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Assign Variable Label

Source: R/label.R
xportr_label.Rd

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)

Arguments

.df

A data frame of CDISC standard.

metadata

A metacore object or 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'

Value

Data frame with label attributes for each variable.

Messaging

If there are any columns present in the '.df' that are not noted in the metadata, they are assigned an empty string as a label and a message will be generated noting the number of those variables.

If there are variables in the metadata that don't exist in '.df', they will be skipped and a message will be generated noting the number of metadata variables skipped.

In both cases, if the value passed to the 'verbose' argument is 'stop', 'warn', or 'message', a complete list of the affected variables will be provided.

Additionally, if a variable label is longer than 40 characters, a complete list of those variables will be provided as a warning, regardless of the value of the 'verbose' argument.

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_xpt 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")