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pfmc-assessments / PacFIN.Utilities

R code to manipulate data from the PacFIN database for assessments
http://pfmc-assessments.github.io/PacFIN.Utilities
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Add additional message or check for unspecified age methods in cleanPacFIN() #128

Open chantelwetzel-noaa opened 2 months ago

chantelwetzel-noaa commented 2 months ago

While working on processing bds data for a select suite of species, I became aware that age records without an ageing method specified were not be being transferred to the Age column in the cleaned data. In the data I was looking at this was primarily occurring for Oregon records where for some years large numbers of the age records did not have an ageing method specified, although there were records from Washington as well. @aliwhitman spot-checked some species identified that had this issue for records in the early- to mid-2000s with this issue and confirmed that they do not have an ageing method in ODFW's internal records.

Given the range of ageing approach across time, the decision to remove these ages with a missing age method may vary on a species-specific based. For example, in the data I was looking at there were a large number of records for widow rockfish with a missing age method where these missing age methods covered period of times when surface reads were prevalent but break-and-burn was also commonly used. In this situation, it may be difficult for the user to determine the correct age method, hence, they may need to be omitted. In contrast, there was also a large number of missing age methods for sablefish across time, but the ages for this species are almost always break-and-burn.

Short Term: cleanPacFIN() does currently print out information on the ages and the age methods removed but this information can be easily missed by the user. Think about ways to alert the user that they may be accidently removing large number of years with age data due to the age method being missing and the data should be further investigated.

Long Term: Investigate whether the ageing method can be determined from existing records or if the ageing labs can identify what periods of time there may have been a single ageing method applied for a species or across species.

aliwhitman commented 2 months ago

ODFW is currently reviewing raw aging records from WDFW and NWFSC to see if we can fill in gaps where the aging method is missing from PacFIN. We're currently focusing on sablefish, yellowtail and widow for the upcoming assessment cycle. We'll keep you updated on progress there.

But the larger issue stands for older age records and I am happy to help as needed!