Error in part 5, Non-numeric argument for mathematical function

[abbyyty]

I ma using the epoch count file converted from 60sec.agd file of actigraph (GT9X).
the code is as follow:

GGIR(datadir=datadir,
outputdir=outputdir,
overwrite=TRUE,
do.imp=TRUE,
idolc=2,
print.filename=TRUE,
storefolderstructure=TRUE,
mode=1:5,
minimumFileSizeMB = 0.1,
dataFormat = "actigraph_csv",
extEpochData_timeformat = "%d/%m/%Y %H:%M:%S",
#--------------
#Read csv
#-------------
rmc.nrow = Inf,
rmc.skip = 0,
rmc.dec = ".",
rmc.firstrow.acc = 11,
rmc.col.acc = 1:3,
rmc.unit.acc = "mg",
rmc.unit.time = "POSIX",
rmc.format.time = "%d/%m/%Y %H:%M:%S",
desiredtz = "Hongkong",
rmc.sf = 60,
rmc.noise = 13,
#--------------
#Part 1
#--------------
windowsizes = c(60,900,3600),
do.cal=TRUE,
do.anglez=TRUE,
do.neishabouricounts = TRUE,
acc.metric = c("NeishabouriCount_x"),
printsummary=TRUE,
#--------------
#Part 2
#--------------
data_masking_strategy = 1,
ndayswindow = 7,
hrs.del.start = 1,
hrs.del.end = 1,
maxdur = 9,
includedaycrit = 20,
M5L5res = 10,
winhr = c(5,10),
qlevels = c(0.1,0.25,0.5,0.75,0.9),
qwindow = c(0,24),
ilevels = c(seq(0,450,50),8000),
mvpathreshold = c(100),
#------------------------------
# Part 3 parameters:
#------------------------------
timethreshold = c(5,10),
anglethreshold = 5,
ignorenonwear = TRUE,
#------------------------------
# Part 4 parameters:
#------------------------------
excludefirstlast = FALSE,
HASPT.algo = "HDCZA",
includenightcrit = 16,
def.noc.sleep = c(1),
outliers.only = FALSE,#so all nights will be printed
relyonguider = FALSE,
do.visual = TRUE,
#-----------------------------
# Part 5 parameters:
#------------------------------
# Key functions: Merging physical activity with sleep analyses
includedaycrit.part5 = 2/3, #how many waking hour is needed for analysis
threshold.lig = 40,
threshold.mod = 100,
threshold.vig = 400,
boutcriter.in = 0.9,
boutcriter.lig = 0.8,
boutcriter.mvpa = 0.8,
boutdur.in = c(10,20,30), #for inactivity
boutdur.lig = c(1,5,10),
boutdur.mvpa = c(1,5,10),
timewindow = c("MM"),
#---------------------------------
# Report generation
#------------------------------
do.report = c(2,4,5)
)

got an error message from part 5:
[1] "Non-numeric argument for mathematical function"
$call
abs(diff(ts$angle[redo1:redo2]))

the attached screenshot is the first few rows of the csv i used, from the first to forth column they are axis 1 (y), axis 2(x), axis 3(z) and vm.

Your help will be greatly appreciated!

Thanks,
Abby

[abbyyty]

Besides, in the visulization report, there is an extremely long sleep duration for all days. is this issue caused by the "anglethreshold =5"? as I am inputting the epoch file but not the raw data?

here is the attached screenshot of the report.
thanks!
abby

[vincentvanhees]

Hi Abby, your question overlaps with https://groups.google.com/g/RpackageGGIR/c/cAQ7QzwvLJA/m/j-GHdMLcBAAJ
please try not to double post questions. I will try to keep an eye on both the google group and this discussion page. As I explained in the google group, please share Rscript and example data to allow me to reproduce the issue.

[vincentvanhees]

Closing because resolved in Google group (see link above).