R/IWScore.R, R/tree_length.R
TreeLength.RdTreeLength() uses the Morphy library (Brazeau et al. 2017)
to calculate a parsimony score for a tree, handling inapplicable data
according to the algorithm of Brazeau et al. (2019)
.
Trees may be scored using equal weights, implied weights
(Goloboff 1993)
, or profile parsimony
(Faith and Trueman 2001)
.
IWScore(tree, dataset, concavity = 10L, ...)
TreeLength(tree, dataset, concavity = Inf)
# S3 method for phylo
TreeLength(tree, dataset, concavity = Inf)
# S3 method for numeric
TreeLength(tree, dataset, concavity = Inf)
# S3 method for list
TreeLength(tree, dataset, concavity = Inf)
# S3 method for multiPhylo
TreeLength(tree, dataset, concavity = Inf)
Fitch(tree, dataset)A tree of class phylo, a list thereof (optionally of class
multiPhylo), or an integer -- in which case tree random trees will be
uniformly sampled.
A phylogenetic data matrix of phangorn class
phyDat, whose names correspond to the labels of any accompanying tree.
Determines the degree to which extra steps beyond the first
are penalized. Specify a numeric value to use implied weighting
(Goloboff 1993)
; 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
(Goloboff et al. 2018; Smith 2019)
.
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.
Specify "profile" to employ profile parsimony (Faith and Trueman 2001)
.
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.
Brazeau MD, Guillerme T, Smith MR (2019).
“An algorithm for morphological phylogenetic analysis with inapplicable data.”
Systematic Biology, 68(4), 619--631.
doi:10.1093/sysbio/syy083
.
Brazeau MD, Smith MR, Guillerme T (2017).
“MorphyLib: a library for phylogenetic analysis of categorical trait data with inapplicability.”
doi:10.5281/zenodo.815372
.
Faith DP, Trueman JWH (2001).
“Towards an inclusive philosophy for phylogenetic inference.”
Systematic Biology, 50(3), 331--350.
doi:10.1080/10635150118627
.
Goloboff PA (1993).
“Estimating character weights during tree search.”
Cladistics, 9(1), 83--91.
doi:10.1111/j.1096-0031.1993.tb00209.x
.
Goloboff PA, Torres A, Arias JS (2018).
“Weighted parsimony outperforms other methods of phylogenetic inference under models appropriate for morphology.”
Cladistics, 34(4), 407--437.
doi:10.1111/cla.12205
.
Smith MR (2019).
“Bayesian and parsimony approaches reconstruct informative trees from simulated morphological datasets.”
Biology Letters, 15(2), 20180632.
doi:10.1098/rsbl.2018.0632
.
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()
data("inapplicable.datasets")
tree <- TreeTools::BalancedTree(inapplicable.phyData[[1]])
TreeLength(tree, inapplicable.phyData[[1]])
#> [1] 1117
TreeLength(tree, inapplicable.phyData[[1]], concavity = 10)
#> [1] 52.75785
TreeLength(tree, inapplicable.phyData[[1]], concavity = "profile")
#> → Inapplicable tokens treated as ambiguous for profile parsimony
#> Warning: Can handle max. 2 informative tokens. Dropping others.
#> Warning: Can handle max. 2 informative tokens. Dropping others.
#> Warning: Can handle max. 2 informative tokens. Dropping others.
#> Warning: Can handle max. 2 informative tokens. Dropping others.
#> Warning: Can handle max. 2 informative tokens. Dropping others.
#> Warning: Can handle max. 2 informative tokens. Dropping others.
#> Warning: Can handle max. 2 informative tokens. Dropping others.
#> Warning: Can handle max. 2 informative tokens. Dropping others.
#> Warning: Can handle max. 2 informative tokens. Dropping others.
#> Warning: Can handle max. 2 informative tokens. Dropping others.
#> Warning: Can handle max. 2 informative tokens. Dropping others.
#> Warning: Can handle max. 2 informative tokens. Dropping others.
#> Warning: Can handle max. 2 informative tokens. Dropping others.
#> Warning: Can handle max. 2 informative tokens. Dropping others.
#> Warning: Can handle max. 2 informative tokens. Dropping others.
#> Warning: Can handle max. 2 informative tokens. Dropping others.
#> Warning: Can handle max. 2 informative tokens. Dropping others.
#> Warning: Can handle max. 2 informative tokens. Dropping others.
#> Warning: Can handle max. 2 informative tokens. Dropping others.
#> Warning: Can handle max. 2 informative tokens. Dropping others.
#> [1] 3941.387
TreeLength(5, inapplicable.phyData[[1]])
#> [1] 1957 1995 1966 1953 1968