| Type: | Package |
| Title: | Calculate 'ActiGraph' Counts from Accelerometer Data |
| Version: | 0.6.6 |
| Description: | Calculate 'ActiGraph' counts from the X, Y, and Z axes of a triaxial accelerometer. This work was inspired by Neishabouri et al. who published the article "Quantification of Acceleration as Activity Counts in 'ActiGraph' Wearables" on February 24, 2022. The link to the article (https://pubmed.ncbi.nlm.nih.gov/35831446) and 'python' implementation of this code (https://github.com/actigraph/agcounts). |
| Depends: | R (≥ 3.5.0) |
| License: | MIT + file LICENSE |
| Encoding: | UTF-8 |
| RoxygenNote: | 7.3.1 |
| Imports: | data.table, gsignal, lubridate, magrittr, Rcpp, GGIR, stats, utils, zoo, reticulate, dplyr, stringr, ggplot2, reactable, shiny, bslib, read.gt3x, DBI, RSQLite |
| Suggests: | parallel, devtools, foreach, testthat (≥ 3.0.0), shinytest2, covr |
| Config/testthat/edition: | 3 |
| LinkingTo: | Rcpp, RcppArmadillo |
| NeedsCompilation: | yes |
| Packaged: | 2024-02-28 18:57:14 UTC; bhelsel |
| Author: | Brian C. Helsel [aut, cre], Paul R. Hibbing [ctb], Robert N. Montgomery [ctb], Eric D. Vidoni [ctb], Jonathan Clutton [ctb], University of Kansas [cph] |
| Maintainer: | Brian C. Helsel <bhelsel@kumc.edu> |
| Repository: | CRAN |
| Date/Publication: | 2024-02-29 20:12:36 UTC |
agcounts: Calculate 'ActiGraph' Counts from Accelerometer Data
Description
Calculate 'ActiGraph' counts from the X, Y, and Z axes of a triaxial accelerometer. This work was inspired by Neishabouri et al. who published the article "Quantification of Acceleration as Activity Counts in 'ActiGraph' Wearables" on February 24, 2022. The link to the article (https://pubmed.ncbi.nlm.nih.gov/35831446) and 'python' implementation of this code (https://github.com/actigraph/agcounts).
Author(s)
Maintainer: Brian C. Helsel bhelsel@kumc.edu
Other contributors:
Paul R. Hibbing [contributor]
Robert N. Montgomery [contributor]
Eric D. Vidoni [contributor]
Jonathan Clutton [contributor]
University of Kansas [copyright holder]
agShinyDeployApp
Description
This function deploys the agcounts Shiny app.
Usage
agShinyDeployApp(...)
Arguments
... |
arguments passed to |
Details
This function deploys the agcounts Shiny app for data visualization and exploration. It also provides an opportunity to compare ActiGraph counts generated from the agcounts package with those from ActiGraph's .agd files.
Value
Deploys a Shiny app on localhost. No data or values are returned.
See Also
fluidPage, titlePanel, reexports, shinyApp
bs_theme
Calibrate acceleration data
Description
This function uses a C++ implementation of the GGIR 'g.calibrate' function.
Usage
agcalibrate(raw, verbose = FALSE, tz = "UTC", ...)
Arguments
raw |
data frame of raw acceleration data obtained from |
verbose |
Print the progress of the calibration for the raw data, Default: FALSE |
tz |
the desired timezone, Default: |
... |
Additional arguments to pass into the agread function |
Details
This function uses a C++ implementation of the GGIR 'g.calibrate' function to return calibrated raw acceleration data.
Value
Returns the calibrated raw acceleration data
See Also
Examples
path <- system.file("extdata/example.gt3x", package = "agcounts")
data <- read.gt3x::read.gt3x(path, asDataFrame = TRUE)
data <- agcalibrate(raw = data)
agcounts: R Package for Extracting Actigraphy Counts from Accelerometer Data.
Description
This R Package reads the X, Y, and Z axes in a GT3X accelerometer file and converts it to Actigraphy counts. This work was inspired by Neishabouri et al. who published the article "Quantification of Acceleration as Activity Counts in ActiGraph Wearables on February 24, 2022. The link to the article and Python implementation of this code https://github.com/actigraph/agcounts.
agcounts functions
Read in raw acceleration data
Description
This function reads in raw acceleration data with the pygt3x Python package, the read.gt3x R package with GGIR autocalibration, or the read.gt3x R package.
Usage
agread(
path,
parser = c("pygt3x", "GGIR", "read.gt3x"),
tz = "UTC",
verbose = FALSE,
...
)
Arguments
path |
Path name to the GT3X file or the dataset with columns time, X, Y, and Z axis |
parser |
The parser to use when reading in the data. Parser values include pygt3x, GGIR, and read.gt3x options. |
tz |
the desired timezone, Default: |
verbose |
Print the read method, Default: FALSE. |
... |
Additional arguments to pass into the agread function |
Details
This function reads in raw acceleration data with the pygt3x Python package, the read.gt3x R package with GGIR autocalibration, or the read.gt3x R package.
Value
Returns the raw acceleration data
See Also
Examples
agread(system.file("extdata/example.gt3x", package = "agcounts"), parser = "pygt3x")
calculate_counts
Description
Calculate ActiGraph activity counts from raw acceleration data
by passing in a data frame with a time stamp, X, Y, and Z axis. This function
allows the ability to work with the raw data from other files, but the data
frame needs to have "start_time" and "stop_time" attributes. This is different
from the get_counts function because it reads a raw
data frame rather than a path name to a GT3X file.
Usage
calculate_counts(raw, epoch, lfe_select = FALSE, tz = "UTC", verbose = FALSE)
Arguments
raw |
data frame of raw acceleration data obtained from
|
epoch |
The epoch length for which the counts should be summed. |
lfe_select |
Apply the Actigraph Low Frequency Extension filter, Default: FALSE |
tz |
the desired timezone, Default: |
verbose |
Print the progress of the Actigraph raw data conversion to counts, Default: FALSE. |
Value
Returns a data.frame containing the ActiGraph count values
Examples
f <- system.file("extdata/example.gt3x", package = "agcounts")
d <- read.gt3x::read.gt3x(f, asDataFrame = TRUE, imputeZeroes = TRUE)
calculate_counts(d, 60)
get_counts
Description
Main function to extract counts from the Actigraph GT3X Files.
Usage
get_counts(
path,
epoch,
lfe_select = FALSE,
write.file = FALSE,
return.data = TRUE,
verbose = FALSE,
tz = "UTC",
parser = c("pygt3x", "GGIR", "read.gt3x"),
...
)
Arguments
path |
Full path name to the GT3X File |
epoch |
The epoch length for which the counts should be summed. |
lfe_select |
Apply the Actigraph Low Frequency Extension filter, Default: FALSE |
write.file |
Export a CSV file of the counts, Default: FALSE |
return.data |
Return the data frame to the R Global Environment, Default: TRUE |
verbose |
Print the progress of the Actigraph raw data conversion to counts, Default: FALSE. |
tz |
the desired timezone, Default: |
parser |
The parser to use when reading in the data. Parser values include pygt3x, GGIR, and read.gt3x options. |
... |
arguments passed to |
Details
Main function to extract counts from the Actigraph GT3X Files.
Value
Writes a CSV file if write.file is TRUE and returns a data.frame if return.data is TRUE
See Also
Examples
get_counts(
path = system.file("extdata/example.gt3x", package = "agcounts"),
epoch = 60, lfe_select = FALSE,
write.file = FALSE, return.data = TRUE
)
Upsample data if frequency is 30, 60, or 90 Hertz
Description
Upsample data if frequency is 30, 60, or 90 Hertz
Arguments
X |
NumericMatrix. The matrix that will be upsampled. |
b_fp |
double. A factor to be multiplied by in the upsampling process. |