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A define's code lists as a report's codelists rows

Source: R/define.R
tfl_define_codelists.Rd

Turns the code lists of the variables a report uses into rows of the spec's codelists sheet: value the coded value, label its decode (blank for an enumerated value: it prints as itself), order its order number. With labels, the variables' labels too, as rows of the variables sheet (attr(, "variables"): output_id, variable, label, note): a variable's heading is that sheet's label (the code list of variable is an earlier form, moved there when a table spec is read). The rows are a draft: nothing is written.

Usage

tfl_define_codelists(
  define,
  variables = NULL,
  output_id,
  datasets = NULL,
  labels = TRUE
)

Arguments

define

A tfl_define (tfl_read_define(), tfl_read_define_spec()), or the path of a define.xml or of a define spec .xlsx (read with the Pinnacle 21 profile).

variables

The variables (names, matched ignoring case); NULL: every variable of datasets that has a code list.

output_id

The report(s) the rows are for (required).

datasets

The datasets to look in; NULL for all.

labels

Add the variables' labels, as variables sheet rows in attr(, "variables").

Value

A data frame of the codelists sheet's columns, all character: output_id, variable, value, label, order, note; with attr(, "set_by_hand") and, with labels, attr(, "variables").

Details

Code lists are per report: every row carries an output_id, so it is required. Several output ids give the rows once for each.

A variable is looked up in the datasets given (all when datasets is NULL). When it is in several with different code lists (PARAMCD of ADVS and of ADLB) that is an error naming them: give datasets. What cannot be taken from the define is listed in attr(, "set_by_hand") (variable, reason): a variable it does not have (also a warning), one with no code list, one whose code list is an external dictionary (MedDRA ...). Each row's note says where it came from (define: CL.SEX; extended for a sponsor's value), and is never read by the spec.

Examples

if (requireNamespace("xml2", quietly = TRUE)) {
  def <- tfl_read_define(system.file("extdata", "define", "define.xml",
                                     package = "tflspec"))
  tfl_define_codelists(def, c("SEX", "AGEGR1", "AGE"),
                       output_id = "T-14-1-1", datasets = "ADSL")
}
#>   output_id variable value  label order              note
#> 1  T-14-1-1      SEX     F Female     2    define: CL.SEX
#> 2  T-14-1-1      SEX     M   Male     1    define: CL.SEX
#> 3  T-14-1-1   AGEGR1   <65   <NA>     1 define: CL.AGEGR1
#> 4  T-14-1-1   AGEGR1  >=65   <NA>     2 define: CL.AGEGR1