Updated docs, also added Fitbit Sleep feature docs
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@ -956,6 +956,84 @@ firstuseafter seconds Seconds until the first unlock e
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An ``unlock`` episode is considered as the time between an ``unlock`` event and a ``lock`` event. iOS recorded these episodes reliable (albeit some duplicated ``lock`` events within milliseconds from each other). However, in Android there are some events unrelated to the screen state because of multiple consecutive ``unlock``/``lock`` events, so we keep the closest pair. In the experiments these are less than 10% of the screen events collected. This happens because ``ACTION_SCREEN_OFF`` and ``ON`` are "sent when the device becomes non-interactive which may have nothing to do with the screen turning off". Additionally in Android it is possible to measure the time spent on the ``lock`` screen onto the ``unlock`` event and the total screen time (i.e. ``ON`` to ``OFF``) events but we are only keeping ``unlock`` episodes (``unlock`` to ``OFF``) to be consistent with iOS.
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.. ------------------------------- Begin Fitbit Section ----------------------------------- ..
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.. _fitbit-sleep-sensor-doc:
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Fitbit: Sleep
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"""""""""""""""""""
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See `Fitbit: Sleep Config Code`_
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**Available Epochs:**
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- daily
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**Available Platforms:**
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- Fitbit
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**Snakefile entry:**
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- Extract Sensor Features:
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| ``expand("data/processed/{pid}/fitbit_sleep_{day_segment}.csv",``
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| ``pid = config["PIDS"],``
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| ``day_segment = config["SLEEP"]["DAY_SEGMENTS"]),``
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**Rule Chain:**
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- **Rule:** ``rules/preprocessing.snakefile/download_dataset`` - See the download_dataset_ rule.
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- **Script:** ``src/data/download_dataset.R`` - See the download_dataset.R_ script.
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- **Rule:** ``rules/preprocessing.snakefile/fitbit_with_datetime`` - See the fitbit_with_datetime_ rule.
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- **Script:** ``src/data/fitbit_readable_datetime.py`` - See the fitbit_readable_datetime.py_ script.
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- **Rule:** ``rules/features.snakefile/fitbit_sleep_features`` - See the fitbit_sleep_features_ rule.
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- **Script:** ``src/features/fitbit_sleep_features.py`` - See the fitbit_sleep_features.py_ script.
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.. _fitbit-sleep-parameters:
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**Fitbit: Sleep Rule Parameters:**
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================================== ===================
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Name Description
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================================== ===================
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day_segment The particular ``day_segment`` that will be analyzed. For this sensor only ``daily`` is used.
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sleep_types The different types of sleep that can be analyzed from the Fitbit: Sleep dataset. The available options are ``main``, ``nap``, ``all``.
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daily_features_from_summary_data The different measures that can be retrieved from the dataset.
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See :ref:`Available Fitbit: Sleep Features <fitbit-sleep-available-features>` Table below
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================================== ===================
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.. _fitbit-sleep-available-features:
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**Available Fitbit: Sleep Features**
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The following table shows a list of the available features for the Fitbit: Sleep dataset.
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======================== =========== =============
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Name Units Description
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======================== =========== =============
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sumdurationafterwakeup minutes Total duration of staying in bed after waking up for ``sleep_type`` during ``day_segment``.
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sumdurationasleep minutes Total duration of sleep for ``sleep_type`` during ``day_segment``.
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sumdurationawake minutes Total duration of being awake but still in bed for ``sleep_type`` during ``day_segment``.
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sumdurationtofallasleep minutes Total duration to fall asleep for ``sleep_type`` during ``day_segment``.
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sumdurationinbed minutes Total duration of staying in bed for ``sleep_type`` during ``day_segment``.
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avgefficiency scores Average of sleep efficiency for ``sleep_type`` during ``day_segment``.
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countepisode episodes Number of sleep episodes for ``sleep_type`` during ``day_segment``.
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======================== =========== =============
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**Assumptions/Observations:**
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N/A
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.. _fitbit-heart-rate-sensor-doc:
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Fitbit: Heart Rate
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@ -1028,22 +1106,24 @@ The following table shows a list of the available features for the Fitbit: Heart
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================== =========== =============
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Name Units Description
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================== =========== =============
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maxhr beats/mins The maximum heart rate.
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minhr beats/mins The minimum heart rate.
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avghr beats/mins The average heart rate.
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medianhr beats/mins The median heart rate.
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modehr beats/mins The mode heart rate.
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stdhr beats/mins The standard deviation of heart rate.
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diffmaxmodehr beats/mins Diff max mode heart rate: The maximum heart rate minus mode heart rate.
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diffminmodehr beats/mins Diff min mode heart rate: The mode heart rate minus minimum heart rate.
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entropyhr Entropy heart rate: The entropy of heart rate.
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lengthoutofrange minutes Length out of range: The duration of time the heart rate is in the ``out_of_range`` zone in minute.
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lengthfatburn minutes Length fat burn: The duration of time the heart rate is in the ``fat_burn`` zone in minute.
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lengthcardio minutes Length cardio: The duration of time the heart rate is in the ``cardio`` zone in minute.
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lengthpeak minutes Length peak: The duration of time the heart rate is in the ``peak`` zone in minute
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restingheartrate beats/mins The number of times your heart beats per minute when participant is still and well rested for ``daily`` epoch.
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calories cals Calories burned during ``heartrate_zone`` for ``daily`` epoch.
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maxhr beats/mins The maximum heart rate during ``day_segment`` epoch.
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minhr beats/mins The minimum heart rate during ``day_segment`` epoch.
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avghr beats/mins The average heart rate during ``day_segment`` epoch.
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medianhr beats/mins The median of heart rate during ``day_segment`` epoch.
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modehr beats/mins The mode of heart rate during ``day_segment`` epoch.
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stdhr beats/mins The standard deviation of heart rate during ``day_segment`` epoch.
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diffmaxmodehr beats/mins The difference between maximum heart rate and mode of heart rate during ``day_segment`` epoch.
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diffminmodehr beats/mins The difference between mode of heart rate and minimum heart rate during ``day_segment`` epoch.
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entropyhr nats Shannon’s entropy measurement based on heart rate during ``day_segment`` epoch.
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length minutes Number of minutes in each ``heartrate_zone`` during ``day_segment`` epoch.
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================== =========== =============
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**Assumptions/Observations:** Heart rate zones contain 4 zones: ``out_of_range`` zone, ``fat_burn`` zone, ``cardio`` zone, and ``peak`` zone. Please refer to the `Fitbit documentation`_ for detailed information of how to define those zones.
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**Assumptions/Observations:**
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Heart rate zones contain 4 zones: ``out_of_range`` zone, ``fat_burn`` zone, ``cardio`` zone, and ``peak`` zone. Please refer to the `Fitbit documentation`_ for detailed information of how to define those zones.
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Calories features might be inaccurate as they depend on users’ Fitbit profile (weight, height, etc.)
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.. _fitbit-steps-sensor-doc:
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@ -1116,24 +1196,26 @@ The following table shows a list of the available features for the Fitbit: Steps
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========================= ========= =============
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Name Units Description
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========================= ========= =============
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sumallsteps steps Sum all steps: The total step count.
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maxallsteps steps Max all steps: The maximum step count
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minallsteps steps Min all steps: The minimum step count
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avgallsteps steps Avg all steps: The average step count
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stdallsteps steps Std all steps: The standard deviation of step count
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countsedentarybout bouts Count sedentary bout: A count of sedentary bouts
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maxdurationsedentarybout minutes Max duration sedentary bout: The maximum duration of sedentary bouts
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mindurationsedentarybout minutes Min duration sedentary bout: The minimum duration of sedentary bouts
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avgdurationsedentarybout minutes Avg duration sedentary bout: The average duration of sedentary bouts
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stddurationsedentarybout minutes Std duration sedentary bout: The standard deviation of the duration of sedentary bouts
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countactivebout bouts Count active bout: A count of active bouts
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maxdurationactivebout minutes Max duration active bout: The maximum duration of active bouts
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mindurationactivebout minutes Min duration active bout: The minimum duration of active bouts
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avgdurationactivebout minutes Avg duration active bout: The average duration of active bouts
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stddurationactivebout minutes Std duration active bout: The standard deviation of the duration of active bouts
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sumallsteps steps The total step count during ``day_segment`` epoch.
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maxallsteps steps The maximum step count during ``day_segment`` epoch.
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minallsteps steps The minimum step count during ``day_segment`` epoch.
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avgallsteps steps The average step count during ``day_segment`` epoch.
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stdallsteps steps The standard deviation of step count during ``day_segment`` epoch.
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countsedentarybout bouts Number of sedentary bouts during ``day_segment`` epoch.
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maxdurationsedentarybout minutes The maximum duration of sedentary bouts during ``day_segment`` epoch.
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mindurationsedentarybout minutes The minimum duration of sedentary bouts during ``day_segment`` epoch.
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avgdurationsedentarybout minutes The average duration of sedentary bouts during ``day_segment`` epoch.
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stddurationsedentarybout minutes The standard deviation of the duration of sedentary bouts during ``day_segment`` epoch.
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countactivebout bouts Number of active bouts during ``day_segment`` epoch.
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maxdurationactivebout minutes The maximum duration of active bouts during ``day_segment`` epoch.
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mindurationactivebout minutes The minimum duration of active bouts during ``day_segment`` epoch.
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avgdurationactivebout minutes The average duration of active bouts during ``day_segment`` epoch.
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stddurationactivebout minutes The standard deviation of the duration of active bouts during ``day_segment`` epoch.
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========================= ========= =============
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**Assumptions/Observations:** If the step count per minute smaller than the ``THRESHOLD_ACTIVE_BOUT`` (default value is 10), it is defined as sedentary status. Otherwise, it is defined as active status. One active/sedentary bout is a period during with the user is under ``active``/``sedentary`` status.
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**Assumptions/Observations:**
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If the step count per minute smaller than the ``THRESHOLD_ACTIVE_BOUT`` (default value is 10), it is defined as sedentary status. Otherwise, it is defined as active status. One active/sedentary bout is a period during with the user is under ``active``/``sedentary`` status.
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.. -------------------------Links ------------------------------------ ..
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@ -1190,9 +1272,12 @@ stddurationactivebout minutes Std duration active bout: The standard
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.. _screen_deltas.R: https://github.com/carissalow/rapids/blob/master/src/features/screen_deltas.R
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.. _screen_features: https://github.com/carissalow/rapids/blob/765bb462636d5029a05f54d4c558487e3786b90b/rules/features.snakefile#L97
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.. _screen_features.py: https://github.com/carissalow/rapids/blob/master/src/features/screen_features.py
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.. _`Fitbit: Heart Rate Config Code`: https://github.com/carissalow/rapids/blob/765bb462636d5029a05f54d4c558487e3786b90b/config.yaml#L113
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.. _fitbit_with_datetime: https://github.com/carissalow/rapids/blob/765bb462636d5029a05f54d4c558487e3786b90b/rules/preprocessing.snakefile#L94
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.. _fitbit_readable_datetime.py: https://github.com/carissalow/rapids/blob/master/src/data/fitbit_readable_datetime.py
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.. _`Fitbit: Sleep Config Code`: https://github.com/carissalow/rapids/blob/e952e27350c7ae02703bd444e8f92979e37d9ba6/config.yaml#L129
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.. _fitbit_sleep_features: https://github.com/carissalow/rapids/blob/e952e27350c7ae02703bd444e8f92979e37d9ba6/rules/features.snakefile#L209
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.. _fitbit_sleep_features.py: https://github.com/carissalow/rapids/blob/master/src/features/fitbit_sleep_features.py
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.. _`Fitbit: Heart Rate Config Code`: https://github.com/carissalow/rapids/blob/765bb462636d5029a05f54d4c558487e3786b90b/config.yaml#L113
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.. _fitbit_heartrate_features: https://github.com/carissalow/rapids/blob/765bb462636d5029a05f54d4c558487e3786b90b/rules/features.snakefile#L151
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.. _fitbit_heartrate_features.py: https://github.com/carissalow/rapids/blob/master/src/features/fitbit_heartrate_features.py
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.. _`Fitbit: Steps Config Code`: https://github.com/carissalow/rapids/blob/765bb462636d5029a05f54d4c558487e3786b90b/config.yaml#L117
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