g.part2 {GGIR}

function to analyse and summarize pre-processed output from g.part1

Description

Loads the output from g.part1 and then applies g.impute and g.analyse, after which the output is converted to .RData-format which will be used by GGIR to generate reports. The variables in these reports are the same variables as described in g.analyse.

Usage

  g.part2(datadir = c(), metadatadir = c(), f0 = c(), f1 = c(),
        myfun = c(), params_cleaning = c(), params_247 = c(),
        params_phyact = c(), params_output = 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 that holds a folder 'meta' and inside this a folder 'basic' which contains the milestone data produced by g.part1. The folderstructure is normally created by g.part1 and GGIR will recognise what the value of metadatadir is.

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_cleaning

See details in GGIR.

params_247

See details in GGIR.

params_phyact

See details in GGIR.

params_output

See details in GGIR.

params_general

See details in GGIR.

verbose

See details in GGIR.

...

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 2 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.part2 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 other functions are called and that their output is stored in the folder structure as created with g.part1.

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

Examples

  ## Not run: 
    metadatadir = "C:/myresults/output_mystudy"
    g.part2(metadatadir)
  
## End(Not run)