## ----setup, include=FALSE-----------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE, comment = "#>", fig.width = 8, fig.height = 4.6
)

## ----paired-slopegraph, eval=requireNamespace("ggplot2", quietly=TRUE)--------
set.seed(20261009)
n_participants <- 36L
demo <- data.frame(
  participant_id = rep(seq_len(n_participants), each = 2L),
  condition = factor(
    rep(c("Baseline", "Stimulus"), n_participants),
    levels = c("Baseline", "Stimulus")
  ),
  response = rep(stats::rnorm(n_participants, 1.4, .28), each = 2L) +
    rep(c(0, .22), n_participants) +
    stats::rnorm(n_participants * 2L, sd = .11)
)
ggplot2::ggplot(
  demo, ggplot2::aes(x = condition, y = response, group = participant_id)
) +
  ggplot2::geom_line(alpha = .27, linewidth = .36, colour = "#718C96") +
  ggplot2::geom_point(
    size = 1.8, alpha = .82, colour = "#387C88"
  ) +
  ggplot2::labs(
    title = "Illustrative participant-level biometric responses",
    subtitle = "Synthetic data; each line joins one participant's observations",
    x = NULL, y = "Synthetic physiological feature (arbitrary units)"
  ) +
  ggplot2::theme_minimal(base_size = 12)

## ----effect-distribution, eval=requireNamespace("ggplot2", quietly=TRUE)------
control <- demo$response[demo$condition == "Baseline"]
stimulus <- demo$response[demo$condition == "Stimulus"]
participant_differences <- stimulus - control
effect <- mean(participant_differences)
replicates <- replicate(
  2000L,
  mean(sample(
    participant_differences,
    size = length(participant_differences), replace = TRUE
  ))
)
bounds <- stats::quantile(replicates, c(.025, .975), names = FALSE)
draws <- data.frame(panel = "Paired difference", effect = replicates)
estimate <- data.frame(
  panel = "Paired difference", effect = effect,
  lower = bounds[1L], upper = bounds[2L]
)
ggplot2::ggplot(draws, ggplot2::aes(x = panel, y = effect)) +
  ggplot2::geom_violin(fill = "#8FBAC3", alpha = .7, width = .54) +
  ggplot2::geom_pointrange(
    data = estimate,
    ggplot2::aes(ymin = lower, ymax = upper),
    colour = "#245B65", linewidth = .7
  ) +
  ggplot2::geom_hline(yintercept = 0, linetype = "dashed") +
  ggplot2::labs(
    title = "Bootstrap distribution of the paired mean difference",
    subtitle = "Synthetic demonstration; 2,000 participant resamples, percentile 95% interval",
    x = NULL, y = "Stimulus minus baseline (arbitrary units)"
  ) +
  ggplot2::theme_minimal(base_size = 12)