initial_cleaning: Initial occurrence data cleaning steps

In kuenm2: Detailed Development of Ecological Niche Models

Initial occurrence data cleaning steps

Description

Simple occurrence data cleaning procedures.

Usage

initial_cleaning(data, species, x, y,
                 other_columns = NULL, keep_all_columns = TRUE,
                 sort_columns = TRUE, remove_na = TRUE, remove_empty = TRUE,
                 remove_duplicates = TRUE, by_decimal_precision = FALSE,
                 decimal_precision = 0, longitude_precision = NULL,
                 latitude_precision = NULL)

sort_columns(data, species, x, y, keep_all_columns = FALSE)

remove_missing(data, columns = NULL, remove_na = TRUE,
               remove_empty = TRUE, keep_all_columns = TRUE)

remove_duplicates(data, columns = NULL, keep_all_columns = TRUE)

remove_corrdinates_00(data, x, y)

filter_decimal_precision(data, x,
                         y, decimal_precision = 0,
                         longitude_precision = NULL,
                         latitude_precision = NULL)

Arguments

data	data.frame with occurrence records.
species	(character) name of the column in data containing species name.
x	(character) name of the column in data containing longitude values.
y	(character) name of the column in data containing latitude values.
other_columns	(character) vector of other column name(s) in data to be considered while performing cleaning steps, default = NULL.
keep_all_columns	(logical) whether to keep all columns in data. Default = TRUE.
sort_columns	(logical) whether to sort species, longitude, and latitude columns in data. Default = TRUE.
remove_na	(logical) whether to remove NA values in the columns considered. Default = TRUE.
remove_empty	(logical) whether to remove empty (missing) values in the columns considered. Default = TRUE.
remove_duplicates	(logical) whether to remove duplicates in the columns considered. Default = TRUE.
by_decimal_precision	(logical) whether to remove certain records with coordinate precision lower than that of the following three parameters. Default = FALSE
decimal_precision	(numeric) decimal precision threshold for coordinates. Default = 0. Ignored if the following two parameters are defined.
longitude_precision	(numeric) decimal precision threshold for longitude. Default = NULL.
latitude_precision	(numeric) decimal precision threshold for latitude. Default = NULL.
columns	(character) vector of additional column name(s) in data to be considered while removing missing or duplicate records, default = NULL.

Details

Function initial_cleaning helps to perform all simple steps of data cleaning.

Value

A data.frame with resulting occurrence records.

See Also

advanced_cleaning

Examples

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

# remove missing data
mis <- remove_missing(data = occ_data_noclean, columns = NULL, remove_na = TRUE,
                      remove_empty = TRUE)

# remove exact duplicates
mis_dup <- remove_duplicates(data = mis, columns = NULL, keep_all_columns = TRUE)

# remove records with 0 for x and y coordinates
mis_dup_00 <- remove_corrdinates_00(data = mis_dup, x = "x", y = "y")

# remove coordinates with low decimal precision.
mis_dup_00_dec <- filter_decimal_precision(data = mis_dup_00, x = "x", y = "y",
                                           decimal_precision = 2)

# 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)

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