holding data - confirm run and adipose clipped

[alvizek]

We need to confirm the run and adipose clipped status of the holding data or if unknown we need to include that.

[liz-fw]

Notes on holding data (run and adipose):

• Battle: USFWS request was for only spring and unknown runs. No adipose_clipped data collected
• Clear: USFWS request were all spring- mutated run column in standard-format markdown. Filtered to chinook in the clear .Rmd. No adipose_clipped data collected
• Deer: no run or adipose_clipped data collected, but raw file for 1986-1996 holding notes that it is the "DEER CREEK ADULT SPRING-RUN SALMON COUNTS BY REACH" ; 1997-present raw file is titled "SRCS" - so we can assume that the run is spring. Updated in standard-format markdown.
• Mill: does not collect holding
• Butte: holding surveys are for spring run chinook (https://www.calfish.org/ProgramsData/ConservationandManagement/CentralValleyMonitoring/SacramentoValleyTributaryMonitoring/ButteCreek.aspx) assuming these are spring, no adipose_clipped data recorded

Action items:

• [ ] Confirm - is it OK to have all Clear data as spring or do we want to change it to NA

[liz-fw]

associated branch: holding-data-checks

[liz-fw]

• [x] Deer - adipose_clipped can be F (no hatchery)
• [x] all other streams (clear and butte), adipose_clipped = "not recorded"
• [x] double check holding (multiple rows for a reach/day/stream, no double counting, check crew column)

[liz-fw]

@alvizek I changed deer adipose_clipped to F and other streams to not recorded.

re: double counting checks, butte creek counts are already processed to be averaged across date and reach. Battle and Clear both have multiple rows for many date/reach combinations. I think the next steps should be:

• [ ] for Battle, group by date and reach and take the average because in the adult data report, Battle's methods state "Three snorkelers swim perpendicular to the flow and count holding Chinook, carcasses and redds.".
• [ ] for Clear, group by date and reach and take the average. According to methods, "Moving downstream with the current, three snorkelers counted adult Chinook, Chinook carcasses, and Chinook redds... Generally, snorkelers were adjacent to each other in a line perpendicular to the flow and would keep track of individual counts within their lane or area of the creek. As needed, snorkelers would confer with each other to make sure no salmon were missed or double counted and then sum and record their counts." (https://www.noaa.gov/sites/default/files/legacy/document/2020/Oct/07354626154.pdf page 4)

There is no additional information in the raw data files that would further distinguish the multiple rows, except in Clear the notes column has WP XYZ values (likely waypoint) that are mostly distinct

[alvizek]

Ashley and Liz discussed and decided to ask data stewards during the Adult Next Steps meeting.

[alvizek]

Battle confirmed that we are not double counting (we do not need to average). Need to ask Clear same questions to close out issue.