Package 'NBDCtools'

Description

This function allows users to add custom metadata (data dictionary, levels table, sessions table) to the package environment. This can be useful for users who want to use their own metadata instead of the ones provided by the package, or for testing and development purposes.

Usage

add_custom_metadata(dd = NULL, levels = NULL, sessions = NULL)

Arguments

Details

The custom metadata will be stored in the package environment can be accessed with any function that contains the "release" argument with release = "custom". For example, get_dd(study = "abcd", release = "custom").

The default value for dd, levels, and sessions is NULL. If any of them is not NULL, it will be added to the package environment. If the argument is NULL, the corresponding metadata will not be added.

Value

invisible TRUE.

Examples

add_custom_metadata(
  dd = tibble::tibble(
    name = "var1",
    table_name = "table1",
    identifier_columns = "participant_id"
  )
)
get_dd(study = "abcd", release = "custom")

Description

This function renames columns in a data frame to another type of column name specified in the data dictionary.

For example, this can be used to convert the ABCD column names introduced in the 6.0 release to the previously used column names. If you instead want to convert the column names in a file, use convert_names_file().

Note: Please use this function with caution and make sure that the data in the converted column is equivalent to the data in the original column. Also, please make sure that the names can be mapped one-to-one. Some variables in the ABCD data dictionary have been collapsed from previous releases and thus might have multiple names in the name_to column that map to a single name (see skip_sep_check argument below).

Usage

convert_names_data(
  data,
  dd,
  name_from = "name",
  name_to,
  ignore_cols = union(get_id_cols_abcd(), get_id_cols_hbcd()),
  skip_sep_check = FALSE
)

Arguments

Value

tibble. The data with renamed column names.

Examples

## Not run: 
# rename columns to previous ABCD names used by NDA
convert_names_data(
  data,
  dd = get_dd("abcd"),
  name_from = "name",
  name_to = "name_nda"
)

# rename columns to Stata names
convert_names_data(
  data,
  dd = get_dd("abcd"),
  name_from = "name",
  name_to = "name_stata"
)

## End(Not run)

Description

This function replaces all matched column names in a file with another type of column name specified in the data dictionary.

For example, this function can be used to convert script files that specified previously used column names to the the ABCD column names introduced in the 6.0 release. If you instead want to convert the column names in a data frame, use convert_names_data().

Note: Please use this function with caution and make sure that the data in the converted column is equivalent to the data in the original column. Also, please make sure that the names can be mapped one-to-one. Some variables in the ABCD data dictionary have been collapsed from previous releases and thus might have multiple names in the name_from column that map to a single name (see skip_sep_check argument below).

Usage

convert_names_file(
  file_in,
  file_out = NULL,
  dd,
  name_from,
  name_to,
  skip_sep_check = FALSE
)

Arguments

Details

Word matching

The function uses word boundaries to match the names in the file. It Uses regex word boundaries (⁠\\b⁠) to ensure exact word matches. This prevents partial matches within larger words. For example, matching "age" will not match "cage" or "page".

Speed

The data dictionary is big from get_dd(), so the function would loop through all the names in the data dictionary. If there are only a few names to replace, it is the best to trim the data dictionary to only those names before using this function.

Value

character. The path to the output file with converted names, invisible.

Examples

## Not run: 
convert_names_file(
  file_in = "analysis_script.R",
  dd = get_dd("abcd"),
  name_from = "name_nda",
  name_to = "name"
)

# Specify custom output file
convert_names_file(
  file_in = "analysis_script.py",
  file_out = "analysis_script_new.py",
  dd = get_dd("abcd"),
  name_from = "name_nda",
  name_to = "name"
)

## End(Not run)

Description

Creates a Brain Imaging Data Structure (BIDS) JSON sidecar file from the metadata (data dictionary and levels table). Returns the JSON object or writes it to a file.

Usage

create_bids_sidecar_data(
  data,
  study,
  release = "latest",
  var_coding = "values",
  metadata_description = "Dataset exported using NBDCtools",
  path_out = NULL,
  pretty = TRUE
)

Arguments

Details

• If you have a labelled dataset, and want to create data specific BIDS sidecar with variable levels from the data, please use create_bids_sidecar_data().

• If you want to create a BIDS sidecar without the underlying data, please use create_bids_sidecar_metadata().

Value

the json object or the path to the json file

See Also

create_bids_sidecar_metadata()

Examples

## Not run: 
data |> create_bids_sidecar_data()
data |> create_bids_sidecar_data(path_out = "data.json")

## End(Not run)

Description

Generates a Brain Imaging Data Structure (BIDS) JSON sidecar using metadata tables (data dictionary and levels) without requiring the underlying data.

Usage

create_bids_sidecar_metadata(
  dd,
  levels,
  vars = NULL,
  tables = NULL,
  metadata_description = "Dataset exported using NBDCtools",
  path_out = NULL,
  pretty = TRUE
)

Arguments

Details

• If you have a labelled dataset, and want to create data specific BIDS sidecar with variable levels from the data, please use create_bids_sidecar_data().

• If you want to create a BIDS sidecar without the underlying data, please use create_bids_sidecar_metadata().

Value

Either a JSON string (when path_out is NULL) or the output file path (invisibly) after writing the JSON sidecar to disk.

See Also

create_bids_sidecar_data()

Examples

create_bids_sidecar_metadata(
  dd = get_dd("abcd"),
  levels = get_levels("abcd"),
  tables = c("ph_y_mctq")
)

Description

This high-level function simplifies the process of creating a dataset from the ABCD or HBCD Study data by allowing users to create an analysis-ready dataset in a single step. It executes the lower-level functions provided in the NBDCtools package in sequence to load, join, and transform the data.

The function expects study data to be stored as one .parquet or .tsv file per database table within a specified directory, provided as dir_data. Variables specified in vars and tables will be full-joined together, while variables specified in vars_add and tables_add will be left-joined to these variables. For more details, see join_tabulated().

In addition to the main create_dataset() function, there are two study-specific variations:

• create_dataset_abcd(): for the ABCD study.

• create_dataset_hbcd(): for the HBCD study.

They have the same arguments as the create_dataset() function, except that the study argument is set to the respective study by default, and should not be set by the user.

Usage

create_dataset(
  dir_data,
  study,
  vars = NULL,
  tables = NULL,
  vars_add = NULL,
  tables_add = NULL,
  release = "latest",
  format = "parquet",
  bypass_ram_check = FALSE,
  ignore_version_mismatch = FALSE,
  categ_to_factor = TRUE,
  add_labels = TRUE,
  value_to_label = FALSE,
  value_to_na = FALSE,
  time_to_hms = FALSE,
  bind_shadow = FALSE,
  ...
)

create_dataset_abcd(...)

create_dataset_hbcd(...)

Arguments

Details

Order

This high-level function executes the different steps in the following order:

1. Read the data/shadow matrix using join_tabulated().

2. Convert categorical variables to factors using transf_factor().

3. Add labels to the variables and values using transf_label().

4. Convert categorical variables' numeric values to labels using transf_value_to_label().

5. Convert categorical missingness/non-response codes to NA using transf_value_to_na().

6. Convert time variables to hms class using transf_time_to_hms().

7. If bind_shadow and the study is "HBCD", replace the missing values in the shadow due to joining multiple datasets using shadow_replace_binding_missing().

8. Bind the shadow matrix to the data using shadow_bind_data().

Not all steps are executed by default. The above order represents the maximal order of execution.

bind_shadow

If bind_shadow is TRUE, the shadow matrix will be added to the data using shadow_bind_data().

• HBCD study: For the HBCD study, this function uses the shadow matrix from the dir_data directory by default (the HBCD Study releases a ⁠_shadow.parquet⁠/⁠_shadow.tsv⁠ file per table that accompanies the data). Alternatively, one can set naniar_shadow = TRUE as part of the ... arguments to use naniar::as_shadow() to create a shadow matrix from the data.

• ABCD study: The ABCD Study does not currently release shadow matrices. If bind_shadow is set to TRUE, the function will create the shadow matrix from the data using naniar::as_shadow(); no extra naniar_shadow = TRUE argument is needed.

Value

A tibble with the analysis-ready dataset.

Examples

## Not run: 
# most common use case
create_dataset(
  dir_data = "6_0/data",
  study = "abcd",
  vars = c("var1", "var2", "var3")
)

# to handle with tagged missingness
create_dataset(
  dir_data = "1_0/data",
  study = "hbcd",
  vars = c("var1", "var2", "var3"),
  value_to_na = TRUE
)

# to bind shadow matrices to the data
create_dataset(
  dir_data = "1_0/data/",
  study = "hbcd",
  vars = c("var1", "var2", "var3"),
  bind_shadow = TRUE
)

# to use the additional arguments
# for example in `value_to_na` option, the underlying function
# `transf_value_to_na()` has 2 more arguments,
# which can be passed to the `create_dataset()` function
create_dataset(
  dir_data = "6_0/data",
  study = "abcd",
  vars = c("var1", "var2", "var3"),
  value_to_na = TRUE,
  missing_codes = c("999", "888", "777", "666", "555", "444", "333", "222"),
  ignore_col_pattern = "__dk$|__dk__l$"
)

# use study specific functions
create_dataset_abcd(
  dir_data = "6_0/data",
  vars = c("var1", "var2", "var3")
)

## End(Not run)

Description

This function filters out columns that are empty.

Usage

filter_empty_cols(
  data,
  id_cols = union(get_id_cols_abcd(), get_id_cols_hbcd())
)

Arguments

Value

A tibble with the filtered data.

Examples

data <- tibble::tibble(
  participant_id = c("sub-001", "sub-002", "sub-003"),
  session_id = c("ses-001", "ses-001", "ses-002"),
  var1 = c(NA, NA, NA),
  var2 = c(NA, NA, 2),
  var3 = c(NA, NA, 3)
)
filter_empty_cols(data)

Description

This function filters out rows that are empty

Usage

filter_empty_rows(
  data,
  id_cols = union(get_id_cols_abcd(), get_id_cols_hbcd())
)

Arguments

Value

A tibble with the filtered data.

Examples

data <- tibble::tibble(
  participant_id = c("sub-001", "sub-002", "sub-003"),
  session_id = c("ses-001", "ses-001", "ses-002"),
  var1 = c(NA, NA, 1),
  var2 = c(NA, NA, 2),
  var3 = c(NA, NA, 3)
)
filter_empty_rows(data)

Description

Given a (set of) condition(s), filters the events included in an ABCD dataset. Conditions can be specified as a vector of strings, where each string can be one of the following conditions:

• "core": events for the ABCD core study

• "annual": annual events for the ABCD core study

• "mid_year": mid-year events for the ABCD core study

• "substudy": events for ABCD substudies

• "covid": events for the COVID substudy

• "sdev": events for the Social Development substudy

• "even": even-numbered events

• "odd": odd-numbered events

• numerical expressions like ⁠>2⁠ or ⁠<=5⁠ to filter events by number

• any other string to be used as filter for the session_id column

The conditions can be combined with logical "and" or "or".

Usage

filter_events_abcd(data, conditions, connect = "and")

Arguments

Value

A tibble with the filtered data.

Examples

data <- tibble::tribble(
  ~session_id,     ~study,     ~type,
  "ses-00S",       "core",     "screener",
  "ses-00M",       "core",     "mid-year",
  "ses-00A",       "core",     "even",
  "ses-01M",       "core",     "mid-year",
  "ses-01A",       "core",     "odd",
  "ses-02M",       "core",     "mid-year",
  "ses-02A",       "core",     "even",
  "ses-03M",       "core",     "mid-year",
  "ses-03A",       "core",     "odd",
  "ses-04M",       "core",     "mid-year",
  "ses-04A",       "core",     "even",
  "ses-05M",       "core",     "mid-year",
  "ses-05A",       "core",     "odd",
  "ses-06M",       "core",     "mid-year",
  "ses-06A",       "core",     "even",
  "ses-C01",       "substudy", "covid",
  "ses-C02",       "substudy", "covid",
  "ses-C03",       "substudy", "covid",
  "ses-C04",       "substudy", "covid",
  "ses-C05",       "substudy", "covid",
  "ses-C06",       "substudy", "covid",
  "ses-C07",       "substudy", "covid",
  "ses-S01",       "substudy", "sdev",
  "ses-S02",       "substudy", "sdev",
  "ses-S03",       "substudy", "sdev",
  "ses-S04",       "substudy", "sdev",
  "ses-S05",       "substudy", "sdev"
)

# ABCD core study events
filter_events_abcd(data, c("core"))

# COVID substudy events
filter_events_abcd(data, c("covid"))

# imaging events
filter_events_abcd(data, c("annual", "even"))

# mid-years before year 5
filter_events_abcd(data, c("mid_year", "<5"))

# COVID or Social Development substudy events
filter_events_abcd(data, c("covid", "sdev"), connect = "or")

Description

Given a vector of ID/events (concatenated like "{participant_id}_{session_id}"), or a dataframe with participant_id and session_id columns, this function filters the data to keep or alternatively remove the rows for the given ID/events.

Usage

filter_id_events(data, id_events, revert = FALSE)

Arguments

Value

A tibble with the filtered data.

Examples

data <- tibble::tribble(
  ~participant_id, ~session_id,
  "sub-001",       "ses-001",
  "sub-001",       "ses-002",
  "sub-002",       "ses-001",
  "sub-002",       "ses-002",
  "sub-003",       "ses-001",
  "sub-003",       "ses-002"
)

# filter using a vector of ID/events
filter_id_events(
  data,
  id_events = c("sub-001_ses-001", "sub-003_ses-002")
)

# filter using a dataframe with participant_id and session_id
data_filter <- tibble::tibble(
  participant_id = c("sub-001", "sub-003"),
  session_id = c("ses-001", "ses-002")
)
filter_id_events(
  data,
  id_events = data_filter
)

# revert filter
filter_id_events(
  data,
  id_events = c("sub-001_ses-001", "sub-003_ses-002"),
  revert = TRUE
)

Description

Retrieves data dictionary for a given study and release version. Allows for filtering by variables and tables. Wrapper around get_metadata().

In addition to the main get_dd() function, there are two study-specific variations:

• get_dd_abcd(): for the ABCD study.

• get_dd_hbcd(): for the HBCD study.

They have the same arguments as the get_dd() function, except that the study argument is set to the respective study by default, and should not be set by the user.

Usage

get_dd(study, release = "latest", vars = NULL, tables = NULL)

get_dd_abcd(...)

get_dd_hbcd(...)

Arguments

Value

Data frame with the data dictionary.

Examples

get_dd("abcd")

get_dd("hbcd", release = "1.0")

get_dd("abcd", vars = c("ab_g_dyn__visit_dtt", "ab_g_dyn__visit_age"))

get_dd("abcd", tables = "ab_g_dyn")

get_dd_abcd()

get_dd_hbcd(release = "1.0")

Description

Retrieves the identifier columns for a given study and release version.

In addition to the main get_id_cols() function, there are two study-specific variations:

• get_id_cols_abcd(): for the ABCD study.

• get_id_cols_hbcd(): for the HBCD study.

They have the same arguments as the get_id_cols() function, except that the study argument is set to the respective study by default, and should not be set by the user.

Usage

get_id_cols(study, release = "latest")

get_id_cols_abcd(...)

get_id_cols_hbcd(...)

Arguments

Value

character vector with the identifier columns.

Examples

get_id_cols("abcd")

get_id_cols("hbcd")

get_id_cols_abcd(release = "6.0")

get_id_cols_hbcd(release = "1.0")

Description

Retrieves levels table for a given study and release version. Allows for filtering by variables and tables. Wrapper around get_metadata().

In addition to the main get_levels() function, there are two study-specific variations:

• get_levels_abcd(): for the ABCD study.

• get_levels_hbcd(): for the HBCD study.

They have the same arguments as the get_levels() function, except that the study argument is set to the respective study by default, and should not be set by the user.

Usage

get_levels(study, release = "latest", vars = NULL, tables = NULL)

get_levels_abcd(...)

get_levels_hbcd(...)

Arguments

Value

Data frame with the levels table.

Examples

get_levels("abcd")

get_levels("hbcd", release = "1.0")

get_levels("abcd", vars = c("ab_g_dyn__visit_type"))

get_levels("abcd", tables = "ab_g_dyn")

get_levels_abcd(release = "6.0")

get_levels_hbcd()

Description

Retrieves metadata (data dictionary, levels table, event map) for a given study and release version. Allows for filtering by variables and tables.

Usage

get_metadata(
  study,
  release = "latest",
  vars = NULL,
  tables = NULL,
  type = "dd"
)

Arguments

Value

Data frame with the metadata.

Examples

get_metadata("abcd", type = "levels")

get_metadata("hbcd", release = "1.0")

get_metadata("abcd", vars = c("ab_g_dyn__visit_dtt", "ab_g_dyn__visit_age"))

get_metadata("abcd", tables = "ab_g_dyn")

get_metadata("abcd", tables = "ab_g_dyn")

get_metadata("abcd", type = "sessions")

Description

These functions retrieve all release version number(s) for a given study, or the latest release version number.

Usage

get_releases(study)

get_releases_abcd()

get_releases_hbcd()

get_latest_release(study)

get_latest_release_abcd()

get_latest_release_hbcd()

Arguments

Value

character. The latest release version number(s) of the specified study.

Examples

get_releases("abcd")
get_releases("hbcd")
get_latest_release("abcd")
get_latest_release("hbcd")

Description

Retrieves the sessions table for a given study and release version. Wrapper around get_metadata().

In addition to the main get_sessions() function, there are two study-specific variations:

• get_sessions_abcd(): for the ABCD study.

• get_sessions_hbcd(): for the HBCD study.

They have the same arguments as the get_sessions() function, except that the study argument is set to the respective study by default, and should not be set by the user.

Usage

get_sessions(study, release = "latest")

get_sessions_abcd(...)

get_sessions_hbcd(...)

Arguments

Value

Data frame with the sessions table.

Examples

get_sessions("abcd")

get_sessions("hbcd")

get_sessions_abcd(release = "6.0")

get_sessions_hbcd(release = "1.0")

Description

Joins selected variables and/or whole tables from the tabulated data/shadow files into a single data frame. Expects the data files to be stored in one directory in .parquet or .tsv format, with one file per table following the naming convention of the respective NBDC dataset (from the ABCD or HBCD studies). Typically, this will be the ⁠rawdata/phenotype/⁠ directory within a BIDS dataset downloaded from the NBDC Data Hub.

Variables specified in vars and tables will be full-joined together, i.e., all rows will be kept, even if they do not have a value for all columns. Variables specified in vars_add will be left-joined to the variables selected in vars and tables, i.e., only the values for already existing rows will be added and no new rows will be created. This is useful for adding variables to the dataset that are important for a given analysis but are not the main variables of interest (e.g., design/nesting or demographic information). By left-joining these variables, one avoids creating new rows that contain only missing values for the main variables of interest selected using vars and tables. If the same variables are specified in vars/tables and vars_add/tables_add, the variables in vars_add/tables_add will be ignored.

In addition to the main join_tabulated() function, there are two study-specific variations:

• join_tabulated_abcd(): for the ABCD study.

• join_tabulated_hbcd(): for the HBCD study.

They have the same arguments as the join_tabulated() function, except that the study argument is set to the respective study by default, and should not be set by the user.

Usage

join_tabulated(
  dir_data,
  study,
  vars = NULL,
  tables = NULL,
  vars_add = NULL,
  tables_add = NULL,
  release = "latest",
  format = "parquet",
  shadow = FALSE,
  remove_empty_rows = TRUE,
  bypass_ram_check = FALSE,
  ignore_version_mismatch = FALSE
)

join_tabulated_abcd(...)

join_tabulated_hbcd(...)

Arguments

Value

A tibble of data or shadow matrix with the joined variables.

Examples

## Not run: 
join_tabulated(
  dir_data = "path/to/data/",
  vars     = c("var_1", "var_2", "var_3"),
  tables   = c("table_1", "table_2"),
  study    = "abcd",
  release  = "6.0"
)

## End(Not run)

Description

Reads in a .tsv or .csv file with correctly formatted column types. Uses readr::read_tsv()/readr::read_csv() internally and specifies the column types explicitly using the col_types argument utilizing information from the data dictionary. Returns only the identifier columns and the columns specified in the data dictionary, i.e., all columns in the file that are not specified in the data dictionary are ignored.

Usage

read_dsv_formatted(file, dd, action = "warn")

Arguments

Details

WHY THIS IS IMPORTANT: readr::read_tsv()/readr::read_csv() (like other commands to load text files in R or other programming languages) by default infers the column types from the data. This doesn't always work perfectly. For example, it may interpret a column with only integers as a double, or a column with only dates as a character. Sometimes a column may even be read in completely empty because, by default, readr::read_tsv()/readr::read_csv() only considers the first 1000 rows when inferring the data type and interprets the column as an empty logical vector if those rows are all empty. The NBDC datasets store categorical data as integers formatted as character. By default, readr::read_tsv()/readr::read_csv() may interpret them as numeric. By specifying the column types explicitly based on what is defined in the data dictionary, we can avoid these issues.

GENERAL RECOMMENDATION: Other file formats like .parquet correctly store the column types and don't need to be handled explicitly. They also offer other advantages like faster reading speed and smaller file sizes. As such, these formats should generally be preferred over .tsv/.csv files. However, if you have to work with .tsv/.csv files, this function can help you avoid common pitfalls.

Value

A tibble with the data/shadow matrix read from the .tsv or .csv file.

Examples

## Not run: 
dd <- NBDCtools::get_dd("abcd", "6.0")
read_tsv_formatted("path/to/file.tsv", dd)

## End(Not run)

Description

This function binds the shadow matrix to the data.

Usage

shadow_bind_data(
  data,
  shadow = NULL,
  naniar_shadow = FALSE,
  id_cols = union(get_id_cols_abcd(), get_id_cols_hbcd()),
  suffix = "_shadow"
)

Arguments

Details

Data requirements

If naniar_shadow = FASLE and shadow is provided, the two dataframes must have the same columns, order of the columns does not matter, but ID columns must be the same in both dataframes. If there are extra rows in the shadow matrix, they will be ignored.

ABCD and HBCD data

NBDC releases HBCD data with shadow matrices, which can be used for the shadow argument. To work with ABCD data, the option for now is to use naniar_shadow = TRUE, which will create a shadow matrix from the data using naniar::as_shadow().

Value

a dataframe of the data matrix with shadow columns. It will be 2x the size of the original data matrix.

Examples

shadow <- tibble::tibble(
  participant_id = c("1", "2", "3"),
  session_id = c("1", "2", "3"),
  var1 = c("Unknown", NA, NA),
  var2 = c("Wish not to answer", NA, NA)
)
data <- tibble::tibble(
  participant_id = c("1", "2", "3"),
  session_id = c("1", "2", "3"),
  var1 = c(NA, NA, 1),
  var2 = c(NA, 2, NA)
)
shadow_bind_data(data, shadow)
if (requireNamespace("naniar", quietly = TRUE)) {
  shadow_bind_data(data, naniar_shadow = TRUE)
}

Description

This function replaces the missing values in the shadow matrices. This is done by checking if the values in shadow matrices are both NA. If they are, the value in the shadow matrix is replaced with ⁠Missing due to joining⁠.

Usage

shadow_replace_binding_missing(
  data,
  shadow,
  id_cols = union(get_id_cols_abcd(), get_id_cols_hbcd()),
  replacement = "Missing due to joining"
)

Arguments

Details

Data and shadow requirements: The two dataframes must have the same columns and the same number of rows. They must have the same column names, but the order of the columns does not matter. It is recommended to use the same column order and the same row order (by ID columns) in both dataframes, which saves some processing time.

Value

A tibble of the shadow matrix with missing values replaced.

Examples

shadow <- tibble::tibble(
  participant_id = c("1", "2", "3"),
  session_id = c("1", "2", "3"),
  var1 = c("Unknown", NA, NA),
  var2 = c("Wish not to answer", NA, NA)
)
data <- tibble::tibble(
  participant_id = c("1", "2", "3"),
  session_id = c("1", "2", "3"),
  var1 = c(NA, NA, 1),
  var2 = c(NA, 2, NA)
)
shadow_replace_binding_missing(data, shadow)

Description

Based on the specifications in the data dictionary, transforms all categorical columns to factor.

Usage

transf_factor(data, study, release = "latest")

Arguments

Value

A tibble with the transformed data.

Examples

## Not run: 
transf_factor(data, study = "abcd")

## End(Not run)

Description

This function can add variable labels and value labels to the data. The variable labels are descriptive information about the column, and the value labels are the levels of the factor variables.

Usage

transf_label(
  data,
  study,
  release = "latest",
  add_var_label = TRUE,
  add_value_label = TRUE,
  id_cols_labels = c(participant_id = "Participant identifier", session_id =
    "Event identifier", run_id = "Run identifier")
)

Arguments

Details

Two types of labels

At least one of add_var_label or add_value_label must be set to TRUE. If both are FALSE, an error will be raised.

Text columns

The transf_factor() function has a convert_text argument, which will convert text columns to unordered factors. When one uses a type transformed data to add labels, the text-factor columns will not have labels at variable level.

Value

A tibble with the labelled data.

See Also

transf_factor() for transforming categorical columns to factors.

Examples

## Not run: 
transf_label(data)

## End(Not run)

Description

This function converts time columns to hms format.

Usage

transf_time_to_hms(data, study, release = "latest")

Arguments

Details

The input data with time columns are expected to have character format of "HH:MM:SS". If it is not in this format, the function will return NA for that row.

Value

A tibble with time columns converted to hms format.

Examples

## Not run: 
transf_time_to_hms(data)

## End(Not run)

Description

Converts the values of categorical/factor columns (e.g., "1", "2") to their labels (e.g., "Male", "Female"). The value labels will be set to the values.

Usage

transf_value_to_label(data, transf_sess_id = FALSE)

Arguments

Details

Input requirements

The data must be type transformed and labelled. See transf_factor() and transf_label() for details.

data <- data |>
  transf_factor() |>
  transf_label()

Value

A tibble with factor columns transformed to labels.

Examples

## Not run: 
transf_value_to_label(data)
transf_value_to_label(data, value_to_na = TRUE)

## End(Not run)

Description

This function converts the missing codes in the dataset to NA in all factor columns. Example of missing codes are 999, 888, 777, etc.

Usage

transf_value_to_na(
  data,
  missing_codes = c("999", "888", "777", "666", "555", "444", "333", "222"),
  ignore_col_pattern = "__dk$|__dk__l$",
  id_cols = union(get_id_cols_abcd(), get_id_cols_hbcd())
)

Arguments

Details

Use case

This function works the best with ABCD data where the missing codes are strictly defined. For HBCD data, the missing codes are still under discussion. The function may work, but for some undecided future missing codes, the function may not work as expected.

In case of HBCD data or other aribitrary missing codes that one wishes to convert to NA, it is recommended to use the sjmisc::set_na_if() function instead.

Input requirements

The data must be type transformed and labelled. See transf_factor() and transf_label() for details.

data <- data |>
  transf_factor() |>
  transf_label()

Value

A tibble of the dataset with missing codes converted to NA

Examples

## Not run: 
data <- data |>
  transf_factor() |>
  transf_label()

transf_value_to_na(data)

## End(Not run)