Overview of a BIDS project | File dataset_description.json | File participants.tsv | Instantiate a BIDS subject | Raw, source, or derivative data | Query subject files by types | Filter & get BIDS entity
Package: bidsr 0.1.1
bidsr: A Brain Imaging Data Structure ('BIDS') Parser
Parse and read the files that comply with the brain imaging data structure, or 'BIDS' format, see the publication from Gorgolewski, K., Auer, T., Calhoun, V. et al. (2016) <doi:10.1038/sdata.2016.44>. Provides query functions to extract and check the 'BIDS' entity information (such as subject, session, task, etc.) from the file paths and suffixes according to the specification. The package is developed and used in the reproducible analysis and visualization of intracranial electroencephalography, or 'RAVE', see Magnotti, J. F., Wang, Z., and Beauchamp, M. S. (2020) <doi:10.1016/j.neuroimage.2020.117341>; see 'citation("bidsr")' for details and attributions.
Authors:
bidsr_0.1.1.tar.gz
bidsr_0.1.1.zip(r-4.7)bidsr_0.1.1.zip(r-4.6)bidsr_0.1.1.zip(r-4.5)
bidsr_0.1.1.tgz(r-4.6-any)bidsr_0.1.1.tgz(r-4.5-any)
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bidsr_0.1.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
bidsr/json (API)
| # Install 'bidsr' in R: |
| install.packages('bidsr', repos = c('https://dipterix.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/dipterix/bidsr/issues
Pkgdown/docs site:https://dipterix.org
Last updated from:ef6099666a. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 137 | ||
| source / vignettes | OK | 193 | ||
| linux-release-x86_64 | OK | 115 | ||
| macos-release-arm64 | OK | 98 | ||
| macos-oldrel-arm64 | OK | 94 | ||
| windows-devel | OK | 84 | ||
| windows-release | OK | 66 | ||
| windows-oldrel | OK | 102 | ||
| wasm-release | OK | 118 |
Exports:as_bids_tabularbids_projectbids_propertybids_property_characterbids_property_choicebids_property_collapsed_characterbids_property_data_framebids_property_deprecatedbids_property_entity_listbids_property_integerishbids_property_listbids_property_named_listbids_property_numericbids_property_optionalbids_property_prohibitedbids_property_recommendedbids_property_requiredbids_property_tabular_column_descriptor_listbids_property_tabular_contentbids_property_tabular_metabids_property_unnamed_listbids_subjectBIDSClassBaseBIDSDatasetDescriptionBIDSDatasetGeneratedByBIDSEntity_any_optionalBIDSEntity_any_prohibitedBIDSEntity_any_requiredBIDSEntity_index_optionalBIDSEntity_index_prohibitedBIDSEntity_index_requiredBIDSEntity_label_optionalBIDSEntity_label_prohibitedBIDSEntity_label_requiredBIDSMapBIDSProjectBIDSSubjectBIDSTabularBIDSTabularColumnDescriptorBIDSTabularMetaSidecarBIDSTabularParticipantsBIDSTabularPhenotypeBIDSTabularSamplesBIDSTabularScansBIDSTabularSessionsBIDSURIdownload_bids_examplesget_bids_dataset_descriptionget_bids_entityget_bids_entity_rulesget_bids_participantsget_bids_phenotype_dataget_bids_samplesnew_bids_classnew_bids_entity_file_classnew_bids_tabular_classparse_path_bids_entityquery_bidsresolve_bids_pathsave_bids_tabularsave_bids_tabular_defaultset_propsvalid_eventually
Dependencies:backportsbitbit64checkmatedata.tablefastmapfsjsonlitelatticenanotimeRcppRcppCCTZRcppDateS7uuidzoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Class definitions and utilities for 'BIDS' tabular | as_bids_tabular BIDSTabular BIDSTabularColumnDescriptor BIDSTabularMetaSidecar new_bids_tabular_class save_bids_tabular save_bids_tabular_default |
| 'BIDS' project class | BIDSProject bids_project |
| ''S7'' property for 'BIDS' classes | bids_property bids_property_character bids_property_choice bids_property_collapsed_character bids_property_data_frame bids_property_deprecated bids_property_entity_list bids_property_integerish bids_property_list bids_property_named_list bids_property_numeric bids_property_optional bids_property_prohibited bids_property_recommended bids_property_required bids_property_tabular_column_descriptor_list bids_property_tabular_content bids_property_tabular_meta bids_property_unnamed_list |
| 'BIDS' subject class | BIDSSubject bids_subject |
| Low-level abstract class for 'bidsr' | BIDSClassBase |
| Class definition for 'BIDS' meta-data ''GeneratedBy'' | BIDSDatasetGeneratedBy |
| Class definitions of 'BIDS' entity | BIDSEntity BIDSEntity_any_optional BIDSEntity_any_prohibited BIDSEntity_any_required BIDSEntity_index_optional BIDSEntity_index_prohibited BIDSEntity_index_required BIDSEntity_label_optional BIDSEntity_label_prohibited BIDSEntity_label_required |
| Low-level nested map to store key-value data with inherited structure | BIDSMap |
| 'BIDS' scans table class | BIDSTabularScans |
| 'BIDS' sessions table class | BIDSTabularSessions |
| 'BIDS' uniform resource indicator ('URI') class definition | BIDSURI |
| Download 'BIDS' example data-sets | download_bids_examples |
| Class definition of 'BIDS' data-set description | BIDSDatasetDescription get_bids_dataset_description |
| Get 'BIDS' entity values from file | get_bids_entity get_bids_entity_rules |
| 'BIDS' participant table class | BIDSTabularParticipants get_bids_participants |
| 'BIDS' phenotype and assessment table class | BIDSTabularPhenotype get_bids_phenotype_data |
| 'BIDS' samples table class | BIDSTabularSamples get_bids_samples |
| Create new 'bidsr' class definition | new_bids_class |
| Class generator for 'BIDS' file class with entities | new_bids_entity_file_class |
| Parse 'BIDS' entities from file path | parse_path_bids_entity |
| Query 'BIDS' | query_bids |
| Resolve path of a 'BIDS' object | resolve_bids_path |
