Post-run content-related changes for 2024 update

[rikudoukarthik]

Content changes (mainly year-related) to be made to steps after trend (and occupancy) model runs.

• [x] Code for fixing to certain version of results (fix_to_printed_results.R) to be checked/updated before resolving and classifying.
• [x] Future-year projected value columns (including extra.years object) to be updated as appropriate (TBD).
• [x] Sensitivity checks for current trend (each year dropped manually)
• [ ] 00_plot_functions.R needs significant update to incorporate one new year in graphs (2022, 2023 coded manually). This will stabilise once CAT reaches 10 years.
• [ ] 20_website_database.R may or may not need updates in file/folder naming (L 97, 98, 102). TBD.

SoIB_mapping_2023.csv still has some columns yet to be mapped. Also, this CSV will be regularly updated to reflect changes, e.g., updates to IUCN status 57ed26b.

• [x] Map the following columns: BLI.Common.Name, BLI.Scientific.Name, IUCN.Category, WPA.Schedule, CITES.Appendix, CMS.Appendix

20_website_SoIB_main.R:

• [ ] proprange2022/Range Coverage columns and BLI name columns to be updated.
• [ ] 2015\u20132023 in may or may not need update (TBD).
• [ ] "2023" in column names and file names --> "2024"

Update: 10 Oct 2024

Occupancy

@rikudoukarthik :

• [x] In run_species_occupancy-presence.R, add code to delete all .csv output files before writing new ones, because file names are of species names, some of which have changed with taxonomy update
• [x] In resolve occupancy, add code to delete old output files before writing new ones (species names changed). Old occupancy result values are needed only for website output, which will be taken directly from SoIB_main.csv anyway.

Resolve trends

@rikudoukarthik :

• [x] Update classification step of subnational level Priority Status: just take Priority from national level, but keep classifying long-term and current trend statuses. Subnational levels do not have range size being classified, so it doesn't make sense to assess separate priority.
  • [ ] Website already only shows national level Priority for subnational levels. When this change made to main pipeline, update website database code appropriately
• [x] Remove fix_to_printed_results.R and associated files/calls in code elsewhere. This was done because main SoIB 2023 run was done before some additional sensitivity checks were put in place for classification, and we wanted to maintain consistency with the report. Now, we are updating these anyway.
• [x] Before writing the output trends.csv file in L878 :
  • [x] Rename the past trends.csv to trends_20xx.csv (can even include an interannual_update conditional, and will need to update metadata object also)
  • [x] Save latest dataframe as trends.csv

Classify and summarise

@ashwinv2005 :

• [x] Read in trends.csv, which is the latest run data (we now only need old trends_20xx.csv during plotting and nowhere else
• [x] Before writing the output SoIB_main.csv file in L501:
  • [x] Retain BR:BU columns from the old SoIB_main.csv file (so load that first) by adding the suffix _MAJ.UPD or _maj_upd, rest all overwritten with latest
  • [x] The new main object will have updated taxonomy (basis latest mapping file), so map to old using this
  • [x] (SoIB_main_wocats.csv will be overwritten entirely, in resolve above, without the two kinds of columns)
• [x] We want to summarising step, but use the latest Statuses and other values
• [ ] Add another conditional step only for interannual updates to compare latest interannual results with previous "major update" results (matrix of status comparisons + actual list of species with major changes)
• [ ] Summarisation section (including High Priority breakup) needs updates, mainly to make code year-agnostic and to decide between major update or latest year update as fallback.

Plotting

@rikudoukarthik :

• [ ] Delete all old plot files (both trends and maps) before writing new ones (species name changes)
• [x] Remove code for generating systematic monitoring plots from all scripts (done last year and won't be done the same way in future)
• [ ] Make all plotting scripts/functions (e.g., plot_import_data(), geom_axisbracket(), etc.) year-agnostic, using soib_year_info()
• [ ] Add conditional for input data for plots (at L418-427 of plot_load_filter_data()):
  • [ ] Single filter on two columns (but year-agnostic): filter((year %in% 1992:2022 & latest_interannual == FALSE) | (year == 2023 & latest_interannual == TRUE))
  • [ ] To make this filter condition year-agnostic, soib_year_info() needs to be updated with a new option to output the year of the latest "major SoIB update"
  • [ ] This filter is only needed when interannual_update == TRUE
• [ ] Update plot features:
  • [ ] x-axis plot settings will all need to be tweaked with trial-and-error to accommodate the new year. Best to automate it as much as possible (as done for y-axis breaks).
  • [ ] Add visual elements for distinguishing the latest interannual data on plots from old data

[rikudoukarthik]

Indian BIRDS checklist related updates made to the mapping file in 7238158c850b72097d51ddca0c1d4f0937f266d5

[rikudoukarthik]

Occupancy code edits made in 03d2ada21d280820280abc95da8cd0d67c87e41d

[rikudoukarthik]

fix_to_printed_results removed entirely 4b84030e9cc695c655362e5c2d912a0fcdf167af