TreeSearch
Phylogenetic Tree Search Using Custom Optimality Criteria
Searches for phylogenetic trees that are optimal using a user-defined criterion.
Implements Profile Parsimony (Faith and Trueman, 2001)
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.
Installation
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')Optimailty criteria
TreeSearch allows the implementation of various optimality criteria, including
- The Profile Parsimony approach introduced by Faith and Trueman (2001).
- Successive Approximations weighting (Farris 1969).
- Fitch parsimony with inapplicable data (Brazeau, Guillerme and Smith, 2017).
It is also possible to specify bespoke optimality criteria.
References
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
News
TreeSearch 0.3.0
New features
- Implement an information theoretic tree distance measure (Smith, in prep)
- Prepare for new random number generator in R3.6.0
Deprecations
- Function
TreeSplitsis deprecated; useTree2Splitsinstead.
Bug fixes
- Correct some mistakes in the documentation
TreeSearch 0.2.2
Bug fixes
- Correct vignette titles
TreeSearch 0.2.1
New features
CollapseNodesandCollapseEdgesallow the creation of polytomiesTree2Splitslists the bipartition splits implied by a tree topology
Enhancements
SplitFrequencynow supports larger trees- Can specify tip labels directly to
ReadTntTree, to avoid reliance on generative file
Bug fixes
- Export missing functions
TreeSearch 0.2.0
New features
RootTreefunction allows rooting of tree on incompletely specified or single-taxon outgroupAllTBRreturns all trees one TBR rearrangement awayTBRMovesreports all possible TBR rearrangementsJackknifeconducts Jackknife resamplingSplitFrequencyreports frequency of clades in a forestSupportColourallows visual marking of support valuesApeTimereports the creation date of an ape-exported treeSortTreeflips nodes into a consistent left-right orderAsBinarysupports 0
Enhancements
- [IW]RatchetConsensus renamed to [IW]MultiRatchet, giving a better description of the function's purpose
- Don't warn about missing EOL when reading Nexus or TNT files
- Add new 12-colour colourblind-friendly palette
- FitchSteps now supports datasets with tips not found in tree
- Improve portability of function
ReadTntTree
Bug fixes
- [IW]MultiRatchet now considers trees identical even if they've been hit a different number of times
TreeSearch 0.1.2
Bug fixes
- Update MorphyLib library to fix C warnings
- Remove non-ASCII characters from data
- Disable slow-building and problematic vignette
- Use local copy of citation style when building vignettes
TreeSearch 0.1.0
New features
- Helper functions to read Nexus and TNT data and trees.
- Brewer palette in local data to allow easier colouring
Enhancements
- Allow additional parameters to be passed to
consensusviaConsensusWithout
Bug fixes
- C11 compliance
IWRatchetConsensusnow relays concavity value to subsequent functionsReadCharactersreturns labels for all characters and states ifcharacter_num = NULL
TreeSearch 0.0.8
New features
- Added NJTree function as shortcut to generate Neighbour-Joining tree from a dataset
- Add functions to allow recovery of all trees one rearrangement from that input
Efficiency gains
- Separate out NNISwap functions to allow more efficient rearrangement of edgeLists
- [9002] Improve efficiency by using three-pass algorithm in place of four-pass precursor
- [9004] Bootstrap search improvements
Bug fixes
- [9003] User now able to specify value of concavity constant (was overridden to k = 4)
- [9003] Bootstrap replicates now scored correctly (and without warning) under implied weights
TreeSearch 0.0.7
Inapplicables:
- Integrated with this package (previously in
inapplicable) - Handle inapplicable data via API to Martin Brazeau's Morphy Phylogenetic Library
Profile Parsimony:
- Integrated with this package (previously in
ProfileParsimony) - Faster calculation of concavity profiles in C
- Persistent memoization with R.cache
TreeSearch 0.0.6
- First CRAN submission