move.lineage: Move tips or clades

In RRphylo: Phylogenetic Ridge Regression Methods for Comparative Studies

Move tips or clades

Description

Move a single tip or an entire clade to a different position within the tree.

Usage

move.lineage(tree,focal,sister,poly=FALSE,rescale=TRUE,rootage=NULL)

Arguments

tree	a phylogenetic tree. The tree needs not to be ultrametric and fully dichotomous.
focal	the lineage to be moved. It can be either a tip name/number or a node number. If tree$node.label is not NULL, a focal clade can be indicated as "Clade NAMEOFTHECLADE" when appropriate. Similarly, an entire genus can be indicated as "Genus NAMEOFTHEGENUS" (see examples below).
sister	the sister tip/node where the focal must be attached. It can be tip name/number or node number. If tree$node.label is not NULL, a focal clade can be indicated as "Clade NAMEOFTHECLADE" when appropriate. Similarly, an entire genus can be indicated as "Genus NAMEOFTHEGENUS" (see examples below).
poly	logical indicating whether the focal and the sister should form a polytomous clade.
rescale	logical. If the most recent common ancestor of the focal clade is older than its new ancestor (i.e. the node right above sister), the user can choose whether the height of the focal clade must be rescaled on the height of the new ancestor (rescale=TRUE), or the topology of the tree must be modified to accommodate the height of focal as it is (rescale=FALSE, in this case scaleTree is applied). This is ignored under poly = TRUE.
rootage	the age of the tree root to be supplied if focal must be attached to it (and poly=FALSE). If rootage=NULL the total height of the tree increases by 10%.

Value

The phylogenetic tree with required topological changes.

Author(s)

Silvia Castiglione, Pasquale Raia

Examples

require(phytools)
DataCetaceans$tree->treecet

### Case 1. Moving a single tip
# sister to a tip
move.lineage(treecet,focal="Orcinus_orca",sister="Balaenoptera_musculus")->mol1
# sister to a clade
move.lineage(treecet,focal="Orcinus_orca",sister=131)->mol2
# sister to a clade by using treecet$node.label
move.lineage(treecet,focal="Balaenoptera_musculus",sister="Clade Delphinida")->mol3
# sister to a specific genus
move.lineage(treecet,focal="Orcinus_orca",sister="Genus Balaenoptera")->mol4
# sister to the tree root with and without rootage
move.lineage(treecet,focal="Balaenoptera_musculus",sister=117)->mol5
move.lineage(treecet,focal="Balaenoptera_musculus",sister=117,rootage=max(diag(vcv(treecet))))->mol6

### Case 2. Moving a clade
# sister to a tip
move.lineage(treecet,focal="Genus Mesoplodon",sister="Balaenoptera_musculus")->mol7
move.lineage(treecet,focal="Clade Delphinida",sister="Balaenoptera_musculus")->mol8
move.lineage(treecet,focal=159,sister="Balaenoptera_musculus")->mol9
# sister to a clade
move.lineage(treecet,focal="Genus Mesoplodon",sister=131)->mol10
move.lineage(treecet,focal="Clade Delphinida",sister=131)->mol11
move.lineage(treecet,focal=159,sister=131)->mol12
# sister to a clade by using treecet$node.label
move.lineage(treecet,focal="Genus Mesoplodon",sister="Clade Plicogulae")->mol13
move.lineage(treecet,focal="Clade Delphinida",sister="Clade Plicogulae")->mol14
move.lineage(treecet,focal=159,sister="Clade Plicogulae")->mol15
# sister to a specific genus
move.lineage(treecet,focal="Genus Mesoplodon",sister="Genus Balaenoptera")->mol16
move.lineage(treecet,focal="Clade Delphinida",sister="Genus Balaenoptera")->mol17
move.lineage(treecet,focal=159,sister="Genus Balaenoptera")->mol18
# sister to the tree root with and without rootage
move.lineage(treecet,focal="Genus Mesoplodon",sister=117)->mol19
move.lineage(treecet,focal="Clade Delphinida",sister=117)->mol20
move.lineage(treecet,focal=159,sister=117)->mol21
move.lineage(treecet,focal="Genus Mesoplodon",
             sister=117,rootage=max(diag(vcv(treecet))))->mol22
move.lineage(treecet,focal="Clade Delphinida",
             sister=117,rootage=max(diag(vcv(treecet))))->mol23
move.lineage(treecet,focal=159,sister=117,rootage=max(diag(vcv(treecet))))->mol24

RRphylo documentation built on April 3, 2025, 9:43 p.m.