Study Config

study_config() provides a robust way of working with the _study.yml configuration file in the {mighty} framework.

A new object is initialized by supplying either the path to a _study.yml file or an in-memory list of the same content. Both are automatically validated against the study.json schema.

study_config() inherits from S7schema::S7schema(). You can validate an object at any time by calling validate() and use write_config() to save it back as a yaml file.

Usage

study_config(file, .data)

Arguments

file

character(1) path to a _study.yml file. Mutually exclusive with .data.

.data

list holding a _study.yml configuration already in memory. Mutually exclusive with file.

Value

A study_config S7 object extending S7schema::S7schema.

study_id

Unique identifier of the study.

study_description

Optional description of the study.

standards

Optional list of standards, each with id and version.

terminology

Optional list of controlled terminologies, each with id and version.

Details

The _study.yml file is validated against the study.json schema on load. The file must contain a study_id field. Additional study-level properties are allowed and are kept as-is.

The optional standards and terminology fields describe the standards and controlled terminologies applied in the study; see vignette("study-schema").

Study-level properties are used by resolve_includes() to evaluate the include conditions of domains, columns, parameters, and rows.

Write Config

Use write_config() to serialize a study_config() object back to a _study.yml file. Supply path to write to a specific file; defaults to the file the object was loaded from.

See also

mighty_study, mighty_config, mighty_domain, write_config()

Examples

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

# Custom print method gives a small overview
print(x)
#> <mighty.metadata::study_config>
#> Study ID: example_study
#> Fields: `study_id`, `standards`, and `terminology`

# Underlying object is a `list`
str(x)
#> <mighty.metadata::study_config> List of 3
#>  $ study_id   : chr "example_study"
#>  $ standards  :List of 1
#>   ..$ :List of 2
#>   .. ..$ id     : chr "ADaM-IG"
#>   .. ..$ version: chr "1.1"
#>  $ terminology:List of 4
#>   ..$ :List of 2
#>   .. ..$ id     : chr "ADAM"
#>   .. ..$ version: chr "2025-08-06"
#>   ..$ :List of 2
#>   .. ..$ id     : chr "SDTM"
#>   .. ..$ version: chr "2025-08-06"
#>   ..$ :List of 2
#>   .. ..$ id     : chr "MedDRA"
#>   .. ..$ version: chr "22.1"
#>   ..$ :List of 2
#>   .. ..$ id     : chr "WHODrug"
#>   .. ..$ version: chr "2023 JAN"
#>  @ schema   : chr "/home/runner/work/_temp/Library/mighty.metadata/schema/study.json"
#>  @ validator: <S7schema::validator>
#>  .. @ context:Classes 'V8', 'environment' <environment: 0x55eb80ac81f0> 
#>  @ file     : chr "/home/runner/work/_temp/Library/mighty.metadata/examples/_study.yml"

# Write back to a file
tmp <- tempfile(fileext = ".yml")
write_config(x, path = tmp)

# Or build one in memory
study_config(
  .data = list(study_id = "example_study", study_description = "A study")
)
#> <mighty.metadata::study_config>
#> Study ID: example_study
#> Fields: `study_id` and `study_description`