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.. _rapids_features:
RAPIDS Features
===============
*How do I compute any of these features?* In your ``config.yaml``, go to the sensor section you are interested in and set the corresponding ``COMPUTE`` option to ``TRUE`` as well as ``DB_TABLE`` to the senor's table name in your database (the default table name is the one assigned by Aware), for example
::
MESSAGES:
COMPUTE: True
DB_TABLE: messages
...
If you want to extract phone_valid_sensed_days.csv, screen features or locaton features based on fused location data don't forget to configure ``[PHONE_VALID_SENSED_BINS][TABLES]`` (see below).
.. _global-sensor-doc:
Global Parameters
"""""""""""""""""
.. _sensor-list:
.. _pid:
- ``PIDS`` - The list of participant ids to be included in the analysis. These should match the names of the files created in the ``data/external`` directory (:ref:`see more details<db-configuration>`).
.. _day-segments:
- ``DAY_SEGMENTS`` - The list of day epochs that features can be segmented into: ``daily``, ``morning`` (6am-12pm), ``afternnon`` (12pm-6pm), ``evening`` (6pm-12am) and ``night`` (12am-6am). This list can be modified globally or on a per sensor basis. See DAY_SEGMENTS_ in ``config`` file.
.. _timezone:
- ``TIMEZONE`` - The time zone where data was collected. Use the timezone names from this `List of Timezones`_. Double check your chosen name is correct, for example US Eastern Time is called New America/New_York, not EST.
.. _database_group:
- ``DATABASE_GROUP`` - The name of your database credentials group, it should match the one in ``.env`` (:ref:`see the datbase configuration<db-configuration>`).
.. _download-dataset:
- ``DOWNLOAD_DATASET``
- ``GROUP``. Credentials group to connect to the database containing ``SENSORS``. By default it points to ``DATABASE_GROUP``.
.. _readable-datetime:
- ``READABLE_DATETIME`` - Configuration to convert UNIX timestamps into readbale date time strings.
- ``FIXED_TIMEZONE``. See ``TIMEZONE`` above. This assumes that all data of all participants was collected within one time zone.
- Support for multiple time zones for each participant coming soon based on the ``timezone`` table collected by Aware.
.. _phone-valid-sensed-bins:
- ``PHONE_VALID_SENSED_BINS``
Contains three attributes: ``COMPUTE``, ``BIN_SIZE`` and ``TABLES``. See the PHONE_VALID_SENSED_BINS_ section in the ``config.yaml`` file
Set the ``COMPUTE`` flag to True if you want to get this file (``data/interim/{pid}/phone_sensed_bins``). Phone valid sensed bins is a matrix of days x bins where we divide every hour of every day into N bins of size ``BIN_SIZE`` (in minutes). Each bin contains the number of rows that were recorded in that interval by all the sensors listed in ``TABLES``. Add as many sensor tables to ``TABLES`` as you have in your database because valid sensed bins are used to compute ``PHONE_VALID_SENSED_DAYS``, the ``episodepersensedminutes`` feature of :ref:`Screen<screen-sensor-doc>` and to resample fused location data if you configure Barnett's/Doryab's location features to use ``RESAMPLE_FUSED``.
The ``COMPUTE`` flag is automatically ignored (set internally to True) if you are extracting PHONE_VALID_SENSED_DAYS or screen or Barnett's location features.
.. _phone-valid-sensed-days:
- ``PHONE_VALID_SENSED_DAYS``.
Contains three attributes: ``COMPUTE``, ``MIN_VALID_HOURS_PER_DAY``, ``MIN_VALID_BINS_PER_HOUR``. See the PHONE_VALID_SENSED_DAYS_ section in ``config.yaml``.
On any given day, Aware could have sensed data only for a few minutes or for 24 hours. Daily estimates of features should be considered more reliable the more hours Aware was running and logging data, for example, 10 calls logged on a day when only one hour of data was recorded is a less reliable feature compared to 10 calls on a day when 23 hours of data were recorded.
Therefore, we define a valid hour as those that contain a minimum number of valid bins. A valid bin are those that contain at least one row of data from any sensor logged within that period (See ``PHONE_VALID_SENSED_BINS`` above). We mark an hour as valid if contains at least ``MIN_VALID_BINS_PER_HOUR`` (out of the total possible number of bins that can be captured in an hour based on their length i.e. 60min/``BIN_SIZE`` bins). In turn, we mark a day as valid if it has at least ``MIN_VALID_HOURS_PER_DAY``. ``MIN_VALID_HOURS_PER_DAY`` could be a list. For different thresholds, we can get different valid sensed days: ``"data/interim/{pid}/phone_valid_sensed_days_{min_valid_hours_per_day}h.csv"``.
Note that at the moment RAPIDS *DOES NOT* filter your feature files automatically, you need to do this after your features have been extracted using ``"data/interim/{pid}/phone_valid_sensed_days_{min_valid_hours_per_day}h.csv"``.
.. _individual-sensor-settings:
.. _messages-sensor-doc:
Messages (SMS)
"""""""""""""""
See `Messages Config Code`_
**Available Epochs (day_segment) :** daily, morning, afternoon, evening, night
**Available Platforms:** Android
**Rule Chain:**
- Rule ``rules/preprocessing.snakefile/download_dataset``
- Rule ``rules/preprocessing.snakefile/readable_datetime``
- Rule ``rules/features.snakefile/messages_features``
.. _messages-parameters:
**Messages Rule Parameters (messages_features):**
============== ===================
Name Description
============== ===================
messages_type The particular ``messages_type`` that will be analyzed. The options for this parameter are ``received`` or ``sent``.
day_segment The particular ``day_segment`` that will be analyzed. The available options are ``daily``, ``morning``, ``afternoon``, ``evening``, ``night``
features Features to be computed, see table below
============== ===================
.. _messages-available-features:
**Available Message Features**
========================= ========= =============
Name Units Description
========================= ========= =============
count messages Number of messages of type ``messages_type`` that occurred during a particular ``day_segment``.
distinctcontacts contacts Number of distinct contacts that are associated with a particular ``messages_type`` during a particular ``day_segment``.
timefirstmessages minutes Number of minutes between 12:00am (midnight) and the first ``message`` of a particular ``messages_type``.
timelastmessages minutes Number of minutes between 12:00am (midnight) and the last ``message`` of a particular ``messages_type``.
countmostfrequentcontact messages Number of messages from the contact with the most messages of ``messages_type`` during a ``day_segment`` throughout the whole dataset of each participant.
========================= ========= =============
**Assumptions/Observations:**
``TYPES`` and ``FEATURES`` keys in ``config.yaml`` need to match. For example, below the ``TYPE`` ``sent`` matches the ``FEATURES`` key ``sent``::
MESSAGES:
...
TYPES: [sent]
FEATURES:
sent: [count, distinctcontacts, timefirstmessages, timelastmessages, countmostfrequentcontact]
.. _call-sensor-doc:
Calls
""""""
See `Call Config Code`_
**Available Epochs (day_segment) :** daily, morning, afternoon, evening, night
**Available Platforms:** Android and iOS
**Rule Chain:**
- Rule ``rules/preprocessing.snakefile/download_dataset``
- Rule ``rules/preprocessing.snakefile/readable_datetime``
- Rule ``rules/features.snakefile/call_features``
.. _calls-parameters:
**Call Rule Parameters (call_features):**
============ ===================
Name Description
============ ===================
call_type The particular ``call_type`` that will be analyzed. The options for this parameter are ``incoming``, ``outgoing`` or ``missed``.
day_segment The particular ``day_segment`` that will be analyzed. The available options are ``daily``, ``morning``, ``afternoon``, ``evening``, ``night``
features Features to be computed. Note that the same features are available for both ``incoming`` and ``outgoing`` calls, while ``missed`` calls has its own set of features. See :ref:`Available Incoming and Outgoing Call Features <available-in-and-out-call-features>` Table and :ref:`Available Missed Call Features <available-missed-call-features>` Table below.
============ ===================
.. _available-in-and-out-call-features:
**Available Incoming and Outgoing Call Features**
========================= ========= =============
Name Units Description
========================= ========= =============
count calls Number of calls of a particular ``call_type`` occurred during a particular ``day_segment``.
distinctcontacts contacts Number of distinct contacts that are associated with a particular ``call_type`` for a particular ``day_segment``
meanduration seconds The mean duration of all calls of a particular ``call_type`` during a particular ``day_segment``.
sumduration seconds The sum of the duration of all calls of a particular ``call_type`` during a particular ``day_segment``.
minduration seconds The duration of the shortest call of a particular ``call_type`` during a particular ``day_segment``.
maxduration seconds The duration of the longest call of a particular ``call_type`` during a particular ``day_segment``.
stdduration seconds The standard deviation of the duration of all the calls of a particular ``call_type`` during a particular ``day_segment``.
modeduration seconds The mode of the duration of all the calls of a particular ``call_type`` during a particular ``day_segment``.
entropyduration nats The estimate of the Shannon entropy for the the duration of all the calls of a particular ``call_type`` during a particular ``day_segment``.
timefirstcall minutes The time in minutes between 12:00am (midnight) and the first call of ``call_type``.
timelastcall minutes The time in minutes between 12:00am (midnight) and the last call of ``call_type``.
countmostfrequentcontact calls The number of calls of a particular ``call_type`` during a particular ``day_segment`` of the most frequent contact throughout the monitored period.
========================= ========= =============
.. _available-missed-call-features:
**Available Missed Call Features**
========================= ========= =============
Name Units Description
========================= ========= =============
count calls Number of ``missed`` calls that occurred during a particular ``day_segment``.
distinctcontacts contacts Number of distinct contacts that are associated with ``missed`` calls for a particular ``day_segment``
timefirstcall minutes The time in hours from 12:00am (Midnight) that the first ``missed`` call occurred.
timelastcall minutes The time in hours from 12:00am (Midnight) that the last ``missed`` call occurred.
countmostfrequentcontact calls The number of ``missed`` calls during a particular ``day_segment`` of the most frequent contact throughout the monitored period.
========================= ========= =============
**Assumptions/Observations:**
Traces for iOS calls are unique even for the same contact calling a participant more than once which renders ``countmostfrequentcontact`` meaningless and ``distinctcontacts`` equal to the total number of traces.
``TYPES`` and ``FEATURES`` keys in ``config.yaml`` need to match. For example, below the ``TYPE`` ``missed`` matches the ``FEATURES`` key ``missed``::
CALLS:
...
TYPES: [missed]
FEATURES:
missed: [count, distinctcontacts, timefirstcall, timelastcall, countmostfrequentcontact]
Aware Android client stores call types 1=incoming, 2=outgoing, 3=missed while Aware iOS client stores call status 1=incoming, 2=connected, 3=dialing, 4=disconnected. We extract iOS call types based on call status sequences: (1,2,4)=incoming=1, (3,2,4)=outgoing=2, (1,4) or (3,4)=missed=3. Sometimes (due to a possible bug in Aware) sequences get logged on the exact same timestamp, thus 3-item sequences can be 2,3,4 or 3,2,4. Although iOS stores the duration of ringing/dialing stages for missed calls, we set it to 0 to match Android.
.. _bluetooth-sensor-doc:
Bluetooth
""""""""""
See `Bluetooth Config Code`_
**Available Epochs (day_segment) :** daily, morning, afternoon, evening, night
**Available Platforms:** Android and iOS
**Snakemake rule chain:**
- Rule ``rules/preprocessing.snakefile/download_dataset``
- Rule ``rules/preprocessing.snakefile/readable_datetime``
- Rule ``rules/features.snakefile/bluetooth_features``
.. _bluetooth-parameters:
**Bluetooth Rule Parameters (bluetooth_features):**
============ ===================
Name Description
============ ===================
day_segment The particular ``day_segment`` that will be analyzed. The available options are ``daily``, ``morning``, ``afternoon``, ``evening``, ``night``
features Features to be computed, see table below
============ ===================
.. _bluetooth-available-features:
**Available Bluetooth Features**
=========================== ========= =============
Name Units Description
=========================== ========= =============
countscans devices Number of scanned devices during a ``day_segment``, a device can be detected multiple times over time and these appearances are counted separately
uniquedevices devices Number of unique devices during a ``day_segment`` as identified by their hardware address
countscansmostuniquedevice scans Number of scans of the most scanned device during a ``day_segment`` across the whole monitoring period
=========================== ========= =============
**Assumptions/Observations:** N/A
.. _wifi-sensor-doc:
WiFi
""""""""""
See `WiFi Config Code`_
**Available Epochs (day_segment) :** daily, morning, afternoon, evening, night
**Available Platforms:** Android and iOS
**Snakemake rule chain:**
- Rule ``rules/preprocessing.snakefile/download_dataset``
- Rule ``rules/preprocessing.snakefile/readable_datetime``
- Rule ``rules/features.snakefile/wifi_features``
.. _wifi-parameters:
**WiFi Rule Parameters (wifi_features):**
============ ===================
Name Description
============ ===================
day_segment The particular ``day_segment`` that will be analyzed. The available options are ``daily``, ``morning``, ``afternoon``, ``evening``, ``night``
features Features to be computed, see table below
============ ===================
.. _wifi-available-features:
**Available WiFi Features**
=========================== ========= =============
Name Units Description
=========================== ========= =============
countscans devices Number of scanned WiFi access points during a ``day_segment``, an access point can be detected multiple times over time and these appearances are counted separately
uniquedevices devices Number of unique access point during a ``day_segment`` as identified by their hardware address
countscansmostuniquedevice scans Number of scans of the most scanned access point during a ``day_segment`` across the whole monitoring period
=========================== ========= =============
**Assumptions/Observations:**
Both phone platforms record the wifi networks a phone is connected to in ``sensor_wifi`` and those networks that are being broadcasted around a phone in ``wifi``. However, iOS cannot record any broadcasting network due to API restrictions, therefore iOS wifi data only exists in ``sensor_wifi``.
.. _accelerometer-sensor-doc:
Accelerometer
""""""""""""""
See `Accelerometer Config Code`_
**Available Epochs (day_segment) :** daily, morning, afternoon, evening, night
**Available Platforms:** Android and iOS
**Rule chain:**
- Rule ``rules/preprocessing.snakefile/download_dataset``
- Rule ``rules/preprocessing.snakefile/readable_datetime``
- Rule ``rules/features.snakefile/accelerometer_features``
.. _Accelerometer-parameters:
**Accelerometer Rule Parameters (accelerometer_features):**
============ ===================
Name Description
============ ===================
day_segment The particular ``day_segment`` that will be analyzed. The available options are ``daily``, ``morning``, ``afternoon``, ``evening``, ``night``
features Features to be computed, see table below
============ ===================
.. _accelerometer-available-features:
**Available Accelerometer Features**
====================== ============== =============
Name Units Description
====================== ============== =============
maxmagnitude m/s\ :sup:`2` The maximum magnitude of acceleration (:math:`\|acceleration\| = \sqrt{x^2 + y^2 + z^2}`).
minmagnitude m/s\ :sup:`2` The minimum magnitude of acceleration.
avgmagnitude m/s\ :sup:`2` The average magnitude of acceleration.
medianmagnitude m/s\ :sup:`2` The median magnitude of acceleration.
stdmagnitude m/s\ :sup:`2` The standard deviation of acceleration.
sumduration minutes Total duration of all exertional or non-exertional activity episodes.
maxduration minutes Longest duration of any exertional or non-exertional activity episode.
minduration minutes Shortest duration of any exertional or non-exertional activity episode.
avgduration minutes Average duration of any exertional or non-exertional activity episode.
medianduration minutes Median duration of any exertional or non-exertional activity episode.
stdduration minutes Standard deviation of the duration of all exertional or non-exertional activity episodes.
====================== ============== =============
**Assumptions/Observations:**
Exertional activity episodes are based on this paper: Panda N, Solsky I, Huang EJ, et al. Using Smartphones to Capture Novel Recovery Metrics After Cancer Surgery. JAMA Surg. 2020;155(2):123–129. doi:10.1001/jamasurg.2019.4702
.. _applications-foreground-sensor-doc:
Applications Foreground
""""""""""""""""""""""""
See `Applications Foreground Config Code`_
**Available Epochs (day_segment) :** daily, morning, afternoon, evening, night
**Available Platforms:** Android
**Snakemake rule chain:**
- Rule ``rules/preprocessing.snakefile/download_dataset``
- Rule ``rules/preprocessing.snakefile/readable_datetime``
- Rule ``rules/preprocessing.snakefile/application_genres``
- Rule ``rules/features.snakefile/applications_foreground_features``
.. _applications-foreground-parameters:
**Applications Foreground Rule Parameters (applications_foreground_features):**
==================== ===================
Name Description
==================== ===================
day_segment The particular ``day_segment`` that will be analyzed. The available options are ``daily``, ``morning``, ``afternoon``, ``evening``, ``night``
single_categories App categories to be included in the feature extraction computation. See ``APPLICATION_GENRES`` in this file to add new categories or use the catalogue we provide and read :ref:`Assumtions and Observations <applications-foreground-observations>` for more information.
multiple_categories You can group multiple categories into meta categories, for example ``social: ["socialnetworks", "socialmediatools"]``.
single_apps Apps to be included in the feature extraction computation. Use their package name, for example, ``com.google.android.youtube`` or the reserved word ``top1global`` (the most used app by a participant over the whole monitoring study).
excluded_categories App categories to be excluded in the feature extraction computation. See ``APPLICATION_GENRES`` in this file to add new categories or use the catalogue we provide and read :ref:`Assumtions and Observations <applications-foreground-observations>` for more information.
excluded_apps Apps to be excluded in the feature extraction computation. Use their package name, for example: ``com.google.android.youtube``
features Features to be computed, see table below
==================== ===================
.. _applications-foreground-available-features:
**Available Applications Foreground Features**
================== ========= =============
Name Units Description
================== ========= =============
count apps Number of times a single app or apps within a category were used (i.e. they were brought to the foreground either by tapping their icon or switching to it from another app).
timeoffirstuse minutes The time in minutes between 12:00am (midnight) and the first use of a single app or apps within a category during a ``day_segment``.
timeoflastuse minutes The time in minutes between 12:00am (midnight) and the last use of a single app or apps within a category during a ``day_segment``.
frequencyentropy nats The entropy of the used apps within a category during a ``day_segment`` (each app is seen as a unique event, the more apps were used, the higher the entropy). This is especially relevant when computed over all apps. Entropy cannot be obtained for a single app.
================== ========= =============
.. _applications-foreground-observations:
**Assumptions/Observations:**
Features can be computed by app, by apps grouped under a single category (genre) and by multiple categories grouped together (meta categories). For example, we can get features for Facebook, for Social Network Apps (including Facebook and others) or for a meta category called Social formed by Social Network and Social Media Tools categories.
Apps installed by default like YouTube are considered systems apps on some phones. We do an exact match to exclude apps where "genre" == ``EXCLUDED_CATEGORIES`` or "package_name" == ``EXCLUDED_APPS``.
We provide three ways of classifying and app within a category (genre): a) by automatically scraping its official category from the Google Play Store, b) by using the catalogue created by Stachl et al. which we provide in RAPIDS (``data/external/``), or c) by manually creating a personalized catalogue.
The way you choose strategy a, b or c is by modifying ``APPLICATION_GENRES`` keys and values. Set ``CATALOGUE_SOURCE`` to ``FILE`` if you want to use a CSV file as catalogue (strategy b and c) or to ``GOOGLE`` if you want to scrape the genres from the Play Store (strategy a). By default ``CATALOGUE_FILE`` points to the catalogue created by Stachl et al. (strategy b) and you can change this path to your own catalogue that follows the same format (strategy c). In addition, set ``SCRAPE_MISSING_GENRES`` to true if you are using a FILE catalogue and you want to scrape from the Play Store any missing genres and ``UPDATE_CATALOGUE_FILE`` to true if you want to save those scrapped genres back into the FILE.
The genre catalogue we provide was shared as part of the Supplemental Materials of Stachl, C., Au, Q., Schoedel, R., Buschek, D., Völkel, S., Schuwerk, T., … Bühner, M. (2019, June 12). Behavioral Patterns in Smartphone Usage Predict Big Five Personality Traits. https://doi.org/10.31234/osf.io/ks4vd
.. _battery-sensor-doc:
Battery
"""""""""
See `Battery Config Code`_
**Available Epochs (day_segment) :** daily, morning, afternoon, evening, night
**Available Platforms:** Android and iOS
**Snakemake rule chain:**
- Rule ``rules/preprocessing.snakefile/download_dataset``
- Rule ``rules/preprocessing.snakefile/readable_datetime``
- Rule ``rules/features.snakefile/battery_deltas``
- Rule ``rules/features.snakefile/battery_features``
.. _battery-parameters:
**Battery Rule Parameters (battery_features):**
============ ===================
Name Description
============ ===================
day_segment The particular ``day_segment`` that will be analyzed. The available options are ``daily``, ``morning``, ``afternoon``, ``evening``, ``night``
features Features to be computed, see table below
============ ===================
.. _battery-available-features:
**Available Battery Features**
===================== ================= =============
Name Units Description
===================== ================= =============
countdischarge episodes Number of discharging episodes.
sumdurationdischarge minutes The total duration of all discharging episodes.
countcharge episodes Number of battery charging episodes.
sumdurationcharge minutes The total duration of all charging episodes.
avgconsumptionrate episodes/minutes The average of all episodes’ consumption rates. An episode’s consumption rate is defined as the ratio between its battery delta and duration
maxconsumptionrate episodes/minutes The highest of all episodes’ consumption rates. An episode’s consumption rate is defined as the ratio between its battery delta and duration
===================== ================= =============
**Assumptions/Observations:**
For Aware iOS client V1 we swap battery status 3 to 5 and 1 to 3, client V2 does not have this problem.
.. _activity-recognition-sensor-doc:
Activity Recognition
""""""""""""""""""""""""""""
See `Activity Recognition Config Code`_
**Available Epochs:** daily, morning, afternoon, evening, night
**Available Platforms:** Android and iOS
**Snakemake rule chain:**
- Rule ``rules/preprocessing.snakefile/download_dataset``
- Rule ``rules/preprocessing.snakefile/readable_datetime``
- Rule ``rules/preprocessing.snakefile/unify_ios_android``
- Rule ``rules/features.snakefile/google_activity_recognition_deltas``
- Rule ``rules/features.snakefile/ios_activity_recognition_deltas``
- Rule ``rules/features.snakefile/activity_features``
.. _activity-recognition-parameters:
**Rule Parameters (activity_features):**
============ ===================
Name Description
============ ===================
day_segment The particular ``day_segment`` that will be analyzed. The available options are ``daily``, ``morning``, ``afternoon``, ``evening``, ``night``
features Features to be computed, see table below
============ ===================
.. _activity-recognition-available-features:
**Available Activity Recognition Features**
====================== ============== =============
Name Units Description
====================== ============== =============
count rows Number of episodes.
mostcommonactivity activity_type The most common ``activity_type``. If this feature is not unique the first ``activity_type`` of the set of most common ``activity_types`` is selected ordered by ``activity_type``.
countuniqueactivities activity_type Number of unique ``activity_type``.
durationstationary minutes The total duration of episodes of still and tilting (phone) activities.
durationmobile minutes The total duration of episodes of on foot, running, and on bicycle activities
durationvehicle minutes The total duration of episodes of on vehicle activity
====================== ============== =============
**Assumptions/Observations:**
iOS Activity Recognition data labels are unified with Google Activity Recognition labels: "automotive" to "in_vehicle", "cycling" to "on_bicycle", "walking" and "running" to "on_foot", "stationary" to "still". In addition, iOS activity pairs formed by "stationary" and "automotive" labels (driving but stopped at a traffic light) are transformed to "automotive" only.
In AWARE, Activity Recognition data for Google (Android) and iOS are stored in two different database tables, RAPIDS (via Snakemake) automatically infers what platform each participant belongs to based on their participant file (``data/external/``) which in turn takes this information from the ``aware_device`` table (see ``optional_ar_input`` function in ``rules/features.snakefile``).
The activties are mapped to activity_types as follows:
=============== ===============
Activity Name Activity Type
=============== ===============
in_vehicle 0
on_bicycle 1
on_foot 2
still 3
unknown 4
tilting 5
walking 7
running 8
=============== ===============
.. _light-doc:
Light
"""""""
See `Light Config Code`_
**Available Epochs (day_segment) :** daily, morning, afternoon, evening, night
**Available Platforms:** Android
**Rule Chain:**
- Rule: ``rules/preprocessing.snakefile/download_dataset``
- Rule: ``rules/preprocessing.snakefile/readable_datetime``
- Rule: ``rules/features.snakefile/light_features``
.. _light-parameters:
**Light Rule Parameters (light_features):**
============ ===================
Name Description
============ ===================
day_segment The particular ``day_segment`` that will be analyzed. The available options are ``daily``, ``morning``, ``afternoon``, ``evening``, ``night``
features Features to be computed, see table below
============ ===================
.. _light-available-features:
**Available Light Features**
=========== ========= =============
Name Units Description
=========== ========= =============
count rows Number light sensor rows recorded.
maxlux lux The maximum ambient luminance.
minlux lux The minimum ambient luminance.
avglux lux The average ambient luminance.
medianlux lux The median ambient luminance.
stdlux lux The standard deviation of ambient luminance.
=========== ========= =============
**Assumptions/Observations:** N/A
.. _location-sensor-doc:
Location (Barnett’s) Features
""""""""""""""""""""""""""""""
Barnett’s location features are based on the concept of flights and pauses. GPS coordinates are converted into a
sequence of flights (straight line movements) and pauses (time spent stationary). Data is imputed before features
are computed. See Ian Barnett, Jukka-Pekka Onnela, Inferring mobility measures from GPS traces with missing data, Biostatistics, Volume 21, Issue 2, April 2020, Pages e98–e112, https://doi.org/10.1093/biostatistics/kxy059. The code for these features was made open source by Ian Barnett (https://scholar.harvard.edu/ibarnett/software/gpsmobility).
See `Location (Barnett’s) Config Code`_
**Available Day Segments (epochs) :** only daily periods of EVERY_DAY_INTERVAL or FLEXIBLE_DAY_INTERVAL (periods that start at 00:00:00 and end at 23:59:59 on the same day)
**Available Platforms:** Android and iOS
**Snakemake rule chain:**
- Rule ``rules/preprocessing.snakefile/download_dataset`` (de duplication and sorting by timestamp)
- Rule ``rules/preprocessing.snakefile/readable_datetime`` (add local date and time components, add local day segment)
- Rule ``rules/preprocessing.snakefile/phone_sensed_bins`` (get the periods of time the phone was sensing data to resample over them)
- Rule ``rules/preprocessing.snakefile/process_location_types`` (filter gps data or resample fused location, deletes (0,0) coordinates)
- Rule ``rules/features.snakefile/locations_r_features`` (RAPIDS executes ``barnett_location_features`` from ``src/features/location/barnett/main.R`)
- Rule ``rules/features.snakefile/join_features_from_providers`` (joins the location features of all python and r providers)
.. _location-parameters:
**Location Rule Parameters (location_barnett_features):**
================= ===================
Name Description
================= ===================
location_to_use *Read the Observations section below*. The specifies what type of location data will be use in the analysis. Possible options are ``ALL``, ``GPS`` OR ``RESAMPLE_FUSED``
accuracy_limit This is in meters. The sensor drops location coordinates with an accuracy higher than this. This number means there's a 68% probability the true location is within this radius specified.
timezone The timezone used to calculate location.
minutes_data_used This is NOT a feature. This is just a quality control check, and if set to TRUE, a new column is added to the output file with the number of minutes containing location data that were used to compute all features. The more data minutes exist for a period, the more reliable its features should be. For fused location, a single minute can contain more than one coordinate pair if the participant is moving fast enough.
features Features to be computed, see table below
================= ===================
.. _location-available-features:
**Available Location Features**
Description taken from `Beiwe Summary Statistics`_.
================ ========= =============
Name Units Description
================ ========= =============
hometime minutes Time at home. Time spent at home in minutes. Home is the most visited significant location between 8 pm and 8 am including any pauses within a 200-meter radius.
disttravelled meters Total distance travelled over a day (flights).
rog meters The Radius of Gyration (rog) is a measure in meters of the area covered by a person over a day. A centroid is calculated for all the places (pauses) visited during a day and a weighted distance between all the places and that centroid is computed. The weights are proportional to the time spent in each place.
maxdiam meters The maximum diameter is the largest distance between any two pauses.
maxhomedist meters The maximum distance from home in meters.
siglocsvisited locations The number of significant locations visited during the day. Significant locations are computed using k-means clustering over pauses found in the whole monitoring period. The number of clusters is found iterating k from 1 to 200 stopping until the centroids of two significant locations are within 400 meters of one another.
avgflightlen meters Mean length of all flights.
stdflightlen meters Standard deviation of the length of all flights.
avgflightdur seconds Mean duration of all flights.
stdflightdur seconds The standard deviation of the duration of all flights.
probpause The fraction of a day spent in a pause (as opposed to a flight)
siglocentropy nats Shannon’s entropy measurement based on the proportion of time spent at each significant location visited during a day.
circdnrtn A continuous metric quantifying a person’s circadian routine that can take any value between 0 and 1, where 0 represents a daily routine completely different from any other sensed days and 1 a routine the same as every other sensed day.
wkenddayrtn Same as circdnrtn but computed separately for weekends and weekdays.
================ ========= =============
**Assumptions/Observations:**
*Types of location data to use*
Aware Android and iOS clients can collect location coordinates through the phone's GPS, the network cellular towers around the phone or Google's fused location API. If you want to use only the GPS provider set ``location_to_use`` to ``GPS``, if you want to use all providers (not recommended due to the difference in accuracy) set ``location_to_use`` to ``ALL``, if your Aware client was configured to use fused location only or want to focus only on this provider, set ``location_to_use`` to ``RESAMPLE_FUSED``. ``RESAMPLE_FUSED`` takes the original fused location coordinates and replicates each pair forward in time as long as the phone was sensing data as indicated by ``phone_sensed_bins`` (see :ref:`Phone valid sensed days <phone-valid-sensed-days>`), this is done because Google's API only logs a new location coordinate pair when it is sufficiently different in time or space from the previous one.
There are two parameters associated with resampling fused location in the ``LOCATIONS`` section of the ``config.yaml`` file. ``RESAMPLE_FUSED_CONSECUTIVE_THRESHOLD`` (in minutes, default 30) controls the maximum gap between any two coordinate pairs to replicate the last known pair (for example, participant A's phone did not collect data between 10.30am and 10:50am and between 11:05am and 11:40am, the last known coordinate pair will be replicated during the first period but not the second, in other words, we assume that we cannot longer guarantee the participant stayed at the last known location if the phone did not sense data for more than 30 minutes). ``RESAMPLE_FUSED_TIME_SINCE_VALID_LOCATION`` (in minutes, default 720 or 12 hours) makes that the last known fused location won't be carried over longer that this threshold even if the phone was sensing data continuously (for example, participant A went home at 9pm and their phone was sensing data without gaps until 11am the next morning, the last known location will only be replicated until 9am). If you have suggestions to modify or improve this imputation, let us know.
*Barnett's et al features*
These features are based on a Pause-Flight model. A pause is defined as a mobiity trace (location pings) within a certain duration and distance (by default 300 seconds and 60 meters). A flight is any mobility trace between two pauses. Data is resampled and imputed before the features are computed. See this paper for more information: https://doi.org/10.1093/biostatistics/kxy059.
In RAPIDS we only expose two parameters for these features (timezone and accuracy). If you wish to change others you can do so in ``src/features/location/barnett/library/MobilityFeatures.R``
*Significant Locations*
Significant locations are determined using K-means clustering on pauses longer than 10 minutes. The number of clusters (K) is increased until no two clusters are within 400 meters from each other. After this, pauses within a certain range of a cluster (200 meters by default) will count as a visit to that significant location. This description was adapted from the Supplementary Materials of https://doi.org/10.1093/biostatistics/kxy059.
*The Circadian Calculation*
For a detailed description of how this is calculated, see Canzian, L., & Musolesi, M. (2015, September). Trajectories of depression: unobtrusive monitoring of depressive states by means of smartphone mobility traces analysis. In Proceedings of the 2015 ACM international joint conference on pervasive and ubiquitous computing (pp. 1293-1304). Their procedure was followed using 30-min increments as a bin size. Taken from `Beiwe Summary Statistics`_.
Location (Doryab's) Features
""""""""""""""""""""""""""""""
Doryab's location features are based on this paper: Doryab, A., Chikarsel, P., Liu, X., & Dey, A. K. (2019). Extraction of Behavioral Features from Smartphone and Wearable Data. ArXiv:1812.10394 [Cs, Stat]. http://arxiv.org/abs/1812.10394
See `Location (Doryab's) Config Code`_
**Available Day Segments (epochs):** any of EVERY_DAY_FREQUENCY, EVERY_DAY_INTERVAL and FLEXIBLE_DAY_INTERVAL
**Available Platforms:** Android and iOS
**Snakemake rule chain:**
- Rule ``rules/preprocessing.snakefile/download_dataset`` (de duplication and sorting by timestamp)
- Rule ``rules/preprocessing.snakefile/readable_datetime`` (add local date and time components, add local day segment)
- Rule ``rules/preprocessing.snakefile/phone_sensed_bins`` (get the periods of time the phone was sensing data to resample over them)
- Rule ``rules/preprocessing.snakefile/process_location_types`` (filter gps data or resample fused location, deletes (0,0) coordinates)
- Rule ``rules/features.snakefile/locations_python_features`` (RAPIDS executes ``doryab_location_features`` from ``src/features/location/doryab/main.py`)
- Rule ``rules/features.snakefile/join_features_from_providers`` (joins the location features of all python and r providers)
.. _location-doryab-parameters:
**Location Rule Parameters (location_doryab_features):**
=================== ===================
Name Description
=================== ===================
day_segment The particular ``day_segment`` that will be analyzed. The available options are ``daily``, ``morning``, ``afternoon``, ``evening``, ``night``
location_to_use *Read the Observations section below*. The specifies what type of location data will be use in the analysis. Possible options are ``ALL``, ``GPS`` OR ``RESAMPLE_FUSED``.
features Features to be computed, see table below.
threshold_static It is the threshold value in km/hr which labels a row as Static or Moving.
dbscan_minsamples The number of samples (or total weight) in a neighborhood for a point to be considered as a core point. This includes the point itself.
dbscan_eps The maximum distance between two samples for one to be considered as in the neighborhood of the other. This is not a maximum bound on the distances of points within a cluster. This is the most important DBSCAN parameter to choose appropriately for your data set and distance function.
maximum_gap_allowed The maximum gap (in seconds) allowed between any two consecutive rows for them to be considered part of the same displacement. If this threshold is too high, it can throw speed and distance calculations off for periods when the the phone was not sensing.
minutes_data_used This is NOT a feature. This is just a quality control check, and if set to TRUE, a new column is added to the output file with the number of minutes containing location data that were used to compute all features. The more data minutes exist for a period, the more reliable its features should be. For fused location, a single minute can contain more than one coordinate pair if the participant is moving fast enough.
sampling_frequency Expected time difference between any two location rows in minutes. If set to '0', the sampling frequency will be inferred automatically as the median of all the differences between any two consecutive row timestamps. This parameter impacts all the time calculations.
=================== ===================
.. _location-doryab-available-features:
**Available Location Features**
============================ ================ =============
Name Units Description
============================ ================ =============
locationvariance :math:`meters^2` The sum of the variances of the latitude and longitude columns.
loglocationvariance Log of the sum of the variances of the latitude and longitude columns.
totaldistance meters Total distance travelled in a ``day_segment`` using the haversine formula.
averagespeed km/hr Average speed in a ``day_segment`` considering only the instances labeled as Moving.
varspeed km/hr Speed variance in a ``day_segment`` considering only the instances labeled as Moving.
circadianmovement "It encodes the extent to which a person’s location patterns follow a 24-hour circadian cycle." (Doryab et. al. 2019)
numberofsignificantplaces places Number of significant locations visited. It is calculated using the DBSCAN clustering algorithm which takes in EPS and MIN_SAMPLES as paramters to identify clusters. Each cluster is a significant place.
numberlocationtransitions transitions Number of movements between any two clusters in a ``day_segment``.
radiusgyration meters Quantifies the area covered by a participant
timeattop1location minutes Time spent at the most significant location.
timeattop2location minutes Time spent at the 2nd most significant location.
timeattop3location minutes Time spent at the 3rd most significant location.
movingtostaticratio Ratio between the number of rows labeled Moving versus Static
outlierstimepercent Ratio between the number of rows that belong to non-significant clusters divided by the total number of rows in a ``day_segment``.
maxlengthstayatclusters minutes Maximum time spent in a cluster (significant location).
minlengthstayatclusters minutes Minimum time spent in a cluster (significant location).
meanlengthstayatclusters minutes Average time spent in a cluster (significant location).
stdlengthstayatclusters minutes Standard deviation of time spent in a cluster (significant location).
locationentropy nats Shannon Entropy computed over the row count of each cluster (significant location), it will be higher the more rows belong to a cluster (i.e. the more time a participant spent at a significant location).
normalizedlocationentropy nats Shannon Entropy computed over the row count of each cluster (significant location) divided by the number of clusters, it will be higher the more rows belong to a cluster (i.e. the more time a participant spent at a significant location).
============================ ================ =============
**Assumptions/Observations:**
*Types of location data to use*
Aware Android and iOS clients can collect location coordinates through the phone's GPS, the network cellular towers around the phone or Google's fused location API. If you want to use only the GPS provider set ``location_to_use`` to ``GPS``, if you want to use all providers (not recommended due to the difference in accuracy) set ``location_to_use`` to ``ALL``, if your Aware client was configured to use fused location only or want to focus only on this provider, set ``location_to_use`` to ``RESAMPLE_FUSED``. ``RESAMPLE_FUSED`` takes the original fused location coordinates and replicates each pair forward in time as long as the phone was sensing data as indicated by ``phone_sensed_bins`` (see :ref:`Phone valid sensed days <phone-valid-sensed-days>`), this is done because Google's API only logs a new location coordinate pair when it is sufficiently different in time or space from the previous one.
There are two parameters associated with resampling fused location in the ``LOCATIONS`` section of the ``config.yaml`` file. ``RESAMPLE_FUSED_CONSECUTIVE_THRESHOLD`` (in minutes, default 30) controls the maximum gap between any two coordinate pairs to replicate the last known pair (for example, participant A's phone did not collect data between 10.30am and 10:50am and between 11:05am and 11:40am, the last known coordinate pair will be replicated during the first period but not the second, in other words, we assume that we cannot longer guarantee the participant stayed at the last known location if the phone did not sense data for more than 30 minutes). ``RESAMPLE_FUSED_TIME_SINCE_VALID_LOCATION`` (in minutes, default 720 or 12 hours) makes that the last known fused location won't be carried over longer that this threshold even if the phone was sensing data continuously (for example, participant A went home at 9pm and their phone was sensing data without gaps until 11am the next morning, the last known location will only be replicated until 9am). If you have suggestions to modify or improve this imputation, let us know.
*Significant Locations Identified*
Significant locations are determined using DBSCAN clustering on locations that a patient visit over the course of the period of data collection.
*Circadian Movement Calculation*
"Circadian movement (Saeb et al. 2015) is calculated using the Lomb-Scargle method" (Doryab et. al. 2019)
.. _screen-sensor-doc:
Screen
""""""""
See `Screen Config Code`_
**Available Epochs (day_segment) :** daily, morning, afternoon, evening, night
**Available Platforms:** Android and iOS
**Snakemake rule chain:**
- Rule ``rules/preprocessing.snakefile/download_dataset``
- Rule ``rules/preprocessing.snakefile/readable_datetime``
- Rule ``rules/preprocessing.snakefile/unify_ios_android``
- Rule ``rules/features.snakefile/screen_deltas``
- Rule ``rules/features.snakefile/screen_features``
.. _screen-parameters:
**Screen Rule Parameters (screen_features):**
============================ ===================
Name Description
============================ ===================
day_segment The particular ``day_segments`` that will be analyzed. The available options are ``daily``, ``morning``, ``afternoon``, ``evening``, ``night``
reference_hour_first_use The reference point from which ``firstuseafter`` is to be computed, default is midnight
ignore_episodes_shorter_than Ignore episodes that are shorter than this threshold (minutes). Set to 0 to disable this filter.
ignore_episodes_longer_than Ignore episodes that are longer than this threshold (minutes). Set to 0 to disable this filter.
features_deltas Features to be computed, see table below
episode_types Currently we only support unlock episodes (from when the phone is unlocked until the screen is off)
============================ ===================
.. _screen-episodes-available-features:
**Available Screen Episodes Features**
========================= ================= =============
Name Units Description
========================= ================= =============
sumduration minutes Total duration of all unlock episodes.
maxduration minutes Longest duration of any unlock episode.
minduration minutes Shortest duration of any unlock episode.
avgduration minutes Average duration of all unlock episodes.
stdduration minutes Standard deviation duration of all unlock episodes.
countepisode episodes Number of all unlock episodes
episodepersensedminutes episodes/minute The ratio between the total number of episodes in an epoch divided by the total time (minutes) the phone was sensing data.
firstuseafter minutes Minutes until the first unlock episode.
========================= ================= =============
**Assumptions/Observations:**
In Android, ``lock`` events can happen right after an ``off`` event, after a few seconds of an ``off`` event, or never happen depending on the phone's settings, therefore, an ``unlock`` episode is defined as the time between an ``unlock`` and a ``off`` event. In iOS, ``on`` and ``off`` events do not exist, so an ``unlock`` episode is defined as the time between an ``unlock`` and a ``lock`` event.
Events in iOS are recorded reliably albeit some duplicated ``lock`` events within milliseconds from each other, so we only keep consecutive unlock/lock pairs. In Android you cand find multiple consecutive ``unlock`` or ``lock`` events, so we only keep consecutive unlock/off pairs. In our experiments these cases are less than 10% of the screen events collected and this happens because ``ACTION_SCREEN_OFF`` and ``ACTION_SCREEN_ON`` are "sent when the device becomes non-interactive which may have nothing to do with the screen turning off". In addition to unlock/off episodes, in Android it is possible to measure the time spent on the lock screen before an ``unlock`` event as well as the total screen time (i.e. ``ON`` to ``OFF``) but these are not implemented at the moment.
To unify the screen processing and use the same code in RAPIDS, we replace LOCKED episodes with OFF episodes (2 with 0) in iOS. However, as mentioned above this is still computing ``unlock`` to ``lock`` episodes.
.. _conversation-sensor-doc:
Conversation
""""""""""""""
See `Conversation Config Code`_
**Available Epochs (day_segment) :** daily, morning, afternoon, evening, night
**Available Platforms:** Android and iOS
**Snakemake rule chain:**
- Rule ``rules/preprocessing.snakefile/download_dataset``
- Rule ``rules/preprocessing.snakefile/readable_datetime``
- Rule ``rules/features.snakefile/conversation_features``
.. _conversation-parameters:
**Conversation Rule Parameters (conversation_features):**
========================= ===================
Name Description
========================= ===================
day_segment The particular ``day_segments`` that will be analyzed. The available options are ``daily``, ``morning``, ``afternoon``, ``evening``, ``night``
recordingMinutes Minutes the plugin was recording audio (default 1 min)
pausedMinutes Minutes the plugin was NOT recording audio (default 3 min)
features Features to be computed, see table below
========================= ===================
.. _conversation-available-features:
**Available Conversation Features**
========================= ================= =============
Name Units Description
========================= ================= =============
minutessilence minutes Minutes labeled as silence
minutesnoise minutes Minutes labeled as noise
minutesvoice minutes Minutes labeled as voice
minutesunknown minutes Minutes labeled as unknown
sumconversationduration minutes Total duration of all conversations
maxconversationduration minutes Longest duration of all conversations
minconversationduration minutes Shortest duration of all conversations
avgconversationduration minutes Average duration of all conversations
sdconversationduration minutes Standard Deviation of the duration of all conversations
timefirstconversation minutes Minutes since midnight when the first conversation for a day segment was detected
timelastconversation minutes Minutes since midnight when the last conversation for a day segment was detected
noisesumenergy L2-norm Sum of all energy values when inference is noise
noiseavgenergy L2-norm Average of all energy values when inference is noise
noisesdenergy L2-norm Standard Deviation of all energy values when inference is noise
noiseminenergy L2-norm Minimum of all energy values when inference is noise
noisemaxenergy L2-norm Maximum of all energy values when inference is noise
voicesumenergy L2-norm Sum of all energy values when inference is voice
voiceavgenergy L2-norm Average of all energy values when inference is voice
voicesdenergy L2-norm Standard Deviation of all energy values when inference is voice
voiceminenergy L2-norm Minimum of all energy values when inference is voice
voicemaxenergy L2-norm Maximum of all energy values when inference is voice
silencesensedfraction Ratio between minutessilence and the sum of (minutessilence, minutesnoise, minutesvoice, minutesunknown)
noisesensedfraction Ratio between minutesnoise and the sum of (minutessilence, minutesnoise, minutesvoice, minutesunknown)
voicesensedfraction Ratio between minutesvoice and the sum of (minutessilence, minutesnoise, minutesvoice, minutesunknown)
unknownsensedfraction Ratio between minutesunknown and the sum of (minutessilence, minutesnoise, minutesvoice, minutesunknown)
silenceexpectedfraction Ration between minutessilence and the number of minutes that in theory should have been sensed based on the record and pause cycle of the plugin (1440 / recordingMinutes+pausedMinutes)
noiseexpectedfraction Ration between minutesnoise and the number of minutes that in theory should have been sensed based on the record and pause cycle of the plugin (1440 / recordingMinutes+pausedMinutes)
voiceexpectedfraction Ration between minutesvoice and the number of minutes that in theory should have been sensed based on the record and pause cycle of the plugin (1440 / recordingMinutes+pausedMinutes)
unknownexpectedfraction Ration between minutesunknown and the number of minutes that in theory should have been sensed based on the record and pause cycle of the plugin (1440 / recordingMinutes+pausedMinutes)
========================= ================= =============
**Assumptions/Observations:**
N/A
.. ------------------------------- Begin Fitbit Section ----------------------------------- ..
.. _fitbit-sleep-sensor-doc:
Fitbit: Sleep
"""""""""""""""""""
See `Fitbit: Sleep Config Code`_
**Available Epochs (day_segment) :** daily
**Available Platforms:**: Fitbit
**Snakemake rule chain:**
- Rule ``rules/preprocessing.snakefile/download_dataset``
- Rule ``rules/preprocessing.snakefile/fitbit_with_datetime``
- Rule ``rules/features.snakefile/fitbit_sleep_features``
.. _fitbit-sleep-parameters:
**Fitbit: Sleep Rule Parameters (fitbit_sleep_features):**
================================== ===================
Name Description
================================== ===================
day_segment The particular ``day_segment`` that will be analyzed. For this sensor only ``daily`` is used.
sleep_types The types of sleep provided by Fitbit: ``main``, ``nap``, ``all``.
daily_features_from_summary_data The sleep features that can be computed based on Fitbit's summary data. See :ref:`Available Fitbit: Sleep Features <fitbit-sleep-available-features>` Table below
================================== ===================
.. _fitbit-sleep-available-features:
**Available Fitbit: Sleep Features**
======================== =========== =============
Name Units Description
======================== =========== =============
sumdurationtofallasleep minutes Time it took the user to fall asleep for ``sleep_type`` during ``day_segment``.
sumdurationawake minutes Time the user was awake but still in bed for ``sleep_type`` during ``day_segment``.
sumdurationasleep minutes Sleep duration for ``sleep_type`` during ``day_segment``.
sumdurationafterwakeup minutes Time the user stayed in bed after waking up for ``sleep_type`` during ``day_segment``.
sumdurationinbed minutes Total time the user stayed in bed (sumdurationtofallasleep + sumdurationawake + sumdurationasleep + sumdurationafterwakeup) for ``sleep_type`` during ``day_segment``.
avgefficiency scores Sleep efficiency average for ``sleep_type`` during ``day_segment``.
countepisode episodes Number of sleep episodes for ``sleep_type`` during ``day_segment``.
======================== =========== =============
**Assumptions/Observations:**
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.
- 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:
- For the ``classic`` type unified_level is one of {0, 1} where 0 means awake and groups ``awake`` + ``restless``, while 1 means asleep and groups ``asleep``.
- For the ``stages`` type, unified_level is one of {0, 1} where 0 means awake and groups ``wake`` while 1 means asleep and groups ``deep`` + ``light`` + ``rem``.
- Short Data. In ``v1.2``, records of type ``stages`` contain ``shortData`` in addition to ``data``. We merge both to extract intraday data.
- ``data`` contains sleep stages and any wake periods > 3 minutes (180 seconds).
- ``shortData`` contains short wake periods representing physiological awakenings that are <= 3 minutes (180 seconds).
- The following columns of Summary data are not computed by RAPIDS but taken directly from columns with a similar name provided by Fitbit's API: ``efficiency``, ``minutes_after_wakeup``, ``minutes_asleep``, ``minutes_awake``, ``minutes_to_fall_asleep``, ``minutes_in_bed``, ``is_main_sleep`` and ``type``
- The following columns of Intraday data are not computed by RAPIDS but taken directly from columns with a similar name provided by Fitbit's API: ``original_level``, ``is_main_sleep`` and ``type``. We compute ``unified_level`` as explained above.
These are examples of intraday and summary data:
- Intraday data (at 30-second intervals for ``stages`` type or 60-second intervals for ``classic`` type)
========= ============== ============= ============= ====== =================== ========== =========== ========= ================= ========== ========== ============ =================
device_id original_level unified_level is_main_sleep type local_date_time local_date local_month local_day local_day_of_week local_time local_hour local_minute local_day_segment
========= ============== ============= ============= ====== =================== ========== =========== ========= ================= ========== ========== ============ =================
did wake 0 1 stages 2020-05-20 22:13:30 2020-05-20 5 20 2 22:13:30 22 13 evening
did wake 0 1 stages 2020-05-20 22:14:00 2020-05-20 5 20 2 22:14:00 22 14 evening
did light 1 1 stages 2020-05-20 22:14:30 2020-05-20 5 20 2 22:14:30 22 14 evening
did light 1 1 stages 2020-05-20 22:15:00 2020-05-20 5 20 2 22:15:00 22 15 evening
did light 1 1 stages 2020-05-20 22:15:30 2020-05-20 5 20 2 22:15:30 22 15 evening
========= ============== ============= ============= ====== =================== ========== =========== ========= ================= ========== ========== ============ =================
- Summary data
========= ========== ==================== ============== ============= ====================== ============== ============= ====== ===================== =================== ================ ============== ======================= =====================
device_id efficiency minutes_after_wakeup minutes_asleep minutes_awake minutes_to_fall_asleep minutes_in_bed is_main_sleep type local_start_date_time local_end_date_time local_start_date local_end_date local_start_day_segment local_end_day_segment
========= ========== ==================== ============== ============= ====================== ============== ============= ====== ===================== =================== ================ ============== ======================= =====================
did 90 0 381 54 0 435 1 stages 2020-05-20 22:12:00 2020-05-21 05:27:00 2020-05-20 2020-05-21 evening night
did 88 0 498 86 0 584 1 stages 2020-05-22 22:03:00 2020-05-23 07:47:03 2020-05-22 2020-05-23 evening morning
========= ========== ==================== ============== ============= ====================== ============== ============= ====== ===================== =================== ================ ============== ======================= =====================
.. _fitbit-heart-rate-sensor-doc:
Fitbit: Heart Rate
"""""""""""""""""""
See `Fitbit: Heart Rate Config Code`_
**Available Epochs (day_segment) :** daily, morning, afternoon, evening, night
**Available Platforms:**: Fitbit
**Snakemake rule chain:**
- Rule ``rules/preprocessing.snakefile/download_dataset``
- Rule ``rules/preprocessing.snakefile/fitbit_with_datetime``
- Rule ``rules/features.snakefile/fitbit_heartrate_features``
.. _fitbit-heart-rate-parameters:
**Fitbit: Heart Rate Rule Parameters (fitbit_heartrate_features):**
============ ===================
Name Description
============ ===================
day_segment The particular ``day_segment`` that will be analyzed. The available options are ``daily``, ``morning``, ``afternoon``, ``evening``, ``night``
features The heartrate features that can be computed. See :ref:`Available Fitbit: Heart Rate Features <fitbit-heart-rate-available-features>` Table below
============ ===================
.. _fitbit-heart-rate-available-features:
**Available Fitbit: Heart Rate Features**
================== =========== =============
Name Units Description
================== =========== =============
restingheartrate beats/mins The number of times your heart beats per minute when participant is still and well rested for ``daily`` epoch.
calories cals Calories burned during ``heartrate_zone`` for ``daily`` epoch.
maxhr beats/mins The maximum heart rate during ``day_segment`` epoch.
minhr beats/mins The minimum heart rate during ``day_segment`` epoch.
avghr beats/mins The average heart rate during ``day_segment`` epoch.
medianhr beats/mins The median of heart rate during ``day_segment`` epoch.
modehr beats/mins The mode of heart rate during ``day_segment`` epoch.
stdhr beats/mins The standard deviation of heart rate during ``day_segment`` epoch.
diffmaxmodehr beats/mins The difference between the maximum and mode heart rate during ``day_segment`` epoch.
diffminmodehr beats/mins The difference between the mode and minimum heart rate during ``day_segment`` epoch.
entropyhr nats Shannon’s entropy measurement based on heart rate during ``day_segment`` epoch.
minutesonZONE minutes Number of minutes the user's heartrate fell within each ``heartrate_zone`` during ``day_segment`` epoch.
================== =========== =============
**Assumptions/Observations:**
There are four heart rate zones: ``out_of_range``, ``fat_burn``, ``cardio``, and ``peak``. Please refer to `Fitbit documentation`_ for more information about the way they are computed.
Calories' accuracy depends on the users’ Fitbit profile (weight, height, etc.).
.. _fitbit-steps-sensor-doc:
Fitbit: Steps
"""""""""""""""
See `Fitbit: Steps Config Code`_
**Available Epochs (day_segment) :** daily, morning, afternoon, evening, night
**Available Platforms:**: Fitbit
**Snakemake rule chain:**
- Rule ``rules/preprocessing.snakefile/download_dataset``
- Rule ``rules/preprocessing.snakefile/fitbit_with_datetime``
- Rule ``rules/features.snakefile/fitbit_step_features``
.. _fitbit-steps-parameters:
**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``
========================== ===================
.. _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.
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 ------------------------------------ ..
.. _PHONE_VALID_SENSED_BINS: https://github.com/carissalow/rapids/blob/4bdc30ffa4e13987b398a2354746d1a1977bef27/config.yaml#L30
.. _`Messages Config Code`: https://github.com/carissalow/rapids/blob/4bdc30ffa4e13987b398a2354746d1a1977bef27/config.yaml#L43
.. _AWARE: https://awareframework.com/what-is-aware/
.. _`List of Timezones`: https://en.wikipedia.org/wiki/List_of_tz_database_time_zones
.. _DAY_SEGMENTS: https://github.com/carissalow/rapids/blob/4bdc30ffa4e13987b398a2354746d1a1977bef27/config.yaml#L6
.. _PHONE_VALID_SENSED_DAYS: https://github.com/carissalow/rapids/blob/4bdc30ffa4e13987b398a2354746d1a1977bef27/config.yaml#L37
.. _`Call Config Code`: https://github.com/carissalow/rapids/blob/4bdc30ffa4e13987b398a2354746d1a1977bef27/config.yaml#L53
.. _`WiFi Config Code`: https://github.com/carissalow/rapids/blob/4bdc30ffa4e13987b398a2354746d1a1977bef27/config.yaml#L172
.. _`Bluetooth Config Code`: https://github.com/carissalow/rapids/blob/4bdc30ffa4e13987b398a2354746d1a1977bef27/config.yaml#L84
.. _`Accelerometer Config Code`: https://github.com/carissalow/rapids/blob/4bdc30ffa4e13987b398a2354746d1a1977bef27/config.yaml#L118
.. _`Applications Foreground Config Code`: https://github.com/carissalow/rapids/blob/4bdc30ffa4e13987b398a2354746d1a1977bef27/config.yaml#L128
.. _`Battery Config Code`: https://github.com/carissalow/rapids/blob/4bdc30ffa4e13987b398a2354746d1a1977bef27/config.yaml#L98
.. _`Activity Recognition Config Code`: https://github.com/carissalow/rapids/blob/4bdc30ffa4e13987b398a2354746d1a1977bef27/config.yaml#L90
.. _`Light Config Code`: https://github.com/carissalow/rapids/blob/4bdc30ffa4e13987b398a2354746d1a1977bef27/config.yaml#L112
.. _`Location (Barnett’s) Config Code`: https://github.com/carissalow/rapids/blob/4bdc30ffa4e13987b398a2354746d1a1977bef27/config.yaml#L74
.. _`Location (Doryab's) Config Code`: https://github.com/carissalow/rapids/blob/4bdc30ffa4e13987b398a2354746d1a1977bef27/config.yaml#L74
.. _`Screen Config Code`: https://github.com/carissalow/rapids/blob/4bdc30ffa4e13987b398a2354746d1a1977bef27/config.yaml#L104
.. _`Fitbit: Sleep Config Code`: https://github.com/carissalow/rapids/blob/4bdc30ffa4e13987b398a2354746d1a1977bef27/config.yaml#L165
.. _`version 1`: https://dev.fitbit.com/build/reference/web-api/sleep-v1/
.. _`version 1.2`: https://dev.fitbit.com/build/reference/web-api/sleep/
.. _`Conversation Config Code`: https://github.com/carissalow/rapids/blob/4bdc30ffa4e13987b398a2354746d1a1977bef27/config.yaml#L191
.. _`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/4bdc30ffa4e13987b398a2354746d1a1977bef27/config.yaml#L141
.. _`Fitbit: Steps Config Code`: https://github.com/carissalow/rapids/blob/29b04b0601b62379fbdb76de685f3328b8dde2a2/config.yaml#L148
.. _`Fitbit documentation`: https://help.fitbit.com/articles/en_US/Help_article/1565
.. _top1global: https://github.com/carissalow/rapids/blob/765bb462636d5029a05f54d4c558487e3786b90b/config.yaml#L136
.. _`Beiwe Summary Statistics`: http://wiki.beiwe.org/wiki/Summary_Statistics
.. _`Pause-Flight Model`: https://academic.oup.com/biostatistics/advance-article/doi/10.1093/biostatistics/kxy059/5145908
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