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Updated docs, also added Fitbit Sleep feature docs

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kaguillera 2020-05-28 12:17:41 -04:00
parent e952e27350
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docs/features/extracted.rst
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@ -956,6 +956,84 @@ firstuseafter seconds Seconds until the first unlock e
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. 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.
.. ------------------------------- Begin Fitbit Section ----------------------------------- ..
.. _fitbit-sleep-sensor-doc:
Fitbit: Sleep
"""""""""""""""""""
See `Fitbit: Sleep Config Code`_
**Available Epochs:**
- daily
**Available Platforms:**
- Fitbit
**Snakefile entry:**
- Extract Sensor Features:
| ``expand("data/processed/{pid}/fitbit_sleep_{day_segment}.csv",``
| ``pid = config["PIDS"],``
| ``day_segment = config["SLEEP"]["DAY_SEGMENTS"]),``
**Rule Chain:**
- **Rule:** ``rules/preprocessing.snakefile/download_dataset`` - See the download_dataset_ rule.
- **Script:** ``src/data/download_dataset.R`` - See the download_dataset.R_ script.
- **Rule:** ``rules/preprocessing.snakefile/fitbit_with_datetime`` - See the fitbit_with_datetime_ rule.
- **Script:** ``src/data/fitbit_readable_datetime.py`` - See the fitbit_readable_datetime.py_ script.
- **Rule:** ``rules/features.snakefile/fitbit_sleep_features`` - See the fitbit_sleep_features_ rule.
- **Script:** ``src/features/fitbit_sleep_features.py`` - See the fitbit_sleep_features.py_ script.
.. _fitbit-sleep-parameters:
**Fitbit: Sleep Rule Parameters:**
================================== ===================
Name Description
================================== ===================
day_segment The particular ``day_segment`` that will be analyzed. For this sensor only ``daily`` is used.
sleep_types The different types of sleep that can be analyzed from the Fitbit: Sleep dataset. The available options are ``main``, ``nap``, ``all``.
daily_features_from_summary_data The different measures that can be retrieved from the dataset.
See :ref:`Available Fitbit: Sleep Features <fitbit-sleep-available-features>` Table below
================================== ===================
.. _fitbit-sleep-available-features:
**Available Fitbit: Sleep Features**
The following table shows a list of the available features for the Fitbit: Sleep dataset.
======================== =========== =============
Name Units Description
======================== =========== =============
sumdurationafterwakeup minutes Total duration of staying in bed after waking up for ``sleep_type`` during ``day_segment``.
sumdurationasleep minutes Total duration of sleep for ``sleep_type`` during ``day_segment``.
sumdurationawake minutes Total duration of being awake but still in bed for ``sleep_type`` during ``day_segment``.
sumdurationtofallasleep minutes Total duration to fall asleep for ``sleep_type`` during ``day_segment``.
sumdurationinbed minutes Total duration of staying in bed for ``sleep_type`` during ``day_segment``.
avgefficiency scores Average of sleep efficiency for ``sleep_type`` during ``day_segment``.
countepisode episodes Number of sleep episodes for ``sleep_type`` during ``day_segment``.
======================== =========== =============
**Assumptions/Observations:**
N/A
.. _fitbit-heart-rate-sensor-doc: .. _fitbit-heart-rate-sensor-doc:
Fitbit: Heart Rate Fitbit: Heart Rate
@ -1028,22 +1106,24 @@ The following table shows a list of the available features for the Fitbit: Heart
================== =========== ============= ================== =========== =============
Name Units Description Name Units Description
================== =========== ============= ================== =========== =============
maxhr beats/mins The maximum heart rate. restingheartrate beats/mins The number of times your heart beats per minute when participant is still and well rested for ``daily`` epoch.
minhr beats/mins The minimum heart rate. calories cals Calories burned during ``heartrate_zone`` for ``daily`` epoch.
avghr beats/mins The average heart rate. maxhr beats/mins The maximum heart rate during ``day_segment`` epoch.
medianhr beats/mins The median heart rate. minhr beats/mins The minimum heart rate during ``day_segment`` epoch.
modehr beats/mins The mode heart rate. avghr beats/mins The average heart rate during ``day_segment`` epoch.
stdhr beats/mins The standard deviation of heart rate. medianhr beats/mins The median of heart rate during ``day_segment`` epoch.
diffmaxmodehr beats/mins Diff max mode heart rate: The maximum heart rate minus mode heart rate. modehr beats/mins The mode of heart rate during ``day_segment`` epoch.
diffminmodehr beats/mins Diff min mode heart rate: The mode heart rate minus minimum heart rate. stdhr beats/mins The standard deviation of heart rate during ``day_segment`` epoch.
entropyhr Entropy heart rate: The entropy of heart rate. diffmaxmodehr beats/mins The difference between maximum heart rate and mode of heart rate during ``day_segment`` epoch.
lengthoutofrange minutes Length out of range: The duration of time the heart rate is in the ``out_of_range`` zone in minute. diffminmodehr beats/mins The difference between mode of heart rate and minimum heart rate during ``day_segment`` epoch.
lengthfatburn minutes Length fat burn: The duration of time the heart rate is in the ``fat_burn`` zone in minute. entropyhr nats Shannon’s entropy measurement based on heart rate during ``day_segment`` epoch.
lengthcardio minutes Length cardio: The duration of time the heart rate is in the ``cardio`` zone in minute. length minutes Number of minutes in each ``heartrate_zone`` during ``day_segment`` epoch.
lengthpeak minutes Length peak: The duration of time the heart rate is in the ``peak`` zone in minute
================== =========== ============= ================== =========== =============
**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. **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.
Calories features might be inaccurate as they depend on users’ Fitbit profile (weight, height, etc.)
.. _fitbit-steps-sensor-doc: .. _fitbit-steps-sensor-doc:
@ -1103,7 +1183,7 @@ See `Fitbit: Steps Config Code`_
Name Description Name Description
======================= =================== ======================= ===================
day_segment The particular ``day_segment`` that will be analyzed. The available options are ``daily``, ``morning``, ``afternoon``, ``evening``, ``night`` day_segment The particular ``day_segment`` that will be analyzed. The available options are ``daily``, ``morning``, ``afternoon``, ``evening``, ``night``
features The different measures that can be retrieved from the dataset. See :ref:`Available Fitbit: Steps Features <fitbit-steps-available-features>` Table below features The different measures that can be retrieved from the dataset. See :ref:`Available Fitbit: Steps Features <fitbit-steps-available-features>` Table below
threshold_active_bout The maximum number of steps per minute necessary for a bout to be ``sedentary``. That is, if the step count per minute is greater than this value the bout has a status of ``active``. threshold_active_bout The maximum number of steps per minute necessary for a bout to be ``sedentary``. That is, if the step count per minute is greater than this value the bout has a status of ``active``.
======================= =================== ======================= ===================
@ -1116,24 +1196,26 @@ The following table shows a list of the available features for the Fitbit: Steps
========================= ========= ============= ========================= ========= =============
Name Units Description Name Units Description
========================= ========= ============= ========================= ========= =============
sumallsteps steps Sum all steps: The total step count. sumallsteps steps The total step count during ``day_segment`` epoch.
maxallsteps steps Max all steps: The maximum step count maxallsteps steps The maximum step count during ``day_segment`` epoch.
minallsteps steps Min all steps: The minimum step count minallsteps steps The minimum step count during ``day_segment`` epoch.
avgallsteps steps Avg all steps: The average step count avgallsteps steps The average step count during ``day_segment`` epoch.
stdallsteps steps Std all steps: The standard deviation of step count stdallsteps steps The standard deviation of step count during ``day_segment`` epoch.
countsedentarybout bouts Count sedentary bout: A count of sedentary bouts countsedentarybout bouts Number of sedentary bouts during ``day_segment`` epoch.
maxdurationsedentarybout minutes Max duration sedentary bout: The maximum duration of sedentary bouts maxdurationsedentarybout minutes The maximum duration of sedentary bouts during ``day_segment`` epoch.
mindurationsedentarybout minutes Min duration sedentary bout: The minimum duration of sedentary bouts mindurationsedentarybout minutes The minimum duration of sedentary bouts during ``day_segment`` epoch.
avgdurationsedentarybout minutes Avg duration sedentary bout: The average duration of sedentary bouts avgdurationsedentarybout minutes The average duration of sedentary bouts during ``day_segment`` epoch.
stddurationsedentarybout minutes Std duration sedentary bout: The standard deviation of the duration of sedentary bouts stddurationsedentarybout minutes The standard deviation of the duration of sedentary bouts during ``day_segment`` epoch.
countactivebout bouts Count active bout: A count of active bouts countactivebout bouts Number of active bouts during ``day_segment`` epoch.
maxdurationactivebout minutes Max duration active bout: The maximum duration of active bouts maxdurationactivebout minutes The maximum duration of active bouts during ``day_segment`` epoch.
mindurationactivebout minutes Min duration active bout: The minimum duration of active bouts mindurationactivebout minutes The minimum duration of active bouts during ``day_segment`` epoch.
avgdurationactivebout minutes Avg duration active bout: The average duration of active bouts avgdurationactivebout minutes The average duration of active bouts during ``day_segment`` epoch.
stddurationactivebout minutes Std duration active bout: The standard deviation of the duration of active bouts stddurationactivebout minutes The standard deviation of the duration of active bouts during ``day_segment`` epoch.
========================= ========= ============= ========================= ========= =============
**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. **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.
.. -------------------------Links ------------------------------------ .. .. -------------------------Links ------------------------------------ ..
@ -1190,9 +1272,12 @@ stddurationactivebout minutes Std duration active bout: The standard
.. _screen_deltas.R: https://github.com/carissalow/rapids/blob/master/src/features/screen_deltas.R .. _screen_deltas.R: https://github.com/carissalow/rapids/blob/master/src/features/screen_deltas.R
.. _screen_features: https://github.com/carissalow/rapids/blob/765bb462636d5029a05f54d4c558487e3786b90b/rules/features.snakefile#L97 .. _screen_features: https://github.com/carissalow/rapids/blob/765bb462636d5029a05f54d4c558487e3786b90b/rules/features.snakefile#L97
.. _screen_features.py: https://github.com/carissalow/rapids/blob/master/src/features/screen_features.py .. _screen_features.py: https://github.com/carissalow/rapids/blob/master/src/features/screen_features.py
.. _`Fitbit: Heart Rate Config Code`: https://github.com/carissalow/rapids/blob/765bb462636d5029a05f54d4c558487e3786b90b/config.yaml#L113
.. _fitbit_with_datetime: https://github.com/carissalow/rapids/blob/765bb462636d5029a05f54d4c558487e3786b90b/rules/preprocessing.snakefile#L94 .. _fitbit_with_datetime: https://github.com/carissalow/rapids/blob/765bb462636d5029a05f54d4c558487e3786b90b/rules/preprocessing.snakefile#L94
.. _fitbit_readable_datetime.py: https://github.com/carissalow/rapids/blob/master/src/data/fitbit_readable_datetime.py .. _fitbit_readable_datetime.py: https://github.com/carissalow/rapids/blob/master/src/data/fitbit_readable_datetime.py
.. _`Fitbit: Sleep Config Code`: https://github.com/carissalow/rapids/blob/e952e27350c7ae02703bd444e8f92979e37d9ba6/config.yaml#L129
.. _fitbit_sleep_features: https://github.com/carissalow/rapids/blob/e952e27350c7ae02703bd444e8f92979e37d9ba6/rules/features.snakefile#L209
.. _fitbit_sleep_features.py: https://github.com/carissalow/rapids/blob/master/src/features/fitbit_sleep_features.py
.. _`Fitbit: Heart Rate Config Code`: https://github.com/carissalow/rapids/blob/765bb462636d5029a05f54d4c558487e3786b90b/config.yaml#L113
.. _fitbit_heartrate_features: https://github.com/carissalow/rapids/blob/765bb462636d5029a05f54d4c558487e3786b90b/rules/features.snakefile#L151 .. _fitbit_heartrate_features: https://github.com/carissalow/rapids/blob/765bb462636d5029a05f54d4c558487e3786b90b/rules/features.snakefile#L151
.. _fitbit_heartrate_features.py: https://github.com/carissalow/rapids/blob/master/src/features/fitbit_heartrate_features.py .. _fitbit_heartrate_features.py: https://github.com/carissalow/rapids/blob/master/src/features/fitbit_heartrate_features.py
.. _`Fitbit: Steps Config Code`: https://github.com/carissalow/rapids/blob/765bb462636d5029a05f54d4c558487e3786b90b/config.yaml#L117 .. _`Fitbit: Steps Config Code`: https://github.com/carissalow/rapids/blob/765bb462636d5029a05f54d4c558487e3786b90b/config.yaml#L117