## ----fig.align='center', fig.width=8, fig.height=8, echo=FALSE---------------- load("dark.rda") tmp<-dark par(las = 1, bty = "n", mfrow = c(1, 1), font = 2, font.lab = 2, cex.lab = 1.5, oma = c(1, 1, 1, 1), mar = c(6, 6, 2, 3) ) XL <- expression(bold(Time ~ (min))) YL <- expression(bold(Threshold ~ (log ~ units))) plot(tmp$time, tmp$thrs, xlab = XL, ylab = YL, pch = 1, cex = 1) axis(1, lwd = 2) axis(2, lwd = 2) lines(tmp$time, tmp$fit, col = 2) CT <- tmp$opt[1] CC <- tmp$opt[2] Tau <- tmp$opt[3] S2 <- tmp$opt[4] Al <- tmp$opt[5] S3 <- tmp$opt[6] Be <- tmp$opt[7] rect(0, CT, Al, max(tmp$thrs), border = NA, col = rgb(1, 1, 0, 0.2)) idx<-tmp$time<Al points(tmp$time[idx], tmp$thrs[idx], pch=16, cex=0.7) Off <- c(1.5, 3) * -0.2 text(Al, max(tmp$thrs), "Cone", adj = Off) Lty = 4 Sym <- expression(theta[1] ~ Cone ~ Threshold) arrows(Be + 10, CT, -2, CT, length = 0.125, angle = 20, lty = Lty) text(Be + 10, CT, Sym, adj = c(0, 0), cex = 1.2) Sym <- expression(theta[2] ~ Cone ~ Coefficient) arrows(Be + 10, CT + CC, -2, CC + CT, length = 0.125, angle = 20, lty = Lty) text(Be + 10, CC + CT, Sym, adj = c(0, 0), cex = 1.2) Sym <- expression(theta[3] ~ Cone ~ Time ~ Constant ~ (tau)) # arrows(Be+10,CT+CC/2, 3, CT+CC/2, length = 0.125, angle = 20, lty=Lty) text(3, CT + CC/2, Sym, adj = c(0, 0), cex = 1.2) ## ----fig.align='center', fig.width=8, fig.height=8, echo=FALSE---------------- source('../R/H.R') source('../R/P7c.R') tmp<-dark par(las = 1, bty = "n", mfrow = c(1, 1), font = 2, font.lab = 2, cex.lab = 1.5, oma = c(1, 1, 1, 1), mar = c(6, 6, 2, 3) ) XL <- expression(bold(Time ~ (min))) YL <- expression(bold(Threshold ~ (log ~ units))) plot(tmp$time, tmp$thrs, xlab = XL, ylab = YL, pch = 1, cex = 1) axis(1, lwd = 2) axis(2, lwd = 2) lines(tmp$time, tmp$fit, col = 2) CT <- tmp$opt[1] CC <- tmp$opt[2] Tau <- tmp$opt[3] S2 <- tmp$opt[4] Al <- tmp$opt[5] S3 <- tmp$opt[6] Be <- tmp$opt[7] rect(Al, P7c(tmp$opt, Be), Be, P7c(tmp$opt, Al), border = NA, col = rgb(1, 0, 0, 0.2)) idx<-tmp$time>Al & tmp$time<Be points(tmp$time[idx], tmp$thrs[idx], pch=16, cex=0.7) mod<-lm(tmp$thrs[idx]~tmp$time[idx]) abline(mod, col=2, lty=2) Off <- c(1, 1) * 3 * -0.08 text(Be, P7c(tmp$opt, Al), "S2", adj = Off) Lty = 4 Sym <- expression(atop(theta[4] ~ Second ~ Rod ~ Recovery, ~Rate ~ (S2))) # arrows(Be+10,CT+CC/2, 3, CT+CC/2, length = 0.125, angle = 20, lty=Lty) text(Be - 3, mean(tmp$thrs) - 0.2, Sym, adj = c(0, 0), cex = 1.2) Sym <- expression(atop(theta[5] ~ Cone ~ Rod, ~Breakpoint ~ (alpha))) arrows(Al - 3, P7c(tmp$opt, Al) - 1.4, Al, P7c(tmp$opt, Al), length = 0.125, angle = 20, lty = Lty) text(Al - 5, P7c(tmp$opt, Al) - 1.8, Sym, adj = c(0.5, 0), cex = 1.2) ## ----fig.align='center', fig.width=8, fig.height=8, echo=FALSE---------------- library(Dark) data(dark) tmp<-dark par(las = 1, bty = "n", mfrow = c(1, 1), font = 2, font.lab = 2, cex.lab = 1.5, oma = c(1, 1, 1, 1), mar = c(6, 6, 2, 3) ) XL <- expression(bold(Time ~ (min))) YL <- expression(bold(Threshold ~ (log ~ units))) plot(tmp$time, tmp$thrs, xlab = XL, ylab = YL, pch = 1, cex = 1) axis(1, lwd = 2) axis(2, lwd = 2) lines(tmp$time, tmp$fit, col = 2) CT <- tmp$opt[1] CC <- tmp$opt[2] Tau <- tmp$opt[3] S2 <- tmp$opt[4] Al <- tmp$opt[5] S3 <- tmp$opt[6] Be <- tmp$opt[7] rect(Be, min(tmp$thrs), max(tmp$time), P7c(tmp$opt, Be), border = NA, col = rgb(1, 0, 1, 0.2)) Off <- c(1, 1) * 3 * -0.08 text(max(tmp$time), P7c(tmp$opt, Be), "S3", Off) idx<-tmp$time>Be points(tmp$time[idx], tmp$thrs[idx], pch=16, cex=0.7) mod<-lm(tmp$thrs[idx]~tmp$time[idx]) abline(mod, col=2, lty=2) Lty = 4 Sym <- expression(atop(theta[6] ~ Third ~ Rod ~ Recovery, ~Rate ~ (-(S2 + S3)))) # arrows(Be+10,CT+CC/2, 3, CT+CC/2, length = 0.125, angle = 20, lty=Lty) text(Be + 12, P7c(tmp$opt, Be) - 0.5, Sym, adj = c(0, 0), cex = 1.2) Sym <- expression(atop(theta[7] ~ Rod ~ Rod, ~Breakpoint ~ (beta))) arrows(Al, P7c(tmp$opt, Be) - 0.4, Be, P7c(tmp$opt, Be), length = 0.125, angle = 20, lty = Lty) text(Al - 5, P7c(tmp$opt, Be) - 0.6, Sym, adj = c(0.5, 0), cex = 1.2)