2020-11-09 19:27:07 +01:00
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RAPIDS
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carissalow/rapids
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Home
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Home
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Table of contents
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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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Setup
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File Structure
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Installation
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Initial Configuration
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Execution
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Example Workflows
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Example Workflows
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Minimal
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Behavioral Features
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Behavioral Features
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Introduction
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Phone
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Phone
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Phone Data Quality
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< a href = "features/phone-accelerometer/" class = "md-nav__link" >
Phone Accelerometer
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Phone Activity Recognition
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Phone Applications Foreground
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Phone Battery
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Phone Bluetooth
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Phone Calls
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Phone Conversation
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Phone Light
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Phone Locations
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Phone Messages
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Phone Screen
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Phone WiFI Connected
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Phone WiFI Visible
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Add New Features
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Developers
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Developers
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Remote Support
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Virtual Environments
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Documentation
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Testing
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Test cases
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< 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 >
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< h1 id = "welcome-to-rapids-documentation" > Welcome to RAPIDS documentation< a class = "headerlink" href = "#welcome-to-rapids-documentation" title = "Permanent link" > ¶ < / a > < / h1 >
2020-11-17 01:12:05 +01:00
< div class = "admonition warning" >
< p class = "admonition-title" > Warning< / p >
< p > The functionality outlined in these docs is implemented in the branch < code > day_segments< / code > which we will merge to < code > master< / code > soon as release < code > 0.1< / code > . The previous (first) release of RAPIDS along with the old < a href = "https://rapidspitt.readthedocs.io/en/latest/" > docs< / a > will be labeled < code > beta< / code > . If you landed on this page feel free to look around, just have in mind that we are polishing the last rough patches before we advertise < code > 0.1< / code > (Nov 16, 2020)< / p >
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2020-11-09 19:27:07 +01:00
< p > Reproducible Analysis Pipeline for Data Streams (RAPIDS) allows you to process smartphone and wearable data to extract < strong > behavioral features< / strong > (a.k.a. digital biomarkers/phenotypes).< / p >
< 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 >
< p > < span class = "twemoji" > < svg xmlns = "http://www.w3.org/2000/svg" viewBox = "0 0 24 24" > < path d = "M6 15a2 2 0 01-2 2 2 2 0 01-2-2 2 2 0 012-2h2v2m1 0a2 2 0 012-2 2 2 0 012 2v5a2 2 0 01-2 2 2 2 0 01-2-2v-5m2-8a2 2 0 01-2-2 2 2 0 012-2 2 2 0 012 2v2H9m0 1a2 2 0 012 2 2 2 0 01-2 2H4a2 2 0 01-2-2 2 2 0 012-2h5m8 2a2 2 0 012-2 2 2 0 012 2 2 2 0 01-2 2h-2v-2m-1 0a2 2 0 01-2 2 2 2 0 01-2-2V5a2 2 0 012-2 2 2 0 012 2v5m-2 8a2 2 0 012 2 2 2 0 01-2 2 2 2 0 01-2-2v-2h2m0-1a2 2 0 01-2-2 2 2 0 012-2h5a2 2 0 012 2 2 2 0 01-2 2h-5z" / > < / svg > < / span > Questions or feedback can be posted on #rapids 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 0 002 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 0012 2z" / > < / svg > < / span > Bugs should be reported 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 00-17 0L58.93 98.81l-22.7-22.12a12 12 0 00-17 0L3.53 92.41a12 12 0 000 17l47.59 47.4a12.78 12.78 0 0017.61 0l15.59-15.62L156.52 69a12.09 12.09 0 00.09-17zm0 159.19a12 12 0 00-17 0l-63.68 63.72-22.7-22.1a12 12 0 00-17 0L3.53 252a12 12 0 000 17L51 316.5a12.77 12.77 0 0017.6 0l15.7-15.69 72.2-72.22a12 12 0 00.09-16.9zM64 368c-26.49 0-48.59 21.5-48.59 48S37.53 464 64 464a48 48 0 000-96zm432 16H208a16 16 0 00-16 16v32a16 16 0 0016 16h288a16 16 0 0016-16v-32a16 16 0 00-16-16zm0-320H208a16 16 0 00-16 16v32a16 16 0 0016 16h288a16 16 0 0016-16V80a16 16 0 00-16-16zm0 160H208a16 16 0 00-16 16v32a16 16 0 0016 16h288a16 16 0 0016-16v-32a16 16 0 00-16-16z" / > < / 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 = "M424.4 214.7L72.4 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 > and then to < a href = "setup/configuration/" > Initial Configuration< / a > < / p >
< 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 >
< li > < strong > Extensible code< / strong > . You can easily add your own behavioral features in R or Python and keep authorship and citations.< / li >
< li > < strong > Timezone aware< / strong > . Your data is adjusted to the specified timezone (multiple timezones suport < em > coming soon< / em > ).< / li >
< li > < strong > Flexible day 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 >
< li > < strong > Tested code< / strong > . We are constantly adding tests to make sure our behavioral features are correct.< / li >
< li > < strong > Reproducible code< / strong > . 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 >
< 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 >
< p > In broad terms the < code > config.yaml< / code > , < code > .env< / code > files, participant files, and day segment files 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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