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Flag duplicated records

Source: R/flag_duplicates.R
flag_duplicates.Rd

This function identifies duplicated records based on species name and coordinates, as well as user-defined additional columns or raster cells. Among duplicated records, the function keeps only one unflagged record, chosen according to a continuous variable (e.g., keeping the most recent), a categorical variable (e.g., prioritizing a specific data source), or randomly.

Usage

flag_duplicates(
  occ,
  species = "species",
  long = "decimalLongitude",
  lat = "decimalLatitude",
  additional_groups = NULL,
  continuous_variable = NULL,
  decreasing = TRUE,
  categorical_variable = NULL,
  priority_categories = NULL,
  by_cell = FALSE,
  raster_variable = 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 species, long and lat arguments.

species

(character) the name of the column containing species names. Default is "species".

long

(character) the name of the column containing longitude values. Default is "decimalLongitude".

lat

(character) the name of the column containing latitude values. Default is "decimalLatitude".

additional_groups

(character) optional vector of additional column names to consider when identifying duplicates. For example, if "year" is included, records with the same coordinates but different collection years will not be flagged. Default is NULL.

continuous_variable

(character) optional name of a numeric column used to sort duplicated records and select one to remain unflagged. Default is NULL, meaning that no sorting will occur and the unflagged record will be selected randomly.

decreasing

(logical) whether to sort records in decreasing order using the continuous_variable (e.g., from most recent to oldest when the variable is "year"). Only applicable when continuous_variable is not NULL. Default is TRUE.

categorical_variable

(character) (character) optional name of a categorical column used to sort duplicated records and select one to remain unflagged. If provided, the order of priority must be specified through priority_categories. Default is NULL.

priority_categories

(character) vector of categories, in the desired order of priority, present in the column specified in categorical_variable. Only applicable when categorical_variable is not NULL. Default is NULL.

by_cell

(logical) whether to use raster cells instead of raw coordinates to identify duplicates (i.e., all records inside the same raster cell are treated as duplicates). If TRUE, a SpatRaster must be supplied in raster_variable. Default is FALSE.

raster_variable

(SpatRaster) a SpatRaster used to identify duplicated records by raster cell. Only applicable when by_cell is TRUE. Default is NULL.

Value

A data.frame that is the original occ data frame augmented with a new column named duplicated_flag. Records identified as duplicated receive FALSE, while all unique retained records receive TRUE.

Examples

# Load example data
data("occurrences", package = "RuHere")
# Duplicate some records as example
occurrences <- rbind(occurrences[1:1000, ], occurrences[1:100,])
# Flag duplicates
occ_dup <- flag_duplicates(occ = occurrences)
sum(!occ_dup$duplicated_flag) #Number of duplicated records
#> [1] 100