{"id":13592468,"url":"https://github.com/OxWearables/biobankAccelerometerAnalysis","last_synced_at":"2025-04-08T23:32:56.057Z","repository":{"id":19486970,"uuid":"22732815","full_name":"OxWearables/biobankAccelerometerAnalysis","owner":"OxWearables","description":"Extracting meaningful health information from large accelerometer datasets","archived":false,"fork":false,"pushed_at":"2024-07-04T07:06:36.000Z","size":26623,"stargazers_count":172,"open_issues_count":26,"forks_count":61,"subscribers_count":22,"default_branch":"master","last_synced_at":"2024-08-10T22:57:28.698Z","etag":null,"topics":["actigraph","activity-tracker","axivity","fitness-tracker","geneactiv","machine-learning","ukbiobank"],"latest_commit_sha":null,"homepage":"https://biobankaccanalysis.readthedocs.io/en/latest/index.html","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/OxWearables.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":"CONTRIBUTING.md","funding":null,"license":"LICENSE.md","code_of_conduct":null,"threat_model":null,"audit":null,"citation":"CITATION.md","codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null}},"created_at":"2014-08-07T18:54:33.000Z","updated_at":"2024-07-24T13:27:58.000Z","dependencies_parsed_at":"2023-02-14T01:16:29.466Z","dependency_job_id":"8e64feef-0bd7-4fdc-ae4e-7726fd2a59bf","html_url":"https://github.com/OxWearables/biobankAccelerometerAnalysis","commit_stats":{"total_commits":845,"total_committers":25,"mean_commits":33.8,"dds":0.5810650887573965,"last_synced_commit":"aebbd74d3da26b10493edbf7987e21208c6346ed"},"previous_names":["activitymonitoring/biobankaccelerometeranalysis"],"tags_count":34,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/OxWearables%2FbiobankAccelerometerAnalysis","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/OxWearables%2FbiobankAccelerometerAnalysis/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/OxWearables%2FbiobankAccelerometerAnalysis/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/OxWearables%2FbiobankAccelerometerAnalysis/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/OxWearables","download_url":"https://codeload.github.com/OxWearables/biobankAccelerometerAnalysis/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":223346778,"owners_count":17130499,"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":["actigraph","activity-tracker","axivity","fitness-tracker","geneactiv","machine-learning","ukbiobank"],"created_at":"2024-08-01T16:01:09.573Z","updated_at":"2025-04-08T23:32:56.052Z","avatar_url":"https://github.com/OxWearables.png","language":"Python","funding_links":[],"categories":["Derivation of variables"],"sub_categories":["Accelerometer"],"readme":"![Accelerometer data processing overview](https://raw.githubusercontent.com/OxWearables/biobankAccelerometerAnalysis/master/docs/source/accelerometerLogo.png)\n\n[![Github all releases](https://img.shields.io/github/release/activityMonitoring/biobankAccelerometerAnalysis.svg)](https://github.com/activityMonitoring/biobankAccelerometerAnalysis/releases/)\n[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.14515076.svg)](https://doi.org/10.5281/zenodo.14515076)\n![install](https://github.com/activityMonitoring/biobankAccelerometerAnalysis/workflows/install/badge.svg)\n\nA tool to extract meaningful health information from large accelerometer datasets. The software generates time-series and summary metrics useful for answering key questions such as how much time is spent in sleep, sedentary behaviour, or doing physical activity.\n\n## Install\n\n*Minimum requirements*: Python 3.7 to 3.10, Java 8 (1.8)\n\nThe following instructions make use of Anaconda to meet the minimum requirements:\n\n1. Download \u0026 install [Miniconda](https://docs.conda.io/en/latest/miniconda.html) (light-weight version of Anaconda).\n1. (Windows) Once installed, launch the **Anaconda Prompt**.\n1. Create a virtual environment:\n    ```console\n    $ conda create -n accelerometer python=3.9 openjdk pip\n    ```\n    This creates a virtual environment called `accelerometer` with Python version 3.9, OpenJDK, and Pip.\n1. Activate the environment:\n    ```console\n    $ conda activate accelerometer\n    ```\n    You should now see `(accelerometer)` written in front of your prompt.\n1. Install `accelerometer`:\n    ```console\n    $ pip install accelerometer\n    ```\n\nYou are all set! The next time that you want to use `accelerometer`, open the Anaconda Prompt and activate the environment (step 4). If you see `(accelerometer)` in front of your prompt, you are ready to go!\n\n## Usage\nTo extract summary movement statistics from an Axivity file (.cwa):\n\n```console\n$ accProcess data/sample.cwa.gz\n\n \u003coutput written to data/sample-outputSummary.json\u003e\n \u003ctime series output written to data/sample-timeSeries.csv.gz\u003e\n```\n\nMovement statistics will be stored in a JSON file:\n```json\n{\n    \"file-name\": \"sample.cwa.gz\",\n    \"file-startTime\": \"2014-05-07 13:29:50\",\n    \"file-endTime\": \"2014-05-13 09:49:50\",\n    \"acc-overall-avg(mg)\": 32.78149,\n    \"wearTime-overall(days)\": 5.8,\n    \"nonWearTime-overall(days)\": 0.04,\n    \"quality-goodWearTime\": 1\n}\n```\n\nSee [Data Dictionary](https://biobankaccanalysis.readthedocs.io/en/latest/datadict.html) for the list of output variables.\n\nActigraph and GENEActiv files are also supported, as well as custom CSV files. See [Usage](https://biobankaccanalysis.readthedocs.io/en/latest/usage.html#basic-usage) for more details.\n\nTo plot the activity profile:\n```console\n$ accPlot data/sample-timeSeries.csv.gz\n \u003coutput plot written to data/sample-timeSeries-plot.png\u003e\n```\n![Time series plot](https://raw.githubusercontent.com/OxWearables/biobankAccelerometerAnalysis/master/docs/source/samplePlot.png)\n\n### Troubleshooting \nSome systems may face issues with Java when running the script. If this is your case, try fixing OpenJDK to version 8:\n```console\n$ conda install -n accelerometer openjdk=8\n```\n\n## Under the hood\nInterpreted levels of physical activity can vary, as many approaches can be\ntaken to extract summary physical activity information from raw accelerometer\ndata. To minimise error and bias, our tool uses published methods to calibrate,\nresample, and summarise the accelerometer data.\n\n![Accelerometer data processing overview](https://raw.githubusercontent.com/OxWearables/biobankAccelerometerAnalysis/master/docs/source/accMethodsOverview.png)\n![Activity classification](https://raw.githubusercontent.com/OxWearables/biobankAccelerometerAnalysis/master/docs/source/accClassification.png)\n\nSee [Methods](https://biobankaccanalysis.readthedocs.io/en/latest/methods.html) for more details.\n\n\n## Citing our work\nWhen using this tool, please consider the works listed in [CITATION.md](https://github.com/OxWearables/biobankAccelerometerAnalysis/blob/master/CITATION.md).\n    \n\n## Licence\nSee [LICENSE.md](https://github.com/OxWearables/biobankAccelerometerAnalysis/blob/master/LICENSE.md).\n\n\n## Acknowledgements\nWe would like to thank all our code contributors and manuscript co-authors.\n\n[Contributors Graph](https://github.com/OxWearables/biobankAccelerometerAnalysis/graphs/contributors)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FOxWearables%2FbiobankAccelerometerAnalysis","html_url":"https://awesome.ecosyste.ms/projects/github.com%2FOxWearables%2FbiobankAccelerometerAnalysis","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FOxWearables%2FbiobankAccelerometerAnalysis/lists"}