Process Count Data

Process Count Data

Process Count Data

Usage

acti_calculate_counts(
  data,
  epoch = 60L,
  resample = TRUE,
  lfe_select = FALSE,
  verbose = TRUE,
  fix_first_second = TRUE,
  round_digits = NULL
)

acti_calculate_wear(
  data,
  method = c("choi", "troiano"),
  use_magnitude = TRUE,
  ...
)

acti_calculate_nonwear(
  data,
  method = c("choi", "troiano"),
  use_magnitude = TRUE,
  ...
)

acti_apply_cole_kripke(data)

acti_apply_sadeh(data, ...)

Arguments

data

A data.frame from acti_calculate_counts that has columns axis1-3 and counts

epoch

epoch length, either in seconds or a string such as "1 min" (see actibase::acti_standardize_epoch()); must be a whole number of seconds. Default is 60 seconds. See agcounts::calculate_counts

resample

(recommended) resample the data to 30Hz using actibase::acti_resample vs. using the resampling method from agcounts::calculate_counts.

lfe_select

Apply the Actigraph Low Frequency Extension filter. See agcounts::calculate_counts

verbose

print diagnostic messages. Either logical or integer, where higher values are higher levels of verbosity.

fix_first_second

Fix the first second bug in agcounts. Appends replicated data of the first record if the first record is not an "even" epoch (e.g. 60 second epoch and data does not start at a 00 second).

round_digits

If not NULL, the number of decimal places the X/Y/Z values are rounded to after resampling and before counting. Use 3 to match ActiLife, which rounds GT3X data to 3 decimals (half away from zero, so 0.0625 becomes 0.063, unlike base::round()). Useful if the data were read with more digits. Default NULL does not round.

method

Method for detecting non-wear, either "choi" or "troiano", corresponding to actigraph.sleepr::apply_choi() or actigraph.sleepr::apply_troiano()

use_magnitude

If TRUE, the magnitude of the vector (axis1, axis2, axis3) is used to measure activity; otherwise the axis1 value is used.

...

additional arguments to pass to actigraph.sleepr function

Value

A data.frame of transformed data

A data.frame of transformed data with columns axis1-3, counts, and counts_log10.

A data.frame of transformed data

Details

The sampling frequency is only needed when resample = FALSE; it is taken from the sample_rate attribute (or estimated from time).

acti_calculate_wear(), acti_apply_cole_kripke(), and acti_apply_sadeh() require 60-second epochs. Cole–Kripke, Sadeh, and acti_calculate_wear(use_magnitude = FALSE) score the vertical axis, so data must contain axis1; vector-magnitude-only counts are an error.

Note

This calls the downstream wear-processing helpers used by actigraph.sleepr

Examples

# \donttest{
path = actiread::acti_example_gt3x()
ac = actiread::acti_read_gt3x(path)
#> ℹ Filling zeros in data
#> ✔ Filled zeros in data
#> ℹ Timezone not applied to data
out = acti_calculate_counts(ac)
#> namespace 'agcounts' is already loaded so argument 'partial' will be ignored.
#> [1] "Creating Downsampled Data"
#> [1] "Filtering Data"
#> [1] "Trimming Data"
#> [1] "Getting data back to 10Hz for accumulation"
#> [1] "Summing epochs"
# }
data = actimetrics::acti_count_data
wear = actimetrics::acti_calculate_wear(data)
tro_wear = actimetrics::acti_calculate_wear(data, method = "troiano")
ck = actimetrics::acti_apply_cole_kripke(data)
tl = actimetrics::acti_apply_tudor_locke(ck)
sadeh = actimetrics::acti_apply_sadeh(ck)