Addition tree

Generates a starting tree by adding each taxon in turn to the most parsimonious location.

Usage

AdditionTree(dataset, concavity = Inf, constraint, sequence)

Arguments

dataset

A phylogenetic data matrix of phangorn class phyDat, whose names correspond to the labels of any accompanying tree. Perhaps load into R using ReadAsPhyDat. Additive (ordered) characters can be handled using Decompose.

concavity

Determines the degree to which extra steps beyond the first are penalized. Specify a numeric value to use implied weighting Goloboff1993TreeSearch; concavity specifies k in k / e + k. A value of 10 is recommended; TNT sets a default of 3, but this is too low in some circumstances Goloboff2018,Smith2019TreeSearch. Better still explore the sensitivity of results under a range of concavity values, e.g. k = 2 ^ (1:7). Specify Inf to weight each additional step equally, (which underperforms step weighting approaches Goloboff2008,Goloboff2018,Goloboff2019,Smith2019TreeSearch). Specify "profile" to employ an approximation of profile parsimony Faith2001TreeSearch.

constraint

Either an object of class phyDat, in which case returned trees will be perfectly compatible with each character in constraint; or a tree of class phylo, all of whose nodes will occur in any output tree. See ImposeConstraint() and vignette for further examples.

sequence

Character or numeric vector listing sequence in which to add taxa. Randomized if not provided.

Value

AdditionTree() returns a tree of class phylo, rooted on sequence[1].

See also

Impose a constraint: TreeTools::ImposeConstraint()

Neighbour-joining trees: TreeTools::NJTree(); TreeTools::ConstrainedNJ()

Other tree generation functions: RandomMorphyTree()

Author

Martin R. Smith (martin.smith@durham.ac.uk)

Examples

data("inapplicable.phyData", package = "TreeSearch")
AdditionTree(inapplicable.phyData[["Longrich2010"]], concavity = 10)
#> 
#> Phylogenetic tree with 20 tips and 19 internal nodes.
#> 
#> Tip labels:
#>   Psittacosaurus_spp, Prenocephale_prenes, Pachycephalosaurus_wyomingensis, Texacephale_langstoni, Hanssuesia_sternbergi, Homalocephale_calathocercos, ...
#> 
#> Rooted; no branch length.