g.part1 {GGIR}

function to load and pre-process acceleration files

Description

Calls function g.getmeta and g.calibrate, and converts the output to .RData-format which will be the input for g.part2. Here, the function generates a folder structure to keep track of various output files. The reason why these g.part1 and g.part2 are not merged as one generic shell function is because g.part1 takes much longer to and involves only minor decisions of interest to the movement scientist. Function g.part2 on the other hand is relatively fast and comes with all the decisions that directly impact on the variables that are of interest to the movement scientist. Therefore, the user may want to run g.part1 overnight or on a computing cluster, while g.part2 can then be the main playing ground for the movement scientist. Function GGIR provides the main shell that allows for operating g.part1 and g.part2.

Usage

  g.part1(datadir = c(), metadatadir = c(), f0 = 1, f1 = c(),
          myfun = c(), params_metrics = c(), params_rawdata = c(),
          params_cleaning = c(), params_general = c(), verbose = TRUE, ...)

Arguments

datadir

Directory where the accelerometer files are stored, e.g. "C:/mydata", or list of accelerometer filenames and directories, e.g. c("C:/mydata/myfile1.bin", "C:/mydata/myfile2.bin").

metadatadir

Directory where the output needs to be stored. Note that this function will attempt to create folders in this directory and uses those folder to keep output.

f0

File index to start with (default = 1). Index refers to the filenames sorted in alphabetical order

f1

File index to finish with (defaults to number of files available, i.e., f1 = 0)

myfun

External function object to be applied to raw data. See details applyExtFunction.

params_metrics

See details in GGIR.

params_rawdata

See details in GGIR.

params_cleaning

See details in GGIR.

params_general

See details in GGIR.

verbose

See details in GGIR.

...

If you are working with a non-standard csv formatted files, g.part1 also takes any input arguments needed for function read.myacc.csv and argument rmc.noise from get_nw_clip_block_params. First test these argument with function read.myacc.csv directly. To ensure compatibility with R scripts written for older GGIR versions, the user can also provide parameters listed in the params_ objects as direct argument.

Details

GGIR comes with many processing parameters, which have been thematically grouped in parameter objects (R list). By running print(load_params()) you can see the default values of all the parameter objects. When g.part 1 is used via GGIR you have the option to specifiy a configuration file, which will overrule the default parameter values. Further, as user you can set parameter values as input argument to both g.part1 and GGIR. Directly specified argument overrule the configuration file and default values.

See the GGIR package vignette or the details section in GGIR for a more elaborate overview of parameter objects and their usage across GGIR.

Value

The function provides no values, it only ensures that the output from other functions is stored in .RData(one file per accelerometer file) in folder structure

Author(s)

Vincent T van Hees <[e-mail]>

References

• van Hees VT, Gorzelniak L, Dean Leon EC, Eder M, Pias M, et al. (2013) Separating Movement and Gravity Components in an Acceleration Signal and Implications for the Assessment of Human Daily Physical Activity. PLoS ONE 8(4): e61691. doi:10.1371/journal.pone.0061691

• van Hees VT, Fang Z, Langford J, Assah F, Mohammad A, da Silva IC, Trenell MI, White T, Wareham NJ, Brage S. Auto-calibration of accelerometer data for free-living physical activity assessment using local gravity and temperature: an evaluation on four continents. J Appl Physiol (1985). 2014 Aug 7

• Aittasalo M, Vaha-Ypya H, Vasankari T, Husu P, Jussila AM, and Sievanen H. Mean amplitude deviation calculated from raw acceleration data: a novel method for classifying the intensity of adolescents physical activity irrespective of accelerometer brand. BMC Sports Science, Medicine and Rehabilitation (2015).

Examples

  ## Not run: 
    datafile = "C:/myfolder/mydata"
    outputdir = "C:/myresults"
    g.part1(datadir,outputdir)
  
## End(Not run)