{"id":16552282,"url":"https://github.com/trybnetic/paat","last_synced_at":"2025-03-21T10:32:18.976Z","repository":{"id":43042169,"uuid":"341190676","full_name":"Trybnetic/paat","owner":"Trybnetic","description":"The physical activity analysis toolbox (PAAT) is a comprehensive toolbox to analyse raw acceleration data from the hip.","archived":false,"fork":false,"pushed_at":"2025-03-17T15:29:37.000Z","size":105038,"stargazers_count":4,"open_issues_count":2,"forks_count":2,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-03-17T16:38:40.644Z","etag":null,"topics":["accelerometry","actigraph","actigraphy","hip","physical-activity"],"latest_commit_sha":null,"homepage":"https://paat.readthedocs.io/","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/Trybnetic.png","metadata":{"files":{"readme":"README.rst","changelog":null,"contributing":"CONTRIBUTING.rst","funding":null,"license":"LICENSE.txt","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2021-02-22T12:19:20.000Z","updated_at":"2025-02-05T12:05:06.000Z","dependencies_parsed_at":"2024-09-09T10:04:36.254Z","dependency_job_id":"8732a3b5-8927-4c1d-a10b-d820c866f109","html_url":"https://github.com/Trybnetic/paat","commit_stats":null,"previous_names":[],"tags_count":4,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Trybnetic%2Fpaat","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Trybnetic%2Fpaat/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Trybnetic%2Fpaat/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Trybnetic%2Fpaat/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Trybnetic","download_url":"https://codeload.github.com/Trybnetic/paat/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":244778008,"owners_count":20508830,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["accelerometry","actigraph","actigraphy","hip","physical-activity"],"created_at":"2024-10-11T19:44:26.527Z","updated_at":"2025-03-21T10:32:13.963Z","avatar_url":"https://github.com/Trybnetic.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"=========================================\nPhysical Activity Analysis Toolbox (PAAT)\n=========================================\n\n    **Note:** This package is currently under development and the API might change\n    anytime! For reproducible versions, see `zenodo \u003chttps://doi.org/10.5281/zenodo.13885749\u003e`_.\n\n\n.. image:: https://github.com/Trybnetic/paat/actions/workflows/python-test.yml/badge.svg\n :target: https://github.com/Trybnetic/paat/actions/workflows/python-test.yml\n :alt: Tests\n\n.. image:: https://codecov.io/gh/Trybnetic/paat/branch/main/graph/badge.svg\n  :target: https://codecov.io/gh/Trybnetic/paat\n  :alt: Coverage\n\n.. image:: https://readthedocs.org/projects/paat/badge/?version=latest\n :target: https://paat.readthedocs.io/en/latest/?badge=latest\n :alt: Documentation Status\n\n.. image:: https://img.shields.io/github/license/trybnetic/paat.svg\n :target: https://github.com/trybnetic/paat/blob/master/LICENSE.txt\n :alt: License\n\n.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.13885749.svg\n  :target: https://doi.org/10.5281/zenodo.13885749\n  :alt: zenodo\n\nThe physical activity analysis toolbox (PAAT) is a comprehensive toolbox to\nanalyze raw acceleration data. We developed all code mainly for analyzing\nActiGraph data (GT3X files) in large sample study settings where manual annotation\nand analysis is not feasible. Most functions come along with scientific papers\ndescribing the methodology in detail. Even though, the package was and is primarily\ndevelop for analyzing ActiGraph data, we warmly welcome contributions for other\nclinical sensors as well!\n\n\nInstallation\n============\n\nAt the moment, the easiest way to install *paat* directly from GitHub by running:\n\n.. code:: bash\n\n    pip install paat\n\n\nUsage\n=====\n\nFor now, several functions to work with raw data from ActiGraph devices are\nimplemented while others are still work in progress. The following code snippet\nshould give you a brief overview and idea on how to use this package. Further\nexamples and more information on the functions can be found in the documentation.\n\n.. code-block:: python\n\n    # Load data from file\n    data, sample_freq = paat.read_gt3x('path/to/gt3x/file')\n\n    # Detect non-wear time\n    data.loc[:, \"Non Wear Time\"] = paat.detect_non_wear_time_hees2011(data, sample_freq)\n\n    # Detect sleep episodes\n    data.loc[:, \"Time in Bed\"] = paat.detect_time_in_bed_weitz2024(data, sample_freq)\n\n    # Classify moderate-to-vigorous and sedentary behavior\n    data.loc[:, [\"MVPA\", \"SB\"]] = paat.calculate_pa_levels(\n      data, \n      sample_freq, \n      mvpa_cutpoint=.069, \n      sb_cutpoint=.015\n    )\n\n    # Merge the activity columns into one labelled column. columns indicates the\n    # importance of the columns, later names are more important and will be kept\n    data.loc[:, \"Activity\"] = paat.create_activity_column(\n      data, \n      columns=[\"SB\", \"MVPA\", \"Time in Bed\", \"Non Wear Time\"]\n    )\n\n    # Remove the other columns after merging\n    data =  data[[\"X\", \"Y\", \"Z\", \"Activity\"]]\n\n\n\nGetting involved\n================\n\nThe *paat* project welcomes help in the following ways:\n\n* Making Pull Requests for\n  `code \u003chttps://github.com/trybnetic/paat/tree/master/paat\u003e`_,\n  `tests \u003chttps://github.com/trybnetic/paat/tree/master/tests\u003e`_\n  or `documentation \u003chttps://github.com/trybnetic/paat/tree/master/doc\u003e`_.\n* Commenting on `open issues \u003chttps://github.com/trybnetic/paat/issues\u003e`_\n  and `pull requests \u003chttps://github.com/trybnetic/paat/pulls\u003e`_.\n* Helping to answer `questions in the issue section\n  \u003chttps://github.com/trybnetic/paat/labels/question\u003e`_.\n* Creating feature requests or adding bug reports in the `issue section\n  \u003chttps://github.com/trybnetic/paat/issues/new\u003e`_.\n\n\nAuthors and Contributers\n========================\n\n*paat* was mainly developed by\n`Marc Weitz \u003chttps://github.com/trybnetic\u003e`_\nand `Shaheen Syed \u003chttps://github.com/shaheen-syed/\u003e`_. For the full list of\ncontributors have a look at `Github's Contributor summary\n\u003chttps://github.com/trybnetic/paat/contributors\u003e`_.\n\nCurrently, it is maintained by `Marc Weitz \u003chttps://github.com/trybnetic\u003e`_. In case\nyou want to contact the project maintainers, please send an email to\nmarc [dot] weitz [at] uit [dot] no\n\n\nAcknowledgments\n===============\n\nThis work was supported by the High North Population Studies at UiT The Arctic\nUniversity of Norway.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftrybnetic%2Fpaat","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ftrybnetic%2Fpaat","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftrybnetic%2Fpaat/lists"}