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Flag occurrence records sourced from iNaturalist

Source: R/flag_inaturalist.R
flag_inaturalist.Rd

This function identifies and flags occurrence records sourced from iNaturalist. It can flag all iNaturalist records or only those that do not have Research Grade status.

Usage

flag_inaturalist(occ, columns = "datasetName", research_grade = FALSE)

Arguments

occ

(data.frame) a data frame containing the occurrence records to be examined, preferably standardized using format_columns(). Must contain the columns specified in columns.

columns

(character) column name in occ where the function will search for the term "iNaturalist". Default is "datasetName".

research_grade

(logical) whether to flag all records from iNaturalist, including those with Research Grade status. Default is FALSE, meaning that only iNaturalist records without Research Grade will be flagged.

Value

A data.frame that is the original occ data frame augmented with a new column named inaturalist_flag. Flagged records receive FALSE, while all other records receive TRUE. As with all other flagging functions in RuHere, TRUE indicates that the record passed this test and is eligible for retention; FALSE indicates it failed and is flagged as potentially problematic, and can be removed using remove_flagged().

Details

According to iNaturalist, Observations become Research Grade when:

  • the iNaturalist community agrees on species-level ID or lower, i.e. when more than 2/3 of identifiers agree on a taxon;

  • the community taxon and the observation taxon agree;

  • or the community agrees on an ID between family and species and votes that the community taxon is as good as it can be.

Examples

# Load example data
data("occurrences", package = "RuHere")
# Flag only iNaturalist records without Research Grade
occ_inat <- flag_inaturalist(occ = occurrences, research_grade = FALSE)
table(occ_inat$inaturalist_flag) # Number of records flagged (FALSE)
#> 
#> TRUE 
#> 4080 
# Flag all iNaturalist records (including Research Grade)
occ_inat <- flag_inaturalist(occ = occurrences, research_grade = TRUE)
table(occ_inat$inaturalist_flag) # Number of records flagged (FALSE)
#> 
#> FALSE  TRUE 
#>   869  3211