get_bids_dataset_description {bidsr} | R Documentation |
Class definition of 'BIDS' data-set description
Description
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 |
parent_directory |
parent directory where the file
|
... |
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
|
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 |
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
|
SourceDatasets |
Used to specify the locations and relevant
attributes of all source data-sets. Valid keys in each object include
|
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). |
Value
A S7
description object that contains all the fields
describing the data set; see 'Examples' for usages.
Author(s)
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$License
dataset_description$GeneratedBy[[1]]$Container
# ---- 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)
}