New vignette on how to compare tree sets.
PathVector() now treats trees with a root node as
rooted.
Fix plot layout in treespace vignette.
Informative failure when not enough memory for
consensus_info().
Replace throw with stop in
C++.
Correct calculation of trustworthiness and continuity metrics.
Depict strain in minimum spanning trees with
StrainCol() and helper function
MSTSegments().
Update tests for consistency with “TreeTools” v1.7.
Use lighter Rcpp headers.
Support ConsensusInfo(p > 0.5).
Address hypervolume comparison in vignettes.
Support uniform manifold approximation and projection in app.
Speed improvements, using optimizations suggested by Alexis Stamatakis’ Bioinformatics group.
Support for parallel computation via
StartParallel().
Progress bars.
Solaris compatibility.
Modest vignette improvements.
spic/scic abbreviation recognition.
ConsensusInfo() quickly calculates the splitwise
information content of the consensus of a set of trees, after Smith
(forthcoming).
SplitwiseInfo() and ClusteringInfo()
gain a p parameter to reflect the reduced information
content of splits with lower support values, and a sum
parameter to allow return of individual split information
content.
KCDiameter() approximates the diameter of the
Kendall-Colijn metric.
Plot3() (experimental) provides pseudo-3D
plotting.
Project()/ProjectionQuality() re-named
to MapTrees()/MappingQuality().
SpectralClustering() re-named to
SpectralEigens().
Add self-organizing map example to treespace vignette.
Allow the specification of custom vectors in the Kendall–Colijn metric.
Faster all-to-all tree distance calculation.
Diagnose and fix memory leaks, including over-long reported matchings.
Explicitly import shiny/shinyjs functions.
Project() launches ‘shiny’ app for projection and
analysis of tree space.
ProjectionQuality() calculates trustworthiness and
continuity of tree space mappings.
Faster calculation of Robinson–Foulds distance (using algorithm of Day (1985)) and clustering information distance.
New class ClusterTable to allow faster distance
computation with Day (1985) algorithm.
Improve error messages in
CalculateTreeDist().
Improvements to vignettes.
Use package ‘vdiffr’ conditionally.
TreeDistance() and related functions now return a
dist object when computing all distances between all pairs
of trees in a list.
Improve floating-point arithmetic in TreeDistance()
functions.
TreeDistance() now returns a distance (as
documented), rather than a similarity.
Fix rounding error in NNI ‘Li’ upper estimate, and improve NNI performance.
Reduce precision of LAPJV so rounding errors do not result in interminable run times.
Improvements to NNIDist() in light of Fack et
al. (2002).
Add NNIDiameter(): approximate diameter of NNI
distance.
Remove vignette ‘Interpreting tree distances’: duplicates https://ms609.github.io/TreeDistData/articles/09-expected-similarity.html.
Remove redundant data object oneOverlap.
Fix an issue when installing on R 3.x (require C++11 to ensure
declaration of UINT_FAST16_MAX).
Fix memory-handling bug in lapjv().