raveio (version 0.9.0)

power_baseline: Calculate power baseline

Description

Calculate power baseline

Usage

power_baseline(
  x,
  baseline_windows,
  method = c("percentage", "sqrt_percentage", "decibel", "zscore", "sqrt_zscore"),
  units = c("Trial", "Frequency", "Electrode"),
  ...
)
# S3 method for rave_prepare_power
power_baseline(
  x,
  baseline_windows,
  method = c("percentage", "sqrt_percentage", "decibel", "zscore", "sqrt_zscore"),
  units = c("Frequency", "Trial", "Electrode"),
  electrodes,
  ...
)
# S3 method for FileArray
power_baseline(
  x,
  baseline_windows,
  method = c("percentage", "sqrt_percentage", "decibel", "zscore", "sqrt_zscore"),
  units = c("Frequency", "Trial", "Electrode"),
  filebase = NULL,
  ...
)
# S3 method for array
power_baseline(
  x,
  baseline_windows,
  method = c("percentage", "sqrt_percentage", "decibel", "zscore", "sqrt_zscore"),
  units = c("Trial", "Frequency", "Electrode"),
  ...
)
# S3 method for ECoGTensor
power_baseline(
  x,
  baseline_windows,
  method = c("percentage", "sqrt_percentage", "decibel", "zscore", "sqrt_zscore"),
  units = c("Trial", "Frequency", "Electrode"),
  filebase = NULL,
  hybrid = TRUE,
  ...
)

Value

Usually the same type as the input: for arrays, filearray, or ECoGTensor, the outputs are also the same type with the same dimensions; for 'rave_prepare_power'

repositories, the results will be stored in its 'baselined' element; see 'Examples'.

Arguments

x

R array, filearray, ECoGTensor, or 'rave_prepare_power' object created by prepare_subject_power.

baseline_windows

list of baseline window (intervals)

method

baseline method; choices are 'percentage', 'sqrt_percentage', 'decibel', 'zscore', 'sqrt_zscore'; see 'Details' in baseline_array

units

the unit of the baseline; see 'Details'

...

passed to other methods

electrodes

the electrodes to be included in baseline calculation; for power repository object produced by prepare_subject_power only; default is all available electrodes in each of signal_types

filebase

where to store the output; default is NULL and is automatically determined

hybrid

whether the array will be

Details

The arrays must be four-mode tensor and must have valid named dimnames. The dimension names must be 'Trial', 'Frequency', 'Time', 'Electrode', case sensitive.

The baseline_windows determines the baseline windows that are used to calculate time-points of baseline to be included. This can be one or more intervals and must pass the validation function validate_time_window.

The units determines the unit of the baseline. It can be one or more of 'Trial', 'Frequency', 'Electrode'. The default value is all of them, i.e., baseline for each combination of trial, frequency, and electrode. To share the baseline across trials, please remove 'Trial' from units. To calculate baseline that should be shared across electrodes (e.g. in some mini-electrodes), remove 'Electrode' from the units.

Examples

if (FALSE) {
# The following code need to download additional demo data
# Please see https://rave.wiki/ for more details

library(raveio)
repo <- prepare_subject_power(
  subject = "demo/DemoSubject",
  time_windows = c(-1, 3),
  electrodes = c(14, 15))

##### Direct baseline on the repository
power_baseline(x = repo, method = "decibel",
               baseline_windows = list(c(-1, 0), c(2, 3)))
power_mean <- repo$power$baselined$collapse(
  keep = c(2,1), method = "mean")
image(power_mean, x = repo$time_points, y = repo$frequency,
      xlab = "Time (s)", ylab = "Frequency (Hz)",
      main = "Mean power over trial (Baseline: -1~0 & 2~3)")
abline(v = 0, lty = 2, col = 'blue')
text(x = 0, y = 20, "Aud-Onset", col = "blue", cex = 0.6)

##### Alternatively, baseline on electrode instances
baselined <- lapply(repo$power$data_list, function(inst) {
  re <- power_baseline(inst, method = "decibel",
                       baseline_windows = list(c(-1, 0), c(2, 3)))
  collapse2(re, keep = c(2,1), method = "mean")
})
power_mean2 <- (baselined[[1]] + baselined[[2]]) / 2

# Same with precision difference
max(abs(power_mean2 - power_mean)) < 1e-6


}