raveio (version 0.9.0)

voltage_baseline: Calculate voltage baseline

Description

Calculate voltage baseline

Usage

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

Value

The same type as the inputs

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

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) {
# 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


}