Searches for phylogenetic trees that are optimal using a
user-defined criterion.
Handles inapplicable data using the algorithm of
Brazeau, Guillerme and Smith (2019)
This package exists to allow parsimony-style tree searches in R.
It extends the basic functionality available in phangorn, with a view to making tree search faster and more efficient, and allowing user-defined optimality criteria to be employed.
Implied weighting and heuristic searches such as the Parsimony Ratchet are implemented (function: Ratchet
).
Browse the vignettes (with vignette(package = "TreeSearch")
to get started.
Install and load the library from CRAN as follows:
install.packages('TreeSearch')
library('TreeSearch')
If you're feeling brave, you can install the development version thus:
if(!require(devtools)) install.packages("devtools")devtools::install_github('ms609/TreeSearch')
TreeSearch allows the implementation of various optimality criteria, including
It is also possible to specify bespoke optimality criteria.
Brazeau, M. D., Guillerme, T. and Smith, M. R. 2017. Morphological phylogenetic analysis with inapplicable data. BioRχiv. doi:10.1101/209775
D. P. Faith, J. W. H. Trueman, Towards an inclusive philosophy for phylogenetic inference. Syst. Biol. 50, 331–350 (2001). doi:10.1080/10635150118627
Farris, J. S. (1969). A successive approximations approach to character weighting. Systematic Biology, 18(4), 374–385. doi:10.2307/2412182
TreeSplits
is deprecated; use Tree2Splits
instead.CollapseNodes
and CollapseEdges
allow the creation of polytomiesTree2Splits
lists the bipartition splits implied by a tree topologySplitFrequency
now supports larger treesReadTntTree
, to avoid reliance on
generative fileRootTree
function allows rooting of tree on incompletely specified
or single-taxon outgroupAllTBR
returns all trees one TBR rearrangement awayTBRMoves
reports all possible TBR rearrangementsJackknife
conducts Jackknife resamplingSplitFrequency
reports frequency of clades in a forestSupportColour
allows visual marking of support valuesApeTime
reports the creation date of an ape-exported treeSortTree
flips nodes into a consistent left-right orderAsBinary
supports 0ReadTntTree
consensus
via ConsensusWithout
IWRatchetConsensus
now relays concavity value to subsequent functionsReadCharacters
returns labels for all characters and states if character_num = NULL
inapplicable
)ProfileParsimony
)