Convert object to Splits
as.Splits() converts a phylogenetic tree to a Splits object representing
its constituent bipartition splits.
as.Splits(x, tipLabels = NULL, ...) ## S3 method for class 'phylo' as.Splits(x, tipLabels = NULL, asSplits = TRUE, ...) ## S3 method for class 'multiPhylo' as.Splits(x, tipLabels = x[[1]]$tip.label, asSplits = TRUE, ...) ## S3 method for class 'Splits' as.Splits(x, tipLabels = NULL, ...) ## S3 method for class 'list' as.Splits(x, tipLabels = NULL, asSplits = TRUE, ...) ## S3 method for class 'matrix' as.Splits(x, tipLabels = NULL, ...) ## S3 method for class 'logical' as.Splits(x, tipLabels = NULL, ...) ## S3 method for class 'Splits' as.logical(x, tipLabels = NULL, ...)
x |
Object to convert into splits: perhaps a tree of class
|
tipLabels |
Character vector specifying sequence in which to order
tip labels. Label order must (currently) match to combine or compare separate
|
... |
Presently unused. |
asSplits |
Logical specifying whether to return a |
as.Splits() returns an object of class Splits, or
(if asSplits = FALSE) a two-dimensional array of raw objects, with
each bit specifying whether or not the leaf corresponding to the respective
bit position is a member of the split.
Splits are named according to the node at the non-root end of the edge that
defines them. In rooted trees, the child of the rightmost root edge names
the split.
Martin R. Smith (martin.smith@durham.ac.uk)
Other Splits operations:
LabelSplits(),
NSplits(),
NTip(),
SplitFrequency(),
SplitsInBinaryTree(),
TipLabels(),
TipsInSplits(),
match()
splits <- as.Splits(BalancedTree(letters[1:6])) summary(splits) TipsInSplits(splits) summary(!splits) TipsInSplits(!splits) length(splits + !splits) length(unique(splits + !splits)) summary(c(splits[[2:3]], !splits[[1:2]])) moreSplits <- as.Splits(PectinateTree(letters[6:1]), tipLabel = splits) print(moreSplits, details = TRUE) match(splits, moreSplits) moreSplits %in% splits
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