camr_add_codebook_entry: Add a Codebook Entry to a Data Frame
In rettopnivek/camrprojects: Portable Functions for R Projects at CAM-MGH

camr_add_codebook_entry

R Documentation

Add a Codebook Entry to a Data Frame

Description

Function to update the attributes for a column in a data frame to contain a codebook entry. This ensures easy portability (at least within the framework of R) of the codebook for a data set.

Usage

camr_add_codebook_entry(
  dtf,
  variable,
  description = "",
  category = "",
  data_type = "",
  subcategory = "",
  values_and_labels = "",
  inventory = "",
  units_of_measurement = "",
  descriptive_summary = "",
  codes_for_missing_data = NULL,
  deidentified = "FALSE",
  collected_over = "",
  created_from = "",
  data_quality_checks = "",
  notes = "",
  custom_category = NULL,
  custom_data_type = NULL,
  custom_subcategory = NULL,
  missing_attribute_label = "missing",
  digits = 2,
  add_missing_to_attr = NULL,
  non_standard = TRUE
)

camr_ace(...)

Arguments

`dtf`	A data frame, preferably one using standardized naming conventions for columns (see camr_column_abbreviations).
`variable`	The column name for the variable whose attributes should be updated to include a codebook entry. Non-standard evaluation possible.
`description`	A character string, a brief human-readable description of what the variable is.
`category`	An optional character string, the category label for the variable. If left blank, the function automatically determines the category via camr_column_abbreviations.
`data_type`	An optional character string, the data type label for the variable. If left blank, the function automatically determines the data type via camr_column_abbreviations.
`subcategory`	An optional character string, the subcategory label for the variable. If left blank, the function automatically determines the subcategory via camr_column_abbreviations.
`values_and_labels`	Either the empty character set or a named list of two vectors, (1) `content` containing the distinct values for the variable, and (2) `additional_content` containing the label associated with each value in (1).
`inventory`	Either (1) output from the camr_inventories function, (2) the empty character set, or (3) a named list of two vectors, where `content` contains details on inventory an `additional_content` labels each type of detail (name, number of items, etc.).
`units_of_measurement`	A character string, the units of measurement for the variable.
`descriptive_summary`	Either the empty character set or a named list of two vectors, (1) `content` containing summary statistics for the variable, and (2) `additional_content` containing the label associated with each statistic in (1).
`codes_for_missing_data`	An optional vector with codes for missing data. If `NULL` uses default codes. If `variable` has an attribute with the codes, the codes in the attribute list override this argument.
`deidentified`	Either `FALSE` if the variable is not deidentified (i.e., contains potential patient health information) or `TRUE` otherwise.
`collected_over`	Either the empty character set or a named list of two vectors, (1) `content` containing distinct values for groups, time points, etc., over which the variable was collected, and (2) `additional_content` containing the column name associated with the values in (1).
`created_from`	An optional character vector, the original REDCap variables from which the variable was created.
`data_quality_checks`	An optional character string, notes on any data quality checks relevant to the variable.
`notes`	An optional character vector, any additional notes to include in the codebook entry.
`custom_category`	An optional matrix with two columns, 'Abbr' and 'Label', for custom abbreviations and labels for variable categories.
`custom_data_type`	An optional matrix with two columns, 'Abbr' and 'Label', for custom abbreviations and labels for data types.
`custom_subcategory`	An optional matrix with two columns, 'Abbr' and 'Label', for custom abbreviations and labels for variable subcategories.
`missing_attribute_label`	A character string, the name of the element in the list of attributes containing codes for missing data.
`digits`	The number of decimal places to round to for the descriptive summaries.
`add_missing_to_attr`	An optional logical value; if `FALSE` will not add codes for missing data to the attributes of `Variable`. If `NULL` defaults to adding if no pre-existing attribute is found.
`non_standard`	A logical value; if `TRUE` uses non-standard evaluation for `variable`.

Value

The data frame dtf, with the attributes for the column specified by variable updated to contain a data frame of additional class codebook_entry.

Author(s)

Kevin Potter

Examples

data( "example_CAM_data_set" )
dtf <- example_CAM_data_set

# Add codebook entry to data frame
dtf <- dtf |>
  camr_add_codebook_entry(
    IDS.INT.Screening,
    description = "Identifier assigned at screening session"
  )

dtf |> camr_pull_codebook_entry( IDS.INT.Screening )

dtf <- dtf |>
  camr_add_codebook_entry(
    IDS.CHR.Participant,
    "Identifier assigned at enrollment"
  )

dtf |> camr_pull_codebook_entry( IDS.CHR.Participant )

dtf <- dtf |>
  camr_add_codebook_entry(
    INV.INT.HADS_anxiety,
    inventory = camr_inventories( "HADS", "Anxiety" ),
    descriptive_summary = "continuous",
    collected_over = camr_ice(
      "combine",
      dtf |> camr_collected_over( INV.INT.HADS_anxiety, SSS.CHR.Session ),
      dtf |> camr_collected_over( INV.INT.HADS_anxiety, SSS.CHR.Event )
    )
  )
dtf |> camr_pull_codebook_entry( INV.INT.HADS_anxiety )

rettopnivek/camrprojects documentation built on March 26, 2024, 9:17 a.m.