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Remove flagged records

Source: R/remove_flagged.R
remove_flagged.Rd

This function removes occurrence records flagged as invalid by one or more flagging functions. Additional manual control is available to force keeping or removing specific records, regardless of their flag values.

Usage

remove_flagged(
  occ,
  flags = "all",
  additional_flags = NULL,
  force_keep = NULL,
  force_remove = NULL,
  remove_NA = FALSE,
  column_id = "record_id",
  save_flagged = FALSE,
  output_dir = NULL,
  overwrite = FALSE,
  output_format = ".gz"
)

Arguments

occ

(data.frame or data.table) a dataset with occurrence records that has been processed by two or more flagging functions. See details.

flags

(character) a character vector with the names of the flag columns to be used for filtering records. See details for the available options. Default is "all".

additional_flags

(character) an optional named character vector with the names of additional logical columns to be used as flags. Default is NULL.

force_keep

(character) an optional character vector with the IDs of records that were flagged but should still be kept. Default is NULL.

force_remove

(character) an optional character vector with the IDs of records that were not flagged but should still be removed. Default is NULL.

remove_NA

(logical) whether to remove records that have NA in the flags specified. Default is FALSE.

column_id

(character) the name of the column containing unique record IDs. Required if force_keep or force_remove is used. Default is NULL.

save_flagged

(logical) whether to save the flagged (removed) records. If TRUE, an output_dir must be provided. Default is FALSE.

output_dir

(character) path to an existing directory where removed flagged records will be saved. Only used when save_flagged = TRUE.

overwrite

(logical) whether to overwrite existing files in output_dir. Only used when save_flagged = TRUE. Default is FALSE.

output_format

(character) output format for saving removed records. Options are ".csv" or ".gz". Only used when save_flagged = TRUE. Default is ".gz".

Value

A data.frame containing only the valid (kept) records according to the flags and additional criteria.

Details

The following flags are available: correct_country, correct_state, cultivated, fossil, inaturalist, faunabr, florabr, wcvp, iucn, duplicated, thin_geo, thin_env, .val, .equ, .zer, .cap, .cen, .sea, .urb, .otl, .gbf, .inst, and .aohi.

Examples

# Load example data
data("occ_flagged", package = "RuHere")

# Remove all flagged records
occ_valid <- remove_flagged(occ = occ_flagged)

# Remove flagged records and force removal of some unflagged records
to_remove <- c("gbif_5987", "specieslink_2301", "gbif_18761")
occ_valid2 <- remove_flagged(occ = occ_flagged,
                             force_remove = to_remove)

# Remove flagged records but keep some flagged ones
to_keep <- c("gbif_14501", "gbif_12002", "gbif_5168")
occ_valid3 <- remove_flagged(occ = occ_flagged,
                            force_keep = to_keep)