Clean GBIF occurrences based on user-selected flags and/or specific gbifIDs
Source:R/clean_occs.R
clean_occs.RdClean GBIF occurrences based on user-selected flags and/or specific gbifIDs
Usage
clean_occs(
checked_occs,
remove_flags = c("flag_no_coords", "flag_cc_capitals", "flag_cc_centroids",
"flag_cc_institutions", "flag_cc_equal", "flag_cc_gbif", "flag_cc_zeros",
"flag_high_uncertainty", "flag_outside_native"),
remove_gbifids = NULL,
gbifid_reason = NULL,
keep_gbifids = NULL
)Arguments
- checked_occs
Result from check_occs() function
- remove_flags
Vector of flag names to use for cleaning. Set to NULL to ignore all automatic flags. Flag names must be: "flag_no_coords" Missing coordinates; "flag_cc_capitals" Near country capitals; "flag_cc_centroids" Near country centroids; "flag_cc_institutions" Near biodiversity institutions; "flag_cc_equal" Equal coordinates; "flag_cc_gbif" GBIF headquarters; "flag_high_uncertainty" High coordinate uncertainty; "flag_outside_native" Outside native range
- remove_gbifids
Vector of gbifIDs to remove from the dataset, or a named list where names are reasons and values are vectors of gbifIDs sharing that reason. Example: list("identification uncertain" = c("1234", "5678"), "habitat mismatch" = c("9012"))
- gbifid_reason
Character string providing the default reason for manual gbifID removal when remove_gbifids is a simple vector.
- keep_gbifids
Vector of gbifIDs to keep in the clean dataset even if they are flagged as problematic by automatic flags. These records will override any flags. Example: c("5101884416", "1252668978")