2067 lines
52 KiB
HTML
2067 lines
52 KiB
HTML
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<title>Installation - RAPIDS</title>
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RAPIDS
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Installation
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Initializing search
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<a href="https://github.com/carissalow/rapids/" title="Go to repository" class="md-source" data-md-component="source">
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carissalow/rapids
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RAPIDS
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carissalow/rapids
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Setup
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Overview
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Minimal Example
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Installation
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Configuration
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Execution
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Citation
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</nav>
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Data Streams
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Introduction
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Phone
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<nav class="md-nav" aria-label="Phone" data-md-level="2">
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Phone
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<a href="../../datastreams/aware-mysql/" class="md-nav__link">
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aware_mysql
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</a>
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</li>
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<li class="md-nav__item">
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<a href="../../datastreams/aware-csv/" class="md-nav__link">
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aware_csv
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</a>
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</li>
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<li class="md-nav__item">
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<a href="../../datastreams/aware-influxdb/" class="md-nav__link">
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aware_influxdb (beta)
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</a>
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</li>
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<li class="md-nav__item">
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<a href="../../datastreams/mandatory-phone-format/" class="md-nav__link">
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Mandatory Phone Format
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</ul>
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</nav>
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<label class="md-nav__link" for="__nav_3_3">
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Fitbit
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<nav class="md-nav" aria-label="Fitbit" data-md-level="2">
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Fitbit
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<a href="../../datastreams/fitbitjson-mysql/" class="md-nav__link">
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<li class="md-nav__item">
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<a href="../../datastreams/fitbitjson-csv/" class="md-nav__link">
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fitbitjson_csv
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<a href="../../datastreams/fitbitparsed-mysql/" class="md-nav__link">
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<li class="md-nav__item">
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<a href="../../datastreams/mandatory-fitbit-format/" class="md-nav__link">
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Mandatory Fitbit Format
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<label class="md-nav__link" for="__nav_3_4">
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<nav class="md-nav" aria-label="Empatica" data-md-level="2">
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<a href="../../datastreams/empatica-zip/" class="md-nav__link">
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<nav class="md-nav" aria-label="Behavioral Features" data-md-level="1">
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<li class="md-nav__item md-nav__item--nested">
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<input class="md-nav__toggle md-toggle" data-md-toggle="__nav_4_2" type="checkbox" id="__nav_4_2" >
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<label class="md-nav__link" for="__nav_4_2">
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Phone
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<nav class="md-nav" aria-label="Phone" data-md-level="2">
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Phone
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<ul class="md-nav__list" data-md-scrollfix>
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<li class="md-nav__item">
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<a href="../../features/phone-accelerometer/" class="md-nav__link">
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Phone Accelerometer
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</a>
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<li class="md-nav__item">
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<a href="../../features/phone-activity-recognition/" class="md-nav__link">
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Phone Activity Recognition
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</a>
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<li class="md-nav__item">
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<a href="../../features/phone-applications-crashes/" class="md-nav__link">
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Phone Applications Crashes
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</a>
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</li>
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<li class="md-nav__item">
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<a href="../../features/phone-applications-foreground/" class="md-nav__link">
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Phone Applications Foreground
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</a>
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</li>
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<li class="md-nav__item">
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<a href="../../features/phone-applications-notifications/" class="md-nav__link">
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Phone Applications Notifications
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</a>
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</li>
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<li class="md-nav__item">
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<a href="../../features/phone-battery/" class="md-nav__link">
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Phone Battery
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</a>
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</li>
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<li class="md-nav__item">
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<a href="../../features/phone-bluetooth/" class="md-nav__link">
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Phone Bluetooth
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</a>
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</li>
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<li class="md-nav__item">
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<a href="../../features/phone-calls/" class="md-nav__link">
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Phone Calls
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</a>
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</li>
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<li class="md-nav__item">
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<a href="../../features/phone-conversation/" class="md-nav__link">
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Phone Conversation
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</a>
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</li>
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<li class="md-nav__item">
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<a href="../../features/phone-data-yield/" class="md-nav__link">
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Phone Data Yield
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</a>
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</li>
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<li class="md-nav__item">
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<a href="../../features/phone-keyboard/" class="md-nav__link">
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Phone Keyboard
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</a>
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</li>
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<li class="md-nav__item">
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<a href="../../features/phone-light/" class="md-nav__link">
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Phone Light
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</a>
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</li>
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<li class="md-nav__item">
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<a href="../../features/phone-locations/" class="md-nav__link">
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Phone Locations
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</a>
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</li>
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<li class="md-nav__item">
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<a href="../../features/phone-log/" class="md-nav__link">
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Phone Log
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</a>
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</li>
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<li class="md-nav__item">
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<a href="../../features/phone-messages/" class="md-nav__link">
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Phone Messages
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</a>
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</li>
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<li class="md-nav__item">
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<a href="../../features/phone-screen/" class="md-nav__link">
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Phone Screen
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</a>
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</li>
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<li class="md-nav__item">
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<a href="../../features/phone-wifi-connected/" class="md-nav__link">
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Phone WiFI Connected
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</a>
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</li>
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<li class="md-nav__item">
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<a href="../../features/phone-wifi-visible/" class="md-nav__link">
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Phone WiFI Visible
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</a>
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</li>
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</ul>
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</nav>
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</li>
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<li class="md-nav__item md-nav__item--nested">
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<input class="md-nav__toggle md-toggle" data-md-toggle="__nav_4_3" type="checkbox" id="__nav_4_3" >
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<label class="md-nav__link" for="__nav_4_3">
|
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Fitbit
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|
<span class="md-nav__icon md-icon"></span>
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</label>
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|
|
<nav class="md-nav" aria-label="Fitbit" data-md-level="2">
|
|
<label class="md-nav__title" for="__nav_4_3">
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<span class="md-nav__icon md-icon"></span>
|
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Fitbit
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|
</label>
|
|
<ul class="md-nav__list" data-md-scrollfix>
|
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<li class="md-nav__item">
|
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<a href="../../features/fitbit-data-yield/" class="md-nav__link">
|
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Fitbit Data Yield
|
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</a>
|
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</li>
|
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<li class="md-nav__item">
|
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<a href="../../features/fitbit-heartrate-summary/" class="md-nav__link">
|
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Fitbit Heart Rate Summary
|
|
</a>
|
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</li>
|
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<li class="md-nav__item">
|
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<a href="../../features/fitbit-heartrate-intraday/" class="md-nav__link">
|
|
Fitbit Heart Rate Intraday
|
|
</a>
|
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</li>
|
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<li class="md-nav__item">
|
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<a href="../../features/fitbit-sleep-summary/" class="md-nav__link">
|
|
Fitbit Sleep Summary
|
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</a>
|
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</li>
|
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<li class="md-nav__item">
|
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<a href="../../features/fitbit-sleep-intraday/" class="md-nav__link">
|
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Fitbit Sleep Intraday
|
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</a>
|
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</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">
|
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<a href="../../features/fitbit-steps-intraday/" class="md-nav__link">
|
|
Fitbit Steps Intraday
|
|
</a>
|
|
</li>
|
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|
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</ul>
|
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</nav>
|
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</li>
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|
|
<li class="md-nav__item md-nav__item--nested">
|
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|
|
|
|
<input class="md-nav__toggle md-toggle" data-md-toggle="__nav_4_4" type="checkbox" id="__nav_4_4" >
|
|
|
|
|
|
|
|
|
|
<label class="md-nav__link" for="__nav_4_4">
|
|
Empatica
|
|
<span class="md-nav__icon md-icon"></span>
|
|
</label>
|
|
|
|
<nav class="md-nav" aria-label="Empatica" data-md-level="2">
|
|
<label class="md-nav__title" for="__nav_4_4">
|
|
<span class="md-nav__icon md-icon"></span>
|
|
Empatica
|
|
</label>
|
|
<ul class="md-nav__list" data-md-scrollfix>
|
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|
|
|
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|
|
|
|
|
|
|
|
<li class="md-nav__item">
|
|
<a href="../../features/empatica-accelerometer/" class="md-nav__link">
|
|
Empatica Accelerometer
|
|
</a>
|
|
</li>
|
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|
|
|
|
|
|
|
|
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|
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|
|
<li class="md-nav__item">
|
|
<a href="../../features/empatica-heartrate/" class="md-nav__link">
|
|
Empatica Heart Rate
|
|
</a>
|
|
</li>
|
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|
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|
|
|
|
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|
|
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|
|
|
|
|
|
<li class="md-nav__item">
|
|
<a href="../../features/empatica-temperature/" class="md-nav__link">
|
|
Empatica Temperature
|
|
</a>
|
|
</li>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<li class="md-nav__item">
|
|
<a href="../../features/empatica-electrodermal-activity/" class="md-nav__link">
|
|
Empatica Electrodermal Activity
|
|
</a>
|
|
</li>
|
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|
|
|
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|
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|
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|
|
<li class="md-nav__item">
|
|
<a href="../../features/empatica-blood-volume-pulse/" class="md-nav__link">
|
|
Empatica Blood Volume Pulse
|
|
</a>
|
|
</li>
|
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|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
<li class="md-nav__item">
|
|
<a href="../../features/empatica-inter-beat-interval/" class="md-nav__link">
|
|
Empatica Inter Beat Interval
|
|
</a>
|
|
</li>
|
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|
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|
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|
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|
|
<li class="md-nav__item">
|
|
<a href="../../features/empatica-tags/" class="md-nav__link">
|
|
Empatica Tags
|
|
</a>
|
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</li>
|
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|
|
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</ul>
|
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</nav>
|
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</li>
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|
<li class="md-nav__item">
|
|
<a href="../../features/add-new-features/" class="md-nav__link">
|
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Add New Features
|
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</a>
|
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</li>
|
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</ul>
|
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</nav>
|
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</li>
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<li class="md-nav__item md-nav__item--section md-nav__item--nested">
|
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<input class="md-nav__toggle md-toggle" data-md-toggle="__nav_5" type="checkbox" id="__nav_5" >
|
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|
<label class="md-nav__link" for="__nav_5">
|
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Visualizations
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|
<span class="md-nav__icon md-icon"></span>
|
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</label>
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|
<nav class="md-nav" aria-label="Visualizations" data-md-level="1">
|
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<label class="md-nav__title" for="__nav_5">
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<span class="md-nav__icon md-icon"></span>
|
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Visualizations
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<h1 id="installation">Installation<a class="headerlink" href="#installation" title="Permanent link">¶</a></h1>
|
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<p>You can install RAPIDS using Docker (the fastest), or native instructions for MacOS and Linux (Ubuntu). Windows is supported through Docker or WSL.</p>
|
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<div class="tabbed-set" data-tabs="1:4"><input checked="checked" id="__tabbed_1_1" name="__tabbed_1" type="radio" /><label for="__tabbed_1_1">Docker</label><div class="tabbed-content">
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<ol>
|
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<li>
|
|
<p>Install <a href="https://docs.docker.com/desktop/">Docker</a></p>
|
|
</li>
|
|
<li>
|
|
<p>Pull our RAPIDS container
|
|
<div class="highlight"><pre><span></span><code>docker pull moshiresearch/rapids:latest
|
|
</code></pre></div></p>
|
|
</li>
|
|
<li>
|
|
<p>Run RAPIDS' container (after this step is done you should see a
|
|
prompt in the main RAPIDS folder with its python environment active)</p>
|
|
<div class="highlight"><pre><span></span><code>docker run -it moshiresearch/rapids:latest
|
|
</code></pre></div>
|
|
</li>
|
|
<li>
|
|
<p>Pull the latest version of RAPIDS</p>
|
|
<div class="highlight"><pre><span></span><code>git pull
|
|
</code></pre></div>
|
|
</li>
|
|
<li>
|
|
<p>Make RAPIDS script executable
|
|
<div class="highlight"><pre><span></span><code>chmod +x rapids
|
|
</code></pre></div></p>
|
|
</li>
|
|
<li>
|
|
<p>Check that RAPIDS is working
|
|
<div class="highlight"><pre><span></span><code>./rapids -j1
|
|
</code></pre></div></p>
|
|
</li>
|
|
<li>
|
|
<p><em>Optional</em>. You can edit RAPIDS files with <code>vim</code> but we recommend using <code>Visual Studio Code</code> and its <code>Remote Containers</code> extension</p>
|
|
<details class="info"><summary>How to configure Remote Containers extension</summary><ul>
|
|
<li>Make sure RAPIDS container is running<ul>
|
|
<li>Install the <a href="https://marketplace.visualstudio.com/items?itemName=ms-vscode-remote.remote-containers">Remote - Containers extension</a></li>
|
|
<li>Go to the <code>Remote Explorer</code> panel on the left hand sidebar</li>
|
|
<li>On the top right dropdown menu choose <code>Containers</code></li>
|
|
<li>Double click on the <code>moshiresearch/rapids</code> container in the<code>CONTAINERS</code> tree</li>
|
|
<li>A new VS Code session should open on RAPIDS main folder inside the container.</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
</details>
|
|
</li>
|
|
</ol>
|
|
<div class="admonition warning">
|
|
<p class="admonition-title">Warning</p>
|
|
<p>If you installed RAPIDS using Docker for Windows on Windows 10, the container will have <a href="https://stackoverflow.com/questions/43460770/docker-windows-container-memory-limit">limits</a> on the amount of RAM it can use. If you find that RAPIDS crashes due to running out of memory, <a href="https://stackoverflow.com/a/56583203/6030343">increase</a> this limit.</p>
|
|
</div>
|
|
</div>
|
|
<input id="__tabbed_1_2" name="__tabbed_1" type="radio" /><label for="__tabbed_1_2">MacOS</label><div class="tabbed-content">
|
|
<p>We tested these instructions in Catalina and Big Sur</p>
|
|
<details class="info"><summary>M1 Macs</summary><p>RAPIDS can run on M1 Macs, the only changes as of Feb 21, 2021 are:</p>
|
|
<ul>
|
|
<li>R needs to be installed via brew under Rosetta (x86 arch) due to incompatibility issues with some R libraries. To do this, run your terminal <a href="https://www.youtube.com/watch?v=nv2ylxro7rM&t=138s">via Rosetta</a>, then proceed with the usual brew installation command. Use x86 brew to install R and restore RAPIDS’ packages (<code>snakemake -j1 renv_install & snakemake -j1 renv_restore</code>). </li>
|
|
<li>There is a bug related to timezone codes. We set the correct <code>TZ_DIR</code> in <code>renv/activate.R</code> (line #19) <code>Sys.setenv("TZDIR" = file.path(R.home(), "share", "zoneinfo"))</code> (RAPIDS does this automatically).</li>
|
|
</ul>
|
|
</details>
|
|
<ol>
|
|
<li>
|
|
<p>Install <a href="https://brew.sh/">brew</a></p>
|
|
</li>
|
|
<li>
|
|
<p>Install MySQL</p>
|
|
<div class="highlight"><pre><span></span><code>brew install mysql
|
|
brew services start mysql
|
|
</code></pre></div>
|
|
</li>
|
|
<li>
|
|
<p>Install R 4.0, pandoc and rmarkdown. If you have other instances of R, we recommend uninstalling them</p>
|
|
<div class="highlight"><pre><span></span><code>brew install r
|
|
brew install pandoc
|
|
Rscript --vanilla -e <span class="s1">'install.packages("rmarkdown", repos="http://cran.us.r-project.org")'</span>
|
|
</code></pre></div>
|
|
</li>
|
|
<li>
|
|
<p>Install miniconda (restart your terminal afterwards)</p>
|
|
<div class="highlight"><pre><span></span><code>brew cask install miniconda
|
|
conda init zsh <span class="c1"># (or conda init bash)</span>
|
|
</code></pre></div>
|
|
</li>
|
|
<li>
|
|
<p>Clone our repo</p>
|
|
<div class="highlight"><pre><span></span><code>git clone https://github.com/carissalow/rapids
|
|
</code></pre></div>
|
|
</li>
|
|
<li>
|
|
<p>Create a python virtual environment</p>
|
|
<div class="highlight"><pre><span></span><code><span class="nb">cd</span> rapids
|
|
conda env create -f environment.yml -n rapids
|
|
conda activate rapids
|
|
</code></pre></div>
|
|
</li>
|
|
<li>
|
|
<p>Install R packages and virtual environment:</p>
|
|
<div class="highlight"><pre><span></span><code>snakemake -j1 renv_install
|
|
snakemake -j1 renv_restore
|
|
</code></pre></div>
|
|
<div class="admonition note">
|
|
<p class="admonition-title">Note<p>This step could take several minutes to complete, especially if you have less than 3Gb of RAM or packages need to be compiled from source. Please be patient and let it run until completion.</p>
|
|
</p>
|
|
</div>
|
|
</li>
|
|
<li>
|
|
<p>Make RAPIDS script executable
|
|
<div class="highlight"><pre><span></span><code>chmod +x rapids
|
|
</code></pre></div></p>
|
|
</li>
|
|
<li>
|
|
<p>Check that RAPIDS is working
|
|
<div class="highlight"><pre><span></span><code>./rapids -j1
|
|
</code></pre></div></p>
|
|
</li>
|
|
</ol>
|
|
</div>
|
|
<input id="__tabbed_1_3" name="__tabbed_1" type="radio" /><label for="__tabbed_1_3">Ubuntu</label><div class="tabbed-content">
|
|
<p>We tested RAPIDS on Ubuntu 18.04 & 20.04. Note that the necessary Python and R packages are available in other Linux distributions, so if you decide to give it a try, let us know and we can update these docs.</p>
|
|
<ol>
|
|
<li>
|
|
<p>Install dependencies</p>
|
|
<div class="highlight"><pre><span></span><code>sudo apt install libcurl4-openssl-dev
|
|
sudo apt install libssl-dev
|
|
sudo apt install libxml2-dev
|
|
sudo apt install libglpk40
|
|
</code></pre></div>
|
|
</li>
|
|
<li>
|
|
<p>Install MySQL</p>
|
|
<div class="highlight"><pre><span></span><code>sudo apt install libmysqlclient-dev
|
|
sudo apt install mysql-server
|
|
</code></pre></div>
|
|
</li>
|
|
<li>
|
|
<p>Add key for R’s repository.</p>
|
|
<div class="highlight"><pre><span></span><code>sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
|
|
</code></pre></div>
|
|
</li>
|
|
<li>
|
|
<p>Add R’s repository</p>
|
|
<div class="tabbed-set" data-tabs="2:2"><input checked="checked" id="__tabbed_2_1" name="__tabbed_2" type="radio" /><label for="__tabbed_2_1">Ubuntu 18.04 Bionic</label><div class="tabbed-content">
|
|
<div class="highlight"><pre><span></span><code>sudo add-apt-repository <span class="s1">'deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran40/'</span>
|
|
</code></pre></div>
|
|
</div>
|
|
<input id="__tabbed_2_2" name="__tabbed_2" type="radio" /><label for="__tabbed_2_2">Ubuntu 20.04 Focal</label><div class="tabbed-content">
|
|
<div class="highlight"><pre><span></span><code>sudo add-apt-repository <span class="s1">'deb https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/'</span>
|
|
</code></pre></div>
|
|
</div>
|
|
</div>
|
|
</li>
|
|
<li>
|
|
<p>Install R 4.0. If you have other instances of R, we recommend uninstalling them</p>
|
|
<div class="highlight"><pre><span></span><code>sudo apt update
|
|
sudo apt install r-base
|
|
</code></pre></div>
|
|
</li>
|
|
<li>
|
|
<p>Install Pandoc and rmarkdown</p>
|
|
<div class="highlight"><pre><span></span><code>sudo apt install pandoc
|
|
Rscript --vanilla -e <span class="s1">'install.packages("rmarkdown", repos="http://cran.us.r-project.org")'</span>
|
|
</code></pre></div>
|
|
</li>
|
|
<li>
|
|
<p>Install git</p>
|
|
<div class="highlight"><pre><span></span><code>sudo apt install git
|
|
</code></pre></div>
|
|
</li>
|
|
<li>
|
|
<p>Install <a href="https://docs.conda.io/projects/conda/en/latest/user-guide/install/linux.html">miniconda</a></p>
|
|
</li>
|
|
<li>
|
|
<p>Restart your current shell</p>
|
|
</li>
|
|
<li>
|
|
<p>Clone our repo:</p>
|
|
<div class="highlight"><pre><span></span><code>git clone https://github.com/carissalow/rapids
|
|
</code></pre></div>
|
|
</li>
|
|
<li>
|
|
<p>Create a python virtual environment:</p>
|
|
<div class="highlight"><pre><span></span><code><span class="nb">cd</span> rapids
|
|
conda env create -f environment.yml -n MY_ENV_NAME
|
|
conda activate MY_ENV_NAME
|
|
</code></pre></div>
|
|
</li>
|
|
<li>
|
|
<p>Install the R virtual environment management package (renv)</p>
|
|
<div class="highlight"><pre><span></span><code>snakemake -j1 renv_install
|
|
</code></pre></div>
|
|
</li>
|
|
<li>
|
|
<p>Restore the R virtual environment</p>
|
|
<div class="tabbed-set" data-tabs="3:3"><input checked="checked" id="__tabbed_3_1" name="__tabbed_3" type="radio" /><label for="__tabbed_3_1">Ubuntu 18.04 Bionic (fast)</label><div class="tabbed-content">
|
|
<p>Run the following command to restore the R virtual environment using <a href="https://packagemanager.rstudio.com/client/#/repos/1/overview">RSPM</a> binaries
|
|
<div class="highlight"><pre><span></span><code>R -e <span class="s1">'renv::restore(repos = c(CRAN = "https://packagemanager.rstudio.com/all/__linux__/bionic/latest"))'</span>
|
|
</code></pre></div></p>
|
|
</div>
|
|
<input id="__tabbed_3_2" name="__tabbed_3" type="radio" /><label for="__tabbed_3_2">Ubuntu 20.04 Focal (fast)</label><div class="tabbed-content">
|
|
<p>Run the following command to restore the R virtual environment using <a href="https://packagemanager.rstudio.com/client/#/repos/1/overview">RSPM</a> binaries
|
|
<div class="highlight"><pre><span></span><code>R -e <span class="s1">'renv::restore(repos = c(CRAN = "https://packagemanager.rstudio.com/all/__linux__/focal/latest"))'</span>
|
|
</code></pre></div></p>
|
|
</div>
|
|
<input id="__tabbed_3_3" name="__tabbed_3" type="radio" /><label for="__tabbed_3_3">Ubuntu (slow)</label><div class="tabbed-content">
|
|
<p>If the fast installation command failed for some reason, you can restore the R virtual environment from source:
|
|
<div class="highlight"><pre><span></span><code>R -e <span class="s1">'renv::restore()'</span>
|
|
</code></pre></div></p>
|
|
</div>
|
|
</div>
|
|
<div class="admonition note">
|
|
<p class="admonition-title">Note<p>This step could take several minutes to complete, especially if you have less than 3Gb of RAM or packages need to be compiled from source. Please be patient and let it run until completion.</p>
|
|
</p>
|
|
</div>
|
|
</li>
|
|
<li>
|
|
<p>Make RAPIDS script executable
|
|
<div class="highlight"><pre><span></span><code>chmod +x rapids
|
|
</code></pre></div></p>
|
|
</li>
|
|
<li>
|
|
<p>Check that RAPIDS is working
|
|
<div class="highlight"><pre><span></span><code>./rapids -j1
|
|
</code></pre></div></p>
|
|
</li>
|
|
</ol>
|
|
</div>
|
|
<input id="__tabbed_1_4" name="__tabbed_1" type="radio" /><label for="__tabbed_1_4">Windows</label><div class="tabbed-content">
|
|
<p>There are several options varying in complexity:</p>
|
|
<ul>
|
|
<li>You can use our Docker instructions (tested)</li>
|
|
<li>You can use our Ubuntu 20.04 instructions on <a href="https://docs.microsoft.com/en-us/windows/wsl/install-win10">WSL2</a> (not tested but it will likely work)</li>
|
|
<li>Native installation (experimental). If you would like to contribute to RAPIDS you could try to install MySQL, miniconda, Python, and R 4.0+ in Windows and restore the Python and R virtual environments using steps 6 and 7 of the instructions for Mac. You can <a href="../../team">get in touch</a> if you would like to discuss this with the team.</li>
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