for these questions - will get back to you with a response (and likely some code fixes) later this week.

[hillarymarler]

@wokenny13 -I fixed the join bug that was creating extra rows in the resulting df.

[hillarymarler]

@wokenny13 - I added stops with messages if the user incorrectly enters params.

[wokenny13]

Would there be any value/ potential interest from users to provide their own custom reference table as an arg input for a user's own crosswalk table (rather than using the internal TADA tables) that would allow users to review this list, and make any edits as needed?

This could potentially be another function that creates a sort of own WQPMonLocTypeToSaltFresh/ATTAINSWaterTypeToSaltFresh ref output for users to only review the unique ATTAINS.WaterType or WQP MonitoringLocationIdentifier and the TADA default of Salt/Fresh from TADA, and then users can customize as desired.

Users would not need to go through this step and can use the default TADA internal Salt/Fresh table if desired. But if they do feel the need to customize they can do so. I was thinking this could help with any tricky classification of waters that could be either salt or fresh.

[hillarymarler]

Would there be any value/ potential interest from users to provide their own custom reference table as an arg input for a user's own crosswalk table (rather than using the internal TADA tables) that would allow users to review this list, and make any edits as needed?

This could potentially be another function that creates a sort of own WQPMonLocTypeToSaltFresh/ATTAINSWaterTypeToSaltFresh ref output for users to only review the unique ATTAINS.WaterType or WQP MonitoringLocationIdentifier and the TADA default of Salt/Fresh from TADA, and then users can customize as desired.

Users would not need to go through this step and can use the default TADA internal Salt/Fresh table if desired. But if they do feel the need to customize they can do so. I was thinking this could help with any tricky classification of waters that could be either salt or fresh.

I like this idea! Yes it makes sense to me that users might want to provide their own crosswalk, particularly to deal with tricky water type like estuaries.

I will make some updates to:

1. Facilitate users being able to see/review the default TADA salt/fresh crosswalk
2. Allow users to supply their own crosswalk if they choose to edit the TADA defaults

@wokenny13 and @cristinamullin would your preference be that I do this additional work as part of this PR or a new one? The major pro to merging this first draft in before the update is that it would allow me to start working on adding this tab in the Shiny app.

[wokenny13]

I think as a separate PR is fine. Other than that suggestion, I think this PR is good to merge in.