data.3 <- read.table("Mesozoic_squamates_lower_jaw_lengths_1.txt", header=T, row.names=1) # max(data.3 [, "Lower_jaw_length__mm"]) par(bg = "white") plot (x = data.3 [, "MID"], y = log10(data.3 [, "Lower_jaw_length__mm"]), xlim = c(157, 66),col = "transparent", xlab = "Time (Ma)", ylab = "Lower jaw length (log10 mm)", yaxt="n") axis(side=2, at=c(1,2,3), labels = c(10, 100, 1000)) polygon (c(157.3, 152.1, 152.1, 157.3), y = c(-1000, -1000, 3000, 3000), border = NA, col = rgb (0, 0, 0, 0.03)) polygon (c(145.0, 139.8, 139.8, 145.0), y = c(-1000, -1000, 3000, 3000), border = NA, col = rgb (0, 0, 0, 0.03)) polygon (c(132.9, 129.4, 129.4, 132.9), y = c(-1000, -1000, 3000, 3000), border = NA, col = rgb (0, 0, 0, 0.03)) polygon (c( 125.0, 113.0,113.0, 125.0), y = c(-1000, -1000, 3000, 3000), border = NA, col = rgb (0, 0, 0, 0.03)) polygon (c(100.5, 93.9, 93.9, 100.5), y = c(-1000, -1000, 3000, 3000), border = NA, col = rgb (0, 0, 0, 0.03)) polygon (c(89.8, 86.3,86.3, 89.8), y = c(-1000, -1000, 3000, 3000), border = NA, col = rgb (0, 0, 0, 0.03)) polygon (c(83.6, 72.1,72.1, 83.6), y = c(-1000, -1000, 3000, 3000), border = NA, col = rgb (0, 0, 0, 0.03)) abline(v = c(145), col = "gray60", lwd = 1) # make gray background abline(v = c(66), col = "gray60", lwd = 1) # make gray background box(col="black", lwd=1.2) midpoints <-data.3 [, "MID"] ucl <- c(data.3 [, "FAD"]) ucl lcl <- c(data.3 [, "LAD"]) lcl size <- log10(data.3 [, "Lower_jaw_length__mm"]) par(new=T) segments(ucl, size, lcl, size, col = rgb (1, 0, 0, 0.2), lwd=1) points (midpoints, size, pch = 21, col = "black", bg = "white", cex=0.7, lwd=1, xlim = c(157, 66)) dev.copy(pdf,"Squamate_size_time_plot_LOG_times.pdf", width=8, height=4.5, family="Times") dev.off() dev.copy(pdf,"Squamate_size_time_plot_LOG_times.V2.pdf", width=5, height=5, family="Times") dev.off()