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Filter data

Source: R/filter_data.R
filter_data.Rd

Filters taxa and distributions data frames, and returns the filtered data and notes.

Usage

filter_data(taxa, distributions, establishment_means = NULL)

Arguments

taxa

Data frame as returned by get_taxa().

distributions

Data frame as returned by get_distributions().

establishment_means

EstablishmentMeans to filter on. Only taxa with matching distributions with establishmentMeans in this vector will be retained. Default is "introduced".

Value

A list with three data frames:

  • taxa: Filtered taxa data frame, with different columns than the input taxa data frame.

  • distributions: Filtered distributions data frame.

  • notes: Data frame with notes on taxa that were not included or replaced in the filtered data.

Filter on establishmentMeans

Defaults to NULL, which means no filter on establishmentMeans. Possible values are "native", "introduced", "nativeReintroduced", "introducedAssistedColonisation", "vagrant", "uncertain" and "nativeEndemic".

Filter details

Taxa are removed if

  • they are not matched with the GBIF backbone (i.e., nubKey is NA),

  • they do not have a matching distribution (i.e., taxonKey is not in distributions$taxonKey),

  • they do not have a matching distribution with establishmentMeans in establishment_means.

Synonyms are replaced by the accepted taxa they are synonyms of (i.e., taxonomicStatus is either "synonym", "ambiguous synonym", "heterotypic synonym", "homotypic synonym", "misapplied" or "proparte synonym).

scientificName is replaced with the scientific name matching the GBIF backbone.

Taxa details

The taxa data frame in the output list has 6 variables:

  • taxonKey: GBIF taxon key of scientificName. This value is replaced with acceptedKey if the taxon is a synonym of an accepted taxon.

  • nubKey: GBIF backbone taxon key.

  • taxonID: Taxon ID of scientificName, as provided in the checklist.

  • scientificName: Scientific name of the taxon. This value is replaced with acceptedName for all records.

  • kingdom: Kingdom of the taxon.

  • taxonRank: Taxonomic rank of the taxon.

Examples

if (FALSE) { # \dontrun{
# Updated checklist of the ants in Belgium
datasetKey <- "32afaa9d-a27f-4885-b30c-ce08c34e1efb"
taxa <- get_taxa(datasetKey)
distributions <- get_distributions(datasetKey, taxa)
filter_data(taxa, distributions, establishment_means = "introduced" )
} # }