inst/doc/Compare-methods.R

In CongreveLamsdell2016: Distance Metrics for Trees Generated by Congreve and Lamsdell

## ----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)