xportr_label: Assign Variable Label

In xportr: Utilities to Output CDISC SDTM/ADaM XPT Files

Assign Variable Label

Description

Assigns variable label from a variable level metadata to a given data frame. This function will give detect if a label is greater than 40 characters which isn't allowed in XPT v5. If labels aren't present for the variable it will be assigned an empty character value. Labels are stored in the 'label' attribute of the column.

Usage

xportr_label(
  .df,
  metadata = NULL,
  domain = NULL,
  verbose = NULL,
  metacore = deprecated()
)

Arguments

.df	A data frame of CDISC standard.
metadata	A data frame containing variable level metadata. See 'Metadata' section for details.
domain	Appropriate CDISC dataset name, e.g. ADAE, DM. Used to subset the metadata object.
verbose	The action this function takes when an action is taken on the dataset or function validation finds an issue. See 'Messaging' section for details. Options are 'stop', 'warn', 'message', and 'none'
metacore	Previously used to pass metadata now renamed with metadata

Value

Data frame with label attributes for each variable.

Messaging

label_log() is the primary messaging tool for xportr_label(). If there are any columns present in the '.df' that are not noted in the metadata, they cannot be assigned a label and a message will be generated noting the number or variables that have not been assigned a label.

If variables were not found in the metadata and the value passed to the 'verbose' argument is 'stop', 'warn', or 'message', a message will be generated detailing the variables that were missing in metadata.

Metadata

The argument passed in the 'metadata' argument can either be a metacore object, or a data.frame containing the data listed below. If metacore is used, no changes to options are required.

For data.frame 'metadata' arguments three columns must be present:

1. Domain Name - passed as the 'xportr.domain_name' option. Default: "dataset". This is the column subset by the 'domain' argument in the function.

2. Variable Name - passed as the 'xportr.variable_name' option. Default: "variable". This is used to match columns in '.df' argument and the metadata.

3. Variable Label - passed as the 'xportr.label' option. Default: "label". These character values to update the 'label' attribute of the column. This is passed to haven::write to note the label.

Examples

adsl <- data.frame(
  USUBJID = c(1001, 1002, 1003),
  SITEID = c(001, 002, 003),
  AGE = c(63, 35, 27),
  SEX = c("M", "F", "M")
)

metadata <- data.frame(
  dataset = "adsl",
  variable = c("USUBJID", "SITEID", "AGE", "SEX"),
  label = c("Unique Subject Identifier", "Study Site Identifier", "Age", "Sex")
)

adsl <- xportr_label(adsl, metadata, domain = "adsl")

xportr documentation built on Oct. 8, 2024, 1:08 a.m.