Data clean edits

[fontikar]

Overall:

• [x] Hide chunks: load dependencies, read parquet and subset columns we want using eval=FALSE

Taxonomic errors:

• [x] Remove counting of taxonRank
• [x] Remove names(arachnids)
• [x] What is the total number of species in the ALA data
• [x] Compute a percentage of species with ALA data that is in the AFD
• [x] "Aname armigera" is a synonym, what is the current 'updated' name in the AFD?
• [x] Fix synonyms

Introduced/Invasive species: WSC:

• [x] A few sentences about WSC
• [x] Remove str_subset(wsc$distribution, "Australia") and str_detect(), keep only introduced_taxa <- wsc |> filter(str_detect(distribution, pattern = "Introduced to.*Australia")) and rest of code in that section

GRIIS:

• [x] Keep code involving in reading in distribution and taxon-edited and joining the files
• [ ] #8
• [x] A sentence for no archanidas in the GRIIS list

Subspecies:

• [x] Remove entire section

Exclude Marine species with WoRMs:

• [x] Hide job::job() chunk with eval=FALSE
• [x] Read in "output/worrms_myg_wm_records_taxamatch.rds"
• [x] Cross match with ALA species and report accordingly

Geographic Errors:

• [x] #6
• [x] Delete section on mainland exclusion as Data retrieval does this already
• [x] Delete selection excluding NA and "0" values in coordinates
• [x] Exclude flagged records by Coordinate Cleaner
• [x] Export clean data as parquet

Deduplication:

• [x] Talk to @payalbal about strategy

[fontikar]

@Ashbyi

Coordinate cleaner

• .val = coordinate validity: non-numeric or missing coordinates and coordinates exceeding the global extent
• .equ = equal: tests for equal absolute longitude and latitude
• .zer = zeros: tests for plain zeros, equal latitude and longitude and a radius around the point 0/0
• .cap = capitals: tests a radius around adm-0 capitals
• .cen = centroids: tests a radius around country centroids
• .sea = seas: tests if coordinates fall into the ocean
• .otl = outliers: tests each species for outlier records
• .gbf = gbif: tests a one-degree radius around the GBIF headquarters in Copenhagen, Denmark
• .inst = institutions: tests a radius around known biodiversity institutions from instiutions

How many records are flagged and therefore removed for each of the above and assess from there advice from @payalbal