Nothing
Resolution and accuracy in Congreve & Lamsdell matrices"
In CongreveLamsdell2016: Distance Metrics for Trees Generated by Congreve and Lamsdell
This page depicts the analytical results of all 100 matrices generated by
Congreve & Lamsdell [-@Congreve2016] using a ternary plotting approach
[@Smith2019], with quartets and partitions used as distance metrics.
library("Ternary")
library("CongreveLamsdell2016")
data("clBremPartitions", "clBremQuartets", "clMkvPartitions", "clMkvQuartets",
"clBootFreqPartitions", "clBootFreqQuartets",
"clBootGcPartitions", "clBootGcQuartets",
"clJackFreqPartitions", "clJackFreqQuartets",
"clJackGcPartitions", "clJackGcQuartets",
"clCI")
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
```{R 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()
## Trees 1--10
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(1)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(2)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(3)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(4)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(5)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(6)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(7)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(8)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(9)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(10)
## Trees 11--20
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(11)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(12)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(13)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(14)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(15)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(16)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(17)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(18)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(19)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(20)
## Trees 21--30
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(21)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(22)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(23)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(24)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(25)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(26)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(27)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(28)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(29)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(30)
## Trees 31--40
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(31)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(32)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(33)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(34)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(35)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(36)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(37)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(38)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(39)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(40)
## Trees 41--50
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(41)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(42)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(43)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(44)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(45)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(46)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(47)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(48)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(49)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(50)
## Trees 51--60
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(51)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(52)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(53)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(54)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(55)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(56)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(57)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(58)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(59)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(60)
## Trees 61--70
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(61)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(62)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(63)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(64)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(65)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(66)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(67)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(68)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(69)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(70)
## Trees 71--80
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(71)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(72)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(73)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(74)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(75)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(76)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(77)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(78)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(79)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(80)
## Trees 81--90
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(81)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(82)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(83)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(84)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(85)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(86)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(87)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(88)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(89)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(90)
## Trees 91--100
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(91)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(92)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(93)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(94)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(95)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(96)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(97)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(98)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(99)
{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(100)
References
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CongreveLamsdell2016 documentation built on May 29, 2024, 2:52 a.m.
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This page depicts the analytical results of all 100 matrices generated by Congreve & Lamsdell [-@Congreve2016] using a ternary plotting approach [@Smith2019], with quartets and partitions used as distance metrics.
library("Ternary") library("CongreveLamsdell2016") data("clBremPartitions", "clBremQuartets", "clMkvPartitions", "clMkvQuartets", "clBootFreqPartitions", "clBootFreqQuartets", "clBootGcPartitions", "clBootGcQuartets", "clJackFreqPartitions", "clJackFreqQuartets", "clJackGcPartitions", "clJackGcQuartets", "clCI")
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
```{R 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()
## Trees 1--10 ```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE} par(mfrow = ROWS, mar = MARGINS); x <- Plottem(1)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE} par(mfrow = ROWS, mar = MARGINS); x <- Plottem(2)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(3)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE} par(mfrow = ROWS, mar = MARGINS); x <- Plottem(4)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(5)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE} par(mfrow = ROWS, mar = MARGINS); x <- Plottem(6)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(7)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE} par(mfrow = ROWS, mar = MARGINS); x <- Plottem(8)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(9)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE} par(mfrow = ROWS, mar = MARGINS); x <- Plottem(10)
## Trees 11--20 ```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE} par(mfrow = ROWS, mar = MARGINS); x <- Plottem(11)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE} par(mfrow = ROWS, mar = MARGINS); x <- Plottem(12)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(13)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE} par(mfrow = ROWS, mar = MARGINS); x <- Plottem(14)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(15)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE} par(mfrow = ROWS, mar = MARGINS); x <- Plottem(16)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(17)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE} par(mfrow = ROWS, mar = MARGINS); x <- Plottem(18)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(19)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE} par(mfrow = ROWS, mar = MARGINS); x <- Plottem(20)
## Trees 21--30 ```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE} par(mfrow = ROWS, mar = MARGINS); x <- Plottem(21)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE} par(mfrow = ROWS, mar = MARGINS); x <- Plottem(22)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(23)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE} par(mfrow = ROWS, mar = MARGINS); x <- Plottem(24)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(25)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE} par(mfrow = ROWS, mar = MARGINS); x <- Plottem(26)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(27)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE} par(mfrow = ROWS, mar = MARGINS); x <- Plottem(28)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(29)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE} par(mfrow = ROWS, mar = MARGINS); x <- Plottem(30)
## Trees 31--40 ```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE} par(mfrow = ROWS, mar = MARGINS); x <- Plottem(31)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE} par(mfrow = ROWS, mar = MARGINS); x <- Plottem(32)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(33)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE} par(mfrow = ROWS, mar = MARGINS); x <- Plottem(34)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(35)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE} par(mfrow = ROWS, mar = MARGINS); x <- Plottem(36)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(37)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE} par(mfrow = ROWS, mar = MARGINS); x <- Plottem(38)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(39)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE} par(mfrow = ROWS, mar = MARGINS); x <- Plottem(40)
## Trees 41--50 ```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE} par(mfrow = ROWS, mar = MARGINS); x <- Plottem(41)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE} par(mfrow = ROWS, mar = MARGINS); x <- Plottem(42)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(43)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE} par(mfrow = ROWS, mar = MARGINS); x <- Plottem(44)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(45)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE} par(mfrow = ROWS, mar = MARGINS); x <- Plottem(46)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(47)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE} par(mfrow = ROWS, mar = MARGINS); x <- Plottem(48)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(49)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE} par(mfrow = ROWS, mar = MARGINS); x <- Plottem(50)
## Trees 51--60 ```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE} par(mfrow = ROWS, mar = MARGINS); x <- Plottem(51)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE} par(mfrow = ROWS, mar = MARGINS); x <- Plottem(52)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(53)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE} par(mfrow = ROWS, mar = MARGINS); x <- Plottem(54)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(55)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE} par(mfrow = ROWS, mar = MARGINS); x <- Plottem(56)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(57)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE} par(mfrow = ROWS, mar = MARGINS); x <- Plottem(58)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(59)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE} par(mfrow = ROWS, mar = MARGINS); x <- Plottem(60)
## Trees 61--70 ```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE} par(mfrow = ROWS, mar = MARGINS); x <- Plottem(61)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE} par(mfrow = ROWS, mar = MARGINS); x <- Plottem(62)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(63)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE} par(mfrow = ROWS, mar = MARGINS); x <- Plottem(64)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(65)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE} par(mfrow = ROWS, mar = MARGINS); x <- Plottem(66)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(67)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE} par(mfrow = ROWS, mar = MARGINS); x <- Plottem(68)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(69)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE} par(mfrow = ROWS, mar = MARGINS); x <- Plottem(70)
## Trees 71--80 ```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE} par(mfrow = ROWS, mar = MARGINS); x <- Plottem(71)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE} par(mfrow = ROWS, mar = MARGINS); x <- Plottem(72)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(73)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE} par(mfrow = ROWS, mar = MARGINS); x <- Plottem(74)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(75)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE} par(mfrow = ROWS, mar = MARGINS); x <- Plottem(76)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(77)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE} par(mfrow = ROWS, mar = MARGINS); x <- Plottem(78)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(79)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE} par(mfrow = ROWS, mar = MARGINS); x <- Plottem(80)
## Trees 81--90 ```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE} par(mfrow = ROWS, mar = MARGINS); x <- Plottem(81)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE} par(mfrow = ROWS, mar = MARGINS); x <- Plottem(82)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(83)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE} par(mfrow = ROWS, mar = MARGINS); x <- Plottem(84)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(85)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE} par(mfrow = ROWS, mar = MARGINS); x <- Plottem(86)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(87)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE} par(mfrow = ROWS, mar = MARGINS); x <- Plottem(88)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(89)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE} par(mfrow = ROWS, mar = MARGINS); x <- Plottem(90)
## Trees 91--100 ```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE} par(mfrow = ROWS, mar = MARGINS); x <- Plottem(91)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE} par(mfrow = ROWS, mar = MARGINS); x <- Plottem(92)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(93)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE} par(mfrow = ROWS, mar = MARGINS); x <- Plottem(94)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(95)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE} par(mfrow = ROWS, mar = MARGINS); x <- Plottem(96)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(97)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE} par(mfrow = ROWS, mar = MARGINS); x <- Plottem(98)
```{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(99)
{R, echo = FALSE, fig.width = 9, fig.height = 6, warning = FALSE}
par(mfrow = ROWS, mar = MARGINS); x <- Plottem(100)
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