{ "_id": "6a4eec0b21b18e15484feff8", "Package": "fmridataset", "Type": "Package", "Title": "Unified Container for fMRI Datasets", "Version": "0.8.9", "Authors@R": "person(\"Bradley\", \"Buchsbaum\", \nemail = \"bbuchsbaum@gmail.com\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0001-5800-9890\"))", "Description": "Provides a unified S3 class 'fmri_dataset' for\nrepresenting functional magnetic resonance imaging (fMRI) data\nfrom various sources including raw NIfTI files, BIDS projects,\npre-loaded NeuroVec objects, and in-memory matrices. Features\nlazy loading, flexible data access patterns, and integration\nwith neuroimaging analysis workflows.", "License": "GPL (>= 3)", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "VignetteBuilder": "knitr", "Remotes": [ "bbuchsbaum/delarr", "bbuchsbaum/albersdown" ], "Additional_repositories": "https://bbuchsbaum.r-universe.dev", "URL": "https://github.com/bbuchsbaum/fmridataset,\nhttps://bbuchsbaum.github.io/fmridataset/", "BugReports": "https://github.com/bbuchsbaum/fmridataset/issues", "Config/Needs/website": "albersdown", "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev", "Repository": "https://bbuchsbaum.r-universe.dev", "Date/Publication": "2026-06-19 12:42:16 UTC", "RemoteUrl": "https://github.com/bbuchsbaum/fmridataset", "RemoteRef": "HEAD", "RemoteSha": "0d3a0a595e77a5d796691d3b5216a05ab0b8e3d2", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-09 00:23:00 UTC", "User": "root" }, "Author": "Bradley Buchsbaum [aut, cre] (ORCID:\n)", "Maintainer": "Bradley Buchsbaum ", "_user": "bbuchsbaum", "_type": "src", "_file": "fmridataset_0.8.9.tar.gz", "_fileid": "https://r2.ropensci.org/b489dcf592f907ed8b0c64adb4bd37c88e55600439fa4ff096200518f6c98867", "_filesize": 833270, "_sha256": "b489dcf592f907ed8b0c64adb4bd37c88e55600439fa4ff096200518f6c98867", "_expires": "2026-10-17T00:32:09.000Z", "_created": "2026-07-09T00:23:00.000Z", "_published": "2026-07-09T00:32:11.050Z", "_jobs": [ { "job": 86012289699, "time": 452, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "8185692973" }, { "job": 86012289763, "time": 449, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8185692329" }, { "job": 86012289716, "time": 251, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "8185636134" }, { "job": 86012289719, "time": 281, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "8185643955" }, { "job": 86011646999, "time": 308, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8185563286" }, { "job": 86012289710, "time": 186, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8185617253" }, { "job": 86012289714, "time": 493, "config": "windows-devel", "r": "4.7.0", "check": "ERROR", "artifact": "8185705531" }, { "job": 86012289718, "time": 455, "config": "windows-oldrel", "r": "4.5.3", "check": "ERROR", "artifact": "8185694079" }, { "job": 86012289721, "time": 488, "config": "windows-release", "r": "4.6.1", "check": "ERROR", "artifact": "8185704245" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bbuchsbaum/actions/runs/28984889555", "_status": "success", "_upstream": "https://github.com/bbuchsbaum/fmridataset", "_commit": { "id": "0d3a0a595e77a5d796691d3b5216a05ab0b8e3d2", "author": "bbuchsbaum ", "committer": "bbuchsbaum ", "message": "refactor: reduce cyclomatic complexity below 15 across 13 files\n\nExtract behavior-preserving internal helpers to bring 19 functions under\nthe cyclocomp_linter(15) threshold (lintr: 19 -> 0). The full test suite\nis byte-identical to baseline (2463 pass / 0 fail) and devtools::document()\nproduces no NAMESPACE or man-page changes.\n\nFunctions refactored (prior complexity):\n- bids_h5_write.R: compress_bids_study (88), .read_scan_confounds (24),\n .write_bids_group (23), .read_scan_events (21), .project_template_with_offset (19)\n- dataset_constructors.R: fmri_dataset (28)\n- study_backend.R: study_backend (26), backend_get_data.study_backend (25)\n- study_backend_seed_s3.R: register_study_backend_seed_methods (25)\n- latent_backend.R: backend_open.latent_backend (24), latent_backend (19)\n- group_verbs.R: sample_subjects (23); group_map.R: group_map (22)\n- as_delarr.R (22), storage_backend.R: validate_backend (22)\n- backend_registry.R: register_backend (19); data_access.R: fmri_cache_info (19)\n- bids_h5_dataset.R (18); fmri_series_resolvers.R: resolve_selector (18)\n\nHelpers use unique `.`-prefixed names and carry no roxygen (no man-page\nchurn). Helper definitions are placed after the functions they serve so\nexported functions keep their roxygen blocks. group_map now forwards the\ncaller's dots via do.call so an arg literally named `skip_sentinel` is\npassed to `.f` instead of colliding with an internal formal.\n\nVerified by four independent adversarial reviews (RNG order in\nsample_subjects, index/concat math in study_backend, check ordering in\nvalidate_backend, latent-mode K threading in compress_bids_study).\n\nCo-Authored-By: Claude Opus 4.8 (1M context) \n", "time": 1781872936 }, "_maintainer": { "name": "Bradley Buchsbaum", "email": "bbuchsbaum@gmail.com", "orcid": "0000-0001-5800-9890" }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.3.0", "role": "Depends" }, { "package": "assertthat", "role": "Imports" }, { "package": "cachem", "role": "Imports" }, { "package": "deflist", "role": "Imports" }, { "package": "delarr", "role": "Imports" }, { "package": "fmrihrf", 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"page": "as_delarr", "title": "Convert backend to a delarr lazy matrix", "topics": [ "as_delarr", "as_delarr.default", "as_delarr.matrix_backend", "as_delarr.nifti_backend", "as_delarr.study_backend" ] }, { "page": "as_delayed_array", "title": "Convert Backend to DelayedArray", "topics": [ "as_delayed_array", "as_delayed_array.default", "as_delayed_array.matrix_backend", "as_delayed_array.nifti_backend", "as_delayed_array.study_backend" ] }, { "page": "as_delayed_array-dataset", "title": "Convert Dataset Objects to DelayedArray", "topics": [ "as_delayed_array,fmri_file_dataset-method", "as_delayed_array,fmri_mem_dataset-method", "as_delayed_array,matrix_dataset-method", "as_delayed_array-dataset" ] }, { "page": "as_fmri_group", "title": "Coerce a data frame into an fmri_group", "topics": [ "as_fmri_group" ] }, { "page": "as_tibble.fmri_series", "title": "Convert fmri_series to Tibble", "topics": [ "as_tibble.fmri_series" ] }, { "page": "as_tibble.fmri_study_dataset", "title": "Convert fmri_study_dataset to a tibble or lazy matrix", "topics": [ "as_tibble.fmri_study_dataset" ] }, { "page": "as.matrix_dataset", "title": "Convert to Matrix Dataset", "topics": [ "as.matrix_dataset" ] }, { "page": "as.matrix.fmri_series", "title": "Convert fmri_series to Matrix", "topics": [ "as.matrix.fmri_series" ] }, { "page": "bids_h5_dataset", "title": "Open a BIDS HDF5 Study Archive", "topics": [ "bids_h5_dataset" ] }, { "page": "blockids", "title": "Get Block IDs from Sampling Frame", "topics": [ "blockids", "blockids.fmri_dataset", "blockids.sampling_frame" ] }, { "page": "blocklens", "title": "Get Block Lengths from Objects", "topics": [ "blocklens", "blocklens.fmri_dataset", "blocklens.sampling_frame" ] }, { "page": "collect_chunks", "title": "Collect all chunks from a chunk iterator", "topics": [ "collect_chunks" ] }, { "page": "compress_bids_study", "title": "Compress a BIDS Study into a Single HDF5 Archive", "topics": [ "compress_bids_study" ] }, { "page": "create_backend", "title": "Create Backend Instance", "topics": [ "create_backend" ] }, { "page": "data_chunk", "title": "Create a Data Chunk Object", "topics": [ "data_chunk" ] }, { "page": "data_chunks", "title": "Create Data Chunks for Processing", "topics": [ "data_chunks" ] }, { "page": "data_chunks.fmri_file_dataset", "title": "Create Data Chunks for fmri_file_dataset Objects", "topics": [ "data_chunks.fmri_file_dataset" ] }, { "page": "data_chunks.fmri_mem_dataset", "title": "Create Data Chunks for fmri_mem_dataset Objects", "topics": [ "data_chunks.fmri_mem_dataset" ] }, { "page": "data_chunks.fmri_study_dataset", "title": "Create Data Chunks for fmri_study_dataset Objects", "topics": [ "data_chunks.fmri_study_dataset" ] }, { "page": "data_chunks.matrix_dataset", "title": "Create Data Chunks for matrix_dataset Objects", "topics": [ "data_chunks.matrix_dataset" ] }, { "page": "dim.fmri_series", "title": "Dimensions of fmri_series", "topics": [ "dim.fmri_series" ] }, { "page": "encoding_info", "title": "Get Encoding Metadata from a Latent-Mode BIDS H5 Dataset", "topics": [ "encoding_info", "encoding_info.bids_h5_study_dataset" ] }, { "page": "exec_strategy", "title": "Create an Execution Strategy for Data Processing", "topics": [ "exec_strategy" ] }, { "page": "filter_subjects", "title": "Filter subjects in an fmri_group", "topics": [ "filter_subjects" ] }, { "page": "fmri_cache_info", "title": "Get cache information and statistics", "topics": [ "fmri_cache_info" ] }, { "page": "fmri_cache_resize", "title": "Resize the fmridataset cache", "topics": [ "fmri_cache_resize" ] }, { "page": "fmri_clear_cache", "title": "Clear fmridataset cache", "topics": [ "fmri_clear_cache" ] }, { "page": "fmri_dataset", "title": "Create an fMRI Dataset Object from a Set of Scans", "topics": [ "fmri_dataset" ] }, { "page": "fmri_dataset_legacy", "title": "Legacy fMRI Dataset Constructor", "topics": [ "fmri_dataset_legacy" ] }, { "page": "fmri_group", "title": "Create an fmri_group (one row per subject)", "topics": [ "fmri_group" ] }, { "page": "fmri_h5_dataset", "title": "Create an fMRI Dataset Object from H5 Files", "topics": [ "fmri_h5_dataset" ] }, { "page": "fmri_latent_dataset", "title": "Create an fMRI Dataset Object from LatentNeuroVec Files or Objects", "topics": [ "fmri_latent_dataset" ] }, { "page": "fmri_mem_dataset", "title": "Create an fMRI Memory Dataset Object", "topics": [ "fmri_mem_dataset" ] }, { "page": "fmri_series", "title": "fmri_series: fMRI Time Series Container", "topics": [ "fmri_series" ] }, { "page": "fmri_series_resolvers", "title": "Helpers for fmri_series spatial and temporal selection", "topics": [ "fmri_series_resolvers" ] }, { "page": "fmri_study_dataset", "title": "Create an fmri_study_dataset", "topics": [ "fmri_study_dataset" ] }, { "page": "fmri_zarr_dataset", "title": "Create an fMRI Dataset from Zarr Arrays", "topics": [ "fmri_zarr_dataset" ] }, { "page": "generics", "title": "Generic Functions for fMRI Dataset Operations", "topics": [ "generics" ] }, { "page": "get_backend_registry", "title": "Get Registered Backend Information", "topics": [ "get_backend_registry" ] }, { "page": "get_component_info", "title": "Get Component Information", "concept": [ "latent_data" ], "topics": [ "get_component_info" ] }, { "page": "get_confounds", "title": "Get Confound Regressors from a BIDS H5 Dataset", "topics": [ "get_confounds", "get_confounds.bids_h5_study_dataset" ] }, { "page": "get_data", "title": "Get Data from fMRI Dataset Objects", "topics": [ "get_data" ] }, { "page": "get_data_matrix", "title": "Get Data Matrix from fMRI Dataset Objects", "topics": [ "get_data_matrix" ] }, { "page": "get_latent_scores", "title": "Get Latent Scores from Dataset", "concept": [ "latent_data" ], "topics": [ "get_latent_scores" ] }, { "page": "get_loadings", "title": "Get Spatial Loadings from a Latent-Mode BIDS H5 Dataset", "topics": [ "get_loadings", "get_loadings.bids_h5_study_dataset" ] }, { "page": "get_mask", "title": "Get Mask from fMRI Dataset Objects", "topics": [ "get_mask" ] }, { "page": "get_run_duration", "title": "Get Run Duration from Sampling Frame", "topics": [ "get_run_duration", "get_run_duration.fmri_dataset", "get_run_duration.sampling_frame" ] }, { "page": "get_run_lengths", "title": "Get Run Lengths from Sampling Frame", "topics": [ "get_run_lengths", "get_run_lengths.fmri_dataset", "get_run_lengths.sampling_frame" ] }, { "page": "get_spatial_loadings", "title": "Get Spatial Loadings from Dataset", "concept": [ "latent_data" ], "topics": [ "get_spatial_loadings" ] }, { "page": "get_total_duration", "title": "Get Total Duration from Sampling Frame", "topics": [ "get_total_duration", "get_total_duration.fmri_dataset", "get_total_duration.sampling_frame" ] }, { "page": "get_TR", "title": "Get TR (Repetition Time) from Sampling Frame", "topics": [ "get_TR", "get_TR.fmri_dataset", "get_TR.sampling_frame" ] }, { "page": "group_map", "title": "Map a function over subjects in an fmri_group", "topics": [ "group_map" ] }, { "page": "group_reduce", "title": "Reduce over subjects in a single pass", "topics": [ "group_reduce" ] }, { "page": "index_selector", "title": "Index-based Series Selector", "topics": [ "index_selector" ] }, { "page": "is_backend_registered", "title": "Check if Backend is Registered", "topics": [ "is_backend_registered" ] }, { "page": "is.fmri_series", "title": "Check if object is an fmri_series", "topics": [ "is.fmri_series" ] }, { "page": "is.sampling_frame", "title": "Test if Object is a Sampling Frame", "topics": [ "is.sampling_frame" ] }, { "page": "iter_subjects", "title": "Iterate subjects one-by-one (streaming)", "topics": [ "iter_subjects" ] }, { "page": "latent_dataset", "title": "Latent Dataset Interface", "concept": [ "latent_data" ], "topics": [ "latent_dataset" ] }, { "page": "left_join_subjects", "title": "Left join additional subject metadata", "topics": [ "left_join_subjects" ] }, { "page": "list_backend_names", "title": "List Registered Backend Names", "topics": [ "list_backend_names" ] }, { "page": "mask_selector", "title": "Mask-based Series Selector", "topics": [ "mask_selector" ] }, { "page": "matrix_dataset", "title": "Matrix Dataset Constructor", "topics": [ "matrix_dataset" ] }, { "page": "mutate_subjects", "title": "Mutate subject-level attributes", "topics": [ "mutate_subjects" ] }, { "page": "n_runs", "title": "Get Number of Runs from Sampling Frame", "topics": [ "n_runs", "n_runs.fmri_dataset", "n_runs.fmri_study_dataset", "n_runs.sampling_frame" ] }, { "page": "n_subjects", "title": "Number of subjects in a group", "topics": [ "n_subjects" ] }, { "page": "n_timepoints", "title": "Get Number of Timepoints from Sampling Frame", "topics": [ "n_timepoints", "n_timepoints.fmri_dataset", "n_timepoints.sampling_frame" ] }, { "page": "ncol.fmri_series", "title": "Number of columns in fmri_series", "topics": [ "ncol.fmri_series" ] }, { "page": "nrow.fmri_series", "title": "Number of rows in fmri_series", "topics": [ "nrow.fmri_series" ] }, { "page": "parcellation_info", "title": "Get Parcellation Information from a BIDS H5 Dataset", "topics": [ "parcellation_info", "parcellation_info.bids_h5_study_dataset" ] }, { "page": "participants", "title": "Get Participant IDs from a Dataset", "topics": [ "participants", "participants.bids_h5_study_dataset" ] }, { "page": "print", "title": "Print Methods for fmridataset Objects", "topics": [ "print", "print.chunkiter", "print.data_chunk", "print.fmri_dataset", "print.matrix_dataset", "summary.fmri_dataset" ] }, { "page": "print.backend_registry", "title": "Print Backend Registry", "topics": [ "print.backend_registry" ] }, { "page": "print.fmri_series", "title": "Print Method for fmri_series Objects", "topics": [ "print.fmri_series" ] }, { "page": "print.series_selector", "title": "Print Methods for Series Selectors", "topics": [ "print.series_selector" ] }, { "page": "read_fmri_config", "title": "read a basic fMRI configuration file", "topics": [ 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