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Date format recognition improved for Actigraph csv files
g.inspectfile now also functional with cwa data
option added to enforce dynamic range with argument dynrange
vignette expanded
vignette expanded
Bugs fixes in relation to new cwa-read functionality c++ routine registration
Documentation added for all underlying functions
vignette added
Bugs fixes in relation to new cwa-read functionality
Bugs fixes in correct number of days recognition in part5
Removed teLindert2013 metric, because it was not used and not verified
Split g.getmeta function into multiple smaller functions
Added IS and IV variables to g.analyse (still in explorative version)
bug fixed related to wav file read errors
function g.cwaread added (credits to E. Mirkes) for reading Axivity .cwa-format data. g.shellGGIR will automatically use this function when input data has .cwa extension
bug fixed related to for GENEactiv starttime recognition which was introduced in version 1.2-11
g.part5 documentation added on its output
bug fixed in functionlity to process only specific days in measurement (credits to J Heywood)
bug fixed in midnight recognition in g.part5
improvement to handling of measurements that start a few minutes before midnight (credits to E Mirkes)
bug fixed related processing files shorter than 1 day, introduced in previous version
documentationa added for Axivity wav-format data
start made with implementing code testing functionality using testthat and covr
documentation improved for argument def.noc.sleep in function g.part4
g.part5 added. g.part5 merges the output from the first four parts
Functionality added to read Axivity wav-format files with acceleration in first three channels. No documentation added yet until I have more confirmation that it works well
Bug fixed related to MVPA variable. The bug was a result of the updates in version 1.2-10
Changed function argument 'mvpa.2014' into 'bout.metric' across the package in preparation for a central defintion of bouts for future GGIR version which will not only provide bout calculations for MVPA but also for inactivity. Further, I added function g.getbout to improve transparency about the bout calculations
Updated documentation for function g.analyse to clarify different bout metric definitions
Improvements to the functionality to only process specific days from a long accelerometer file using the argument selectdaysfile
Timestamps are now in ISO 8601 format. I have updated the code such that it can still handle old timestamp format, but newly processed files will produce timestamps in the ISO 8601 format. The practical difference is that it will include a numeric timezone indicator.
Bugs fixed in data selection in g.getmeta function. In the old code it tended to drop the last 30-45 minutes of a file.
Added more optional features to be generated by g.getmeta, including rolling medians of the acceleration signals.
Updated documentation for function g.analyse to clarify different mvpa bout definitions
mvpa.2014 = TRUE turned back on again (was disable in last version)
mvpa.2014 TRUE/FALSE was swapped, FALSE is now the default
mvpa.2014 = TRUE disabled
Modified warning message in relation to the change in MVPA bout defintion
Accelerometer non-wear time is now also reported in the output of part 4
Part 1 is now able to only process specific days of a measurement via argument selectdaysfile. This is useful when measurement lasts for a week and the participant is instructed to only wear the accelerometer on one or two specific days.
Argument mvpa.2014 and closedbout added to function g.analyse. The calculation of MVPA (moderate and vigorous physical activity) has been available since 2014. This calculation has been improved, but the user has the option to continue using the old calculation.
Bug fixed in the loading of data files with (very) large amounts of data
Bug fixed in starttime allocation for measurements starting in the 15 minutes before midnight
Literature reference for sleep detection updated
Argument backup.cal.coef now with improved feedback if something goes wrong
Report generation for part 4 much faster now
Bug fixed in part 4 in assignment of dayname when a person sleeps during the day
g.shell.GGIR now capable of handling minimal input argument specifications
Console output from part 3 and 4 more compact now
Package expanded with functions for detecting sleep (g.part3 and g.part4)
Additional bugs fixs related to dealing with csv-format data from the Actigraph accelerometer brand
g.part2 now also stores its output as milestone data just like g.part1. This to facilitate parallel processing of large amounts of data files on clusters.
The orginal report generation functionality in g.part2 has now been moved to shell function g.shell.GGIR because part3, 4 and 5 which are scheduled for later this year will combine milestone data from multiple analysis parts. It therefore, is more logical to control all report generation from the top level in the function hierarchy (g.shell.GGIR).
g.part1 now comes with the option to provide backup calibration coefficients in case auto-calibration is unsuccessful. This function is primarily designed for studies with short lasting experiments.
g.part2 now has the option to export epoch values to a csv-file. Note that these same epoch values are also stored in the .RData milestone file from part2. The export option is mainly to ease access to epoch level data outside the R environment.
g.shell.GGIR now offers the option to overwrite previously generated milestone data with variable 'overwrite'. The default setting (FALSE) is still to skip previously analysed files, which is intended to avoid having to do the same analyses twice after an interruption. However, overwriting previously generated milestone data could be useful when modifications are being made to the input arguments.
g.shell.GGIR now offers the option to record the folderstructure in which an accelerometer file is located, especially useful for studies where accelerometer files are stored hierarchally in line with the study design.
Additional bugs fixs related to recognising data format in Actigraph data
Angle variables are now extracted based on 5 second rolling median as opposed to 501 sample rolling median
Package expanded with functions: g.part1, g.part2, and g.shell.GGIR. These shell functions should help movement scientists to utilize the package without too much prior knowledge about R
Additional bugs fixs related to recognising data format in Actigraph data
Package expanded with axis angle metrics
Package expanded with metric for replicating teLindert2013 counts, see g.getmeta
Package expanded with metric ENMOa, see function tutorial g.getmeta
Bug fixed related to recognising date format in csv-file header from Actigraph accelerometer brand
Literature reference added to function g.calibrate
function g.getmeta expanded with argument 'chunksize'
Implemented functionality for csv-fromat data from GENEActiv and Actigraph. It seems to work for the test files I have, more testing may be necessary
Cleaned up some of the NaN and NA output to aim for consistent annotation of missing data
Fixed bug in modified g.analyse in version 1.0-2
Expanded g.analyse with estimates of time spent in moderate and vigorous activity (a construct popular among physical activity researchers)
Re-named a number of variables in the output from g.analyse to be more friendly for re-use in stata or sas. The majority of variable names are now shorter and do not include spaces, dots or commas
Fixed Linux-Windows sensitivty in g.getmeta. Certain damaged files can only be read with mmap.load set to FALSE in package GENEAread. Function g.getmeta in GGIR catches this problem and turns mmap.load to FALSE if necessary. This catch worked well under Linux, but not for R in Windows. I have now fixed this
Added examples
Expanded documentation for function g.analyse
Fixed bug in extraction of starttime that caused the starttime to be truncated to 00:00:00 in a fraction of measurements.
Fixed bug in extract of temperature in function g.calibrate
Deleted three explorative variables that were only extracted in g.analyse if argument doangle was set to TRUE in function g.getmeta. A number of bugs and the lack of referable journal publications made me decide to remove these variables while working on them. I intend on re-releasing these variables during the course of 2014. Please contact me if this causes you problems
This was the first version