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Coerce variable type

Source: R/type.R
xportr_type.Rd

XPT v5 datasets only have data types of character and numeric. xportr_type attempts to collapse R classes to those two XPT types. The 'xportr.character_types' option is used to explicitly collapse the class of a column to character using as.character. Similarly, 'xportr.numeric_types' will collapse a column to a numeric type. If no type is passed for a variable, it is assumed to be numeric and coerced with as.numeric().

Usage

xportr_type(
  .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

[Deprecated] Previously used to pass metadata now renamed with metadata

Value

Returns the modified table.

Details

Certain care should be taken when using timing variables. R serializes dates based on a reference date of 01/01/1970 where XPT uses 01/01/1960. This can result in dates being 10 years off when outputting from R to XPT if you're using a date class. For this reason, xportr will try to determine what should happen with variables that appear to be used to denote time.

Messaging

type_log() is the primary messaging tool for xportr_type(). The number of column types that mismatch the reported type in the metadata, if any, is reported by by xportr_type(). If there are any type mismatches, and the 'verbose' argument is 'stop', 'warn', or 'message', each mismatch will be detailed with the actual type in the data and the type noted in the 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 four 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 Type - passed as the 'xportr.type_name'. Default: "type". This is used to note the XPT variable "type" options are numeric or character.

  4. (Option only) Character Types - The list of classes that should be explicitly coerced to a XPT Character type. Default: c( "character", "char", "text", "date", "posixct", "posixt", "datetime", "time", "partialdate", "partialtime", "partialdatetime", "incompletedatetime", "durationdatetime", "intervaldatetime")`

  5. (Option only) Numeric Types - The list of classes that should be explicitly coerced to a XPT numeric type. Default: c("integer", "numeric", "num", "float")

Examples

metadata <- data.frame(
  dataset = "test",
  variable = c("Subj", "Param", "Val", "NotUsed"),
  type = c("numeric", "character", "numeric", "character")
)

.df <- data.frame(
  Subj = as.character(123, 456, 789),
  Different = c("a", "b", "c"),
  Val = c("1", "2", "3"),
  Param = c("param1", "param2", "param3")
)

df2 <- xportr_type(.df, metadata, "test")
#> 
#> ── Variable type mismatches found. ──
#> 
#> ✔ 2 variables coerced