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RAPIDS
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RAPIDS
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Home
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Home
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How does it work?
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What are the benefits of using RAPIDS?
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How is it organized?
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Setup
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Installation
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Configuration
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Execution
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Example Workflows
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Example Workflows
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< li class = "md-nav__item" >
< a href = "workflow-examples/minimal/" class = "md-nav__link" >
Minimal
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< / li >
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Analysis
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< / ul >
< / nav >
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< li class = "md-nav__item md-nav__item--section md-nav__item--nested" >
< input class = "md-nav__toggle md-toggle" data-md-toggle = "__nav_4" type = "checkbox" id = "__nav_4" >
< label class = "md-nav__link" for = "__nav_4" >
Behavioral Features
< span class = "md-nav__icon md-icon" > < / span >
< / label >
< nav class = "md-nav" aria-label = "Behavioral Features" data-md-level = "1" >
< label class = "md-nav__title" for = "__nav_4" >
< span class = "md-nav__icon md-icon" > < / span >
Behavioral Features
< / label >
< ul class = "md-nav__list" data-md-scrollfix >
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< li class = "md-nav__item" >
< a href = "features/feature-introduction/" class = "md-nav__link" >
Introduction
< / a >
< / li >
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< li class = "md-nav__item md-nav__item--nested" >
< input class = "md-nav__toggle md-toggle" data-md-toggle = "__nav_4_2" type = "checkbox" id = "__nav_4_2" >
< label class = "md-nav__link" for = "__nav_4_2" >
Phone
< span class = "md-nav__icon md-icon" > < / span >
< / label >
< nav class = "md-nav" aria-label = "Phone" data-md-level = "2" >
< label class = "md-nav__title" for = "__nav_4_2" >
< span class = "md-nav__icon md-icon" > < / span >
Phone
< / label >
< ul class = "md-nav__list" data-md-scrollfix >
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< li class = "md-nav__item" >
< a href = "features/phone-accelerometer/" class = "md-nav__link" >
Phone Accelerometer
< / a >
< / li >
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< li class = "md-nav__item" >
< a href = "features/phone-activity-recognition/" class = "md-nav__link" >
Phone Activity Recognition
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< / li >
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< li class = "md-nav__item" >
< a href = "features/phone-applications-foreground/" class = "md-nav__link" >
Phone Applications Foreground
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< li class = "md-nav__item" >
< a href = "features/phone-battery/" class = "md-nav__link" >
Phone Battery
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< / li >
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< li class = "md-nav__item" >
< a href = "features/phone-bluetooth/" class = "md-nav__link" >
Phone Bluetooth
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< li class = "md-nav__item" >
< a href = "features/phone-calls/" class = "md-nav__link" >
Phone Calls
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< li class = "md-nav__item" >
< a href = "features/phone-conversation/" class = "md-nav__link" >
Phone Conversation
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< / li >
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< li class = "md-nav__item" >
< a href = "features/phone-data-yield/" class = "md-nav__link" >
Phone Data Yield
< / a >
< / li >
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< li class = "md-nav__item" >
< a href = "features/phone-light/" class = "md-nav__link" >
Phone Light
< / a >
< / li >
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< li class = "md-nav__item" >
< a href = "features/phone-locations/" class = "md-nav__link" >
Phone Locations
< / a >
< / li >
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< li class = "md-nav__item" >
< a href = "features/phone-messages/" class = "md-nav__link" >
Phone Messages
< / a >
< / li >
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< li class = "md-nav__item" >
< a href = "features/phone-screen/" class = "md-nav__link" >
Phone Screen
< / a >
< / li >
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< li class = "md-nav__item" >
< a href = "features/phone-wifi-connected/" class = "md-nav__link" >
Phone WiFI Connected
< / a >
< / li >
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< li class = "md-nav__item" >
< a href = "features/phone-wifi-visible/" class = "md-nav__link" >
Phone WiFI Visible
< / a >
< / li >
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< / ul >
< / nav >
< / li >
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< li class = "md-nav__item md-nav__item--nested" >
< input class = "md-nav__toggle md-toggle" data-md-toggle = "__nav_4_3" type = "checkbox" id = "__nav_4_3" >
< label class = "md-nav__link" for = "__nav_4_3" >
Fitbit
< span class = "md-nav__icon md-icon" > < / span >
< / label >
< nav class = "md-nav" aria-label = "Fitbit" data-md-level = "2" >
< label class = "md-nav__title" for = "__nav_4_3" >
< span class = "md-nav__icon md-icon" > < / span >
Fitbit
< / label >
< ul class = "md-nav__list" data-md-scrollfix >
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< li class = "md-nav__item" >
< a href = "features/fitbit-heartrate-summary/" class = "md-nav__link" >
Fitbit Heart Rate Summary
< / a >
< / li >
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< li class = "md-nav__item" >
< a href = "features/fitbit-heartrate-intraday/" class = "md-nav__link" >
Fitbit Heart Rate Intraday
< / a >
< / li >
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< li class = "md-nav__item" >
< a href = "features/fitbit-sleep-summary/" class = "md-nav__link" >
Fitbit Sleep Summary
< / a >
< / li >
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< li class = "md-nav__item" >
< a href = "features/fitbit-steps-summary/" class = "md-nav__link" >
Fitbit Steps Summary
< / a >
< / li >
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< li class = "md-nav__item" >
< a href = "features/fitbit-steps-intraday/" class = "md-nav__link" >
Fitbit Steps Intraday
< / a >
< / li >
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< / ul >
< / nav >
< / li >
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< li class = "md-nav__item" >
< a href = "features/add-new-features/" class = "md-nav__link" >
Add New Features
< / a >
< / li >
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< / ul >
< / nav >
< / li >
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< li class = "md-nav__item md-nav__item--section md-nav__item--nested" >
< input class = "md-nav__toggle md-toggle" data-md-toggle = "__nav_5" type = "checkbox" id = "__nav_5" >
< label class = "md-nav__link" for = "__nav_5" >
Visualizations
< span class = "md-nav__icon md-icon" > < / span >
< / label >
< nav class = "md-nav" aria-label = "Visualizations" data-md-level = "1" >
< label class = "md-nav__title" for = "__nav_5" >
< span class = "md-nav__icon md-icon" > < / span >
Visualizations
< / label >
< ul class = "md-nav__list" data-md-scrollfix >
< li class = "md-nav__item" >
< a href = "visualizations/data-quality-visualizations/" class = "md-nav__link" >
Data Quality
< / a >
< / li >
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< li class = "md-nav__item" >
< a href = "visualizations/feature-visualizations/" class = "md-nav__link" >
Features
< / a >
< / li >
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< / ul >
< / nav >
< / li >
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< li class = "md-nav__item md-nav__item--section md-nav__item--nested" >
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< label class = "md-nav__link" for = "__nav_6" >
Developers
< span class = "md-nav__icon md-icon" > < / span >
< / label >
< nav class = "md-nav" aria-label = "Developers" data-md-level = "1" >
< label class = "md-nav__title" for = "__nav_6" >
< span class = "md-nav__icon md-icon" > < / span >
Developers
< / label >
< ul class = "md-nav__list" data-md-scrollfix >
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< li class = "md-nav__item" >
< a href = "developers/remote-support/" class = "md-nav__link" >
Remote Support
< / a >
< / li >
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< li class = "md-nav__item" >
< a href = "developers/virtual-environments/" class = "md-nav__link" >
Virtual Environments
< / a >
< / li >
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< li class = "md-nav__item" >
< a href = "developers/documentation/" class = "md-nav__link" >
Documentation
< / a >
< / li >
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< li class = "md-nav__item" >
< a href = "developers/testing/" class = "md-nav__link" >
Testing
< / a >
< / li >
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< li class = "md-nav__item" >
< a href = "developers/test-cases/" class = "md-nav__link" >
Test cases
< / a >
< / li >
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< / ul >
< / nav >
< / li >
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< li class = "md-nav__item md-nav__item--section md-nav__item--nested" >
< input class = "md-nav__toggle md-toggle" data-md-toggle = "__nav_7" type = "checkbox" id = "__nav_7" >
< label class = "md-nav__link" for = "__nav_7" >
Others
< span class = "md-nav__icon md-icon" > < / span >
< / label >
< nav class = "md-nav" aria-label = "Others" data-md-level = "1" >
< label class = "md-nav__title" for = "__nav_7" >
< span class = "md-nav__icon md-icon" > < / span >
Others
< / label >
< ul class = "md-nav__list" data-md-scrollfix >
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< li class = "md-nav__item" >
< a href = "migrating-from-old-versions/" class = "md-nav__link" >
Migrating from beta
< / a >
< / li >
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< li class = "md-nav__item" >
< a href = "code_of_conduct/" class = "md-nav__link" >
Code of Conduct
< / a >
< / li >
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< li class = "md-nav__item" >
< a href = "faq/" class = "md-nav__link" >
FAQ
< / a >
< / li >
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< li class = "md-nav__item" >
< a href = "team/" class = "md-nav__link" >
Team
< / a >
< / li >
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< li class = "md-nav__item" >
< a href = "change-log/" class = "md-nav__link" >
Change Log
< / a >
< / li >
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< li class = "md-nav__item" >
< a href = "citation/" class = "md-nav__link" >
Citation
< / a >
< / li >
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< / ul >
< / nav >
< / li >
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< / ul >
< / nav >
< / div >
< / div >
< / div >
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< div class = "md-sidebar md-sidebar--secondary" data-md-component = "sidebar" data-md-type = "toc" >
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< div class = "md-sidebar__scrollwrap" >
< div class = "md-sidebar__inner" >
< nav class = "md-nav md-nav--secondary" aria-label = "Table of contents" >
< label class = "md-nav__title" for = "__toc" >
< span class = "md-nav__icon md-icon" > < / span >
Table of contents
< / label >
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< ul class = "md-nav__list" data-md-component = "toc" data-md-scrollfix >
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< li class = "md-nav__item" >
< a href = "#how-does-it-work" class = "md-nav__link" >
How does it work?
< / a >
< / li >
< li class = "md-nav__item" >
< a href = "#what-are-the-benefits-of-using-rapids" class = "md-nav__link" >
What are the benefits of using RAPIDS?
< / a >
< / li >
< li class = "md-nav__item" >
< a href = "#how-is-it-organized" class = "md-nav__link" >
How is it organized?
< / a >
< / li >
< / ul >
< / nav >
< / div >
< / div >
< / div >
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< div class = "md-content" data-md-component = "content" >
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< article class = "md-content__inner md-typeset" >
< a href = "https://github.com/carissalow/rapids/edit/master/docs/index.md" title = "Edit this page" class = "md-content__button md-icon" >
< svg xmlns = "http://www.w3.org/2000/svg" viewBox = "0 0 24 24" > < path d = "M20.71 7.04c.39-.39.39-1.04 0-1.41l-2.34-2.34c-.37-.39-1.02-.39-1.41 0l-1.84 1.83 3.75 3.75M3 17.25V21h3.75L17.81 9.93l-3.75-3.75L3 17.25z" / > < / svg >
< / a >
< h1 id = "welcome-to-rapids-documentation" > Welcome to RAPIDS documentation< a class = "headerlink" href = "#welcome-to-rapids-documentation" title = "Permanent link" > ¶ < / a > < / h1 >
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< p > Reproducible Analysis Pipeline for Data Streams (RAPIDS) allows you to process smartphone and wearable data to < a href = "features/feature-introduction/" > extract< / a > and < a href = "features/add-new-features/" > create< / a > < strong > behavioral features< / strong > (a.k.a. digital biomarkers), < a href = "visualizations/data-quality-visualizations/" > visualize< / a > mobile sensor data and < a href = "workflow-examples/analysis/" > structure< / a > your analysis into reproducible workflows.< / p >
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< p > RAPIDS is open source, documented, modular, tested, and reproducible. At the moment we support smartphone data collected with < a href = "https://awareframework.com/" > AWARE< / a > and wearable data from Fitbit devices.< / p >
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< div class = "admonition tip" >
< p class = "admonition-title" > Tip< / p >
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< p > < span class = "twemoji" > < svg xmlns = "http://www.w3.org/2000/svg" viewBox = "0 0 24 24" > < path d = "M6 15a2 2 0 0 1-2 2 2 2 0 0 1-2-2 2 2 0 0 1 2-2h2v2m1 0a2 2 0 0 1 2-2 2 2 0 0 1 2 2v5a2 2 0 0 1-2 2 2 2 0 0 1-2-2v-5m2-8a2 2 0 0 1-2-2 2 2 0 0 1 2-2 2 2 0 0 1 2 2v2H9m0 1a2 2 0 0 1 2 2 2 2 0 0 1-2 2H4a2 2 0 0 1-2-2 2 2 0 0 1 2-2h5m8 2a2 2 0 0 1 2-2 2 2 0 0 1 2 2 2 2 0 0 1-2 2h-2v-2m-1 0a2 2 0 0 1-2 2 2 2 0 0 1-2-2V5a2 2 0 0 1 2-2 2 2 0 0 1 2 2v5m-2 8a2 2 0 0 1 2 2 2 2 0 0 1-2 2 2 2 0 0 1-2-2v-2h2m0-1a2 2 0 0 1-2-2 2 2 0 0 1 2-2h5a2 2 0 0 1 2 2 2 2 0 0 1-2 2h-5z" / > < / svg > < / span > Questions or feedback can be posted on the #rapids channel in AWARE Framework's < a href = "http://awareframework.com:3000/" > slack< / a > . < / p >
< p > < span class = "twemoji" > < svg xmlns = "http://www.w3.org/2000/svg" viewBox = "0 0 24 24" > < path d = "M12 2A10 10 0 0 0 2 12c0 4.42 2.87 8.17 6.84 9.5.5.08.66-.23.66-.5v-1.69c-2.77.6-3.36-1.34-3.36-1.34-.46-1.16-1.11-1.47-1.11-1.47-.91-.62.07-.6.07-.6 1 .07 1.53 1.03 1.53 1.03.87 1.52 2.34 1.07 2.91.83.09-.65.35-1.09.63-1.34-2.22-.25-4.55-1.11-4.55-4.92 0-1.11.38-2 1.03-2.71-.1-.25-.45-1.29.1-2.64 0 0 .84-.27 2.75 1.02.79-.22 1.65-.33 2.5-.33.85 0 1.71.11 2.5.33 1.91-1.29 2.75-1.02 2.75-1.02.55 1.35.2 2.39.1 2.64.65.71 1.03 1.6 1.03 2.71 0 3.82-2.34 4.66-4.57 4.91.36.31.69.92.69 1.85V21c0 .27.16.59.67.5C19.14 20.16 22 16.42 22 12A10 10 0 0 0 12 2z" / > < / svg > < / span > Bugs and feature requests should be posted on < a href = "https://github.com/carissalow/rapids/issues" > Github< / a > . < / p >
< p > < span class = "twemoji" > < svg xmlns = "http://www.w3.org/2000/svg" viewBox = "0 0 512 512" > < path d = "M139.61 35.5a12 12 0 0 0-17 0L58.93 98.81l-22.7-22.12a12 12 0 0 0-17 0L3.53 92.41a12 12 0 0 0 0 17l47.59 47.4a12.78 12.78 0 0 0 17.61 0l15.59-15.62L156.52 69a12.09 12.09 0 0 0 .09-17zm0 159.19a12 12 0 0 0-17 0l-63.68 63.72-22.7-22.1a12 12 0 0 0-17 0L3.53 252a12 12 0 0 0 0 17L51 316.5a12.77 12.77 0 0 0 17.6 0l15.7-15.69 72.2-72.22a12 12 0 0 0 .09-16.9zM64 368c-26.49 0-48.59 21.5-48.59 48S37.53 464 64 464a48 48 0 0 0 0-96zm432 16H208a16 16 0 0 0-16 16v32a16 16 0 0 0 16 16h288a16 16 0 0 0 16-16v-32a16 16 0 0 0-16-16zm0-320H208a16 16 0 0 0-16 16v32a16 16 0 0 0 16 16h288a16 16 0 0 0 16-16V80a16 16 0 0 0-16-16zm0 160H208a16 16 0 0 0-16 16v32a16 16 0 0 0 16 16h288a16 16 0 0 0 16-16v-32a16 16 0 0 0-16-16z" / > < / svg > < / span > Join our discussions on our algorithms and assumptions for feature < a href = "https://github.com/carissalow/rapids/issues?q=is%3Aissue+is%3Aopen+label%3Adiscussion" > processing< / a > .< / p >
< p > < span class = "twemoji" > < svg xmlns = "http://www.w3.org/2000/svg" viewBox = "0 0 448 512" > < path d = "M424.4 214.7 72.4 6.6C43.8-10.3 0 6.1 0 47.9V464c0 37.5 40.7 60.1 72.4 41.3l352-208c31.4-18.5 31.5-64.1 0-82.6z" / > < / svg > < / span > Ready to start? Go to < a href = "setup/installation/" > Installation< / a > , then to < a href = "setup/configuration/" > Configuration< / a > , and then to < a href = "setup/execution/" > Execution< / a > < / p >
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< h2 id = "how-does-it-work" > How does it work?< a class = "headerlink" href = "#how-does-it-work" title = "Permanent link" > ¶ < / a > < / h2 >
< p > RAPIDS is formed by R and Python scripts orchestrated by < a href = "https://snakemake.readthedocs.io/en/stable/" > Snakemake< / a > . We suggest you read Snakemake’ s docs but in short: every link in the analysis chain is atomic and has files as input and output. Behavioral features are processed per sensor and per participant.< / p >
< h2 id = "what-are-the-benefits-of-using-rapids" > What are the benefits of using RAPIDS?< a class = "headerlink" href = "#what-are-the-benefits-of-using-rapids" title = "Permanent link" > ¶ < / a > < / h2 >
< ol >
< li > < strong > Consistent analysis< / strong > . Every participant sensor dataset is analyzed in the exact same way and isolated from each other.< / li >
< li > < strong > Efficient analysis< / strong > . Every analysis step is executed only once. Whenever your data or configuration changes only the affected files are updated.< / li >
< li > < strong > Parallel execution< / strong > . Thanks to Snakemake, your analysis can be executed over multiple cores without changing your code.< / li >
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< li > < strong > Code-free features< / strong > . Extract any of the behavioral features offered by RAPIDS without writing any code.< / li >
< li > < strong > Extensible code< / strong > . You can easily add your own behavioral features in R or Python, share them with the community, and keep authorship and citations.< / li >
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< li > < strong > Timezone aware< / strong > . Your data is adjusted to the specified timezone (multiple timezones suport < em > coming soon< / em > ).< / li >
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< li > < strong > Flexible time segments< / strong > . You can extract behavioral features on time windows of any length (e.g. 5 minutes, 3 hours, 2 days), on every day or particular days (e.g. weekends, Mondays, the 1< sup > st< / sup > of each month, etc.) or around events of interest (e.g. surveys or clinical relapses).< / li >
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< li > < strong > Tested code< / strong > . We are constantly adding tests to make sure our behavioral features are correct.< / li >
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< li > < strong > Reproducible code< / strong > . If you structure your analysis within RAPIDS, you can be sure your code will run in other computers as intended thanks to R and Python virtual environments. You can share your analysis code along your publications without any overhead.< / li >
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< li > < strong > Private< / strong > . All your data is processed locally.< / li >
< / ol >
< h2 id = "how-is-it-organized" > How is it organized?< a class = "headerlink" href = "#how-is-it-organized" title = "Permanent link" > ¶ < / a > < / h2 >
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< p > In broad terms the < code > config.yaml< / code > , < a href = "../setup/configuration/#database-credentials" > < code > .env< / code > file< / a > , < a href = "../setup/configuration/#participant-files" > participants files< / a > , and < a href = "../setup/configuration/#time-segments" > time segment files< / a > are the only ones that you will have to modify. All data is stored in < code > data/< / code > and all scripts are stored in < code > src/< / code > . For more information see RAPIDS’ < a href = "file-structure/" > File Structure< / a > .< / p >
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