Data Overview Edits

[fontikar]

Taxonomic overview

• [x] Write a few sentences in taxonRank section about unranked and NA taxon rank taxa.

Spatial overview

• [x] Remove states that are not Australian mainland/Tasmania for the state level overview using filter
• [x] Remove stateProvince == NA
• [x] Report top 3 species with most obs per state

Record overview

• [x] Exclude OBSERVATION and OCCURRENCE from basisOfRecord before tabulating
• [x] Provide definitions of remaining basisofRecord values

Assertions

• [x] A few sentences about assertions, what are the used for and what the logicals (1,0) mean.
• [x] A few sentences that we have taken a "taxonomic" and "spatial" approach in looking at assertions

Spatial assertions

• [x] Remove all coordinate related code from RMD for now

• [x] Sentences explaining that we investigated a range of spatial assertions and found the following are safe to ignore:

• COORDINATE_UNCERTAINTY_METERS_INVALID

• COORDINATE_ROUNDED

• [x] A few sentences on we will use the following Spatial assertions to refine out data download:

• PRESUMED_NEGATED_LONGITUDE + PRESUMED_NEGATED_LATITUDE

• PRESUMED_SWAPPED_COORDINATE

• ZERO_COORDINATE

• COORDINATE_OUT_OF_RANGE

Taxonomic assertions

• [x] Move the taxonomic assertions work from 02.1_ala_data_assertions_overview here for the following assertions:

• TAXON_MATCH_FUZZY

• [x] A sentence prompting expert to check whether TAXON_MATCH_FUZZY are valid

[fontikar]

~Fonti to use COORDINATE_OUT_OF_RANGE to exclude in data download~

[fontikar]

~Fonti to add PRESUMED_NEGATED_LATITUDE to exclude in data download~

[fontikar]

• ~TAXON_QUESTION_SPECIES~
• ~TAXON_EXCLUDED should be excluded by fonti in data download~

[fontikar]

Taxonomic assertions:

• ~recordID~
• ~recordedBy~
• ~collectionCode~
• ~institionCode~
• ~dataREsourceName~

@fontikar

[fontikar]

Fonti to:

• [x] Clean up, delete some code for Overview
• [x] All collect() calls at the start
• [x] one collect() for all data
• [x] one collect() for no citizen science data or a filter by boR as a second step.
• [ ] Follow up on this "facebook group/admin" - for taxa that can be identified by photo...what to do? First sort by BB JM? then reach out to hobbyists?

[fontikar]

Once @fontikar has done the above:

@JoshNitschke:

• [ ] Two sections one for all data, another for only preserved samples/material samples data (ie. no citizen science data)
• [ ] Redeploy report as a website then
• [ ] send to BB and JM for taxonomic review and comments. Gentle encouragement to use Github issue.

[fontikar]

There is a known issue with Arrow at the moment with open_dataset() we need to reinstall using:

install.packages('arrow', repos = c('https://apache.r-universe.dev'))

Details here: https://github.com/apache/arrow/issues/40667#issuecomment-2007942987