Calculate voltage baseline

Usage

voltage_baseline(
  x,
  baseline_windows,
  method = c("percentage", "zscore", "subtract_mean"),
  units = c("Trial", "Electrode"),
  ...
)

# S3 method for class 'rave_prepare_subject_raw_voltage_with_epoch'
voltage_baseline(
  x,
  baseline_windows,
  method = c("percentage", "zscore", "subtract_mean"),
  units = c("Trial", "Electrode"),
  electrodes,
  baseline_mean,
  baseline_sd,
  ...
)

# S3 method for class 'rave_prepare_subject_voltage_with_epoch'
voltage_baseline(
  x,
  baseline_windows,
  method = c("percentage", "zscore", "subtract_mean"),
  units = c("Trial", "Electrode"),
  electrodes,
  baseline_mean,
  baseline_sd,
  ...
)

# S3 method for class 'FileArray'
voltage_baseline(
  x,
  baseline_windows,
  method = c("percentage", "zscore", "subtract_mean"),
  units = c("Trial", "Electrode"),
  filebase = NULL,
  ...
)

# S3 method for class 'array'
voltage_baseline(
  x,
  baseline_windows,
  method = c("percentage", "zscore", "subtract_mean"),
  units = c("Trial", "Electrode"),
  ...
)

Arguments

x: R array, filearray, or 'rave_prepare_power' object created by prepare_subject_raw_voltage_with_epoch.
baseline_windows: list of baseline window (intervals)
method: baseline method; choices are 'percentage' and '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
baseline_mean, baseline_sd: internally used by 'RAVE' repository, provided baseline is not contained in the data. This is useful for calculating the baseline with data from other blocks.
filebase: where to store the output; default is NULL and is automatically determined

Value

The same type as the inputs

Details

The arrays must be three-mode tensor and must have valid named dimnames. The dimension names must be 'Trial', '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 either or both of 'Trial', 'Electrode'. The default value is both, i.e., baseline for each combination of trial and electrode.

Examples


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

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

##### Direct baseline on repository
voltage_baseline(
  x = repo, method = "zscore",
  baseline_windows = list(c(-1, 0), c(2, 3))
)

voltage_mean <- repo$raw_voltage$baselined$collapse(
  keep = c(1,3), method = "mean")
matplot(voltage_mean, type = "l", lty = 1,
        x = repo$raw_voltage$dimnames$Time,
        xlab = "Time (s)", ylab = "Voltage (z-scored)",
        main = "Mean coltage over trial (Baseline: -1~0 & 2~3)")
abline(v = 0, lty = 2, col = 'darkgreen')
text(x = 0, y = -0.5, "Aud-Onset ", col = "darkgreen", cex = 0.6, adj = c(1,1))

##### Alternatively, baseline on each electrode channel
voltage_mean2 <- sapply(repo$raw_voltage$data_list, function(inst) {
  re <- voltage_baseline(
    x = inst, method = "zscore",
    baseline_windows = list(c(-1, 0), c(2, 3)))
  rowMeans(re[])
})

# Same with floating difference
max(abs(voltage_mean - voltage_mean2)) < 1e-8


} # }