surprisingly small CPUE values for DFO-QCS

[zoekitchel]

Noticed surprisingly low CPUE values for DFO-QCS

[zoekitchel]

Found issue in cleaning code where wgt/m^2 is divided by 1000000 m^2/km^2 instead of multiplied, fixed in lines 107-115 of get_dfo-qcs.R

[zoekitchel]

Same changes for Hectate Strait, Strait of Georgia, West Coast Haida Gwaii and West Coast Vancouver Island cleaning codes. Made all changes, but the code threw a few errors:

-get_dfo-sog.R on Line 369: `######### Apply trimming per survey_unit method 2

dat_new_method2 <- apply_trimming_per_survey_unit_method2(clean_sog) summarise() has grouped output by 'survey_unit'. You can override using the .groups argument. Error in if (ext@xmin > -360.01 & ext@xmax < 360.01 & ext@ymin > -90.01 & : missing value where TRUE/FALSE needed`

-get_wchg.R on Line 369: `######### Apply trimming per survey_unit method 2

dat_new_method2 <- apply_trimming_per_survey_unit_method2(clean_wchg) Adding missing grouping variables: survey, haul_id, source, timestamp, country, sub_area, continent, stat_rec, station, stratum, month, day, quarter, season, haul_dur, area_swept, gear, depth, sbt, sst, verbatim_name summarise() has grouped output by 'survey_unit'. You can override using the .groups argument. Joining withby = join_by(survey, haul_id, source, timestamp, country, sub_area, continent, stat_rec, station, stratum, month, day, quarter, season, haul_dur, area_swept, gear, depth, sbt, sst, verbatim_name, survey_unit, year, location, latitude, longitude, cell) Error in dplyr::group_by(): ! Must group by variables found in.data. ✖ Column haul_id is not found. Runrlang::last_trace()` to see where the error occurred.```

I went ahead and pushed these 'cleaned' files to google drive, but they does NOT have flagging columns filled

[AquaAuma]

I'll re-run these cleaning scripts and trouble shoot where needed, thanks for modifying the codes!! I see where problems are, and there also seems to be more issues with the trimming methods outputs, I'll look into it

[AquaAuma]

@zoekitchel, I found out why you encountered issues:

• for DFO-SOG, the minimum criteria to apply trimming require for each survey unit to include at least two year of survey (works for DFO-SOG), and a minimum duration of 10 years (for DFO-SOG, min year is 2012, and max year is 2015, so the duration is 4 years), therefore we end up with an empty data frame and an error in the function. I've modified the function to add a print message and remove the warnings. The survey summary was also missing for DFO-SOG, since it's only 2 years, the graphs are not all interesting, but now it's there. https://github.com/AquaAuma/FishGlob_data/blob/8337fb7088e6ead057ac6267efd158959186b602/functions/apply_trimming_method2.R#L47 https://github.com/AquaAuma/FishGlob_data/blob/8337fb7088e6ead057ac6267efd158959186b602/functions/apply_trimming_method2.R#L289
• for DFO-WCHG, there was a problem with the full_join() function so I fixed the code to add a join that does not create duplicates. https://github.com/AquaAuma/FishGlob_data/blob/8337fb7088e6ead057ac6267efd158959186b602/functions/apply_trimming_method2.R#L203
• I've also found unwanted duplicates in the hauls.removed files, that I fixed in the function here https://github.com/AquaAuma/FishGlob_data/blob/8337fb7088e6ead057ac6267efd158959186b602/functions/apply_trimming_method2.R#L220 and I'll re-run all trimming functions for all surveys to fix the files