allSplits: Splits representation of graphs and trees.

Description

as.splits produces a list of splits or bipartitions.

Usage

allSplits(k, labels = NULL)
allCircularSplits(k, labels = NULL)
as.splits(x, ...)
# S3 method for splits
as.matrix(x, zero.print = 0L, one.print = 1L, ...)
# S3 method for splits
as.Matrix(x, ...)
# S3 method for splits
print(x, maxp = getOption("max.print"), zero.print = ".",
  one.print = "|", ...)
# S3 method for splits
c(..., recursive = FALSE)
# S3 method for splits
unique(x, incomparables = FALSE, unrooted = TRUE, ...)
# S3 method for phylo
as.splits(x, ...)
# S3 method for multiPhylo
as.splits(x, ...)
# S3 method for networx
as.splits(x, ...)
# S3 method for splits
as.prop.part(x, ...)
# S3 method for splits
as.bitsplits(x)
# S3 method for bitsplits
as.splits(x, ...)
compatible(obj1, obj2 = NULL)

Value

as.splits returns an object of class splits, which is mainly a list of splits and some attributes. Often a splits object will contain attributes confidences for bootstrap or Bayesian support values and weight storing edge weights. compatible return a lower triangular matrix where an 1 indicates that two splits are incompatible.

Arguments

k: number of taxa.
labels: names of taxa.
x: An object of class phylo or multiPhylo.
...: Further arguments passed to or from other methods.
zero.print: character which should be printed for zeros.
one.print: character which should be printed for ones.
maxp: integer, default from options(max.print), influences how many entries of large matrices are printed at all.
recursive: logical. If recursive = TRUE, the function recursively descends through lists (and pairlists) combining all their elements into a vector.
incomparables: only for compatibility so far.
unrooted: todo.
obj1, obj2: an object of class splits.

Author

Klaus Schliep klaus.schliep@gmail.com

Examples

Run this code


(sp <- as.splits(rtree(5)))
write.nexus.splits(sp)
spl <- allCircularSplits(5)
plot(as.networx(spl))