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Order variables of a dataset according to Spec

Source: R/order.R
xportr_order.Rd

The dplyr::arrange() function is used to order the columns of the dataframe. Any variables that are missing an order value are appended to the end of the dataframe after all of the variables that have an order.

Usage

xportr_order(.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

Dataframe that has been re-ordered according to spec

Messaging

There are three primary messages output by xportr_order().

The first identifies the "moved" variables. These are the variables that were either not found in the metadata file or had missing order values, and therefore moved to the end of the dataset. A message will be generated noting the number, if any, of variables that were moved to the end of the dataset.

The second message identifies the "reordered" variables. These are the variables that were in the dataset, but not in the correct order. A message will be generated noting the number, if any, of variables that have been reordered.

The third message identifies the "skipped" metadata variables. These are the metadata variables missing from the dataset and therefore skipped from processing. A message will be generated noting the number, if any, of metadata variables that have been skipped.

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

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 Order - passed as the 'xportr.order_name' option. Default: "order". These values used to arrange the order of the variables. If the values of order metadata are not numeric, they will be coerced to prevent alphabetical sorting of numeric values.

Examples

adsl <- data.frame(
  BRTHDT = c(1, 1, 2),
  STUDYID = c("mid987650", "mid987650", "mid987650"),
  TRT01A = c("Active", "Active", "Placebo"),
  USUBJID = c(1001, 1002, 1003)
)

metadata <- data.frame(
  dataset = c("adsl", "adsl", "adsl", "adsl"),
  variable = c("STUDYID", "USUBJID", "TRT01A", "BRTHDT"),
  order = 1:4
)

adsl <- xportr_order(adsl, metadata, domain = "adsl")
#> 
#> ── All variables in dataset are found in `metadata` ──
#> 
#> ── 3 reordered in dataset ──
#>