Mighty Domain — mighty_domain • mighty.metadata

mighty_domain() provides a robust way of working with ADaM metadata in the {mighty} framework.

A new object is initialized by supplying either an existing yaml metadata file or an in-memory list of the same content. This package provides helpers to update column, parameter, and row entries. See the references below for help:

mighty_domain() inherits from S7schema::S7schema() and the yaml file is automatically validated when loaded. The helper functions above also always validates the new configuration before returning.

You can at anytime validate an object by calling validate() and use write_config() to save it as a yaml file again.

Usage

mighty_domain(file, .data)

Arguments

file: character(1) path to a yaml file defining an ADaM dataset. Mutually exclusive with .data.
.data: list holding an ADaM dataset specification already in memory. Mutually exclusive with file.

Value

A mighty_domain S7 object extending S7schema::S7schema. The underlying list contains the parsed and validated YAML metadata including id, label, class, keys, columns, parameters, and rows.

Examples

x <- mighty_domain(
  file = system.file("examples", "advs.yml", package = "mighty.metadata")
)

# Custom print method gives a small overview
print(x)
#> <mighty.metadata::mighty_domain>
#> ADVS: Vital Signs Analysis Dataset
#> Class: BASIC DATA STRUCTURE
#> Keys: USUBJID, PARAMCD, and AVISITN

# Underlying object is a `list`
str(x)
#> <mighty.metadata::mighty_domain> List of 9
#>  $ id        : chr "ADVS"
#>  $ label     : chr "Vital Signs Analysis Dataset"
#>  $ class     : chr "BASIC DATA STRUCTURE"
#>  $ structure : chr "One record per vital sign parameter, per visit, per subject"
#>  $ keys      : chr [1:3] "USUBJID" "PARAMCD" "AVISITN"
#>  $ population:List of 2
#>   ..$ base  :List of 1
#>   .. ..$ :List of 3
#>   .. .. ..$ domain : chr "VS"
#>   .. .. ..$ depends: chr "VSTESTCD"
#>   .. .. ..$ filter : chr "VSTESTCD != \"\""
#>   ..$ global:List of 1
#>   .. ..$ :List of 2
#>   .. .. ..$ filter : chr "SAFFL == \"Y\""
#>   .. .. ..$ depends: chr "SAFFL"
#>  $ columns   :List of 11
#>   ..$ :List of 4
#>   .. ..$ id    : chr "STUDYID"
#>   .. ..$ label : chr "Study Identifier"
#>   .. ..$ method: chr "VS.STUDYID"
#>   .. ..$ core  : chr "Req"
#>   ..$ :List of 4
#>   .. ..$ id    : chr "USUBJID"
#>   .. ..$ label : chr "Unique Subject Identifier"
#>   .. ..$ method: chr "VS.USUBJID"
#>   .. ..$ core  : chr "Req"
#>   ..$ :List of 4
#>   .. ..$ id    : chr "SAFFL"
#>   .. ..$ label : chr "Safety Population Flag"
#>   .. ..$ method: chr "ADSL.SAFFL"
#>   .. ..$ core  : chr "Req"
#>   ..$ :List of 4
#>   .. ..$ id    : chr "TRTP"
#>   .. ..$ label : chr "Planned Treatment"
#>   .. ..$ method: chr "ADSL.TRT01P"
#>   .. ..$ core  : chr "Req"
#>   ..$ :List of 4
#>   .. ..$ id    : chr "VISITNUM"
#>   .. ..$ label : chr "Visit Number"
#>   .. ..$ method: chr "VS.VISITNUM"
#>   .. ..$ core  : chr "Perm"
#>   ..$ :List of 4
#>   .. ..$ id    : chr "AVISITN"
#>   .. ..$ label : chr "Analysis Visit (N)"
#>   .. ..$ method: chr "Derived from VISITNUM"
#>   .. ..$ core  : chr "Req"
#>   ..$ :List of 4
#>   .. ..$ id    : chr "AVISIT"
#>   .. ..$ label : chr "Analysis Visit"
#>   .. ..$ method: chr "Derived from VISIT converted to title case"
#>   .. ..$ core  : chr "Req"
#>   ..$ :List of 4
#>   .. ..$ id    : chr "PARAMCD"
#>   .. ..$ label : chr "Parameter Code"
#>   .. ..$ method: chr "VS.VSTESTCD"
#>   .. ..$ core  : chr "Req"
#>   ..$ :List of 4
#>   .. ..$ id    : chr "PARAM"
#>   .. ..$ label : chr "Parameter"
#>   .. ..$ method: chr "VS.VSTEST"
#>   .. ..$ core  : chr "Req"
#>   ..$ :List of 4
#>   .. ..$ id    : chr "AVAL"
#>   .. ..$ label : chr "Analysis Value"
#>   .. ..$ method: chr "VS.VSSTRESN"
#>   .. ..$ core  : chr "Req"
#>   ..$ :List of 3
#>   .. ..$ id   : chr "AVALC"
#>   .. ..$ label: chr "Analysis Value (C)"
#>   .. ..$ core : chr "Perm"
#>  $ rows      :List of 1
#>   ..$ :List of 2
#>   .. ..$ id    : chr "BASELINE"
#>   .. ..$ method: chr "Add baseline visit as a new row"
#>  $ parameters:List of 2
#>   ..$ :List of 3
#>   .. ..$ id     : chr "BMI"
#>   .. ..$ label  : chr "Body Mass Index (kg/m^2)"
#>   .. ..$ columns:List of 1
#>   .. .. ..$ :List of 2
#>   .. .. .. ..$ id    : chr "AVAL"
#>   .. .. .. ..$ method: chr "Derived from height and weight"
#>   ..$ :List of 3
#>   .. ..$ id     : chr "BMIGRP"
#>   .. ..$ label  : chr "Body Mass Index Group"
#>   .. ..$ columns:List of 2
#>   .. .. ..$ :List of 2
#>   .. .. .. ..$ id    : chr "AVALC"
#>   .. .. .. ..$ method: chr "BMI grouped in <20, 20-<25, 25-<30, 30+"
#>   .. .. ..$ :List of 2
#>   .. .. .. ..$ id    : chr "AVAL"
#>   .. .. .. ..$ method: chr "Numeric representation of AVALC"
#>  @ schema   : chr "/home/runner/work/_temp/Library/mighty.metadata/schema/adam.json"
#>  @ validator: <S7schema::validator>
#>  .. @ context:Classes 'V8', 'environment' <environment: 0x55eb84031380> 
#>  @ file     : chr "/home/runner/work/_temp/Library/mighty.metadata/examples/advs.yml"

# Or build one in memory
mighty_domain(
  .data = list(
    id = "ADVS",
    label = "Vital Signs Analysis Dataset",
    class = "BASIC DATA STRUCTURE",
    structure = "One record per parameter, per visit, per subject",
    keys = c("USUBJID", "PARAMCD"),
    columns = list(
      list(id = "USUBJID", label = "Unique Subject Identifier")
    )
  )
)
#> <mighty.metadata::mighty_domain>
#> ADVS: Vital Signs Analysis Dataset
#> Class: BASIC DATA STRUCTURE
#> Keys: USUBJID and PARAMCD