Sympathetic skin response (SSR) analysis

Extracts the sympathetic skin response evoked by each stimulus from a skin conductance recording: the response onset latency, the baseline-to-peak amplitude, the waveform morphology (monophasic / biphasic) and a present/absent classification. A per-channel summary reports the response rate, mean latency and amplitude, an amplitude-habituation slope across the repeated stimuli, and the clinical absent-SSR flag.

Usage

edaSSR(
  x,
  stimulus_events,
  assay_name = NULL,
  response_window = c(0.5, 8),
  baseline_sec = 2,
  amplitude_min = 0.05,
  recovery_frac = 0.1,
  onset_frac = 0.05,
  morphology_frac = 0.3,
  events_unit = c("auto", "index", "seconds")
)

Arguments

x: A PhysioExperiment object with a skin conductance assay.
stimulus_events: Stimulus times, as sample indices or times in seconds (see events_unit).
assay_name: Input assay (default: defaultAssay(x)).
response_window: Numeric c(start, end) seconds after each stimulus in which the SSR is sought (default c(0.5, 8)).
baseline_sec: Length in seconds of the pre-stimulus window used to estimate and remove the tonic trend (default 2).
amplitude_min: Minimum detrended peak amplitude (uS) for a response to count as present (default 0.05).
recovery_frac: Fraction of the peak amplitude the trace must fall back after the peak for the response to be accepted as phasic (rather than a monotone drift; default 0.1).
onset_frac: Fraction of the SSR amplitude above baseline at which the response onset (and hence latency) is marked (default 0.05).
morphology_frac: Fraction of the SSR amplitude an opposite-going deflection must reach for the response to be classed biphasic (default 0.3).
events_unit: Unit of stimulus_events: "auto" (default), "index" or "seconds".

Value

An eda_ssr object with responses (one row per stimulus per channel: channel, stimulus, stim_time, present, latency, amplitude, peak_time, morphology) and summary (one row per channel: channel, n_stimuli, n_present, response_rate, mean_latency, mean_amplitude, habituation_slope, ssr_absent).

Details

The tonic trend estimated from the pre-stimulus baseline is subtracted from each response window, so slow skin-conductance drift is neither counted as a response nor mistaken for a biphasic deflection. In the detrended window the phasic peak is located; a response is accepted only if it exceeds amplitude_min and recovers (rises then falls), and the latency is measured from the stimulus to the onset of that phasic deflection (Vetrugno et al. 2003).

References

Vetrugno, R. et al. (2003). Sympathetic skin response: basic mechanisms and clinical applications. Clin Auton Res 13(4):256-270.

Examples

# 3 stimuli at 10, 40 and 70 s, each followed by an SCR
pe <- edaSimulate(n_time = 900, sr = 10, scr_count = 0, seed = 1)
sig <- as.numeric(SummarizedExperiment::assay(pe))
sr <- 10
for (st in c(10, 40, 70)) {
  t <- (seq_along(sig) - 1) / sr - st
  sig <- sig + 0.5 * ifelse(t > 0, (exp(-t / 3) - exp(-t / 0.75)), 0)
}
SummarizedExperiment::assay(pe) <- matrix(sig, ncol = 1)
res <- edaSSR(pe, stimulus_events = c(10, 40, 70), events_unit = "seconds")
res$summary
#>   channel n_stimuli n_present response_rate mean_latency mean_amplitude
#> 1    EDA1         3         3             1          0.5       0.243441
#>   habituation_slope ssr_absent
#> 1      -0.001389532      FALSE