IWScore | R Documentation |
TreeLength()
uses the Morphy library \insertCiteBrazeau2017TreeSearch
to calculate a parsimony score for a tree, handling inapplicable data
according to the algorithm of \insertCiteBrazeau2019;textualTreeSearch.
Trees may be scored using equal weights, implied weights
\insertCiteGoloboff1993TreeSearch, or profile parsimony
\insertCiteFaith2001TreeSearch.
IWScore(tree, dataset, concavity = 10L, ...)
TreeLength(tree, dataset, concavity = Inf)
## S3 method for class 'phylo'
TreeLength(tree, dataset, concavity = Inf)
## S3 method for class 'numeric'
TreeLength(tree, dataset, concavity = Inf)
## S3 method for class 'list'
TreeLength(tree, dataset, concavity = Inf)
## S3 method for class 'multiPhylo'
TreeLength(tree, dataset, concavity = Inf)
Fitch(tree, dataset)
tree |
A tree of class |
dataset |
A phylogenetic data matrix of phangorn class
|
concavity |
Determines the degree to which extra steps beyond the first
are penalized. Specify a numeric value to use implied weighting
\insertCiteGoloboff1993TreeSearch; |
... |
unused; allows additional parameters specified within ... to be received by the function without throwing an error. |
TreeLength()
returns a numeric vector containing the score for
each tree in tree
.
Martin R. Smith (using Morphy C library, by Martin Brazeau)
Conduct tree search using MaximizeParsimony()
(command line),
EasyTrees()
(graphical user interface), or TreeSearch()
(custom optimality criteria).
See score for each character: CharacterLength()
.
Other tree scoring:
CharacterLength()
,
LengthAdded()
,
MinimumLength()
,
MorphyTreeLength()
,
TaxonInfluence()
data("inapplicable.datasets")
tree <- TreeTools::BalancedTree(inapplicable.phyData[[1]])
TreeLength(tree, inapplicable.phyData[[1]])
TreeLength(tree, inapplicable.phyData[[1]], concavity = 10)
TreeLength(tree, inapplicable.phyData[[1]], concavity = "profile")
TreeLength(5, inapplicable.phyData[[1]])
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