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Update step features of extracted.rst

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Meng Li 2020-06-26 18:06:05 -04:00
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docs/features/extracted.rst
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@ -802,7 +802,7 @@ Only features from summary data are available at the momement.
The `fitbit_with_datetime` rule will extract Summary data (`fitbit_sleep_summary_with_datetime.csv`) and Intraday data (`fitbit_sleep_intraday_with_datetime.csv`). There are two versions of Fitbit's sleep API (`version 1`_ and `version 1.2`_), and each provides raw sleep data in a different format:
- Sleep level. In ``v1``, sleep level is an integer with three possible values (1, 2, 3) while in ``v1.2`` is a string. We convert integer levels to strings, ``asleep``,``restless`` or ``awake`` respectively.
- Sleep level. In ``v1``, sleep level is an integer with three possible values (1, 2, 3) while in ``v1.2`` is a string. We convert integer levels to strings, ``asleep``, ``restless`` or ``awake`` respectively.
- Count summaries. For Summary data, ``v1`` contains ``count_awake``, ``duration_awake``, ``count_awakenings``, ``count_restless``, and ``duration_restless`` fields for every sleep record while ``v1.2`` does not.
- Types of sleep records. ``v1.2`` has two types of sleep records: ``classic`` and ``stages``. The ``classic`` type contains three sleep levels: ``awake``, ``restless`` and ``asleep``. The ``stages`` type contains four sleep levels: ``wake``, ``deep``, ``light``, and ``rem``. Sleep records from ``v1`` will have the same sleep levels as `v1.2` classic type; therefore we set their type to ``classic``.
- Unified level of sleep. For intraday data, we unify sleep levels of each sleep record with a column named ``unified_level``. Based on `this Fitbit forum post`_ , we merge levels into two categories:
@ -915,46 +915,50 @@ See `Fitbit: Steps Config Code`_
**Fitbit: Steps Rule Parameters (fitbit_step_features):**
======================= ===================
Name Description
======================= ===================
day_segment The particular ``day_segment`` that will be analyzed. The available options are ``daily``, ``morning``, ``afternoon``, ``evening``, ``night``
features The features that can be computed. See :ref:`Available Fitbit: Steps Features <fitbit-steps-available-features>` Table below
threshold_active_bout Every minute with Fitbit step data wil be labelled as ``sedentary`` if its step count is below this threshold, otherwise, ``active``.
include_zero_step_rows Whether or not to include day segments with a 0 step count
exclude_sleep Whether or not to exclude step rows that happen during sleep
exclude_sleep_type If ``exclude_sleep`` is True, then you can choose between ``FIXED`` or ``FITBIT_BASED``. ``FIXED`` will exclude all step rows that happen between a start and end time (see below). ``FITBIT_BASED`` will exclude step rows that happen during main sleep segments as measured by the Fitbit device (``config[SLEEP][DB_TABLE]`` should be a valid table in your database, it usually is the same table that contains your STEP data)
exclude_sleep_fixed_start Start time of the fixed sleep period to exclude. Only relevant if ``exclude_sleep`` is True and ``exclude_sleep_type`` is ``FIXED``
exclude_sleep_fixed_end Start time of the fixed sleep period to exclude. Only relevant if ``exclude_sleep`` is True and ``exclude_sleep_type`` is ``FIXED``
======================= ===================
========================== ===================
Name Description
========================== ===================
day_segment The particular ``day_segment`` that will be analyzed. The available options are ``daily``, ``morning``, ``afternoon``, ``evening``, ``night``
features The features that can be computed. See :ref:`Available Fitbit: Steps Features <fitbit-steps-available-features>` Table below
threshold_active_bout Every minute with Fitbit step data wil be labelled as ``sedentary`` if its step count is below this threshold, otherwise, ``active``.
include_zero_step_rows Whether or not to include day segments with a 0 step count
exclude_sleep Whether or not to exclude step rows that happen during sleep
exclude_sleep_type If ``exclude_sleep`` is True, then you can choose between ``FIXED`` or ``FITBIT_BASED``. ``FIXED`` will exclude all step rows that happen between a start and end time (see below). ``FITBIT_BASED`` will exclude step rows that happen during main sleep segments as measured by the Fitbit device (``config[SLEEP][DB_TABLE]`` should be a valid table in your database, it usually is the same table that contains your STEP data)
exclude_sleep_fixed_start Start time of the fixed sleep period to exclude. Only relevant if ``exclude_sleep`` is True and ``exclude_sleep_type`` is ``FIXED``
exclude_sleep_fixed_end Start time of the fixed sleep period to exclude. Only relevant if ``exclude_sleep`` is True and ``exclude_sleep_type`` is ``FIXED``
========================== ===================
.. _fitbit-steps-available-features:
**Available Fitbit: Steps Features**
========================= ========= =============
Name Units Description
========================= ========= =============
sumallsteps steps The total step count during ``day_segment`` epoch.
maxallsteps steps The maximum step count during ``day_segment`` epoch.
minallsteps steps The minimum step count during ``day_segment`` epoch.
avgallsteps steps The average step count during ``day_segment`` epoch.
stdallsteps steps The standard deviation of step count during ``day_segment`` epoch.
countsedentarybout bouts Number of sedentary bouts during ``day_segment`` epoch.
maxdurationsedentarybout minutes The maximum duration of any sedentary bout during ``day_segment`` epoch.
mindurationsedentarybout minutes The minimum duration of any sedentary bout during ``day_segment`` epoch.
avgdurationsedentarybout minutes The average duration of sedentary bouts during ``day_segment`` epoch.
stddurationsedentarybout minutes The standard deviation of the duration of sedentary bouts during ``day_segment`` epoch.
countactivebout bouts Number of active bouts during ``day_segment`` epoch.
maxdurationactivebout minutes The maximum duration of any active bout during ``day_segment`` epoch.
mindurationactivebout minutes The minimum duration of any active bout during ``day_segment`` epoch.
avgdurationactivebout minutes The average duration of active bouts during ``day_segment`` epoch.
stddurationactivebout minutes The standard deviation of the duration of active bouts during ``day_segment`` epoch.
========================= ========= =============
========================== ========= =============
Name Units Description
========================== ========= =============
sumallsteps steps The total step count during ``day_segment`` epoch.
maxallsteps steps The maximum step count during ``day_segment`` epoch.
minallsteps steps The minimum step count during ``day_segment`` epoch.
avgallsteps steps The average step count during ``day_segment`` epoch.
stdallsteps steps The standard deviation of step count during ``day_segment`` epoch.
countepisodesedentarybout bouts Number of sedentary bouts during ``day_segment`` epoch.
sumdurationsedentarybout minutes Total duration of all sedentary bouts during ``day_segment`` epoch.
maxdurationsedentarybout minutes The maximum duration of any sedentary bout during ``day_segment`` epoch.
mindurationsedentarybout minutes The minimum duration of any sedentary bout during ``day_segment`` epoch.
avgdurationsedentarybout minutes The average duration of sedentary bouts during ``day_segment`` epoch.
stddurationsedentarybout minutes The standard deviation of the duration of sedentary bouts during ``day_segment`` epoch.
countepisodeactivebout bouts Number of active bouts during ``day_segment`` epoch.
sumdurationactivebout minutes Total duration of all active bouts during ``day_segment`` epoch.
maxdurationactivebout minutes The maximum duration of any active bout during ``day_segment`` epoch.
mindurationactivebout minutes The minimum duration of any active bout during ``day_segment`` epoch.
avgdurationactivebout minutes The average duration of active bouts during ``day_segment`` epoch.
stddurationactivebout minutes The standard deviation of the duration of active bouts during ``day_segment`` epoch.
========================== ========= =============
**Assumptions/Observations:**
Active and sedentary bouts. If the step count per minute is smaller than ``THRESHOLD_ACTIVE_BOUT`` (default value is 10), that minute is labelled as sedentary, otherwise, is labelled as active. Active and sedentary bouts are periods of consecutive minutes labelled as ``active`` or ``sedentary``.
``validsensedminutes`` feature is not available for Step sensor as we cannot determine the valid minutes based on the raw Fitbit step data.
.. -------------------------Links ------------------------------------ ..
@ -982,7 +986,7 @@ Active and sedentary bouts. If the step count per minute is smaller than ``THRES
.. _`this Fitbit forum post`: https://community.fitbit.com/t5/Alta/What-does-Restless-mean-in-sleep-tracking/td-p/2989011
.. _shortData: https://dev.fitbit.com/build/reference/web-api/sleep/#interpreting-the-sleep-stage-and-short-data
.. _`Fitbit: Heart Rate Config Code`: https://github.com/carissalow/rapids/blob/0c53fd275e628819cf79cf5b87006ce1ad9e597c/config.yaml#L138
.. _`Fitbit: Steps Config Code`: https://github.com/carissalow/rapids/blob/0c53fd275e628819cf79cf5b87006ce1ad9e597c/config.yaml#L145
.. _`Fitbit: Steps Config Code`: https://github.com/carissalow/rapids/blob/29b04b0601b62379fbdb76de685f3328b8dde2a2/config.yaml#L145
.. _`Fitbit documentation`: https://help.fitbit.com/articles/en_US/Help_article/1565
.. _top1global: https://github.com/carissalow/rapids/blob/765bb462636d5029a05f54d4c558487e3786b90b/config.yaml#L108
.. _`Beiwe Summary Statistics`: http://wiki.beiwe.org/wiki/Summary_Statistics