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Get consensus across multiple flags

Source: R/flag_consensus.R
flag_consensus.Rd

This functions creates a new column representing the consensus across multiple flag columns. The consensus can be computed in two ways:

  • "all_true": A record passes the consensus (TRUE) only if all specified flags are TRUE.

  • "any_true": A record passes the consensus (TRUE) if at least one specified flag is TRUE.

Usage

flag_consensus(
  occ,
  flags,
  consensus_rule = "all_true",
  flag_name = "consensus_flag",
  remove_flag_columns = FALSE
)

Arguments

occ

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

flags

(character) a string vector with the names of the flags to be used in the consensus evaluation. See details for see the options.

consensus_rule

(character) A string specifying how the consensus should be computed. Options are "all_true" (record passes the consensus only when all flags are TRUE) or "any_true" (record passes the consensus when at least one flag is TRUE). Default is "all_true"

flag_name

(character) name of the column that will store the consensus result. Default is "consensus_flag".

remove_flag_columns

(logical) whether to remove the original flag columns specified in flags from the final output. Default is FALSE.

Value

The original occ with an additional logical column defined by flag_name, indicating the consensus result based on the selected consensus_rule. As with all other flagging functions in RuHere, TRUE indicates that the record passed the consensus criterion and is eligible for retention, while FALSE indicates it failed and is flagged as potentially problematic.

Details

The following flags are available: correct_country, correct_state, cultivated, fossil, inaturalist, faunabr, florabr, wcvp, iucn, duplicated, thin_geo, thin_env, year, .val, .equ, .zer, .cap, .cen, .sea, .urb, .otl, .gbf, .inst, and .aohi. Flags may be combined from any category (metadata-based, range-based, or thinning-related).

Examples

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

# Get consensus using florabr, wcvp, and iucn flags
 # Valid (TRUE) only when all flags are TRUE
occ_consensus_all <- flag_consensus(occ = occ_flagged,
                                    flags = c("florabr", "wcvp", "iucn"),
                                    consensus_rule = "all_true")
# Valid (TRUE) when at least one flag is TRUE
occ_consensus_any <- flag_consensus(occ = occ_flagged,
                                    flags = c("florabr", "wcvp", "iucn"),
                                    consensus_rule = "any_true")