1151 lines
36 KiB
HTML
1151 lines
36 KiB
HTML
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<!doctype html>
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<html lang="en" class="no-js">
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<head>
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<meta charset="utf-8">
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<meta name="viewport" content="width=device-width,initial-scale=1">
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<link rel="shortcut icon" href="../../assets/images/favicon.png">
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<meta name="generator" content="mkdocs-1.1.2, mkdocs-material-6.1.4+insiders-1.9.0">
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<title>Introduction - RAPIDS</title>
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<link rel="stylesheet" href="../../assets/stylesheets/main.a2a6bca7.min.css">
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<link rel="stylesheet" href="../../assets/stylesheets/palette.c308bc62.min.css">
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<link href="https://fonts.gstatic.com" rel="preconnect" crossorigin>
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<link rel="stylesheet" href="https://fonts.googleapis.com/css?family=Roboto:300,400,400i,700%7CRoboto+Mono&display=fallback">
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<style>body,input{font-family:"Roboto",-apple-system,BlinkMacSystemFont,Helvetica,Arial,sans-serif}code,kbd,pre{font-family:"Roboto Mono",SFMono-Regular,Consolas,Menlo,monospace}</style>
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<link rel="stylesheet" href="../../stylesheets/extra.css">
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<body dir="ltr" data-md-color-scheme="default" data-md-color-primary="blue" data-md-color-accent="blue">
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<script>var palette=JSON.parse(localStorage.getItem("__palette")||"{}");if(void 0!==palette.color)for(var key in palette.color)document.body.setAttribute("data-md-color-"+key,palette.color[key])</script>
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<label class="md-overlay" for="__drawer"></label>
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<div data-md-component="skip">
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<a href="#behavioral-features-introduction" class="md-skip">
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<header class="md-header" data-md-component="header">
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<nav class="md-header-nav md-grid" aria-label="Header">
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<a href="../.." title="RAPIDS" class="md-header-nav__button md-logo" aria-label="RAPIDS">
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<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M19 18.31V20a2 2 0 01-2 2H7a2 2 0 01-2-2v-3.7c-.46-.18-1.05-.3-2-.3a1 1 0 01-1-1 1 1 0 011-1c.82 0 1.47.08 2 .21V12.3c-.46-.18-1.05-.3-2-.3a1 1 0 01-1-1 1 1 0 011-1c.82 0 1.47.08 2 .21V8.3C4.54 8.12 3.95 8 3 8a1 1 0 01-1-1 1 1 0 011-1c.82 0 1.47.08 2 .21V4a2 2 0 012-2h10a2 2 0 012 2v2.16c1.78.31 2.54.97 2.71 1.13.39.39.39 1.03 0 1.42-.39.39-.91.38-1.42 0 0 0-1.04-.71-3.29-.71-1.26 0-2.09.41-3.05.9-1.04.51-2.21 1.1-3.95 1.1-.36 0-.69 0-1-.04V7.95c.3.05.63.05 1 .05 1.26 0 2.09-.41 3.05-.89C14.09 6.59 15.27 6 17 6V4H7v16h10v-2c1.5 0 1.97.29 2 .31M17 10c-1.73 0-2.91.59-3.95 1.11-.96.48-1.79.89-3.05.89-.37 0-.7 0-1-.05v2.01c.31.04.64.04 1 .04 1.74 0 2.91-.59 3.95-1.1.96-.48 1.79-.9 3.05-.9 2.25 0 3.29.71 3.29.71.51.39 1.03.39 1.42 0 .39-.39.39-1.02 0-1.42C21.5 11.08 20.25 10 17 10m0 4c-1.73 0-2.91.59-3.95 1.11-.96.48-1.79.89-3.05.89-.37 0-.7 0-1-.05v2.01c.31.04.64.04 1 .04 1.74 0 2.91-.59 3.95-1.1.96-.48 1.79-.9 3.05-.9 2.25 0 3.29.71 3.29.71.51.39 1.03.39 1.42 0 .39-.39.39-1.02 0-1.42C21.5 15.08 20.25 14 17 14z"/></svg>
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</a>
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<label class="md-header-nav__button md-icon" for="__drawer">
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<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M3 6h18v2H3V6m0 5h18v2H3v-2m0 5h18v2H3v-2z"/></svg>
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</label>
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<div class="md-header-nav__title" data-md-component="header-title">
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<div class="md-header-nav__ellipsis">
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<div class="md-header-nav__topic">
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<span class="md-ellipsis">
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RAPIDS
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</span>
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</div>
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<div class="md-header-nav__topic" data-md-component="header-topic">
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<span class="md-ellipsis">
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Introduction
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<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M17 7H7a5 5 0 00-5 5 5 5 0 005 5h10a5 5 0 005-5 5 5 0 00-5-5m0 8a3 3 0 01-3-3 3 3 0 013-3 3 3 0 013 3 3 3 0 01-3 3z"/></svg>
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<button class="md-header-nav__button md-icon" title="Switch to dark mode" aria-label="Switch to dark mode" data-md-option="palette" data-md-color-scheme="slate" data-md-color-primary="blue" data-md-color-accent="blue" data-md-state="hidden">
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<label class="md-header-nav__button md-icon" for="__search">
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<div class="md-search" data-md-component="search" role="dialog">
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<label class="md-search__overlay" for="__search"></label>
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<form class="md-search__form" name="search">
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<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M9.5 3A6.5 6.5 0 0116 9.5c0 1.61-.59 3.09-1.56 4.23l.27.27h.79l5 5-1.5 1.5-5-5v-.79l-.27-.27A6.516 6.516 0 019.5 16 6.5 6.5 0 013 9.5 6.5 6.5 0 019.5 3m0 2C7 5 5 7 5 9.5S7 14 9.5 14 14 12 14 9.5 12 5 9.5 5z"/></svg>
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<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M20 11v2H8l5.5 5.5-1.42 1.42L4.16 12l7.92-7.92L13.5 5.5 8 11h12z"/></svg>
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</form>
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<div class="md-search__output">
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<div class="md-search-result__meta">
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Initializing search
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</div>
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<ol class="md-search-result__list"></ol>
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</div>
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</div>
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</div>
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</div>
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</div>
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<div class="md-header-nav__source">
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<a href="https://github.com/carissalow/rapids/" title="Go to repository" class="md-source">
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<div class="md-source__icon md-icon">
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<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><path d="M439.55 236.05L244 40.45a28.87 28.87 0 00-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 01-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 000 40.81l195.61 195.6a28.86 28.86 0 0040.8 0l194.69-194.69a28.86 28.86 0 000-40.81z"/></svg>
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</div>
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<div class="md-source__repository">
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carissalow/rapids
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</div>
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</a>
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</div>
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</nav>
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</header>
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<div class="md-container" data-md-component="container">
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<main class="md-main" data-md-component="main">
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<div class="md-main__inner md-grid">
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<nav class="md-nav md-nav--primary" aria-label="Navigation" data-md-level="0">
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<label class="md-nav__title" for="__drawer">
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<a href="../.." title="RAPIDS" class="md-nav__button md-logo" aria-label="RAPIDS">
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<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M19 18.31V20a2 2 0 01-2 2H7a2 2 0 01-2-2v-3.7c-.46-.18-1.05-.3-2-.3a1 1 0 01-1-1 1 1 0 011-1c.82 0 1.47.08 2 .21V12.3c-.46-.18-1.05-.3-2-.3a1 1 0 01-1-1 1 1 0 011-1c.82 0 1.47.08 2 .21V8.3C4.54 8.12 3.95 8 3 8a1 1 0 01-1-1 1 1 0 011-1c.82 0 1.47.08 2 .21V4a2 2 0 012-2h10a2 2 0 012 2v2.16c1.78.31 2.54.97 2.71 1.13.39.39.39 1.03 0 1.42-.39.39-.91.38-1.42 0 0 0-1.04-.71-3.29-.71-1.26 0-2.09.41-3.05.9-1.04.51-2.21 1.1-3.95 1.1-.36 0-.69 0-1-.04V7.95c.3.05.63.05 1 .05 1.26 0 2.09-.41 3.05-.89C14.09 6.59 15.27 6 17 6V4H7v16h10v-2c1.5 0 1.97.29 2 .31M17 10c-1.73 0-2.91.59-3.95 1.11-.96.48-1.79.89-3.05.89-.37 0-.7 0-1-.05v2.01c.31.04.64.04 1 .04 1.74 0 2.91-.59 3.95-1.1.96-.48 1.79-.9 3.05-.9 2.25 0 3.29.71 3.29.71.51.39 1.03.39 1.42 0 .39-.39.39-1.02 0-1.42C21.5 11.08 20.25 10 17 10m0 4c-1.73 0-2.91.59-3.95 1.11-.96.48-1.79.89-3.05.89-.37 0-.7 0-1-.05v2.01c.31.04.64.04 1 .04 1.74 0 2.91-.59 3.95-1.1.96-.48 1.79-.9 3.05-.9 2.25 0 3.29.71 3.29.71.51.39 1.03.39 1.42 0 .39-.39.39-1.02 0-1.42C21.5 15.08 20.25 14 17 14z"/></svg>
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</a>
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RAPIDS
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</label>
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<div class="md-nav__source">
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<a href="https://github.com/carissalow/rapids/" title="Go to repository" class="md-source">
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<div class="md-source__icon md-icon">
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<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><path d="M439.55 236.05L244 40.45a28.87 28.87 0 00-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 01-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 000 40.81l195.61 195.6a28.86 28.86 0 0040.8 0l194.69-194.69a28.86 28.86 0 000-40.81z"/></svg>
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</div>
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<div class="md-source__repository">
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carissalow/rapids
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</div>
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</a>
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Setup
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<span class="md-nav__icon md-icon"></span>
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Setup
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File Structure
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<a href="../../setup/installation/" class="md-nav__link">
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Installation
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<a href="../../setup/configuration/" class="md-nav__link">
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Configuration
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<li class="md-nav__item">
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<a href="../../setup/execution/" class="md-nav__link">
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Execution
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Example Workflows
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<span class="md-nav__icon md-icon"></span>
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Example Workflows
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<ul class="md-nav__list" data-md-scrollfix>
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<a href="../../workflow-examples/minimal/" class="md-nav__link">
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Minimal
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<li class="md-nav__item md-nav__item--active md-nav__item--section md-nav__item--nested">
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<input class="md-nav__toggle md-toggle" data-md-toggle="nav-4" type="checkbox" id="nav-4" checked>
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<label class="md-nav__link" for="nav-4">
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Behavioral Features
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<span class="md-nav__icon md-icon"></span>
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<nav class="md-nav" aria-label="Behavioral Features" data-md-level="1">
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Behavioral Features
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<label class="md-nav__link md-nav__link--active" for="__toc">
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Introduction
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<a href="./" class="md-nav__link md-nav__link--active">
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Introduction
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<span class="md-nav__icon md-icon"></span>
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Table of contents
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<article class="md-content__inner md-typeset">
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<a href="https://github.com/carissalow/rapids/edit/master/docs/features/feature-introduction.md" title="Edit this page" class="md-content__button md-icon">
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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="behavioral-features-introduction">Behavioral Features Introduction<a class="headerlink" href="#behavioral-features-introduction" title="Permanent link">¶</a></h1>
|
|
<p>Every phone or Fitbit sensor has a corresponding config section in <code>config.yaml</code>, these sections follow a similar structure and we’ll use <code>PHONE_ACCELEROMETER</code> as an example to explain this structure.</p>
|
|
<div class="admonition hint">
|
|
<p class="admonition-title">Hint</p>
|
|
<ul>
|
|
<li>We recommend reading this page if you are using RAPIDS for the first time</li>
|
|
<li>All computed sensor features are stored under <code>/data/processed/features</code> on files per sensor, per participant and per study (all participants).</li>
|
|
<li>Every time you change any sensor parameters, provider parameters or provider features, all the necessary files will be updated as soon as you execute RAPIDS.</li>
|
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</ul>
|
|
</div>
|
|
<div class="admonition example">
|
|
<p class="admonition-title">Config section example for <code>PHONE_ACCELEROMETER</code></p>
|
|
<div class="highlight"><pre><span></span><code><span class="c1"># 1) Config section</span>
|
|
<span class="nt">PHONE_ACCELEROMETER</span><span class="p">:</span>
|
|
<span class="c1"># 2) Parameters for PHONE_ACCELEROMETER</span>
|
|
<span class="nt">TABLE</span><span class="p">:</span> <span class="l l-Scalar l-Scalar-Plain">accelerometer</span>
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|
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<span class="c1"># 3) Providers for PHONE_ACCELEROMETER</span>
|
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<span class="nt">PROVIDERS</span><span class="p">:</span>
|
|
<span class="c1"># 4) RAPIDS provider</span>
|
|
<span class="nt">RAPIDS</span><span class="p">:</span>
|
|
<span class="c1"># 4.1) Parameters of RAPIDS provider of PHONE_ACCELEROMETER</span>
|
|
<span class="nt">COMPUTE</span><span class="p">:</span> <span class="l l-Scalar l-Scalar-Plain">False</span>
|
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<span class="c1"># 4.2) Features of RAPIDS provider of PHONE_ACCELEROMETER</span>
|
|
<span class="nt">FEATURES</span><span class="p">:</span> <span class="p p-Indicator">[</span><span class="s">"maxmagnitude"</span><span class="p p-Indicator">,</span> <span class="s">"minmagnitude"</span><span class="p p-Indicator">,</span> <span class="s">"avgmagnitude"</span><span class="p p-Indicator">,</span> <span class="s">"medianmagnitude"</span><span class="p p-Indicator">,</span> <span class="s">"stdmagnitude"</span><span class="p p-Indicator">]</span>
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|
<span class="nt">SRC_FOLDER</span><span class="p">:</span> <span class="s">"rapids"</span> <span class="c1"># inside src/features/phone_accelerometer</span>
|
|
<span class="nt">SRC_LANGUAGE</span><span class="p">:</span> <span class="s">"python"</span>
|
|
|
|
<span class="c1"># 5) PANDA provider</span>
|
|
<span class="nt">PANDA</span><span class="p">:</span>
|
|
<span class="c1"># 5.1) Parameters of PANDA provider of PHONE_ACCELEROMETER</span>
|
|
<span class="nt">COMPUTE</span><span class="p">:</span> <span class="l l-Scalar l-Scalar-Plain">False</span>
|
|
<span class="nt">VALID_SENSED_MINUTES</span><span class="p">:</span> <span class="l l-Scalar l-Scalar-Plain">False</span>
|
|
<span class="c1"># 5.2) Features of PANDA provider of PHONE_ACCELEROMETER</span>
|
|
<span class="nt">FEATURES</span><span class="p">:</span>
|
|
<span class="nt">exertional_activity_episode</span><span class="p">:</span> <span class="p p-Indicator">[</span><span class="s">"sumduration"</span><span class="p p-Indicator">,</span> <span class="s">"maxduration"</span><span class="p p-Indicator">,</span> <span class="s">"minduration"</span><span class="p p-Indicator">,</span> <span class="s">"avgduration"</span><span class="p p-Indicator">,</span> <span class="s">"medianduration"</span><span class="p p-Indicator">,</span> <span class="s">"stdduration"</span><span class="p p-Indicator">]</span>
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<span class="nt">nonexertional_activity_episode</span><span class="p">:</span> <span class="p p-Indicator">[</span><span class="s">"sumduration"</span><span class="p p-Indicator">,</span> <span class="s">"maxduration"</span><span class="p p-Indicator">,</span> <span class="s">"minduration"</span><span class="p p-Indicator">,</span> <span class="s">"avgduration"</span><span class="p p-Indicator">,</span> <span class="s">"medianduration"</span><span class="p p-Indicator">,</span> <span class="s">"stdduration"</span><span class="p p-Indicator">]</span>
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<span class="nt">SRC_FOLDER</span><span class="p">:</span> <span class="s">"panda"</span> <span class="c1"># inside src/features/phone_accelerometer</span>
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<span class="nt">SRC_LANGUAGE</span><span class="p">:</span> <span class="s">"python"</span>
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</code></pre></div>
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</div>
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<h2 id="sensor-parameters">Sensor Parameters<a class="headerlink" href="#sensor-parameters" title="Permanent link">¶</a></h2>
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<p>Each sensor configuration section has a “parameters” subsection (see <code>#2</code> in the example). These are parameters that affect different aspects of how the raw data is downloaded, and processed. The <code>TABLE</code> parameter exists for every sensor, but some sensors will have extra parameters like <a href="../phone-locations/"><code>[PHONE_LOCATIONS]</code></a>. We explain these parameters in a table at the top of each sensor documentation page.</p>
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<h2 id="sensor-providers">Sensor Providers<a class="headerlink" href="#sensor-providers" title="Permanent link">¶</a></h2>
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<p>Each sensor configuration section can have zero, one or more behavioral feature <strong>providers</strong> (see <code>#3</code> in the example). A provider is a script created by the core RAPIDS team or other researchers that extracts behavioral features for that sensor. In this example, accelerometer has two providers: RAPIDS (see <code>#4</code>) and PANDA (see <code>#5</code>).</p>
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<h3 id="provider-parameters">Provider Parameters<a class="headerlink" href="#provider-parameters" title="Permanent link">¶</a></h3>
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<p>Each provider has parameters that affect the computation of the behavioral features it offers (see <code>#4.1</code> or <code>#5.1</code> in the example). These parameters will include at least a <code>[COMPUTE]</code> flag that you switch to <code>True</code> to extract a provider’s behavioral features. </p>
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<p>We explain every provider’s parameter in a table under the <code>Parameters description</code> heading on each provider documentation page.</p>
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<h3 id="provider-features">Provider Features<a class="headerlink" href="#provider-features" title="Permanent link">¶</a></h3>
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<p>Each provider offers a set of behavioral features (see <code>#4.2</code> or <code>#5.2</code> in the example). For some providers these features are grouped in an array (like those for <code>RAPIDS</code> provider in <code>#4.2</code>) but for others they are grouped in a collection of arrays depending on the meaning and purpose of those features (like those for <code>PANDAS</code> provider in <code>#5.2</code>). In either case, you can delete the features you are not interested in and they will not be included in the sensor’s output feature file. </p>
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<p>We explain each behavioral feature in a table under the <code>Features description</code> heading on each provider documentation page.</p>
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