Day Segment Analysis - Error: undefined columns selected
Kieu Pham
Hi all,
I have issues processing accelerometer data for a participant using the Day Segment Analysis approach in GGIR (v3.0-5).
The data was collected using GENEActiv wrist-worn accelerometers (100Hz) under natural conditions, where participants recorded their location and corresponding time per day. The purpose of using the Day Segment Analysis approach was to include only days of interest. This is the shell code:
GGIR(
#======================
#GENERAL PARAMS
#======================
mode = mode,
datadir = datadir,
outputdir = outputdir,
f0 = f0,
f1 = f1,
overwrite = TRUE,
do.imp = TRUE,
idloc = 2,
print.filename = TRUE,
storefolderstructure = FALSE,
#======================
# PART 1
#======================
windowsizes = c(5, 900, 3600),
do.cal = TRUE,
do.enmo = TRUE,
do.anglex = TRUE,
chunksize = 0.5,
printsummary = TRUE,
#=====================
#PART 2
#=====================
data_masking_strategy = 1,
hrs.del.start = 0,
hrs.del.end = 0,
maxdur = 0,
includedaycrit = 16,
M5L5res = 10,
winhr = 5,
qlevels = NULL,
qwindow = qwindow, #file
directory to the activity diary in .csv format
qwindow_dateformat = qwindow_dateformat,
desiredtz = "Australia/Brisbane",
ilevels = NULL,
mvpathreshold = 100.6,
#=====================
#PART 3
#=====================
timethreshold = 10,
anglethreshold = 5,
ignorenonwear = FALSE,
#====================
#PART 4
#====================
includenightcrit = 16,
def.noc.sleep = 1,
loglocation = NULL,
outliers.only = FALSE,
criterror = 0,
relyonguider = FALSE,
do.visual = TRUE,
#===================
#PART 5
#===================
threshold.lig = 45.8,
threshold.mod = 93.2,
threshold.vig = 418.3,
excludefirstlast = FALSE,
boutcriter = 0.8,
boutcriter.in = 0.9,
boutcriter.lig = 0.8,
boutcriter.mvpa = 0.8,
boutdur.in = c(10,20,30),
boutdur.lig = c(1, 5, 10),
boutdur.mvpa = c(1, 5, 10),
timewindow = c("WW"),
#=====================
#REPORT
#=====================
do.report=c(2,5),
visualreport = TRUE,
dofirstpage = TRUE,
viewingwindow = 1
)
The code works because I successfully processed a different participant. The difference between the two are their activities. The participant that I have issues processing the accelerometer data, had additional days of recording that are not of interest, which I excluded in the activity log. An example of their activity log specified via the `qwindow()`function:
However, I receive the following error:
In the output folder, it does not contain any files relating to Part 5. In part2_daysummary.csv, there aren’t metrics computed in the file for the days of interest (highlighted in yellow below), but only the number of hours per segment:
This is the quality plot:
If anyone can point out the issue or need more details please let me know!
Regards,
Kieu
Kieu Pham
Lena Kushleyeva
Kieu Pham
Checking that user has write access permission for directory specified by argument outputdir: Yes GGIR version: 3.0.5 Do not forget to cite GGIR in your publications via a version number and Migueles et al. 2019 JMPB. doi: 10.1123/jmpb.2018-0063. See also: https://cran.r-project.org/package=GGIR/vignettes/GGIR.html#citing-ggir To make your research reproducible and interpretable always report: (1) Accelerometer brand and product name (2) How you configured the accelerometer (3) Study protocol and wear instructions given to the participants (4) GGIR version (5) How GGIR was used: Share the config.csv file or your R script. (6) How you post-processed / cleaned GGIR output (7) How reported outcomes relate to the specific variable names in GGIR _____________________________________________________________________________________________________________________________ Part 1 Checking that user has read access permission for all files in data directory: Yes 1 File name: stuart_left wrist_066987_2023-12-15 10-33-41.bin P1 file 1 Investigate calibration of the sensors with function g.calibrate: Loading chunk: 1 2 3 4 5 6 7 8 9 10 11 12 13 Summary of autocalibration procedure: Status: recalibration done, no problems detected Calibration error (g) before: 0.00744 Calibration error (g) after: 0.00262 Offset correction x: -0.000848898932656745 Offset correction y: -0.00333971016037461 Offset correction z: -0.00269655031067978 Scale correction x: 0.998516101046556 Scale correction y: 0.999426045898622 Scale correction z: 0.97109432599226 Number of hours used: 78 Number of 10 second windows around the sphere: 16889 Temperature used (if available): TRUE Temperature offset (if temperature is available) x: -0.000651854643415637 Temperature offset (if temperature is available) y: -0.00202529824092677 Temperature offset (if temperature is available) z: 0.000734026697565913 Extract signal features (metrics) with the g.getmeta function: Loading chunk: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 Save .RData-file with: calibration report, file inspection report and all signal features... _____________________________________________________________________________________________________________________________ Part 2 1 _____________________________________________________________________________________________________________________________ Part 3 1 _____________________________________________________________________________________________________________________________ Part 4 1 _____________________________________________________________________________________________________________________________ Part 5 1 _____________________________________________________________________________________________________________________________ Report part 2 1Error in `[.data.frame`(df, 16:ncol(df)) : undefined columns selected
Lena Kushleyeva
Kieu Pham
Vincent van Hees
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