Natal

• Now R version 4.0 compatible
• Part 1 Clipping detection expanded: If any value in block more than 150 percent
  dynamic range then ignore entire block.
• Part 2 report now able to handle changing variable count due to missing data
• Part 2 L5M5 better able to handle small qwindow intervals
• Part 3 HDCZA algorithm expanded to be able to detect daysleepers
• Part 3 various improvements to qc plots.
• Part 5 now also stores full and cleaned output
• Part 5 now better handles missing days in part 4 output.
• Part 5 behavioral class SIB removed from daytime
• Part 5 time series export more user-friendly.
• Part 5 function code split up in 7 new functions.
• Part 4 + 5 argument data_cleaning_file added.
• Part 4 + 5 output variable names improved and documented in vignette
• Numunpack function moved back to c++
• Various updates to visualreport (plot5 function)
• External function embedding feature added
• We now consistently refer to ID (not id) and calendar_date, spelling was
  inconsistent.
• Vignette now has documentation on sleep and time-use analysis.

ElPasado

• Metric ENMOa now facilitated for MVPA calculation
• Bug fixed with part4 daysleeper handling
• Part5 WW window calculation improved, first day now uses sleeplog or HDCZA algorithm estimate, and last day is ignored if no sleep estimates are available. This also affects csv exports by argument save_ms5rawlevels.
• Added explanation to vignette on how to use published cut-points.
• Axivity AX6 (acc + gyro) in cwa format now supported for file reading, actually using the gyro data for feature calculation is future work.
• In the mean time, gyro signal will be ignored by the rest of GGIR.
• Axivity AX3 acc data in cwa format can now also be read if dynamic range is not 8g. Previously this was not possible.
• Fixed bug related to visual report generation when qwindow is set to non-default value.
• Added way to handle Actigraph files which start with several days of zeros which complicates the auto-calibration.
• Default for desiredtz to timezone of machine.

ElCrispin

• Fixed bug that emerged in previous version with GENEActiv .bin data not being processed by g.getmeta for some files.
• read.myacc.csv is now able to resample data with irregular sample rates and handle timestamps in character format.
• function resample can now handle any matrix size, previous only 3 columns.
• Fixed bug when using multiple non-angle metrics in part1 and trying to calculate
  1to6am average metric value in part 2.
• Expanded Actigraph date format recognition ability.
• visualisationreport (function g.plot5) enhanced with colour coding for activity
  classes.
• Fixed bug in sleep period time recognition for first day of measurement.

Pallague

• Fixed functionality to supply calibration coefficients file to backup.cal.coef.
• Fixed OSx flavor not being released on CRAN in previous version.
• Upgrades to foreach loop to ease package maintenance
• Documentation part4 expanded to clarify difference between full and cleaned report.
• Non-wear detection now possible at 1 minute resolution, previously 5 minute.
• Function read.myacc.csv now able to utilize 3rd party wear detection.

ElCedral

• Device serial number recognition in Axivity cwa files fixed
• New GitHub release, because previous version did not install.

Arumaque

• Fixed bug introduced in version 1.10-1 in the conversion from numeric to character sleep times
• Dependencies of dependencies removed from the DESCRIPTION file
• Fixed 1to6am variables, which was wrong in version 1.10-1
• Added functionality to handle accelerometer data from any accelerometer brand stored in csv files via read.myacc.csv. Pass on the arguments of this function to g.shell.GGIR to use this functionality.
• Added reference to new GGIR paper to the documentation

Pendare

• Configuration file option now added to g.shell.GGIR and documented in vignette

• metric lfen added (low-pass filter signels followed by Euclidean norm)

• issues fixed with passing on of hb and lb arguments

• argument backup.cal.coef can now also handle data_quality_reports.csv files

• part 1 now automatically uses previously generated calibration coefficients if the datafile was previously processed, see documentation g.part1 for further details.

• Enabled multiple values for argument winhr, by which part2 can now calculated for example L3M3, L5M5, L6M6, L10M10 all in one go. Further, option added (qM5L5) to extract percentiles (quantiles) from the value distribution corresponding to these windows.

• Moved IVIS calculation to seperate function, and split up function g.analyse.

• Now possible to specify time windows that need to be ignored for imputation, see TimeSegments2ZeroFile.

• Default value for argument mode changed from mode = c(1,2) to mode = 1:5, to perform all the parts.

• Checks added for user write and read access permission, and subsequent warnings given..

• Parts 1, 2, 3, and 5 can now use multi CPU cores which speeds up the processing.

• Argument minimumFileSizeMB added to g.part1 to aid filtering out too small data files.

Jidina

• Added functionality to work with studies where accelerometer is configured in one timezone and used in other timezone. Only functional for AX3 cwa data at the moment. See argument 'configtz'.
• Sleep estimation is now skipped if a day only has one sustained inactivity bout
• Arguments ignorenonwear default value changed to TRUE and def.noc.sleep default changed to 1 in line with literature.
• Fixed AX3 csv format starttimestamp recognition

Extra clarification:
Argument 'ignorenonwear' is now set to TRUE by default. Previously, I set it to TRUE in my own work and also in the examples I gave in the vignette. However, if ignorenonwear was not provided by the user then GGIR used FALSE as a default. What does that mean: If it is TRUE then GGIR will not count non-wear periods towards sleep. The only scenario I can think of where you may want to set this to FALSE is if you know that the accelerometer was not worn during the night and if you want to force the analyses to treat all the non-wear time as sleep, or if you strongly believe that monitor non-wear always coincides with sleep.

Further, I have now made sure that argument 'def.noc.sleep' is set by default to use the HDCZA algorithm I added last year (https://www.nature.com/articles/s41598-018-31266-z). In the example function calls in the vignette I already used it this way, but within GGIR it was not the default. This means that if you now use a sleeplog, GGIR will use the sleeplog first, if sleeplog is missing it will use the HDCZA algorithm, if the HDCZA algorithm for whatever reason fails to provide estimates then it used the L5 +/- 6 algorithm.

Curacautin

• Fixed part5 output midnight-midnight window when monitor not worn during first days.
• Fixed assumption that when using argument idloc=2 the ID has a letter at the end, and automatically
  removes the last value in the index. The code now first checks for this assumption.
• Update vignette with a more elaborate explanation of the optional arguments to g.shell.GGIR.

Ayaviri

• functionality storefilestructure should now store filestructure in output of part 2, 4 and 5.
• filelocationkey.csv that was previously written by storefilestructure was redundant and removed.
• sessioninfo storage improved.
• Fixed bug that caused part2 to provide incorrect window specific estimates on first day.
  of measurement if day is incomplete (not 23, 24 or 25 hours).
• Calibrate function now better able to handle files with more than a week of data, where
  auto-calibration struggles to find enough sphere data in the first week.