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Batch Circadian Analysis of Multiple AGD Files

Source: R/circadian_workbook.R
circadian.batch.Rd

Reads a set of ActiGraph .agd files, runs the full circadian analysis on each, and returns one combined summary row per file, the package equivalent of uploading a batch of files. Files that fail to read or analyse are reported in an error column rather than aborting the run. Optionally writes a single Excel workbook whose Summary sheet has one row per file.

Usage

circadian.batch(
  files,
  file = NULL,
  metric = c("axis1", "vm"),
  include_period_ci = FALSE,
  n_boot = 200,
  epoch_length = NULL,
  verbose = TRUE
)

Arguments

files

Character vector of .agd paths, or a single directory (all its .agd files are used).

file

Optional output .xlsx path for a combined-summary workbook.

metric

Activity metric: "axis1" (default) or "vm" (vector magnitude).

include_period_ci

Bootstrap the period CI per file (default FALSE for batch speed).

n_boot

Bootstrap replicates when include_period_ci is TRUE.

epoch_length

Epoch length in seconds; NULL (default) infers it per file from the timestamps.

verbose

Print per-file progress (default TRUE).

Value

A data frame with one row per file (a file column, an error column, and every summary metric). Returned invisibly when a workbook file is written.

See also

circadian.workbook

Examples

# \donttest{
# Pass a folder to analyse a whole batch; a single file is used here.
batch <- circadian.batch(example_agd(), verbose = FALSE)
batch[, c("file", "IS", "IV", "RA", "rhythm_p_value")]
#>                      file     IS     IV   RA rhythm_p_value
#> 1 MOS2E39230594_60sec.agd 0.2279 1.0008 0.98    0.002396228
# }