Package index • cleanepi

Exported functions

cleanepi functions available to end-users

add_to_dictionary(): Add an element to the data dictionary

add_to_report(): Add an element to the report object

check_date_sequence(): Check whether the order of the sequence of date-events is valid

check_subject_ids(): Check whether the subject IDs comply with the expected format. When incorrect IDs are found, the function sends a warning and the user can call the correct_subject_ids() function to correct them.

clean_data(): Clean and standardize data

clean_using_dictionary(): Perform dictionary-based cleaning

common_na_strings: Common strings representing missing values

convert_numeric_to_date(): Convert numeric to date

convert_to_numeric(): Convert columns into numeric

correct_subject_ids(): Correct the wrong subject IDs based on the user-provided values.

find_duplicates(): Identify and return duplicated rows in a data frame or linelist.

print_report(): Generate report from data cleaning operations

remove_constants(): Remove empty rows and columns and constant column

remove_duplicates(): Remove duplicates

replace_missing_values(): Replace missing values with NA

scan_data(): Scan a data frame to determine the percentage of missing, numeric, Date, character, and logical values in every column.

standardize_column_names(): Standardize column names of a data frame or linelist

standardize_dates(): Standardize date variables

timespan(): Calculate time span between dates

Shared helpers

get_target_column_names(): Get the names of the columns from which duplicates will be found

add_to_report(): Add an element to the report object

get_sum(): Get sum of numbers from a string

numbers_only(): Detects whether a string contains only numbers or not.

Clean data

Performs several cleaning operations at once

clean_data(): Clean and standardize data

Check data structure

Scan through the input data to determine its composition

scan_data(): Scan a data frame to determine the percentage of missing, numeric, Date, character, and logical values in every column.

scan_columns(): Calculate the percentage of missing and other data type values in a vector containing different data types such as numeric, Date, character, and logical.

Print data cleaning report

print_report(): Generate report from data cleaning operations

Standardise column names

Harmonise on the usage of English characters in column names

standardize_column_names(): Standardize column names of a data frame or linelist

Retrieve Date from numeric values

convert_numeric_to_date(): Convert numeric to date

Convert numbers written in letters into numeric

convert_to_numeric(): Convert columns into numeric

detect_to_numeric_columns(): Detect the numeric columns that appears as characters due to the presence of some character values in the column.

Standardise dates

Coerce date values to the ISO format Ymd (2024-31-01)

standardize_dates(): Standardize date variables

date_check_column_existence(): Check if date column exists in the given dataset

date_check_timeframe(): Check date time frame

date_choose_first_good(): Choose the first non-missing date from a data frame of dates

date_convert(): Convert characters to dates

date_convert_and_update(): Convert and update the date values

date_detect_complex_format(): Detect complex date format

date_detect_day_or_month(): Detect the appropriate abbreviation for day or month value

date_detect_format(): Detect a date format with only 1 separator

date_detect_separator(): Detect the special character that is the separator in the date values

date_detect_simple_format(): Get format from a simple Date value

date_get_format(): Detect date format from a date column

date_get_part1(): Get part1 of date value

date_get_part2(): Get part2 of date value

date_get_part3(): Get part3 of date value

date_guess(): Try and guess dates from a characters

date_guess_convert(): Guess if a character vector contains Date values, and convert them to date

date_i_extract_string(): Extract date from a character string

date_i_find_format(): Guess date format of a character string

date_make_format(): Build the auto-detected format

date_match_format_and_column(): Check whether the number of provided formats matches the number of target columns to be standardized.

date_process(): Process date variable

date_rescue_lubridate_failures(): Find the dates that lubridate couldn't

date_trim_outliers(): Trim dates outside of the defined boundaries

convert_numeric_to_date(): Convert numeric to date

Dictionary-based substitution

Substitute given options from columns in a data frame with their corresponding values

dictionary_make_metadata(): Make data dictionary for 1 field

add_to_dictionary(): Add an element to the data dictionary

clean_using_dictionary(): Perform dictionary-based cleaning

make_readcap_dictionary(): Convert Redcap data dictionary into {matchmaker} dictionary format

construct_misspelled_report(): Build the report for the detected misspelled values during dictionary-based data cleaning operation

detect_misspelled_options(): Detect misspelled options in columns to be cleaned

print_misspelled_values(): Print the detected misspelled values

Find and remove duplicates

find_duplicates(): Identify and return duplicated rows in a data frame or linelist.

remove_duplicates(): Remove duplicates

Remove constant data

Remove constant columns, empty rows and columns

remove_constants(): Remove empty rows and columns and constant column

Replace missing values with NA

replace_missing_values(): Replace missing values with NA

Calculate time span between the variables of type Date

timespan(): Calculate time span between dates

Detect incorrect subject ids and correct them if required

check_subject_ids(): Check whether the subject IDs comply with the expected format. When incorrect IDs are found, the function sends a warning and the user can call the correct_subject_ids() function to correct them.

correct_subject_ids(): Correct the wrong subject IDs based on the user-provided values.

Check sequence of date events

check_date_sequence(): Check whether the order of the sequence of date-events is valid

is_date_sequence_ordered(): Check order of a sequence of date-events