Nothing
test_that("Deprecation", {
expect_equal(MinimumLength(1:3), expect_warning(MinimumSteps(1:3)))
})
test_that("Step counts are correctly calculated", {
library("TreeTools")
expect_equal(MinimumLength(rep(1, 3)), 0)
expect_equal(MaximumLength(rep(1, 3)), 0)
expect_equal(MinimumLength(1:3), 1)
expect_equal(MaximumLength(1:3), 1)
# ..+, .+., .++, +.+
expect_equal(MinimumLength(c(1:3, 5)), 1)
expect_equal(MinimumLength(c(6, 7, 14)), 0)
expect_equal(MinimumLength(0:3), 1) # 0 representing the inapplicable token
# ++++, .++., ..++
expect_equal(0, MinimumLength(c(2046, 384, 1152)))
# ++++, +..., .++., ..++
expect_equal(1, MinimumLength(c(15, 8, 6, 3)))
# ++++++, +....., .++..., .+.+.., ...++.
expect_equal(2, MinimumLength(c(63, 32, 24, 20, 6)))
dudDat <- TreeTools::StringToPhyDat("----{-,1}22", letters[1:7])
expect_equal("----<-,1>22", TreeTools::PhyDatToString(dudDat, ">", ","))
expect_equal(0, attr(PrepareDataIW(dudDat), "min.length"))
dudTwo <- TreeTools::StringToPhyDat("{-1}{-2}{-3}2233", letters[1:7])
expect_equal("{-1}{-2}{-3}2233", TreeTools::PhyDatToString(PrepareDataIW(dudTwo)))
morphyObj <- SingleCharMorphy("{-1}{-2}{-3}2233")
expect_equal(MorphyTreeLength(TreeTools::PectinateTree(7), morphyObj), 1)
morphyObj <- UnloadMorphy(morphyObj)
owch2 <- "{-1}{-2}22{-3}33"
tr2 <- ape::read.tree(text=("(a, ((b, (c, d)), (e, (f, g))));"))
# PlotCharacter(tr2, StringToPhyDat(owch2, letters[1:7]))
morphyObj <- SingleCharMorphy(owch2)
expect_equal(MorphyTreeLength(TreeTools::PectinateTree(7), morphyObj), 1)
morphyObj <- UnloadMorphy(morphyObj)
owch3 <- "-1-222-333"
tr3 <- ape::read.tree(text=("((a1, a2), (((b1, b2), (c, d)), ((e1, e2), (f, g))));"))
# PlotCharacter(tr3, StringToPhyDat(owch3, TipLabels(tr3)))
morphyObj <- SingleCharMorphy(owch3)
expect_equal(MorphyTreeLength(TreeTools::PectinateTree(10), morphyObj), 2)
expect_equal(MorphyTreeLength(tr3, morphyObj), 2)
morphyObj <- UnloadMorphy(morphyObj)
expect_equal(2, MinimumLength("-{-1}{-2}{-3}2233"))
expect_equal(1, MinimumLength("--{-1}{-2}{-3}2233"))
expect_equal(0, attr(PrepareDataIW(dudDat), "min.length"))
tr <- ape::read.tree(text="(((a, b), c), (d, (e, ((f, g), (h, (i, (j, k)))))));")
expect_equal(CharacterLength(tr, compress = TRUE,
TreeTools::StringToPhyDat("11---22--33", letters[1:11])),
MinimumLength(c(0, 0, 0, 0, 0, 0, 2, 2, 4, 4, 8, 8)))
# 04, 14, 24, 34, 05, 16, 27, 38, 9A
# In this case, chosing the most common state (4) means that we have to choose 567&8 too
# 012&3 is a better solution
# We also have to choose one of 9 or A, but it doesn't matter which.
expect_equal(4, MinimumLength(c(
2^0 + 2^4,
2^1 + 2^4,
2^2 + 2^4,
2^3 + 2^4,
2^0 + 2^5,
2^1 + 2^6,
2^2 + 2^7,
2^3 + 2^8,
2^9 + 2^10
)))
data("inapplicable.datasets")
expect_equal(c(1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 2, 1, 1, 1, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 1, 1, 1, 2, 1, 1, 2, 1,
1, 2, 1, 1, 4, 3, 1, 1, 1, 1, 2, 1, 1, 1, 1, 1, 1, 1, 2, 4, 1,
1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 2, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1),
MinimumLength(inapplicable.phyData[[4]], compress = TRUE))
})
test_that("MaximumLength() edge cases are handled correctly", {
expect_equal(MaximumLength("00000000000111"), 3)
expect_equal(MaximumLength("001122{12}"), 4)
expect_equal(MaximumLength("0123 0123 0123 ????"), 3 * 3)
expect_equal(MaximumLength( "00112233{01}{23}{012}?"), 3 + 3 + 1)
})
test_that("MaximumLength() handles inapplicable tokens", {
# Number of regions = number of inapplicable tokens - 1
# One extra step allowable for each extra region
expect_equal(MaximumLength("11111--"), 0)
if (interactive()) {
tree <- ape::read.tree(
text = ("(a, (b, (c, (i1, (i2, (i3, e))))));"))
char <- "1110001"
charDat <- StringToPhyDat(char, TipLabels(tree))
PlotCharacter(tree, charDat)
}
expect_equal(MaximumLength("111---1"), 1)
if (interactive()) {
tree <- ape::read.tree(
text = ("(a, (b, (c, ((i1, (i2, d)), (i3, (i4, e))))));"))
char <- "111001001"
charDat <- StringToPhyDat(char, TipLabels(tree))
PlotCharacter(tree, charDat)
}
expect_equal(MaximumLength("111--1--1"), 2)
if (interactive()) {
tree <- ape::read.tree(
text = ("(a, (b, (i0, (((i1, d), (i2, e)), ((i3, c), (i4, f))))));"))
char <- "11001010101"
charDat <- StringToPhyDat(char, TipLabels(tree))
PlotCharacter(tree, charDat) # Treated as independent losses
tree <- ape::read.tree(
text = ("(a, (b, (c, (i0, (((i1, d), (i2, e)), (i3, (i4, f)))))));"))
char <- "11100101001"
charDat <- StringToPhyDat(char, TipLabels(tree))
PlotCharacter(tree, charDat) # Can support four distinct regions
}
expect_equal(MaximumLength("111--1---1"), 3)
expect_equal(MaximumLength("111-----"), 2)
expect_equal(MinimumLength("011-----"), 1)
expect_equal(MaximumLength("011-----"), 2)
expect_equal(MaximumLength("0111-----"), 3)
twoPair <- StringToPhyDat("0011-----", tips = letters[1:9])
colnames(attr(twoPair, "contrast")) <- NULL
expect_equal(MaximumLength(twoPair), 3)
expect_equal(MaximumLength("1--1---0"), 2)
expect_equal(MaximumLength("--1---1"), 1)
expect_equal(MinimumLength("--1---0"), 1)
expect_equal(MinimumLength("--1---0"), 1)
expect_equal(MaximumLength("--1---"), 0)
expect_equal(MaximumLength("-----"), 0)
expect_equal(MaximumLength("001122{12}---"), 4 + 1)
expect_equal(MaximumLength("0123 0123 0123 ----"), 3 * 3 + 2)
expect_equal(MaximumLength("00112233{01}{23}{012}----"), 3 + 3 + 1 + 2)
})
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