function (Nsim = 10000) { par(mfrow = c(1, 1), mar = c(5, 4, 4, 2) + 0.1) SIR = flux$SIR FLUX = flux$FLUX m.SIR = mean(SIR) SIR.X = mean(SIR[FLUX == "X"]) SIR.Y = mean(SIR[FLUX == "Y"]) mm = min(SIR[FLUX == "X"], SIR[FLUX == "Y"]) MM = max(SIR[FLUX == "X"], SIR[FLUX == "Y"]) qqplot(SIR[FLUX == "X"], SIR[FLUX == "Y"], xlab = expression("SIR with Flux X (" ~ log[10](Ohm) ~ ")"), ylab = expression("SIR with Flux Y ( " ~ log[10](Ohm) ~ ")"), xlim = c(mm, MM), ylim = c(mm, MM), pch = 16, col = "red") abline(0, 1) readline("Hit return\n") qqplot(SIR[FLUX == "X"], SIR[FLUX == "Y"], xlab = expression("SIR with Flux X (" ~ log[10](Ohm) ~ ")"), ylab = expression("SIR with Flux Y ( " ~ log[10](Ohm) ~ ")"), xlim = c(0, 20), ylim = c(0, 20), pch = 16, col = "red") abline(0, 1) readline("Hit return\n") boxplot(SIR ~ FLUX, data = flux, ylab = expression("SIR ( " ~ log[10](Ohm) ~ ")"), xlab = "Flux") text(1.5, 12.5, substitute(bar(FLUX)[Y] - bar(FLUX)[X] == flux.diff, list(flux.diff = format(signif(SIR.Y - SIR.X, 4)))), adj = 0) points(rep(0.95, 9), flux$SIR[flux$FLUX == "X"], col = "red", pch = 16) points(rep(1.95, 9), flux$SIR[flux$FLUX == "Y"], col = "blue", pch = 16) out.AD = AD.test(flux$SIR[flux$FLUX == "Y"], flux$SIR[flux$FLUX == "X"]) DIFF = SIR.Y - SIR.X readline("Hit return\n") randomization.ref.dist = combn(1:18, 9, fun = mean.fun, y = SIR) D = 2 * (randomization.ref.dist - m.SIR) p1 = mean(D < DIFF) p2 = mean(D > -DIFF) hist(D, nclass = 200, probability = T, col = c("red", "blue"), main = expression("Randomization Reference Distribution of" ~ bar(SIR)[Y] - bar(SIR)[X]), xlab = expression(bar(Y) - bar(X) == bar(SIR)[Y] - bar(SIR)[X])) abline(v = c(DIFF, -DIFF), lwd = 2, col = "orange") text(1.05 * DIFF, 0.3, substitute(P(bar(Y) - bar(X) <= yxdiff) == p1, list(yxdiff = signif(DIFF, 4), p1 = signif(p1, 4))), adj = 0.5, srt = 90) text(-1.05 * DIFF, 0.3, substitute(P(bar(Y) - bar(X) >= yxdiff) == p2, list(yxdiff = signif(-DIFF, 4), p2 = signif(p2, 4))), adj = 0.5, srt = -90) readline("Hit return\n") qqnorm(D, ylab = expression(bar(Y) - bar(X)), pch = ".") qqline(D, col = "blue") readline("Hit return\n") W = D/sqrt(sum((SIR - m.SIR)^2)) t.SIR = sort((W/sqrt(1 - 9 * 9 * W^2/18)) * sqrt(18 - 2)/sqrt(1/9 + 1/9)) N.perm = length(t.SIR) t.quant = qt((1:N.perm)/(N.perm + 1), 16) plot(t.quant, t.SIR, pch = ".", xlab = expression(t[16] ~ "quantiles"), ylab = "ordered randomization t-statitics") abline(0, 1, col = "blue") readline("Hit return\n") t.sample = sort(rt(N.perm, 16)) mt = t.sample[1] Mt = t.sample[N.perm] plot(t.quant, t.sample, pch = ".", xlab = expression(t[16] ~ "quantiles"), ylab = "simulated t-statitics", xlim = c(mt, Mt), ylim = c(mt, Mt)) abline(0, 1, col = "blue") readline("Hit return\n") sim.ref.dist = NULL for (i in 1:Nsim) { SIR.star = sample(SIR) sim.ref.dist = c(sim.ref.dist, mean(SIR.star[1:9])) } D.star = 2 * (sim.ref.dist - m.SIR) m = min(D.star, D) M = max(D.star, D) qqplot(D, D.star, xlab = expression(bar(y) - bar(x) ~ "for all combinations"), , xlim = c(m, M), ylim = c(m, M), ylab = substitute(bar(y) - bar(x) ~ "for all" ~ Nsim ~ "sampled combinations", list(Nsim = Nsim)), pch = ".") abline(0, 1, col = "blue") p1.hat = mean(D.star < DIFF) p2.hat = mean(D.star > -DIFF) p1.hat = signif(p1.hat, 4) p2.hat = signif(p2.hat, 4) p1 = signif(p1, 4) p2 = signif(p2, 4) text(m, M, substitute(hat(p)[1] == p1.hat, list(p1.hat = p1.hat)), adj = 0, cex = 1) text(m, 0.87 * M, substitute(hat(p)[2] == p2.hat, list(p2.hat = p2.hat)), adj = 0, cex = 1) text(M, 0.9 * m, substitute(p[1] == p1, list(p1 = p1)), adj = 1, cex = 1) text(M, m, substitute(p[2] == p2, list(p2 = p2)), adj = 1, cex = 1) out = list(out.AD = out.AD, SIR.X = SIR.X, SIR.Y = SIR.Y, DIFF = DIFF, p1 = p1, p2 = p2) }