advanced_cleaning: Advanced occurrence data cleaning

In kuenm2: Detailed Development of Ecological Niche Models

Advanced occurrence data cleaning

Description

Advanced processes of data cleaning involving duplicate removal and movement of records.

Usage

advanced_cleaning(data, x, y, raster_layer, cell_duplicates = TRUE,
                  move_points_inside = FALSE, move_limit_distance = NULL,
                  verbose = TRUE)

remove_cell_duplicates(data, x, y,
                       raster_layer)

move_2closest_cell(data, x, y, raster_layer,
                   move_limit_distance, verbose = TRUE)

Arguments

data	data.frame with occurrence records. Rows with NA values will be omitted.
x	(character) name of the column in data containing longitude values.
y	(character) name of the column in data containing latitude values.
raster_layer	a raster layer (object of class SpatRaster).
cell_duplicates	(logical) whether to remove duplicate coordinates considering raster cells. Default = TRUE.
move_points_inside	(logical) whether to move records outside of raster cells with valid values to the closest cell with values. Default = FALSE.
move_limit_distance	maximum distance to move records outside cells with valid values. Default = NULL. Must be defined if move_points_inside = TRUE.
verbose	(logical) whether to print messages of progress. Default = TRUE.

Details

Data used in this functions should have gone through initial processes of cleaning and filtering.

Value

A data.frame with occurrence records resulting from advanced cleaning procedures. Other columns will be added to describe changes made in the original data.

See Also

initial_cleaning()

Examples

# Import occurrences
data(occ_data_noclean, package = "kuenm2")

# Import raster layers
var <- terra::rast(system.file("extdata", "Current_variables.tif",
                   package = "kuenm2"))

# Keep only one layer
var <- var$bio_1

# all basic cleaning steps
clean_init <- initial_cleaning(data = occ_data_noclean, species = "species",
                               x = "x", y = "y", remove_na = TRUE,
                               remove_empty = TRUE, remove_duplicates = TRUE,
                               by_decimal_precision = TRUE,
                               decimal_precision = 2)

# Advanced cleaning steps
# exclude duplicates based on raster cell (pixel)
celldup <- remove_cell_duplicates(data = clean_init, x = "x", y = "y",
                                  raster_layer = var)

# move records to valid pixels
moved <- move_2closest_cell(data = celldup, x = "x", y = "y",
                            raster_layer = var, move_limit_distance = 10)

# the steps at a time
clean_data <- advanced_cleaning(data = clean_init, x = "x", y = "y",
                                raster_layer = var, cell_duplicates = TRUE,
                                move_points_inside = TRUE,
                                move_limit_distance = 10)

kuenm2 documentation built on April 21, 2026, 1:07 a.m.