## ----initialize, echo = FALSE, message = FALSE-------------------------------- library("Ternary") library("CongreveLamsdell2016") data("clBremPartitions", "clBremQuartets", "clMkvPartitions", "clMkvQuartets", "clBootFreqPartitions", "clBootFreqQuartets", "clBootGcPartitions", "clBootGcQuartets", "clJackFreqPartitions", "clJackFreqQuartets", "clJackGcPartitions", "clJackGcQuartets", "clCI") ## ----initialize-variables, echo = FALSE--------------------------------------- PCH <- c( brem = 2, bootG = 0, bootF = 5, jackG = 3, jackF = 4, none = NA, mk = 1, markov = 1, equal = 61, # "=" eq = 61, dot = 183, # "." k1 = 4, implied1 = 4, k2 = 183, implied2 = 183, k3 = 183, implied3 = 183, k5 = 3, implied5 = 3, kX = 183, implied10 = 183, implied20 = 183, implied200 = 183, kC = 17, impliedC = 17 # triupfilled ) COL <- c( black = paste0(cbPalette8[1], "99"), markov = paste0(cbPalette8[4], "99"), mk = paste0(cbPalette8[4], "99"), equal = paste0(cbPalette8[8], "99"), eq = paste0(cbPalette8[8], "99"), implied1 = paste0(cbPalette8[6], "42"), k1 = paste0(cbPalette8[6], "42"), implied2 = paste0(cbPalette8[6], "42"), k2 = paste0(cbPalette8[6], "42"), implied3 = paste0(cbPalette8[6], "42"), k3 = paste0(cbPalette8[6], "42"), implied5 = paste0(cbPalette8[6], "42"), k5 = paste0(cbPalette8[6], "42"), implied10 = paste0(cbPalette8[6], "99"), kX = paste0(cbPalette8[6], "99"), implied20 = paste0(cbPalette8[6], "42"), implied200 = paste0(cbPalette8[6], "42"), kC = paste0(cbPalette8[2], "99"), impliedC = paste0(cbPalette8[2], "99") ) MARGINS <- c(2.8, 0.3, 0.3, 0.3) ROWS <- c(1, 3) TernaryQuarts<-function(TREE = TREE, zoom = 1, padding = 0.1) { clInitializeTernaryQuarts(zoom, padding) clPlotQuartets(clBootGcQuartets, TREE, cex = 1.1, pch = PCH) clPlotQuartets(clMkvQuartets, TREE, cex = 1.1, pch = PCH["mk"]) # Return: invisible() } TernaryParts<-function(TREE = TREE) { clInitializeTernarySplits() clPlotSplits(clBootGcPartitions, TREE, cex = 1.1, pch = PCH) clPlotSplits(clMkvPartitions, TREE, cex = 1.1, pch = PCH["mk"]) # Return: invisible() } AddLegend <- function(pos = "bottomright") { legend(pos, cex = 0.8, bty = "n", lty = 1, pch = PCH[c("mk", "eq", "kX", "k5", "k3", "k1", "kC")], pt.cex = 1.1, col = COL[c("mk", "eq", "kX", "k5", "k3", "k1", "kC")], legend = c("Markov", "Equal weights", paste0("Implied, k = ", c(10, 5, "2, 3", 1, "2..10")))) } Plottem <- function (i) { TernaryQuarts(TREE = i) title(main = paste0("\nQuartets"), cex.main = 0.8) arrows(sqrt(3/4) * 0.5, 0.5, sqrt(3/4) * 0.8, 0.5, length = 0.1) text (sqrt(3/4) * 0.65, 0.5, pos = 3, "Decreasing resolution", cex = 0.8) arrows(sqrt(3/4) * 0.98, 0.40, sqrt(3/4) * 0.98, 0.20, length = 0.1) text (sqrt(3/4) * 1.01, 0.30, pos = 3, "Increasing divergence", cex = 0.8, srt = 270) TernaryQuarts(TREE = i, zoom = 3, padding = 0.01) title(main = paste0("\nDataset ", i, ": CI = ",round(clCI[i], 2)), cex.main = 1.2) TernaryParts(TREE = i) arrows(sqrt(3/4) * 0.98, 0.40, sqrt(3/4) * 0.98, 0.20, length = 0.1) text (sqrt(3/4) * 1.01, 0.30, pos = 3, "Increasing RF distance", cex = 0.8, srt = 270) AddLegend() } ## ----Summary, echo = FALSE, fig.height = 3, fig.width = 9, warning = FALSE---- x <- Sys.setlocale("LC_ALL", "C") # allows PCH = 183 par(mfrow = c(1, ROWS[2]), mar = MARGINS) clInitializeTernaryQuarts() clPlotAverageQuartets(clBootGcQuartets, cex = 1.1, pch = PCH) clPlotAverageQuartets(clMkvQuartets, cex = 1.1, pch = PCH["mk"]) title(main = paste0("\nQuartets"), cex.main = 0.8) arrows(sqrt(3/4) * 0.5, 0.5, sqrt(3/4) * 0.8, 0.5, length = 0.1) text (sqrt(3/4) * 0.65, 0.5, pos = 3, "Decreasing resolution", cex = 0.8) arrows(sqrt(3/4) * 0.98, 0.40, sqrt(3/4) * 0.98, 0.20, length = 0.1) text (sqrt(3/4) * 1.01, 0.30, pos = 3, "Increasing divergence", cex = 0.8, srt = 270) clInitializeTernaryQuarts(zoom = 3, padding = 0.01) clPlotAverageQuartets(clBootGcQuartets, cex = 1.1, pch = PCH) clPlotAverageQuartets(clMkvQuartets, cex = 1.1, pch = PCH["mk"]) title("\nResults for all datasets (means)", cex.main = 1.2) clInitializeTernarySplits() clPlotAverageSplits(clBootGcPartitions, cex = 1.1, pch = PCH) clPlotAverageSplits(clMkvPartitions, cex = 1.1, pch = PCH["mk"]) arrows(sqrt(3/4) * 0.98, 0.40, sqrt(3/4) * 0.98, 0.20, length = 0.1) text (sqrt(3/4) * 1.01, 0.30, pos = 3, "Increasing RF distance", cex = 0.8, srt = 270) AddLegend() ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(1) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(2) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(3) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(4) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(5) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(6) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(7) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(8) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(9) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(10) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(11) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(12) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(13) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(14) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(15) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(16) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(17) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(18) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(19) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(20) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(21) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(22) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(23) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(24) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(25) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(26) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(27) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(28) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(29) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(30) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(31) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(32) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(33) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(34) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(35) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(36) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(37) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(38) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(39) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(40) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(41) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(42) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(43) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(44) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(45) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(46) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(47) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(48) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(49) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(50) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(51) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(52) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(53) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(54) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(55) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(56) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(57) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(58) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(59) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(60) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(61) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(62) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(63) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(64) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(65) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(66) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(67) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(68) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(69) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(70) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(71) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(72) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(73) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(74) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(75) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(76) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(77) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(78) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(79) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(80) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(81) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(82) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(83) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(84) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(85) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(86) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(87) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(88) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(89) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(90) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(91) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(92) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(93) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(94) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(95) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(96) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(97) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(98) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(99) ## ----echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE------------- par(mfrow = ROWS, mar = MARGINS); x <- Plottem(100)