Checks the content of a linelist object

This function evaluates the validity of a linelist object by checking the object class, its tags, and the types of the tagged variables. It combines validations checks made by validate_types() and validate_tags(). See 'Details' section for more information on the checks performed.

Usage

validate_linelist(x, allow_extra = FALSE, ref_types = tags_types())

Arguments

x

a linelist object

allow_extra

a logical indicating if additional data tags not currently recognized by linelist should be allowed; if FALSE, unknown tags will trigger an error

ref_types

a list providing allowed types for all tags, as returned by tags_types()

Value

If checks pass, a linelist object (invisibly); otherwise issues an error.

Details

The following checks are performed:

• x is a linelist object

• x has a well-formed tags attribute

• all default tags are present (even if NULL)

• all tagged variables correspond to existing columns

• all tagged variables have an acceptable class

• (optional) x has no extra tag beyond the default tags

See also

• tags_types() to change allowed types

• validate_types() to check if tagged variables have the right classes

• validate_tags() to perform a series of checks on the tags

Examples

if (require(outbreaks)) {

  ## create a valid linelist
  x <- measles_hagelloch_1861 |>
    make_linelist(
      id = "case_ID",
      date_onset = "date_of_prodrome",
      age = "age",
      gender = "gender"
    )
  x

  ## validation
  validate_linelist(x)

  ## create an invalid linelist - onset date is a factor
  x <- measles_hagelloch_1861 |>
    make_linelist(
      id = "case_ID",
      date_onset = "gender",
      age = "age"
    )
  x

  ## the below issues an error
  ## note: tryCatch is only used to avoid a genuine error in the example
  tryCatch(validate_linelist(x), error = paste)
}
#> 'x' is a valid linelist object
#> [1] "Error: Some tags have the wrong class:\n  - date_onset: Must inherit from class 'integer'/'numeric'/'Date'/'POSIXct'/'POSIXlt', but has class 'factor'\n\n"