Skipping files that are too small for analysis or list object cannot be coerced to type doble

[Mª Purificación Ballester Navarro]

Hi! TY in advance for the help 

I am trying to analyze a unique .csv file that contains proper code for 8 nights with the following code. Is attached to this message as well. 

GGIR(
  mode=c(1,2,3,4,5),
  datadir="//hersheymed.net/files/psychiatry/Research/Sleep/Faculty/Mendoza/Teaching/Postdoctoral Fellows/Ballester Navarro, Pura/Datasets/PSCC/Test-Data/Data",
  outputdir="//hersheymed.net/files/psychiatry/Research/Sleep/Faculty/Mendoza/Teaching/Postdoctoral Fellows/Ballester Navarro, Pura/Datasets/PSCC/Test-Data/Output",
  do.report=c(2,4,5),
  #=====================
  # read.myacc.csv arguments
  #=====================
  rmc.nrow=Inf, rmc.skip = c(0), rmc.dec=".",
  rmc.firstrow.acc = c(12), rmc.firstrow.header=c(11),
  rmc.header.length = c(9),
  rmc.col.acc = 2:4,
  rmc.col.time=c(),
  rmc.unit.acc = "g",
  rmc.unit.time = "POSIX",
  rmc.format.time = "%H:%M:%OS",
  rmc.bitrate = c(), rmc.dynamic_range = c(),
  rmc.unsignedbit = TRUE,
  rmc.origin = "1970-01-01",
  rmc.desiredtz = NULL,
  rmc.configtz = NULL,
  rmc.sf = c(),
  rmc.headername.sf = c(),
  rmc.headername.sn = c(),
  rmc.headername.recordingid = c(),
  rmc.header.structure = c(),
  rmc.check4timegaps = FALSE,
  rmc.col.wear = c(),
  rmc.doresample = FALSE,
  rmc.scalefactor.acc = 1,
  interpolationType=1,
  PreviousLastValue = c(0, 0, 1),
  PreviousLastTime = NULL,
  desiredtz = "US/Pennsylvania",
  configtz = "US/Pennsylvania",
  header = NULL)

and I am getting the following error message 

Error: No files to analyse. Check that there are accelerometer files in the directory specified with argument datadir In addition: Warning message: Skipping files that are too small for analysis: V2 60secDataTable.csv (configurable with parameter minimumFileSizeMB).

NOTE: File is valid, is in the datadir folder, and is the unique file there.

when I try with this code (see bellow), that contains a chunk of code that actually opens the .csv file, there is also an error message popping up.

GGIR(
  mode=c(1,2,3,4,5),
  datadir="//hersheymed.net/files/psychiatry/Research/Sleep/Faculty/Mendoza/Teaching/Postdoctoral Fellows/Ballester Navarro, Pura/Datasets/PSCC/Test-Data/Data",
  outputdir="//hersheymed.net/files/psychiatry/Research/Sleep/Faculty/Mendoza/Teaching/Postdoctoral Fellows/Ballester Navarro, Pura/Datasets/PSCC/Test-Data/Output",
  do.report=c(2,4,5), parametersVignette (minimumFileSizeMB=0.01),
read.myacc.csv(rmc.file=c("//hersheymed.net/files/psychiatry/Research/Sleep/Faculty/Mendoza/Teaching/Postdoctoral Fellows/Ballester Navarro, Pura/Datasets/PSCC/Test-Data/Data/V2 60secDataTable.csv"), rmc.nrow=Inf, rmc.skip = c(0), rmc.dec=".",
               rmc.firstrow.acc = c(12), rmc.firstrow.header=c(11),
               rmc.header.length = c(9),
               rmc.col.acc = 2:4,
               rmc.col.time=c(),
               rmc.unit.acc = "g",
               rmc.unit.time = "POSIX",
               rmc.format.time = "%H:%M:%OS",
               rmc.bitrate = c(), rmc.dynamic_range = c(),
               rmc.unsignedbit = TRUE,
               rmc.origin = "1970-01-01",
               rmc.desiredtz = NULL,
               rmc.configtz = NULL,
               rmc.sf = c(),
               rmc.headername.sf = c(),
               rmc.headername.sn = c(),
               rmc.headername.recordingid = c(),
               rmc.header.structure = c(),
               rmc.check4timegaps = FALSE,
               rmc.col.wear = c(),
               rmc.doresample = FALSE,
               rmc.scalefactor.acc = 1,
               interpolationType=1,
               PreviousLastValue = c(0, 0, 1),
               PreviousLastTime = NULL,
               desiredtz = "US/Pennsylvania",
               configtz = "US/Pennsylvania",
               header = NULL))

Checking that user has write access permission for directory specified by argument outputdir: Yes Error in GGIR(mode = c(1, 2, 3, 4, 5), datadir = "//hersheymed.net/files/psychiatry/Research/Sleep/Faculty/Mendoza/Teaching/Postdoctoral Fellows/Ballester Navarro, Pura/Datasets/PSCC/Test-Data/Data", : 'list' object cannot be coerced to type 'double'

[Lena Kushleyeva]

Hi!

Is there a reason why you are using "parametersVignette (minimumFileSizeMB=0.01)" instead of just setting minimumFileSizeMB?

Also, why did you add a call to read.myacc.csv() there, in the argument list?

try removing both of these things  you added:

parametersVignette (minimumFileSizeMB=0.01),
read.myacc.csv(rmc.file=c("//hersheymed.net/files/psychiatry/Research/Sleep/Faculty/Mendoza/Teaching/Postdoctoral Fellows/Ballester Navarro, Pura/Datasets/PSCC/Test-Data/Data/V2 60secDataTable.csv"),

and instead only add this:

minimumFileSizeMB=0.01,

hope this helps!

-Lena

[Michael Rueschman]

Adding to Lena's comments: It appears you are trying to process an ActiGraph 60-second epoch CSV file (i.e., not raw accelerometry data). Do you have the raw data (e.g., a .gt3x file)? Those are likely easier to get running through GGIR than your 60-second epoch file (observations based on personal experience).

To use the 60-second epoch CSV file you will need to look at additional configuration parameters such as:

data_format = "actigraph_csv"

extEpochData_timeformat = "%m/%d/%Y %H:%M:%S"

(likely others)

References:

• https://cran.r-project.org/web/packages/GGIR/vignettes/GGIRParameters.html
• https://cran.r-project.org/web/packages/GGIR/GGIR.pdf (search "actigraph_csv" to see example code snippets)
  
• https://github.com/wadpac/GGIR/tree/master/inst/testfiles (see ActiGraph CSV files as comparisons to your own files)

Best of luck!