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Initial occurrence data cleaning steps

initial_cleaning.Rd

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.

Value

A data.frame with resulting occurrence records.

Details

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

See also

advanced_cleaning