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 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

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