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Fix .SortTokens() crash for states only seen inside a polymorphism #142

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Merged
ms609 merged 1 commit into from
Aug 7, 2026
Merged

Fix .SortTokens() crash for states only seen inside a polymorphism #142

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13 changes: 11 additions & 2 deletions R/Consistency.R
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Original file line number Diff line number Diff line change
Expand Up @@ -220,8 +220,17 @@ ExpectedLength <- function(dataset, tree, nRelabel = 1000, compress = FALSE) {
2 ^ seq_along(tokensToSort)

nAssigned <- log2(nWhole) + 1
wholes <- mapping[2 ^ (seq_len(nAssigned) - 1)]

wholeBits <- 2 ^ (seq_len(nAssigned) - 1)
# A state that never occurs on its own -- only ever within an ambiguous
# (polymorphic) token -- has no row in `mapping` yet. Give it its own
# unused code so that ambiguous tokens referencing it still sum to a
# meaningful value, rather than silently contributing zero.
unassigned <- wholeBits[mapping[wholeBits] == 0]
if (length(unassigned)) {
mapping[unassigned] <- 2 ^ (length(tokensToSort) + seq_along(unassigned))
}
wholes <- mapping[wholeBits]

ambigTokens <- contr[ambig & seq_along(contr) %fin% char]
mapping[ambigTokens] <- apply(matrix(as.logical(intToBits(contr[ambig])), 32),
2, function(x) sum(wholes[x]))
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23 changes: 21 additions & 2 deletions tests/testthat/test-Consistency.R
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Expand Up @@ -92,6 +92,20 @@ test_that("Consistency() handles `-`", {
)
})

test_that("ExpectedLength() handles a state only seen within a polymorphism", {
# A state that never appears on its own -- only ever inside an ambiguous
# (polymorphic) token -- must not crash .SortTokens()'s wholes/ambiguity
# remapping. Regression test for a crash reported downstream of the
# #88/#87/#94/#112 fix:
# Error in names(object) <- nm :
# 'names' attribute [4] must be the same length as the vector [2]
tree <- TreeTools::BalancedTree(paste0("t", 1:4))
dat <- StringToPhyDat("00(12)(12)", TipLabels(tree))
expect_silent(el <- ExpectedLength(dat, tree, nRelabel = 20))
expect_type(el, "double")
expect_length(el, 1)
})

test_that(".SortTokens() works", {
contrast <- structure(c(0, 0, 1, 1, 0, 0, 0, 1, 0,
1, 0, 1, 0, 0, 0, 0, 0, 1,
Expand Down Expand Up @@ -119,8 +133,13 @@ test_that(".SortTokens() works", {
# Inapplicables with ambiguity
# TODO it would be nice to return 7 in place of 63, but
# unnecessarily complex to implement at the moment
expect_equal(TreeSearch:::.SortTokens(rep(c(1, 2, 3, 4, 8, 9),
expect_equal(TreeSearch:::.SortTokens(rep(c(1, 2, 3, 4, 8, 9),
c(2, 3, 4, 5, 1, 1)), cont, inapp = 1),
rep(c(4, 2, 63, 1, 3, 6), c(2, 3, 4, 5, 1, 1)))


# States that only ever occur within a polymorphism (never on their own)
# must not be silently mapped to zero -- regression test for a crash in
# ExpectedLength() when a character like "00(12)(12)" is scored.
expect_equal(TreeSearch:::.SortTokens(rep(1:2, 2:2), c(1, 6), NA),
rep(c(2, 12), 2:2))
})
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