RuHere (version 1.0.1)

flag_consensus: Get consensus across multiple flags

Description

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
)

Value

The original occ with an additional logical column defined by flag_name, indicating the consensus result based on the selected consensus_rule.

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.

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")