Correction for the detection of duplicated measurementType/measurementTypeID and addition of a check for exact duplicated emofs

[cyrilrader]

In the details of the commit, you can see the changes between the BODC files of this month and the ones from april but it's weird because the repo don't contain the ones from april anymore. I don't think it should be a problem since it wants to make changes in a file that doesn't exist anymore.

[Copilot]

Pull Request Overview

This PR enhances duplicate detection for eMoF records, adds an exact duplicate check, and updates unit definitions and documentation accordingly.

• Added R logic to flag duplicate measurementType and measurementTypeID at both occurrence and event levels, plus an exact-eMoF duplicate check.
• Updated README.md to describe the new duplicate checks.
• Cleaned up BODCunits_20250701.csv by removing duplicates and appending new unit codes.

Reviewed Changes

Copilot reviewed 3 out of 8 changed files in this pull request and generated 3 comments.

File	Description
R/checkdataset.R	New blocks for duplicate measurementType/measurementTypeID and exact eMoF checks
README.md	Added entries for the new duplicate checks in the general issues table
files/BODCunits_20250701.csv	Removed duplicate unit entries and inserted new codes

Comments suppressed due to low confidence (2)

R/checkdataset.R:647

• [nitpick] For the measurementTypeID duplicate check, consider setting field = 'measurementTypeID' instead of 'measurementType' to clearly indicate which column is in error.

                            mutate (field = 'measurementType', 

README.md:80

• [nitpick] The description uses "duplicated measurementTypes" but the next entries refer to measurementTypeID; consider consistent singular/plural naming, e.g. "Check if there are duplicated measurementTypeIDs linked to the same occurrenceID."

| Check if there are duplicated measurementTypes linked to the same occurrenceID / Does the same measurement occurs more than once for the same occurrenceID? | Duplicate measurementType linked to the same occurrence | IPTreport\$dtb\$general_issues | Ideally a given occurrenceID can be linked to the same measurementType only once. E.g. It doesn't make sense to say that one same occurrenceID contains adults in one record but larvae in another record, it must be or either adults or larvae or both, but all expressed in only one record. | 

[Copilot]

In duplicated_measurementTypeID_ev(), you’re selecting and grouping by id instead of eventID. It should use eventID to match the filter on event-level records.

Suggested change

	select (id, measurementTypeID) %>%
	group_by (id, measurementTypeID) %>%
	summarize(count = n()) %>%
	filter (count >1 ) %>%
	inner_join((eMoF) %>% mutate (row = row_number()),
	by = c("id", "measurementTypeID") ) %>%
	select (eventID, measurementTypeID) %>%
	group_by (eventID, measurementTypeID) %>%
	summarize(count = n()) %>%
	filter (count >1 ) %>%
	inner_join((eMoF) %>% mutate (row = row_number()),
	by = c("eventID", "measurementTypeID") ) %>%

[Copilot]

The filter for duplicate measurementType currently excludes measurementTypeID but does not ensure measurementType is not NA. Consider adding !is.na(measurementType) to avoid grouping NA values.

Suggested change

	duplicated_measurementType_oc <- eMoF %>% filter (!is.na(occurrenceID),is.na(measurementTypeID)) %>%
	duplicated_measurementType_oc <- eMoF %>% filter (!is.na(occurrenceID), !is.na(measurementType), is.na(measurementTypeID)) %>%

[Copilot]

[nitpick] New unit codes are inserted in multiple spots; consider keeping the CSV in sorted or grouped order to simplify future maintenance.

[cyrilrader]

Will redo but on dev branch