Specification document to metacore object — spec_to

This function takes the location of an excel specification document and reads it in as a meta core object. At the moment it only supports specification in the format of pinnacle 21 specifications. But, the section level spec builder can be used as building blocks for bespoke specification documents.

Usage

spec_to_metacore(
  path,
  quiet = deprecated(),
  where_sep_sheet = TRUE,
  verbose = "message"
)

Arguments

path

string of file location

quiet

Option to quietly load in, this will suppress warnings, but not errors. Expects either TRUE or FALSE. Default behaviour is FALSE. From v0.3.0 this argument is deprecated in favour of verbose.

where_sep_sheet

Option to tell if the where is in a separate sheet, like in older p21 specs or in a single sheet like newer p21 specs.

verbose

A character string specifying the desired verbosity level. Must be one of:

"message": (default) Messages and warnings are handled normally.
"warn": Messages are suppressed, but warnings are allowed.
"collapse": Warnings are collapsed into a single message indicating the number of suppressed warnings.
"silent": Both messages and warnings are suppressed.

Value

given a spec document it returns a metacore object

Examples

# Run `spec_to_metacore` with `verbose = "collapse"`
spec_path <- metacore_example("p21_mock.xlsx")
metacore <- spec_to_metacore(
path = spec_path,
verbose = "collapse"
)
#> ✔ Metadata successfully imported
#> ℹ To use the Metacore object with metatools package, first subset a dataset
#>   using `metacore::select_dataset()`
#> ℹ Operation performed with 5 suppressed warnings. Set `verbose = "warn"` to
#>   show.

# Run `spec_to_metacore` with `verbose = "warn"`
metacore <- spec_to_metacore(
path = spec_path,
verbose = "warn"
)
#> Warning: The following word in value_spec$origin is not allowed:
#> ℹ edt
#> Warning: `core` from the `ds_vars` table only contains missing values.
#> Warning: `supp_flag` from the `ds_vars` table only contains missing values.
#> Warning: The following derivations are never used:
#> ℹ SUPPAE.QVAL, SUPPDM.QVAL
#> Warning: The following codelists are never used:
#> ℹ DRUG DICTIONARY, MEDICAL HISTORY DICTIONARY