EasyTrees() ‘shiny’ graphical user interface for tree
search
AdditionTree() adds each taxon in sequence to the most
parsimonious place on the tree, generating a more parsimonious starting
tree than neighbour-joining
PlotCharacter() reconstructs character distributions on
trees
ConstrainedNJ() constructs starting trees that respect
a constraint
ImposeConstraint() reconciles a tree with a
constraint
SiteConcordance() calculates exact site
concordance
ConcordantInformation() evaluates signal:noise of
dataset implied by a given tree
PrepareDataProfile() simplifies dataset to allow
partial search when multiple applicable tokens are present
Resample() conducts bootstrap and jackknife
resampling
Consistency() calculates consistency and retention
‘indices’
MinimumLength() calculates minimum length of character
in a dataset on any tree.
Improvements
TreeLength() supports lists of trees
Set handling of ‘gap’ token (-) when creating Morphy object with
gap =
Label nodes with split frequencies using
JackLabels(plot = FALSE)
Support for topological constraints during tree search
Remove redundant function AsBinary()
Drop nTip parameter in RandomTreeScore()
(infer from morphyObj)
C implementations of rearrangement functions
Improved command line interface for search progress messaging
Deprecations
Remove redundant internal function
LogisticPoints()
TreeSearch 0.4.3 (2020-07-09)
Update tests for compatibility with ‘TreeTools’ v1.1.0
Improve memory and pointer handling
TreeSearch 0.4.2 (2020-07-07)
Update tests for compatibility with ‘TreeTools’ v1.1.0
TreeSearch 0.4.1 (2020-06-09)
Compatibility with ‘TreeTools’ v1.0.0
TreeSearch 0.4.0 (2020-02-06)
New features
PhyDatToMatrix(), complementing
MatrixToPhyDat()
Documentation with ‘pkgdown’
JackLabels() helper function
Changes
Move tree distance measures to new package ‘TreeDist’
Move tree utility functions to new package ‘TreeTools’
Rename functions
MinimumSteps()→MinimumLength() and
FitchSteps()→CharacterLength()
Enhancements
Improve speed of tests (by increasing probability of false
positives)
Use message in place of cat, to allow use
of suppressMessages()
TreeSearch 0.3.2 (2019-06-03)
Improve text, content and build speed of vignettes
TreeSearch 0.3.1
New features
NyeTreeSimilarity() function implements the tree
similarity metric of Nye et al. (2006)
MatchingSplitDistance() function implementing the
Matching Split distance of Bogdanowicz & Giaro (2012)
Bug fixes
Check whether input tree is bifurcating before attempting
rearrangements, to avoid crashes on unsupported input
TreeSearch 0.3.0 (2019-03-21)
New features
Implement an information theoretic tree distance measure (Smith,
2020)
Prepare for new random number generator in R3.6.0
Deprecations
Function TreeSplits() is deprecated; use
as.Splits() instead
Bug fixes
Correct some mistakes in the documentation
TreeSearch 0.2.2 (2019-01-02)
Correct vignette titles
TreeSearch 0.2.1 (2018-12-07)
New features
CollapseNodes() and CollapseEdges() allow
the creation of polytomies
Tree2Splits() lists the bipartition splits implied by a
tree topology
Enhancements
SplitFrequency() now 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 (2018-09-10)
New features
RootTree() allows rooting of tree on incompletely
specified or single-taxon outgroup
AllTBR() returns all trees one TBR rearrangement
away
TBRMoves() reports all possible TBR rearrangements
Jackknife() conducts Jackknife resampling
SplitFrequency() reports frequency of clades in a
forest
SupportColour() allows visual marking of support
values
ApeTime() reports the creation date of an ape-exported
tree
SortTree() flips nodes into a consistent left-right
order
AsBinary() supports 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 (2018-03-20)
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 (2018-03-14)
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 consensus()
via ConsensusWithout()
Bug fixes
C11 compliance
IWRatchetConsensus() now relays concavity value to
subsequent functions
ReadCharacters() returns labels for all characters and
states if character_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
Inapplicable tokens:
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)