*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
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 ``TABLES_FOR_SENSED_BINS`` (see below).
-``TABLES_FOR_SENSED_BINS`` - Add as many sensor tables as you have in your database. All sensors included are used to compute ``phone_sensed_bins.csv`` (bins of time when the smartphone was sensing data). In turn, these bins are used to compute ``PHONE_VALID_SENSED_DAYS`` (see below), ``episodepersensedminutes`` feature of :ref:`Screen<screen-sensor-doc>` and to resample fused location data if you configure Barnett's location features to use ``RESAMPLE_FUSED``. See TABLES_FOR_SENSED_BINS_ variable in ``config`` file (therefore, when you are extracting screen or Barnett's location features, screen and locations tables are mandatory).
-``PID`` - 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`` - 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`` - 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`` - The name of your database credentials group, it should match the one in ``.env`` (:ref:`see the datbase configuration<db-configuration>`).
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. In turn, a valid bin are those that contain at least one row of data from any sensor logged within that period. We divide an hour into N bins of size ``BIN_SIZE`` (in minutes) and we mark an hour as valid if contains at least ``MIN_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). Days with valid sensed hours less than ``MIN_VALID_HOURS`` will be excluded form the output of this file. See PHONE_VALID_SENSED_DAYS_ in ``config.yaml``.
Note that RAPIDS *DOES NOT* filter your feature files automatically, you need to do this manually based on ``"data/interim/{pid}/phone_valid_sensed_days.csv"``.
You can get access to every phone's sensed bins matrix (days x bins) in ``data/interim/{pid}/phone_sensed_bins.csv``. As mentioned above, RAPIDS uses this file to compute ``phone_valid_sensed_days.csv``, ``episodepersensedminutes`` feature of :ref:`Screen<screen-sensor-doc>` and to resample fused location data if you configure Barnett's location features to use ``RESAMPLE_FUSED``.
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``
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.
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.
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``.
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.
countmostfrequentcontact calls The number of ``missed`` calls during a particular ``day_segment`` of the most frequent contact throughout the monitored period.
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.
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.
day_segment The particular ``day_segment`` that will be analyzed. The available options are ``daily``, ``morning``, ``afternoon``, ``evening``, ``night``
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
day_segment The particular ``day_segment`` that will be analyzed. The available options are ``daily``, ``morning``, ``afternoon``, ``evening``, ``night``
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
day_segment The particular ``day_segment`` that will be analyzed. The available options are ``daily``, ``morning``, ``afternoon``, ``evening``, ``night``
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
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``
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.
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
day_segment The particular ``day_segment`` that will be analyzed. The available options are ``daily``, ``morning``, ``afternoon``, ``evening``, ``night``
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
day_segment The particular ``day_segment`` that will be analyzed. The available options are ``daily``, ``morning``, ``afternoon``, ``evening``, ``night``
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``).
day_segment The particular ``day_segment`` that will be analyzed. The available options are ``daily``, ``morning``, ``afternoon``, ``evening``, ``night``
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).
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``, ``ALL_EXCEPT_FUSED`` 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.
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.
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.
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.
Aware Android and iOS clients can collect location coordinates through the phone's GPS or Google's fused location API. If your Aware client was ONLY configured to use GPS set ``location_to_use`` to ``ALL``, if your client was configured to use BOTH GPS and fused location you can use ``ALL`` or set ``location_to_use`` to ``ALL_EXCEPT_FUSED`` to ignore fused coordinates, if your client was configured to use fused location only, 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 from the previous one.
There are two parameters associated with resampling fused location in the ``RESAMPLE_FUSED_LOCATION`` section of the ``config.yaml`` file. ``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). ``TIME_SINCE_VALID_LOCATION`` (in minutes, default 720 or 12 hours) 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 are determined using K-means clustering on locations that a patient visit over the course of the period of data collection. By setting K=K+1 and repeat clustering until two significant locations are within 100 meters of one another, the results from the previous step (K-1) can be used as the total number of significant locations. Taken from `Beiwe Summary Statistics`_.
(i.e., The length of time and distance a person has to be around the same place to be labelled as a pause)
This is based on a Pause-Flight model, The parameters used are a minimum pause duration of 300sec and a minimum pause distance of 60m. See the `Pause-Flight Model`_.
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`_.
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
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.
An ``unlock`` episode is considered as the time between an ``unlock`` event and a ``lock`` event. iOS recorded these episodes reliably (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 our experiments these cases 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 before an ``unlock`` event as well as the total screen time (i.e. ``ON`` to ``OFF``) but we are only keeping ``unlock`` episodes (``unlock`` to ``OFF``) to be consistent with iOS.
day_segment The particular ``day_segments`` that will be analyzed. The available options are ``daily``, ``morning``, ``afternoon``, ``evening``, ``night``
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
sumenergy L2-norm Sum of all energy values
avgenergy L2-norm Average of all energy values
sdenergy L2-norm Standard Deviation of all energy values
minenergy L2-norm Minimum of all energy values
maxenergy L2-norm Maximum of all energy values
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)
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
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``.
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.
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
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.).
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``
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``.
