Add electrofishing site data to `habitat_confirmations.xls`

[NewGraphEnvironment]

some documentation of this process here. https://github.com/NewGraphEnvironment/fish_passage_template_reporting/issues/8

Sites were only enclosed at Thompson downstream sites which also have a second pass on the following day. We tested our efficiency by seeing how many of our captured fish had tags the next day (ie. we put the fish back into our enclosed sites after our first pass and fished them again the next day)

NOTE - for Thompson h/p should not be 2 teh second day since the fish were put back in. Also - the downstream sites were enclosed. temperature, conductivity and Turbidity were likely different second day too - card will tell us - should be recorded

[NewGraphEnvironment]

Actually - I think we are going to need to leave h/p as 2 for Thompson second day to avoid other complexity. We can just put a note in Step 2 that fish were returned to the site after the first pass.

[lucy-schick]

A couple sites that were a bit funky and have missing data:

• 8478_ds_ef1 - Trib to McDonell Lake

  • missing site length

• 8478_ds_ef3 - Trib to McDonell Lake

  • missing ef seconds. Looks like all sites were added to one sheet, seconds are present for ef1 and ef2 but looks like they forgot to write down ef3, should we just guess?

[lucy-schick]

Next time, update/add data in step_4_stream_site_data spreadsheet from fiss and fish cards, then when you run the scripts in extract_inputs.R to populate step_2_fish_coll_data you will have all the correct data. I edited that data once it was already in step_2_fish_coll_data which meant I also had to edit the data in step_4_stream_site_data... still learning!

Data that was added by hand. Noting this down in case it needs to be re done... which would not be fun! Beware that some info was taken from fish cards and some from fiss cards

• sampling_method, ef_seconds, enclosure, voltage, frequency for all sites

• 198215 - Dale Creek all ef sites.

  • Temp, conductivity added from fish card
  • Turbidity added from fiss card

• 123377 Thompson Creek

  • ds sites with haul pass = 2, Temp, conductivity, turbitidy, added from fish card
  • us sites, temp, conductivity, turbitidy, added from fiss card
  • ds_ef1 added site length from fiss card

• 8478 Trib to McDonell Lake

  • ds sites, Temp, conductivity added from fiss card
  • _us site, fiss card labelled 8547_us but I'm pretty sure is should be 8478_us because there is a fish card with data labelled 8478_us (and no fish card labelled 8547_us), Temp, conductivity, turbidity added from fiss card
  • ds_ef1 widths added from fiss card to step 4, then avg width added to site width in step 2

• 198217_ds sites - trib to Skeena

  • Turbidity added from fiss card

[NewGraphEnvironment]

This is great! Thank you.

Next time, update/add data in step_4_stream_site_data spreadsheet from fiss and fish cards, then when you run the scripts in extract_inputs.R to populate step_2_fish_coll_data you will have all the correct data.

Another (and potentially preferred option from my perspective) would be to add the data to data_field/2023/form_fiss_site_2023.gpkg in QQIS, track the changes in version control in the repo via fpr_sp_gpkg_backup, export to csv with scripts/fiss_site_tidy.R (template file is here https://github.com/NewGraphEnvironment/dff-2022/blob/master/scripts/fiss_site_tidy.R but likley now needs updateing) and copy paste over step_2_fish_coll_data

[lucy-schick]

Yes I agree I think that is the best way to do it (see slack message).

[NewGraphEnvironment]

logging ad hoc changes required to build reporting objects here as am doing so in main fish submission spreadsheet. Related to https://github.com/NewGraphEnvironment/fish_passage_skeena_2023_reporting/issues/102

step_3_individual_fish_data

• [x] sampling_method
• [x] method_number (usually 1 unless multiple methods employed - not the case in 2023)
• [ ] Gramophone dipnetting site correction - https://github.com/NewGraphEnvironment/fish_passage_skeena_2023_reporting/issues/37#issuecomment-2099726377
• [x] Thompson downstream site ids to 4, 5 and 6 for mark recapture events. haul pass moved to 1 (not implemented in main) - https://github.com/NewGraphEnvironment/fish_passage_skeena_2023_reporting/issues/99

step_2_fish_coll_data

• [x] enclosure first letter non-capitalization in first row of raw FDS template is inconsistent with drop down menus for remaining rows. Not sure why or if it matters much but open vs Open in rows where it is not in the drop down menu could glitch data dump to provincial databases. may as well correct