Error in Report part 5

[david levitan]

Hello everyone,

I'm currently using GGIR to process raw data extracted from a Garmin Vivosmart 5 through Labfront. However, I'm encountering an error in Part 5 of the report generation.

Here is the code I am using:

library(GGIR)

# Define the file paths
datadir <- "C:/garmin test/David/test2/"
outputdir <- "C:/garmin test/1/"

# Ensure the output directory exists
if (!dir.exists(outputdir)) {
  dir.create(outputdir, recursive = TRUE)
}

# Ensure the meta directory exists
meta_dir <- file.path(outputdir, "meta")
if (!dir.exists(meta_dir)) {
  dir.create(meta_dir, recursive = TRUE)
}

# Run GGIR with correct parameters
GGIR(
  mode = 1:5,
  datadir = datadir,
  outputdir = outputdir,
  f0 = 1,
  f1 = 9,
  do.imp = TRUE,
  do.enmo = TRUE,
  do.anglez = TRUE,
  studyname = "Garmin",
  minimumFileSizeMB = 0,
  #=====================
  # read.myacc.csv arguments
  #=====================
  rmc.nrow = Inf,
  rmc.dec = ".",
  rmc.firstrow.acc = 11,  # Row where data starts
  rmc.col.acc = 2:4,  # Columns for accX, accY, accZ
  rmc.col.time = 1,  # Column for unixTimestampInMs
  rmc.unit.acc = "g",  # Adjust to match your data
  rmc.unit.time = "UNIXsec",
  desiredtz = "Asia/Jerusalem",
  rmc.sf = 25
)

The output and error

hecking that user has write access permission for directory specified by argument outputdir: Yes GGIR version: 3.1.1 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 Busy processing ... see C:/garmin test/1//output_test2/meta/basic for progress ________________________________________________________________________________________________ Part 2 Busy processing ... see C:/garmin test/1//output_test2/meta/ms2.out for progress ________________________________________________________________________________________________ Part 3 Busy processing ... see C:/garmin test/1//output_test2/meta/ms3.out for progress ________________________________________________________________________________________________ Part 4 1 2 3 4 5 6 ________________________________________________________________________________________________ Part 5 Busy processing ... see C:/garmin test/1//output_test2/meta/ms5.out for progress ________________________________________________________________________________________________ Report part 2 1File aaa1.csv.RData not available in part 2 2 3 4 5 6 7 8 9 ________________________________________________________________________________________________ Report part 4 loading all the milestone data from part 4 this can take a few minutes report not stored, because no results available ________________________________________________________________________________________________ Report part 5 loading all the milestone data from part 5 this can take a few minutes generating csv report for every parameter configurations... MM-40-100-400-T5A5Error in if (input == "" || length(grep("\\n|\\r", input))) { : missing value where TRUE/FALSE needed In addition: Warning message: No summary data available to be stored in csv-reports

Any insights or suggestions on how to resolve this issue would be greatly appreciated.

Thank you,
David Levitan 

[Vincent van Hees]

Hello David,

When I google the error message it brings me to the fread function in the data.table package (https://github.com/cran/data.table/blob/master/R/fread.R#L55-L56). This indicates that there is no data to be stored. I see you are trying to force GGIR to even consider files with 0MB with parameter minimumFileSizeMB = 0. So, that could be the problem: GGIR is not designed for handling recordings that have only a few minutes or no data. If you have a series of shorter recordings that together could form a continuous multi-day recording then consider parameter 'maxRecordingInterval' which allows you to append those recordings. Otherwise it seems best to skip the very short recordings.

Best,

Vincent

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