What prameters need to modify in my NHP work?

[wang xc]

Hi, Dear all

      I am using a home made acc device to monitor the no human primate activity and sleep time. 

       The acc device is embeded in a collar.They lived in home cage most of the time, in a animal facility with light  cycle controled ON from 7;00 AM to 7 PM. Some times they go out in the weekday,normally less than 3 hours,,that will make he device lose some data in the day time. 

       

        I know the GGIR is based on human, so based on those diffrences, wht special  parameters i need to make attention in our data with GGIR  package. 

      

[Vincent van Hees]

I have no experience with primate data, but in the basis I do not see why this would require a different approach compared with processing human data. Assuming they have typically one long sleep period per day as humans do (?).

Vincent

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[wang xc]

Hi, Vincent

Thanks for your reply and this R package. I totally agree there is no diffrence on the sleep cycle between human and primate. But as the primate living envirienment is diffrent, their acc will be smaller than human.My question is what vars i need to change compared to human as the criteria and threshold will be diffrent. I only need to know the names  Arguments/parameters, and maybe refer those parameters to the childrens' standards.

By the way i met a Error with the following code when run my .csv file :

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

library(GGIR)
GGIR(datadir   = "F:/Code/accData/",
     outputdir = "F:/Code/saveFiles/",
     mode      = 1:5,
     f1        = 0,
     f0        = 1,
     idloc     = 6,
     #do.enmo   = TRUE,
     
     acc.metric     = "ENMO",
     print.filename = TRUE,
     printsummary   = TRUE,
     do.visual      = TRUE,
     do.parallel    = TRUE,
     do.report      = c(2,4,5,6),
     do.en          = TRUE,
     do.cal         = TRUE,
     visualreport   = TRUE,
     #=====================
     # read.myacc.csv arguments
     #=====================
     rmc.nrow          = Inf,      
     rmc.skip          = 0,
     rmc.dec           = ".",
     rmc.firstrow.acc  = 2,
     rmc.col.acc       = 2:4,
     #rmc.col.temp     = " ",
     rmc.col.time      = 1,
     rmc.unit.acc      = "g",
     rmc.unit.temp     = "C",
     rmc.unit.time     = "POSIX",
     rmc.format.time   = "%Y-%m-%d  %H:%M:%OS",
     rmc.desiredtz     = "Europe/London",
     #desiredtz         = "CST",
     rmc.sf            = 1,
     configtz          = " ",
     rmc.origin        = "1970-01-01",
     rmc.check4timegaps= TRUE,
     rmc.doresample    = TRUE,
     interpolationType = 2,
     frequency_tol   =  0.1,
     hb = 15,
     lb = 0.2,
     #n  = 2,
     
     #=====================
     # Part 2 Physical activity Parameters
     #=====================
     mvpathreshold = c(10,20), ##### care this
     boutcriter    = 0.8,
     boutcriter.in        = 0.9,
     boutcriter.lig       = 0.8,
     boutcriter.mvpa      = 0.8,
     threshold.mod        = c(100),
     threshold.vig        = c(400),
     threshold.lig        = c(40),
     boutdur.in           = c(1,10,30),
     boutdur.lig          = c(1,10),
     boutdur.mvpa         = c(1, 5, 10),
     #=====================
     # Part 3 24/7 Parameters
     #=====================
     
     qwindow            = c(7,11,13,17,19),  
     qlevels            = c(0.1,0.5,0.75),
     IVIS_acc_threshold = 5,##### care this
     #Guider         = " ",
     #=====================
     # Part  Cleaning Parameters
     #=====================
     includedaycrit        = 16,
     data_masking_strategy = 2,
     #hrs.del.start = 0,          
     #hrs.del.end = 0,
     maxdur                = 0,                
     excludefirstlast      = FALSE,
     includenightcrit      = 16,
     includedaycrit.part5  = 2/3,
   
     #=====================
     # Part 4 Sleep Parameters
     #=====================
     anglethreshold        = c(3,5),##### care this
     timethreshold         = 5,
     ignorenonwear         = TRUE,
     HASPT.algo            = "HDCZA",
     HASIB.algo            = "vanHees2015",#报错Loading chunk: 1Error in butter.default(n, Wc, type = c("pass")) :
     #butter: critical frequencies must be in (0 1)
     Sadeh_axis            = "Y",
     #longitudinal_axis     = " ",
     HASPT.ignore.invalid  = FALSE,
     def.noc.sleep        = c(19,7) ,
     sleepwindowType       = "SPT",
     possible_nap_window  = c(11,14),
     possible_nap_dur     = c(20,60),
     HDCZA_threshold      = 0.2,
     #=====================
     #  Output Parameters
     #=====================
     outliers.only         = TRUE,
     criterror             = 3, #Numeric (default = 3). In g.part4: Only used if do.visual = TRUE and
     # outliers.only = TRUE. criterror specifies the number of minimum number of hours difference
     # between sleep log and accelerometer estimate for the night to be included in the visualisation.
     do.sibreport         = FALSE,

     #=====================
     # Part 5
     #=====================
     timewindow     = c("MM")
    )

~~~~~~~~~~~~~~~~~~~~~
Part 4 1Error in g.part4(datadir = datadir, metadatadir = metadatadir, f0 = f0, : cannot find 'defaultGuider'

and warnings:

1-50: In as.POSIXlt.POSIXct(x) : unknown timezone ' '

[wang xc]

for this error   Part 4 1Error in g.part4(datadir = datadir, metadatadir = metadatadir, f0 = f0, : cannot find 'defaultGuider'
I run the part 3, it passed and no errors.

[Vincent van Hees]

Hi,

Yes, that error was recently fixed.

I cannot answer questions about how to configure GGIR as that decision is more research question than a technical question. If you want to get a deeper understanding of how GGIR works, your may want to consider our training options https://www.accelting.com/ggir-training/

Best,

Vincent

Dr. Vincent van Hees | Independent consultant | https://accelting.com/

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