AdditionTree | R Documentation |
Generates a starting tree by adding each taxon in turn to the most parsimonious location.
AdditionTree(dataset, concavity = Inf, constraint, sequence)
dataset |
A phylogenetic data matrix of phangorn class
|
concavity |
Numeric specifying concavity constant for implied step
weighting.
The most appropriate value will depend on the dataset, but values around
10–15 often perform well \insertCiteGoloboff2018,Smith2019TreeSearch.
The character string "profile" employs an approximation of profile parsimony
\insertCiteFaith2001TreeSearch.
Set as |
constraint |
Either an object of class |
sequence |
Character or numeric vector listing sequence in which to add taxa. Randomized if not provided. |
AdditionTree()
returns a tree of class phylo
, rooted on
sequence[1]
.
Martin R. Smith (martin.smith@durham.ac.uk)
Impose a constraint: TreeTools::ImposeConstraint()
Neighbour-joining trees: TreeTools::NJTree()
;
TreeTools::ConstrainedNJ()
Other tree generation functions:
RandomMorphyTree()
data("inapplicable.phyData", package = "TreeSearch")
AdditionTree(inapplicable.phyData[["Longrich2010"]], concavity = 10)
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