TreeSearch 0.2.2

Bug fixes

SplitFrequency now supports larger trees
Can specify tip labels directly to ReadTntTree, to avoid reliance on generative file

RootTree function 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

[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

[IW]MultiRatchet now considers trees identical even if they’ve been hit a different number of times

C11 compliance
IWRatchetConsensus now relays concavity value to subsequent functions
ReadCharacters returns labels for all characters and states if character_num = NULL

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

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

[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

Integrated with this package (previously in inapplicable)
Handle inapplicable data via API to Martin Brazeau’s Morphy Phylogenetic Library