PCMBase (version 1.2.10)

PCMTreeInsertSingletons: Insert singleton nodes on chosen edges

Description

Insert singleton nodes on chosen edges

Usage

PCMTreeInsertSingletons(tree, nodes, positions)
PCMTreeInsertSingletonsAtEpoch(tree, epoch, minLength = 0.1)

Arguments

tree

a phylo object

nodes

an integer vector denoting the terminating nodes of the edges on which a singleton node is to be inserted. This vector should not have duplicated nodes - if there is a need to insert two or more singleton nodes at distinct positions of the same edge, this should be done by calling the function several times with the longest position first and so on .

positions

a positive numeric vector of the same length as nodes denoting the root-ward distances from nodes at which the singleton nodes should be inserted.

epoch

a numeric indicating a distance from the root at which a singleton node should be inserted in all lineages that are alive at that time.

minLength

a numeric indicating the minimum allowed branch-length after dividing a branch by insertion of a singleton nodes. No singleton node is inserted if this would result in a branch shorter than `minLength`. Note that this condition is checked only in `PCMTreeInsertSingletonsAtEpoch`.

Value

a modified version of tree with inserted singleton nodes at the specified locations

Functions

• PCMTreeInsertSingletonsAtEpoch:

See Also

PCMTreeEdgeTimes PCMTreeLocateEpochOnBranches PCMTreeLocateMidpointsOnBranches

Examples

# NOT RUN {
set.seed(1, kind = "Mersenne-Twister", normal.kind = "Inversion")
tree <- PCMTree(ape::rtree(25))
PCMTreeSetPartRegimes(
  tree, c(`26`="a", `28`="b", `45`="c", `47`="d"), setPartition = TRUE)
# }
# NOT RUN {
PCMTreePlot(
  tree,
  palette=c(a = "red", b = "green", c = "blue", d = "magenta")) +
  ggtree::geom_nodelab(angle = 45) + ggtree::geom_tiplab(angle = 45)
# }
# NOT RUN {
cbind(tree$edge, PCMTreeEdgeTimes(tree))

id47 <- PCMTreeMatchLabels(tree, "47")
length47 <- PCMTreeGetBranchLength(tree, id47)

# insert a singleton at 0.55 (root-ward) from node 47
tree <- PCMTreeInsertSingletons(tree, nodes = "47", positions = (length47/2))
# }
# NOT RUN {
PCMTreePlot(
  tree,
  palette=c(a = "red", b = "green", c = "blue", d = "magenta")) +
  ggtree::geom_nodelab(angle = 45) + ggtree::geom_tiplab(angle = 45)
# }
# NOT RUN {
# this fails, because the branch leading to node "47" is shorter now (0.55).
ggplot2::should_stop(
  tree <- PCMTreeInsertSingletons(
    tree, nodes = "47", positions= 2* length47 / 3))

# the tree is the same
# }
# NOT RUN {
PCMTreePlot(
  tree, palette=c(a = "red", b = "green", c = "blue", d = "magenta")) +
  ggtree::geom_nodelab(angle = 45) + ggtree::geom_tiplab(angle = 45)
# }
# NOT RUN {
# we can insert at a position within the edge:
tree <- PCMTreeInsertSingletons(tree, nodes = "47", positions = length47/3)
# }
# NOT RUN {
PCMTreePlot(
  tree, palette=c(a = "red", b = "green", c = "blue", d = "magenta")) +
  ggtree::geom_nodelab(angle = 45) + ggtree::geom_tiplab(angle = 45)
# }
# NOT RUN {
# Insert singletons at all branches crossing a given epoch. This will skip
# inserting singleton nodes where the resulting branches would be shorter
# than 0.1.
tree <- PCMTreeInsertSingletonsAtEpoch(tree, 2.3)
# }
# NOT RUN {
PCMTreePlot(
  tree, palette=c(a = "red", b = "green", c = "blue", d = "magenta")) +
  ggtree::geom_nodelab(angle = 45) + ggtree::geom_tiplab(angle = 45)
# }
# NOT RUN {
# Insert singletons at all branches crossing a given epoch
tree <- PCMTreeInsertSingletonsAtEpoch(tree, 2.3, minLength = 0.001)
# }
# NOT RUN {
PCMTreePlot(
  tree,
  palette=c(a = "red", b = "green", c = "blue", d = "magenta")) +
  ggtree::geom_nodelab(angle = 45) + ggtree::geom_tiplab(angle = 45)
# }