GENEAcore 1.3.0

New features

Added mean x, y, z jerk as optional measures out of geneacore_part3().
apply_updown() has been deprecated. Use new function call apply_elevation().
Arm rotation in radians replaces arm rotation in degrees in epochs and events outputs.
Added daily number of bouts and events to daily summary measures.
Updated rest and non-wear output measures. See Breaking Changes.
Daily wear and non-wear durations are now reported for all days in daily measures summary.
Millisecond precision is preserved in the MPI (ConfigTimeISO and ExtractTimeISO) where available.
Bin file free text fields containing non-ASCII characters are now handled more robustly using UTF-8 conversion where possible.
Step statistics for epochs or events with cadence below 20 steps/min or above 175 steps/min are set to 0.
Updated slow and fast cadence limits to 80 steps/min.
SDOverDuration is no longer written to bouts output.
Rest intervals can overlap an analysis day boundary.
Two distinct sleep thresholds are applied for sleep bout classification, one for inside the rest interval and one for outside the rest interval.
Minimum duration for a valid day is increased from 5 seconds to 60 seconds.

During rest interval detection, rest intervals incorrectly overlapped non-wear periods, now fixed.
During rest interval detection and nonwear rest coverage, still bouts that extended over the end of a day was ignored, now fixed.
Older versions of R now correctly specify the POSIXct origin 1970-01-01 during timestamp conversion.
Files containing fewer pages than expected no longer terminate processing. The recorded page count is automatically corrected and processing continues.
Added support for GENEAsleep, GENEAir and GENEAction device types.
Fixed MPI_summary() so that NumberDays is correctly reported when available.
CSV output now writes missing values as blank cells instead of NA.
Temporary suppression of scientific notation prevents integer timestamps from being written in exponential format.
Days containing insufficient data for changepoint analysis are now skipped rather than producing an error.
Files with an invalid configuration time (0001-01-01 00:00:00) are now identified as invalid and generate a warning.
Timestamp alignment issues affecting non-wear and rest coverage in 85.7 Hz files now fixed.

geneacore() main wrapper is restructured to a 4-part analysis architecture
geneacore() wrapper optional parameters are passed to the function as a configurable controls list
Integration of new behavioural bout functions to be run with events outputs only in geneabout()
Produce daily aggregate activity and sleep measures with option to include participant information
Function to generate COEL Behavioural Atoms JSON

New measurement device ‘GENEActiv 1.3’ added to apply_calibration()
Non-contiguous files will be read and aggregated as normal with a new last timestamp
Output folders and MPI files are not created for non-valid GENEActiv bin files

Improved handling of invalid inputs: folders without .bin files or single files without the .bin suffix

Added overloads for get_UniqueBinFileIdentifier() to enable it to also read a filename or a directory path

The StepDiff measure is now included in outputs as default when output_steps = TRUE
Create a bin file summary from geneacore() by passing parameter summary = TRUE
geneacore() can now take either a path to a directory of bin files or a path to a single bin file
MPI file_history now records parameters passed during function calls
MPI now records the GENEAcore package version used during execution
A new MPI is created if package version is not listed in the existing MPI
New DateTimeUTC column has been added to the events and epochs CSV files
Button press (event marker) timestamps are now recorded in the MPI
A new MPI is created when a version number does

geneacore() steps error resolved when there are not enough events in the day
geneacore() events are created when a day has only a single transition (when non-wear spans across multiple days)

detect_nonmovement() uses a new sd_threshold value
detect_transitions() uses new default changepoint penalty values
apply_all() function applies AGSA, ENMO, Elevation and Radians measures in a single function
detect_transitions() runs changepoint only if a different 24-hour cut time is set
sample_binfile() has new parameter option to allow raw sample RDS to be saved
detect_transitions() removes short changeover transition between days
Partial epochs are removed from aggregation output
Aggregated events and epochs output have added day index column and AGSA.sd and ENMO.sd columns have been removed
Standardised format of start time and duration for still bouts and non-wear bouts
Certainty field removed from non-wear bouts
MPI reports first and last timestamps as integer values

sample_binfile() outputs an improved message with time zone offset when reading subset of file

Updated naming conventions for MPI outputs, parameters and functions, see breaking-changes.html

Released to CRAN