{ "_id": "6a284235732311cd875828f3", "Package": "ggseg.formats", "Title": "Brain Atlas Data Structures for the 'ggsegverse' Ecosystem", "Version": "0.0.2.9002", "Authors@R": "c(person(\"Athanasia Mo\", \"Mowinckel\", , \"a.m.mowinckel@psykologi.uio.no\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-5756-0223\")),\nperson(\"Center for Lifespan Changes in Brain and Cognition (LCBC), University of Oslo\",\nrole = \"cph\"))", "Description": "Provides the 'ggseg_atlas' S3 class used across the\n'ggsegverse' ecosystem for 2D and 3D brain visualisation. Ships\nfour bundled atlases ('Desikan-Killiany', 'FreeSurfer' 'aseg',\n'TRACULA', 'SUIT') and functions for querying, subsetting,\nrenaming, and enriching atlas objects. Also includes readers\nfor 'FreeSurfer' statistics files.", "License": "MIT + file LICENSE", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "Config/Needs/website": "ggsegverse/ggseg.docs", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "URL": "https://github.com/ggsegverse/ggseg.formats,\nhttps://ggsegverse.github.io/ggseg.formats/", "BugReports": "https://github.com/ggsegverse/ggseg.formats/issues", "Repository": "https://drmowinckels.r-universe.dev", "Date/Publication": "2026-06-09 14:09:45 UTC", "RemoteUrl": "https://github.com/ggsegverse/ggseg.formats", "RemoteRef": "HEAD", "RemoteSha": "026b30359515b65f8eae2283fbdc3cdcfaabddaf", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-09 16:38:00 UTC", "User": "root" }, "Author": "Athanasia Mo Mowinckel [aut, cre] (ORCID:\n),\nCenter for Lifespan Changes in Brain and Cognition (LCBC), University\nof Oslo [cph]", "Maintainer": "Athanasia Mo Mowinckel ", "MD5sum": "6f3d7368d714d601ff18582cf1c401aa", "_user": "drmowinckels", "_type": "src", "_file": "ggseg.formats_0.0.2.9002.tar.gz", "_fileid": "a663226cf126c79eaece9c10a41b30d1ae6e1a5de2102ee629d8824ad57e77d8", "_filesize": 4367465, "_sha256": "a663226cf126c79eaece9c10a41b30d1ae6e1a5de2102ee629d8824ad57e77d8", "_created": "2026-06-09T16:38:00.000Z", "_published": "2026-06-09T16:41:25.456Z", "_distro": "noble", "_jobs": [ { "job": 80375959469, "time": 154, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7514128449" }, { "job": 80375959532, "time": 154, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7514128665" }, { "job": 80375959487, "time": 156, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7514131223" }, { "job": 80375959485, "time": 105, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7514128691" }, { "job": 80375054848, "time": 274, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7514064920" }, { "job": 80375959452, "time": 112, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7514111981" }, { "job": 80375959472, "time": 134, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7514120877" }, { "job": 80375959592, "time": 114, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7514112700" }, { "job": 80375959466, "time": 110, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7514111501" } ], "_buildurl": "https://github.com/r-universe/drmowinckels/actions/runs/27220858972", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/ggsegverse/ggseg.formats", "_commit": { "id": "026b30359515b65f8eae2283fbdc3cdcfaabddaf", "author": "Athanasia Monika Mowinckel <14014329+drmowinckels@users.noreply.github.com>", "committer": "GitHub ", "message": "refactor: reduce cyclomatic complexity below goodpractice threshold (#13)\n\n* refactor: reduce cyclomatic complexity below goodpractice threshold\n\nDecompose the seven functions flagged by goodpractice (cyclocomp > 15) into\nfocused, internal helpers. Behaviour is unchanged (754 tests pass); the helpers\nare @noRd so the public surface and NAMESPACE are untouched.\n\n- migrate_atlas_files (27 -> 13): migrate_rda_file / migrate_atlas_object /\n migration_target_geom\n- validate_meshes (27 -> 5): validate_one_mesh / mesh_geometry_empty /\n validate_mesh_part\n- as.data.frame.ggseg_atlas (25 -> 3): as_sf_for_data_frame /\n merge_core_into_sf / infer_cortical_hemi\n- atlas_region_op (25 -> 12): region_op_sf_data / region_op_combine /\n region_op_view / add_op_region_meta\n- as_ggseg_atlas.brain_atlas (24 -> 13): flatten the dispatch, fold the\n duplicate convert_legacy_brain_data branch\n- infer_vertices_from_meshes (23 -> low): mesh_vertex_index / coord_keys /\n region_coords_from_mesh / match_ggseg_vertices\n- atlas_view_gather (19 -> low): gather_without_sf\n\nCo-Authored-By: Claude Opus 4.8 (1M context) \n\n* refactor: apply /simplify feedback to complexity refactor\n\n- region_op_sf_data() returns sf_data + was_polygon_only so data_sf() is\n called once (was twice)\n- region_op_view() takes a single `op` context list instead of 9 positional\n args, removing the error-prone positional call\n- as_ggseg_atlas.brain_atlas: any(!vapply(...)) reads clearer than\n !all(vapply(...)) for \"any slot non-null\"\n\nBehaviour unchanged (754 tests pass); no function exceeds cyclocomp 15.\n\nCo-Authored-By: Claude Opus 4.8 (1M context) \n\n* refactor: vectorise for loops where behaviour-preserving\n\n- reposition_views: running x position is a cumsum of preceding widths+gaps;\n offset each view with Map instead of a stateful loop\n- remap_palette_to_labels: lapply + unlist over palette regions (drops the\n nested for/for), order preserved\n- polygons_unnest area: su", "time": 1781014185 }, "_maintainer": { "name": "Athanasia Mo Mowinckel", "email": "a.m.mowinckel@psykologi.uio.no", "login": "drmowinckels", "mastodon": "@Drmowinckels@fosstodon.org", "bluesky": "@drmowinckels.io", "orcid": "0000-0002-5756-0223", "description": "Staff researcher at @LCBC-UiO (www.oslobrains.no) and @Lifebrain (www.lifebrain.uio.no/). PhD in Cognitive Neuroscience. Chapter head for @rladies Oslo", "uuid": 14014329 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "cli", "role": "Imports" }, { "package": "lifecycle", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "sfheaders", "role": "Imports" }, { "package": "covr", "role": "Suggests" }, { "package": "devtools", "role": "Suggests" }, { "package": "here", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "sf", "role": "Suggests" }, { "package": "spelling", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "withr", "role": "Suggests" } ], "_owner": "ggsegverse", "_selfowned": true, "_usedby": 21, "_updates": [ { "week": "2026-06", "n": 17 }, { "week": "2026-07", "n": 29 }, { "week": "2026-08", "n": 3 }, { "week": "2026-14", "n": 13 }, { "week": "2026-23", "n": 3 }, { "week": "2026-24", "n": 3 } ], "_tags": [ { "name": "v0.0.1", "date": "2026-02-15" }, { "name": "v0.0.2", "date": "2026-04-03" } ], "_stars": 0, "_contributors": [ { "user": "drmowinckels", "count": 69, "uuid": 14014329 }, { "user": "copilot", "count": 1, "uuid": 198982749 } ], "_userbio": { "uuid": 14014329, "type": "user", "name": "Athanasia Monika Mowinckel", "description": "Staff researcher at @LCBC-UiO (www.oslobrains.no) and @Lifebrain (www.lifebrain.uio.no/). PhD in Cognitive Neuroscience. Chapter head for @rladies Oslo" }, "_downloads": { "count": 1169, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/ggseg.formats" }, "_mentions": 9, "_devurl": "https://github.com/ggsegverse/ggseg.formats", "_pkgdown": "https://ggsegverse.github.io/ggseg.formats/", "_searchresults": 64, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/ggseg.formats.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/ggsegverse/ggseg.formats", "_realowner": "ggsegverse", "_cranurl": true, "_releases": [ { "version": "0.0.1", "date": "2026-02-18" }, { "version": "0.0.2", "date": "2026-04-03" } ], "_exports": [ "as_brain_atlas", "as_ggseg_atlas", "as_polygon_atlas", "as_sf_atlas", "aseg", "atlas_context_remove", "atlas_core_add", "atlas_geom", "atlas_geometry_type", "atlas_labels", "atlas_meshes", "atlas_palette", "atlas_polygons", "atlas_region_contextual", "atlas_region_keep", "atlas_region_op", "atlas_region_remove", "atlas_region_rename", "atlas_regions", "atlas_sf", "atlas_type", "atlas_vertices", "atlas_view_gather", "atlas_view_keep", "atlas_view_remove", "atlas_view_remove_region", "atlas_view_remove_small", "atlas_view_reorder", "atlas_views", "brain_atlas", "brain_data_cortical", "brain_data_subcortical", "brain_data_tract", "brain_labels", "brain_regions", "brain_views", "convert_legacy_brain_atlas", "dk", "get_brain_mesh", "get_cerebellar_mesh", "ggseg_atlas", "ggseg_data_cerebellar", "ggseg_data_cortical", "ggseg_data_subcortical", "ggseg_data_tract", "is_atlas_polygon", "is_atlas_sf", "is_brain_atlas", "is_cerebellar_atlas", "is_cortical_atlas", "is_ggseg_atlas", "is_ggseg3d_atlas", "is_subcortical_atlas", "is_tract_atlas", "migrate_atlas_files", "read_atlas_files", "read_freesurfer_stats", "read_freesurfer_table", "suit", "tracula", "unify_legacy_atlases" ], 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views", "topics": [ "atlas_context_remove", "atlas_core_add", "atlas_manipulation", "atlas_region_contextual", "atlas_region_keep", "atlas_region_op", "atlas_region_remove", "atlas_region_rename", "atlas_view_gather", "atlas_view_keep", "atlas_view_remove", "atlas_view_remove_region", "atlas_view_remove_small", "atlas_view_reorder" ] }, { "page": "atlas_meshes", "title": "Get atlas meshes for 3D rendering", "topics": [ "atlas_meshes" ] }, { "page": "atlas_palette", "title": "Get atlas palette", "topics": [ "atlas_palette" ] }, { "page": "atlas_polygons", "title": "Get atlas polygons for 2D rendering", "topics": [ "atlas_polygons" ] }, { "page": "atlas_regions", "title": "Extract unique region names from an atlas", "topics": [ "atlas_regions", "brain_regions" ] }, { "page": "atlas_sf", "title": "Get atlas data for 2D rendering", "topics": [ "atlas_sf" ] }, { "page": "atlas_type", "title": "Detect atlas type", "topics": [ "atlas_type" ] }, { "page": "atlas_vertices", "title": "Get atlas vertices for 3D rendering", "topics": [ "atlas_vertices" ] }, { "page": "atlas_views", "title": "Get available views in atlas", "topics": [ "atlas_views", "brain_views" ] }, { "page": "convert_legacy_brain_atlas", "title": "Convert legacy ggseg atlases to ggseg_atlas format", "topics": [ "convert_legacy_brain_atlas", "unify_legacy_atlases" ] }, { "page": "dk", "title": "Desikan-Killiany Cortical Atlas", "concept": [ "cortical_atlases", "ggseg_atlases" ], "topics": [ "dk" ] }, { "page": "get_brain_mesh", "title": "Get brain surface mesh", "topics": [ "get_brain_mesh" ] }, { "page": "get_cerebellar_mesh", "title": "Get SUIT cerebellar surface mesh", "topics": [ "get_cerebellar_mesh" ] }, { "page": "ggseg_atlas", "title": "Constructor for ggseg atlas", "topics": [ "brain_atlas", "ggseg_atlas" ] }, { "page": "ggseg_data_cerebellar", "title": "Create cerebellar atlas data", "topics": [ "ggseg_data_cerebellar" ] }, { "page": "ggseg_data_cortical", "title": "Create cortical atlas data", "topics": [ "brain_data_cortical", "ggseg_data_cortical" ] }, { "page": "ggseg_data_subcortical", "title": "Create subcortical atlas data", "topics": [ "brain_data_subcortical", "ggseg_data_subcortical" ] }, { "page": "ggseg_data_tract", "title": "Create tract atlas data", "topics": [ "brain_data_tract", "ggseg_data_tract" ] }, { "page": "is_ggseg_atlas", "title": "Check ggseg atlas class", "topics": [ "is_brain_atlas", "is_cerebellar_atlas", "is_cortical_atlas", "is_ggseg_atlas", "is_subcortical_atlas", "is_tract_atlas" ] }, { "page": "is_ggseg3d_atlas", "title": "Check if object is a legacy ggseg3d atlas", "topics": [ "is_ggseg3d_atlas" ] }, { "page": "migrate_atlas_files", "title": "Migrate atlas '.rda' files to the sf-optional polygon format", "topics": [ "migrate_atlas_files" ] }, { "page": "read_atlas_files", "title": "Read in atlas data from all subjects", "topics": [ "read_atlas_files" ] }, { "page": "read_freesurfer_stats", "title": "Read in raw FreeSurfer stats file", 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