Nothing
## ----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)
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