Gear grouping standards

[kellijohnson-NOAA]

Is your enhancement request related to a problem? Please describe.

For lingcod (2021) I grouped some catches from gill nets with the trawl fleet when they should of been part of the fixed gear fleet because they are a set net. Thanks to John Field for pointing this out.

Describe the solution you'd like

A programmatically created lookup table to translate gear codes to fleet and example code on how to use the table. The method should accommodate data from PacFIN, WCGOP, and RecFIN.

Tasks

• document discussion from 2022-05-10 nwfsc-assess office hour here in this issue
• create a lookup table using R code and store it in {PEPtools} for now
• create code to use the lookup table and document various use cases
• create process for grouping data using area-specific breaks with port codes (brought up by @brianlangseth-NOAA) PEPtools#5
• make code stored by @andi-stephens-NOAA public in the {nwfsDiscard} package nwfscDiscard#2
• create summary tools to explore the data to facilitate decisions such as will discard rates of the trawl fleet be informed from all gear groups within the trawl fleet that have data or just the bottom-trawl gear groups that have more information, are any gear groups within a fleet different from other gear groups; can any fleets be combined due to similar behaviour? I think {ggridges} could be helpful here
• translate 9 PacFIN groups to 6 WCGOP groups
• create a list of items that should be included in the data-workshop with gear grouping decisions being one of the items

References

WCGOP categories

• Bottom trawl
• Fixed gear
• Hook and line
• Midwater trawl
• Pot
• Shrimp trawl

Gear groupings

• PacFIN hierarchical gear codes
• FAO list of Standard Statistical Classification of Fishing Gear

R code

• dplyr::recode()
• dplyr::recode(, !!!) with splicing
• match()
• %in%

[iantaylor-NOAA]

Here's a note on midwater trawl related to this issue.

The getGearGroup() function groups midwater trawl and bottom trawl in the TWL group with species-specific modifications to break it out for sablefish and spiny dogfish. Both use a MSC = miscellaneous group and spiny dogfish additionally separates midwater trawl from bottom trawl but lumps shrimp trawl with bottom trawl.

Widow Rockfish and Yellowtail Rockfish that are being assessed in 2025 are frequently caught by targeted midwater rockfish gear (Widow has a separate "midwater" fleet), so making it easy to explore the midwater catch separate from bottom trawl catch will be helpful.

@kellijohnson-NOAA you may have already covered this in your ongoing changes to this package, but it could be helpful to add to something to the README on gear groupings, perhaps including a suggestion to run something like dplyr::mutate(geargroup = ifelse(GRID == "MDT", yes = "MDT", no = geargroup)) to separate the midwater trawl for those who are interested.

Although the documentation makes it clear that the gear groupings come from https://pacfin.psmfc.org/pacfin_pub/data_rpts_pub/code_lists/gr.txt I don't understand how that information gets converted into the GearTable object used by getGearGroup(). Perhaps it's via get_codelist() but I don't see where that function is run, so some additional notes in the code might be helpful.

[kellijohnson-NOAA]

In my recent edits that I am working on I have only fixed this for sablefish to create three groups.

If you follow the link in the previous comment, all GRID (which is what is present in the data downloaded from PacFIN) are translated to Gear Group and the gear groups are used for fleets. This will more than likely create too many fleets for what a user actually wants but it is at least a start. In the future it could be modified for more species behind the scenes but that is difficult because those methods are hidden from the average user so I have chosen to leave it as is.