Class definition of 'BIDS' data-set description — get_bids_dataset

See https://bids-specification.readthedocs.io/en/stable/modality-agnostic-files.html#dataset_descriptionjson for specification.

Usage

get_bids_dataset_description(x, parent_directory, ...)

BIDSDatasetDescription(
  Name = character(0),
  BIDSVersion = character(0),
  DatasetLinks = list(),
  HEDVersion = character(0),
  DatasetType = character(0),
  License = character(0),
  Authors = character(0),
  GeneratedBy = list(),
  SourceDatasets = list(),
  Acknowledgements = character(0),
  HowToAcknowledge = character(0),
  Funding = character(0),
  EthicsApprovals = character(0),
  ReferencesAndLinks = character(0),
  DatasetDOI = character(0),
  parent_directory = character(0)
)

Arguments

x: R object to be interpreted as 'BIDS' data description; default support list, path to the 'json' file, 'json' string, etc.
parent_directory: parent directory where the file 'dataset_description.json' is stored. This input is ignored if x is the path to 'dataset_description.json', otherwise is a must.
...: passed to methods
Name: (required, string) Name of the data-set.
BIDSVersion: (required, string) The version of the BIDS standard that was used.
DatasetLinks: (required if 'BIDS-URI' is used) Used to map a given data-set name from a 'BIDS-URI' of the form bids:<dataset-name>:path/within/dataset to a local or remote location.
HEDVersion: (recommended strings) The version of the 'HED' schema used to validate 'HED' tags for study. May include a single schema or a base schema and one or more library schema.
DatasetType: (recommended string) Must be one of "raw" or "derivative"; package bidsr automatically assigns "raw" is not given.
License: (recommended string) The license for the data-set
Authors: (recommended strings) Vector of individuals who contributed to the creation/curation of the data-set
GeneratedBy: (recommended) will be converted to BIDSDatasetGeneratedBy
SourceDatasets: Used to specify the locations and relevant attributes of all source data-sets. Valid keys in each object include "URL", "DOI", and "Version" with string values; Package bidsr does not check the names
Acknowledgements: (optional string) Text acknowledging contributions of individuals or institutions beyond those listed in Authors or Funding.
HowToAcknowledge: (optional string) Text containing instructions on how researchers using this dataset should acknowledge the original authors. This field can also be used to define a publication that should be cited in publications that use the dataset.
Funding: (optional strings) List of sources of funding (grant numbers).
EthicsApprovals: (optional strings) List of ethics committee approvals of the research protocols and/or protocol identifiers.
ReferencesAndLinks: (optional strings) List of references to publications that contain information on the data-set. A reference may be textual or a URI.
DatasetDOI: (optional string) The Digital Object Identifier of the data-set (not the corresponding paper). 'DOIs' should be expressed as a valid 'URI'

Value

A S7 description object that contains all the fields describing the data set; see 'Examples' for usages.

Author

Zhengjia Wang

Examples


# ---- Manually enter entries ----------------------------------------
dataset_description <- BIDSDatasetDescription(
  # a parent directory is mandatory as it defines what data
  # dataset_description.json applies to

  parent_directory = "/path/to/BIDS/folder",

  Name = "A dummy experiments",
  BIDSVersion = "1.6.0",
  License = "CC0",
  Authors = c("Zhengjia Wang"),
  Acknowledgements = c(
    "Package `bidsr` is a 3rd-party BIDS reader developed by",
    "a RAVE (https://rave.wiki) team member with procrastination."
  ),
  HowToAcknowledge = c(
    "Please cite this paper:",
    "https://doi.org/10.1016/j.neuroimage.2020.117341"
  ),
  Funding = c(
    "NIH R01MH133717",
    "NIH U01NS113339",
    "NIH 1R24MH117529"
  ),
  ReferencesAndLinks = c(
    "https://rave.wiki"
  ),
  DatasetDOI = "https://doi.org/10.1016/j.neuroimage.2020.117341",
  HEDVersion = "8.0.0",
  GeneratedBy = list(
    list(
      Name = "Dipterix",
      Version = "0.0.1",
      Container = list(
        Type = "r-package",
        Tag = "dipterix/bidsr:0.0.1"
      )
    )
  )
)

# access the information
dataset_description$License
#> [1] "CC0"

dataset_description$GeneratedBy[[1]]$Container
#> $Type
#> [1] "r-package"
#> 
#> $Tag
#> [1] "dipterix/bidsr:0.0.1"
#> 

# ---- Read from file ---------------------------------------------

# Run `download_bids_examples()` first
examples <- download_bids_examples(test = TRUE)
if(!isFALSE(examples)) {
  example_descr <- file.path(
    examples, "ieeg_epilepsy_ecog", "dataset_description.json")

  x <- get_bids_dataset_description(example_descr)
  x

  # ---- Formatting --------------------------------------------------
  # convert to R list (use recursive to expand field `GeneratedBy`)
  as.list(x, recursive = TRUE)

  # JSON string
  format(x)
}