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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 is considered valid (TRUE) only if all specified flag are valid (TRUE).

  • "any_true": A record is considered valid (TRUE) if at least one specified flag is valid (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 is considered valid only when all flags are TRUE or "any_true"(record is considered valid 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.

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.

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")