Lists which paths present in a master tree are present when leaves are dropped.
KeptPaths(paths, keptVerts, all = TRUE)
# S3 method for data.frame
KeptPaths(paths, keptVerts, all = TRUE)
# S3 method for matrix
KeptPaths(paths, keptVerts, all = TRUE)data.frame of paths in master tree, perhaps generated using
PathLengths().
Logical specifying whether each entry is retained in the
reduced tree, perhaps generated using KeptVerts().
Logical: if TRUE, return all paths that occur in the reduced
tree; if FALSE, return only those paths that correspond to a single edge.
that correspond to edges in the reduced tree.
Ignored if paths is a matrix.
KeptPaths() returns a logical vector specifying whether each path
in paths occurs when keptVerts vertices are retained.
Other tree manipulation:
AddTip(),
CollapseNode(),
ConsensusWithout(),
DropTip(),
EnforceOutgroup(),
ImposeConstraint(),
KeptVerts(),
LeafLabelInterchange(),
MakeTreeBinary(),
RenumberTips(),
RenumberTree(),
Renumber(),
RootTree(),
SortTree(),
Subtree(),
TipTimedTree(),
TrivialTree
master <- BalancedTree(9)
paths <- PathLengths(master)
keptTips <- c(1, 5, 7, 9)
keptVerts <- KeptVerts(master, keptTips)
KeptPaths(paths, keptVerts)
#> [1] TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> [13] FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE
#> [25] FALSE FALSE TRUE TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE
#> [37] FALSE TRUE FALSE FALSE FALSE FALSE
paths[KeptPaths(paths, keptVerts, all = FALSE), ]
#> start end length
#> 2 11 1 3
#> 16 11 5 2
#> 22 15 7 2
#> 28 15 9 2
#> 30 10 11 1
#> 38 10 15 1