spec_type_to_value_spec: Spec to value_spec

In metacore: A Centralized Metadata Object Focus on Clinical Trial Data Programming Workflows

Spec to value_spec

Description

Creates the value_spec from a list of datasets (optionally filtered by the sheet input). The named vector cols is used to determine which is the correct sheet and renames the columns

Usage

spec_type_to_value_spec(
  doc,
  cols = c(dataset = "[D|d]ataset|[D|d]omain", variable = "[N|n]ame|[V|v]ariables?",
    origin = "[O|o]rigin", type = "[T|t]ype", code_id = "[C|c]odelist|Controlled Term",
    sig_dig = "[S|s]ignificant", where = "[W|w]here", derivation_id = "[M|m]ethod",
    predecessor = "[P|p]redecessor"),
  sheet = NULL,
  where_sep_sheet = TRUE,
  where_cols = c(id = "ID", where = c("Variable", "Comparator", "Value")),
  var_sheet = "[V|v]ar"
)

Arguments

doc	Named list of datasets @seealso read_all_sheets() for exact format
cols	Named vector of column names. The column names can be regular expressions for more flexibility. But, the names must follow the given pattern
sheet	Regular expression for the sheet name
where_sep_sheet	Boolean value to control if the where information in a separate dataset. If the where information is on a separate sheet, set to true and provide the column information with the where_cols inputs.
where_cols	Named list with an id and where field. All columns in the where field will be collapsed together
var_sheet	Name of sheet with the Variable information on it. Metacore expects each variable will have a row in the value_spec. Because many specification only have information in the value tab this is added. If the information already exists in the value tab of your specification set to NULL

Value

a dataset formatted for the metacore object

See Also

Other spec builder: spec_type_to_codelist(), spec_type_to_derivations(), spec_type_to_ds_spec(), spec_type_to_ds_vars(), spec_type_to_var_spec()

metacore documentation built on March 7, 2023, 7:45 p.m.