Stop_Num Processing

[IJBG]

• [x] Some ebird data ie: https://ebird.org/checklist/S18551742 does have the stop information in the notes from each bird. Create a workflow for extracting this data from the ebird imports. List of these routes in scratch file 'routes_w_stop_level' (once finished add scratch files back to .gitignore (scratch**)
• ,,,,,,1,,,,
• Stops: 0,1,0
• Stops = 0,1,0,
• 1=0, 2=15,3=
• stop 5 =1, stop 9 = 18,
• st14=2; st18=1;
• st 6 or Stop 3 (where the count is not recorded in species_comments but instead in the count column, and then all others aside from that stop should be assigned to a count of 0)
• [x] Get information from in overall checklist note by quarter stops
• [x] Process csv files in inst/extdata/ that have the stop level information
• Hurlbert_stops
• Pippin_Durham_pre2010stops
• Norm Budnitz
• Patsy Bailey (ensure that descriptive data for each route comes from pre-existing information we have, and doesn't set Marsha Stevens as the primary observer)
• [ ] Function to add stop_num = 1 to routes in a year that have 20 stops and every other stop_num BUT stop 1
• [ ] Write function to filter mbbs dataset(s) to just data that has stop-level information (UPDATE: write a function that REPLACES mbbs data with stop-level information when available. Yes, then have the functions that turn it either entirely stop-based on entirely route-based)
• [ ] To the above function, going to need a step that fills in the missing 0s for species that weren't seen in given years. This can be a nice tidy function to call, so it can be used in any cases
• [x] Incorporate transcribed paper files into the mbbs (this workflow can be completed even before the transcriptions are done)
• [ ] Find a way to extract stop-num that may be less fragile (import_ebird_data.R) and therefore captures the missing extracts from ebird
• [x] create .csv version of species_comments and hist_xls so that the functions do not have to be run every time we need the data, as the files are stable and not expected to change.
• [x] create .csv file from transcribed paper files
• [ ] this pull request may also involve finishing the granulate_to_stop_level function and creating that stop-level dataset.

[IJBG]

There's only one checklist where the information is in the overall checklist note by quarter stops. I played around with getting this information through regex statements, but there's so much chasing down of typos, and it needed a whole function built. I just wound up editing this checklist to have the stop information in the notes from each bird. Any 1-5 went to route 1, 6-10 went to route 6, etc. https://ebird.org/checklist/S18852699 This edit, and one I made to a Chatham to fix a typo during while getting the stop level from species_comments, will get caught the next time all the ebird data gets downloaded.

[IJBG]

After checking there's no lingering work and doing the CRAN checks, go ahead and pull request + merge + close the species_comments branch. Pivoting the datasets and the other marks on this checklist can be their own branch.

[IJBG]

Species comments, historical data, and the transcripbed paper files should all be set to save to a .csv and not need to be updated every year. These will be static documents, don't need to be part of a yearly update. They can get updated manually if more data comes in and they need to be.

This will also prevent needing to add more exceptions to species comments every time someone adds a stray comment with a number to their species description on ebird