mpathsenser 1.2.4

Major changes

• link_db() is now defunct. Please use link() instead.
• Bump minimum R requirement to 4.2.0 as the native pipe |> is used in this package.
• Added add_timezone_to_db() function to add the timezone "measurements" to each measurement of sensor data. This allows you to more easily take into account which timezone a participant was in instead of only relying on UTC.
• Added with_localtime() function to easily add the relevant timezone to a timestamp, even if multiple timezones are present in the data. Note that this does not work in-database.

Minor changes

• import() now supports the new output format for connectivity where connectivity_status can be a list of statuses as well.
• mpathsenser no longer gives a warning for unimplemented 'mpathinfo' meta data.
• bin_data() gained a .name argument to specify the name of the column containing the binned data.
• The use of progressr::progress() has been removed from the documentation is this function is now defunct.

Bugfixes

• Fixed a bug in import() where files could not be read in correctly if they did not contain any measurement with a sensorEndTime.
• Fixed unzip_data() not correctly detecting which files not to overwrite if overwrite = FALSE and the zip files have a non-standard name.
• import() now correctly reads study_id if it contains an underscore _.

mpathsenser 1.2.3

This is a hotfix release to fix a bug in import().

Minor changes

• Added a contribution statement to the project. The previous contribution statement was actually a code of conduct which has now been appropriately assigned as such.

Bugfixes

• Fixed bugs in the import functions of AppUsage, Device, and Location that may have prevented files from being imported.

mpathsenser 1.2.2

Major changes

mpathsenser now supports the new data format as of m-Path Sense 4.2.6. This comes with a large number of changes. Most importantly, this means that import() had to be updated to handle the new data format. Both the old and new data format are now supported by this package. With the new data format there are some changes to the database.

First, some fields have been removed:

• The x, y, and z fields from Accelerometer have been removed from import() and all subsequent functions. These fields were only used when m-Path Sense still collected continuous data, and for some time now only summary data is collected. No continuous data has ever been collected outside of pilot testing, and hence these fields have been removed.
• The x_mean, y_mean, z_mean, x_mean_sq, y_mean_sq, z_mean_sq, and n fields from Gyroscope have been removed as m-Path Sense will currently collect continuous data. These fields were implemented in anticipation of this change but instead, for now, gyroscopic information has been removed from the app altogether. Thus, these fields are removed from simplicity and clarity.
• The timezone field has been removed from all sensor tables. This field was once added in m-Path Sense but this never made it to the final version. It has been removed from the database and all subsequent functions.

Second, some fields have been added:

• The Accelerometer has gained many new data fields:
  • end_time is the time at which the sample of the data ended, where time denotes the start time.
  • n, the number of samples, was already present but has been moved in the ordering of the fields.
  • x_mean, y_mean, and z_mean are the mean values of the accelerometer data. These were already present in the data and remain unchanged.
  • x_median, y_median, and z_median are the median values of the accelerometer data.
  • x_std, y_std, and z_std are the standard deviations of the accelerometer data.
  • x_aad, y_aad, and z_aad are the average absolute deviations of the accelerometer data.
  • x_min, y_min, and z_min are the minimum values of the accelerometer data.
  • x_max, y_max, and z_max are the maximum values of the accelerometer data.
  • x_max_min_diff, y_max_min_diff, and z_max_min_diff are the differences between the maximum and minimum values of the accelerometer data.
  • x_mad, y_mad, and z_mad are the median absolute deviations of the accelerometer data.
  • x_iqr, y_iqr, and z_iqr are the interquartile ranges of the accelerometer data.
  • x_neg_n, y_neg_n, and z_neg_n are the number of negative values of the accelerometer data.
  • x_pos_n, y_pos_n, and z_pos_n are the number of positive values of the accelerometer data.
  • x_above_mean, y_above_mean, and z_above_mean are the number of values above the mean of the accelerometer data.
  • x_energy, y_energy, and z_energy are similar to x_mean_sq, y_mean_sq, and z_mean_sq, being the average sum of squares.
  • avg_res_acc is the average resultant acceleration, being average of the square roots of the values in each of the three axis squared and added together.
  • sma is the signal magnitude area, being the sum of absolute values of the three axis averaged over a window.
• The AppUsage table has gained 2 new fields:
  • end_time is the time at which the sample of the data ended, where time denotes the start time. Note that this timestamp may vary slightly from the end field in the data.
  • package_name is the full application package name.
  • last_foreground is the time at which the application was last in the foreground. If the app had not yet been in the foreground, this is NA.
• The Bluetooth table has gained 2 new fields:
  • start_scan is the time at which the scan started.
  • end_scan is the time at which the scan ended.
• The Device table has gained 2 new fields:
  • operating_system_version is the version of the operating system.
  • sdk is the version of the Android SDK or the iOS kernel.
• A new sensor Heartbeat has been added to the data. This table has the following fields:
  • measurement_id, participant_id, date, and time like every other sensor.
  • period denotes the time period over which the a heartbeat should be registered, in minutes.
  • device_type denotes the type of device of this heartbeat.
  • device_role_name is the role name of the device in the protocol.
• The Light table has gained 1 new field:
  • end_time is the time at which the sample of the data ended, where time denotes the start time.
• Location has gained 3 new fields:
  • vertical_accuracy is the estimated vertical accuracy of this location, in meters.
  • heading_accuracy is the estimated bearing accuracy of this location, in degrees. Only available on Android.
  • is_mock is a boolean indicating whether this location was mocked or not. Always FALSE on iOS. Moreover, because SQLite does not support booleans, this is stored as an integer.
• The Noise table has gained 1 new field:
  • end_time is the time at which the sample of the data ended, where time denotes the start time.
• Timezone has been added a separate sensor. This table has the following fields:
  • measurement_id, participant_id, date, and time like every other sensor.
  • timezone is the time zone of the device at the time of the measurement.

Data collected with previous version of m-Path Sense (henceforth referred to as legacy data) can still be read by import() and subsequent functions, but all new fields will have missing values.

Minor changes

• mpathsenser::sensors now holds 27 sensors, being updated with Heartbeat and Timezone
• Added the correct citation for this package.
• Coverage plots with absolute numbers coverage(relative = FALSE) now show correct colours. The colours are now based on the relative values within each sensor, such that the highest sample is fully red and zero being fully blue.
• vacuum_db() is a newly exported function within this package. Once called upon a database, it shrinks the database to its minimal size by cleaning up remnants from import().
• The maggrittr package has been dropped as a dependency, favouring R's native pipe |> over the maggrittr pipe %>%.
• Added a vignette 'Data overview' to clarify which fields are available in the database and what they mean.
• Added a format argument to geocode_rev() to allow for different output formats from Nominatim's API.
• geocode_rev() and app_category() now return NA if the client or API is offline, as per CRAN guidelines.

Bugfixes

• Fixed an issue in fix_jsons() where files with illegal ASCII characters could be not fixed because the file was still locked from reading.
• A new case has been added to fix_jsons() where JSON files could incorrectly end with }}, followed by a closing bracket ] on a new line. This trailing comma is now removed by fix_jsons().
• If recursive = TRUE in unzip_data() and to = NULL, the output path of the JSON files will be the local directories through which the recursive path is traversed rather than the main directory.
• Replaced double quotation marks with single quotation marks in the description, per CRAN guidelines.

Full Changelog: 1.2.2...1.2.2

mpathsenser 1.1.3

This is a release with breaking changes due to removal of deprecated arguments. Please review
carefully before updating.

This release also supports changes from the new release of m-Path Sense (01/02/2023). Most notably,
the accelerometer and gyroscope are no longer samples of a continuous stream, but rather summaries
of these streams. Old versions are still supported by all functions.

Major changes

• Thanks to a new version of m-Path Sense, accelerometer and gyroscope have gained extra columns:
  • x_mean: The average acceleration or gyroscopic value along the x axis within a sample;
  • y_mean: The average acceleration or gyroscopic value along the y axis within a sample;
  • z_mean: The average acceleration or gyroscopic value along the z axis within a sample;
  • x_mean_sq: The square root of the x values within the sample;
  • y_mean_sq: The square root of the y values within the sample;
  • z_mean_sq: The square root of the z values within the sample;
    From these values, one could calculate the L1 norm and L2 norm like before.
• Added a new value timezone to all sensor data. Confusingly, this is not the timezone of the
  data itself (as this is always in UTC), but rather the timezone the participant was in at the time
  of the measurement.

Deprecations

• Removed deprecated parallel argument in fix_jsons(), test_jsons(), unzip_data(), and
  import().
• Removed deprecated overwrite_db and dbname arguments from import().
• Removed deprecated path and db_name arguments from copy_db().

Minor changes

• Provided support for dplyr 1.1.0.
• link() no longer adds an extra row before (if add_before = TRUE) or after (if
  add_after = TRUE) if the first or last measurement equals the start or end time respectively.
• Changed link_db() lifecycle status to deprecated as link_db() depends on link(). Eventually,
  link() might see changes in its functionality that will cause link_db() to break, so it is
  better to deprecate it already to motivate users to stop using this function.

Bugfixes

• Fix cross-reference to undeclared package ‘future’ in documentation.

• Fixed bug #8 where bin_data() incorrectly handled days occurring after DST change.

• step_count()

These functions delivered incorrect output and only allowed summaries by a fixed time frame, e.g.
by hour or day. These functions will be reimplemented (some with a different name) in mpathsenser
2.0.0.

Minor changes

• When add_before or add_after is TRUE in link(), no extra row is added if there already is
  a row with a timestamp exactly equal to the start of the interval (for add_before = TRUE) or to
  the end of the interval ⁠(add_after = TRUE).
• moving_average() now allows a lazy tibble to allow further computations in-database after
  having called moving_average().
• identify_gaps() is now slightly more efficient.
• get_data() is now case insensitive. In a future update, all sensor names throughout all
  functions will be made case insensitive.
• When using add_before = TRUE, link() no longer adds an extra measurement if the first
  measurement in the interval equals the start time of the interval exactly.
• get_data() now allows multiple participant_ids to be used.
• external_time has been added as an argument to link_db(), to be able to specify the time
  column in external_data in accordance with the change in link() above.

Bugfixes

• link() now correctly handles natural joins (when by = NULL) and cross joins (when
  by = character()).
• The column original_time was not added for any other nested data row except the first one,
  if add_before or add_after was true.
• link() no longer suffers from future's max object restriction (500MB by default).
• When x and y use different time zones in link() and add_before = TRUE, link() now
  correctly leaves all time zones equal to the input.
• link() incorrectly assigned the time zone of x to the nested data of y, if add_before or
  add_after was true. This is now changed to the time zone of y, to ensure consistency. Note that
  if the time zones of x and y are different, matching will be correct but the nested data may
  seem off as it will keep y's input time zone.

mpathsenser 1.1.2

Major changes

• link() gained 3 new arguments:
  • time: The name of the column containing the timestamps in x.
  • end_time: Optionally, the name of the column containing the end time in x.
  • y_time: The name of the column containing the timestamps in y.
  • name: The name of the nested y data, defaulting to "data".
    Using end_time, it is now possible to specify custom time intervals instead of only fixed
    intervals through offset_before or offset_after. Note that these two functionality cannot
    be specified at the same time.
• time and y_time in link() must now be explicitly named, though for the time being default
  to 'time' with a warning.
• Added continue argument to add_gaps() that controls whether the last measurement(s) should be
  continued after a gap.
• link_db() is now soft deprecated as it provides only marginal added functionality compared to
  link().
• decrypt_gps() now takes a vector of encrypted GPS coordinates instead of a whole data frame
  with fixed variables names (latitude and longitude). This allows more flexibility in its use.
  Also, parallelisation has been added similar to other functions in this package (i.e. by setting
  a future plan, e.g.future::plan("multisession")).

Deprecations

The following functions are now made defunctional and internal:

• activity_duration()
• app_usage()
• n_screen_on()
• n_screen_unlocks()
• screen_duration(),
• step_count()

These functions delivered incorrect output and only allowed summaries by a fixed time frame, e.g.
by hour or day. These functions will be reimplemented (some with a different name) in mpathsenser
2.0.0.

Minor changes

• When add_before or add_after is TRUE in link(), no extra row is added if there already is
  a row with a timestamp exactly equal to the start of the interval (for add_before = TRUE) or to
  the end of the interval ⁠(add_after = TRUE).
• moving_average() now allows a lazy tibble to allow further computations in-database after
  having called moving_average().
• identify_gaps() is now slightly more efficient.
• get_data() is now case insensitive. In a future update, all sensor names throughout all
  functions will be made case insensitive.
• When using add_before = TRUE, link() no longer adds an extra measurement if the first
  measurement in the interval equals the start time of the interval exactly.
• get_data() now allows multiple participant_ids to be used.
• external_time has been added as an argument to link_db(), to be able to specify the time
  column in external_data in accordance with the change in link() above.

Bugfixes

• link() now correctly handles natural joins (when by = NULL) and cross joins (when
  by = character()).
• The column original_time was not added for any other nested data row except the first one,
  if add_before or add_after was true.
• link() no longer suffers from future's max object restriction (500MB by default).
• When x and y use different time zones in link() and add_before = TRUE, link() now
  correctly leaves all time zones equal to the input.
• link() incorrectly assigned the time zone of x to the nested data of y, if add_before or
  add_after was true. This is now changed to the time zone of y, to ensure consistency. Note that
  if the time zones of x and y are different, matching will be correct but the nested data may
  seem off as it will keep y's input time zone.

mpathsenser 1.1.1

Major changes

• identify_gaps() now allows multiple sensors to be used. This is particularly useful when there
  are no sensors with high frequency sampling (like accelerometer and gyroscope) or to ensure there
  can be no measurements within the gaps from any sensor.
• Changed the arguments names of copy_db() from_db and to_db to source_db and target_db
  respectively.
• Set activity_duration(), screen_duration(), n_screen_on(), n_screen_unlocks(), and
  step_count() to internal until it is clear how these functions should behave and, more
  importantly, what their output should be.
• Reworked moving_average() to work correctly on multiple participants.

Deprecations

• Deprecated functionality for on-the-fly database creation in several functions. This disentangles
  the functionalities of create_db() and the other functions, where the latter implicitly depended
  on the former. The following arguments are thereby rendered disabled:
  • dbname and overwrite_db arguments in import()
  • path and db_name in copy_db()
• Deprecated the parallel argument in several functions. If you wish to process in parallel, you
  must now specify this beforehand using a future plan, e.g.
  future::plan("multisession"). As a consequence, the package future is no longer a dependency
  (but furrr is).
• Deprecated the plot argument in coverage. To plot a coverage chart, you can now use the
  default plot() function with the output from coverage.

Minor changes

• All functions gained basic argument checking, ensuring that at least the proper type has been
  input.
• The package now provides more nicely formatted errors, warnings, and messages through
  rlang::abort, rlang::warn, and rlang::inform.
• Partially rewrote import() to be more manageable in code. As a consequence, the dependency on
  rjson and dbx can be dropped in favour of jsonlite and native SQL.
• Added lifecycle as a dependency for deprecating arguments.
• Added a warning section in identify_gaps() and friends to inform the user of a possible
  inconsistency when identifying gaps.
• Switched identify_gaps() from using the lag of each measurements towards using the lead. This
  makes no difference in the output but is a little easier to read.

Bug fixes

• Fixed a note when first running link() or link_gaps() in a session, stating that using
  external vectors dplyr::select() is ambiguous.
• bin_data() now correctly includes measurements in bins that do not have a stop time. This was in
  particular a problem with the last measurement of a series.
• Fixed a non-working example in bin_data().
• Fixed a bug in add_gaps() where multiple gaps in succession (i.e. without other data in between)
  were incorrectly handled.
• Fixed app_category() not being able to find the exact app name in the search results, thereby
  defaulting to the nth result (default 1).

mpathsenser 1.1.0

Major changes

• Added several functions:
  • link_gaps: For linking gap data to other data, i.e. how many gaps occur within an interval.
  • add_gaps: To interleave gaps with other data.
  • bin_data: To subdivide data into bins, e.g. all measurements within an hour or day.
• Added lifecycle badge to signal the state of functions.
• link has been revised and expanded:
  • Replaced offset with offset_before and offset_after, allowing both to be specified at the
    same time (#3).
  • Added new add_before and add_after argument to allow the last row before the measurement
    and first row after the measurement respectively to be added to the data.
  • Added a new split argument, allowing computation to be split among many parts thereby
    lowering computational burden.
• app_category is now case insensitive and gained the new argument "exact" to be able to match the
  package name exactly based on a partial match.
• Added a (start of a) vignette to further highlight the package use.

Minor changes

• Changed get_activity to activity_duration.
• Changed link2 to link_db.

Bug fixes

• Fixed issue where link runs out of memory when there are too many matches (#2). link is now
  much more memory efficient and slightly faster.
• Fixed issue in get_data which allowed multiple sensors to be requested from one function call,
  sometimes leading to crashes (#4).
• Fixed issue in link where column original_time is missing if no records before or after the
  interval are found (#6).
• Fixed a bug in import where sensor data not present in first file of the batch are dropped for the
  other files well.
• Fixed app_category to work with the updated Google Play website.

mpathsenser 1.0.3

• Fix final tests not yet using TMPDIR
• mpathsenser now passes on all platforms on CRAN

mpathsenser 1.0.2

• Changed some unit tests to use TMPDIR

mpathsenser 1.0.0

• Initial release on CRAN
• Changed the name to mpathsenser