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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.

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