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Flag occurrence records of cultived individuals

Source: R/flag_cultivated.R
flag_cultivated.Rd

This function identifies records of cultivated individuals based on record description.

Usage

flag_cultivated(
  occ,
  columns = c("occurrenceRemarks", "habitat", "locality"),
  cultivated_terms = NULL,
  not_cultivated_terms = NULL
)

Arguments

occ

(data.frame) a data frame containing the occurrence records to be examined, preferably standardized using format_columns(). Must contain the columns specified in columns.

columns

columns (character) vector of column names in occ where the function will search for cultivated-related expressions. Default is c("occurrenceRemarks", "habitat", "locality").

cultivated_terms

(character) optional vector of additional terms that indicate a cultivated individual. Default is NULL, meaning it will use the cultivated-related expressions available in RuHere::cultivated$cultivated.

not_cultivated_terms

(character) optional vector of additional terms that indicate a non-cultivated individual. Default is NULL, meaning it will use the non cultivated-related expressions available in RuHere::cultivated$not_cultivated.

Value

A data.frame that is the original occ data frame augmented with a new column named cultivated_flag. Records identified as cultivated receive FALSE, while all other records receive TRUE. As with all other flagging functions in RuHere, TRUE indicates that the record passed this test and is eligible for retention; FALSE indicates it failed and is flagged as potentially problematic, and can be removed using remove_flagged().

Examples

# Load example data
data("occurrences", package = "RuHere")
# Flag fossil records
occ_cultivated <- flag_cultivated(occ = occurrences)