NEWS
Quartet 1.2.7
VizualizeQuartet()
now returns calculation results.
- Use spectrum legend in
VisualizeQuartet()
.
- Include CSL file within package to remove external dependency.
Quartet 1.2.6 (2024-02-09)
- Drop obsolete C++11 specification.
- Update minimum R version to 3.5 (for Ternary).
- R <3.6 is no longer formally supported.
Quartet 1.2.5 (2022-07-08)
Quartet 1.2.4 (2022-05-02)
QuartetStates()
handles absent leaves gracefully.
- Copy-edit documentation.
Quartet 1.2.3
- Replace deprecated function
TreeTools::in.Splits()
.
- Update test cases in readiness for TreeTools v1.7.0.
Quartet 1.2.2 (2020-12-09)
- Package 'vdiffr' now used conditionally.
Quartet 1.2.0 (2020-10-21)
New features
CompareQuartetsMulti()
compares quartet status in one tree with status in
multiple others.
VisualizeQuartets()
depicts contribution of splits to quartet score.
SimilarityToReference()
allows comparison against specified reference
topology.
Changes
- Deprecate
RobinsonFoulds()
: renamed to RawSymmetricDifference()
.
QuartetState[s]()
now uses sister-of-4 notation, rather than sister-of-1,
to give values within [0, 3].
ManyToManyQuartetAgreement()
now returns entries for N
and Q
.
Improvements
- Faster C++ implementation of
AllQuartets()
and QuartetStates()
.
QuartetStatus()
now supports non-identical leaf samples.
SimilarityMetrics()
now handles single tree comparisons.
- Correctly calculate resolution of unrooted trees with unconventional node
numbering conventions.
- Remove errant name when comparing unnamed tree pairs.
- Small improvements to
PlotQuartet()
.
- Minor efficiency improvements.
- Documentation improvements.
Quartet 1.1.0 (2020-01-28)
- Pass trees directly to C, without writing to temporary intermediate file.
- Use
TreeTools
in place of TreeSearch
, supporting new Splits
class.
- Facilitate comparison between lists of multiple trees.
- Fix Latex error in vignettes.
Quartet 1.0.3 (2019-12-30)
- Remove deprecated C function
ptr_fun
.
- Clarify some documentation pages.
Quartet 1.0.2 (2019-03-06)
- Force R 3.5.0-style random number generation in examples,
to ensure backward compatibility.
- Add caterpillar trees to
sq_trees
, to illustrate issues with partition-based
distance metrics.
Quartet 1.0.1 (2019-01-22)
- Improved portability of C++ code.
Quartet 1.0.0 (2019-01-16)
New features
- Add functions to generate ternary plots from tree similarity measures.
Improvements
- Use tqDist for all quartet calculations.
- Remove single "splits" from splits objects.
- Simplify installation via
github_install
.
- Add missing details to documentation.
Modifications
- Function
SimilarityMetrics
now takes the output of QuartetStatus(trees)
,
rather than a list of trees.
- Function
SplitStatus
now returns output using the same column headers as QuartetStatus
- Column
N
added to QuartetStatus
output.
- Function names changed, to become more precise:
QuartetMetrics
→ SimilarityMetrics
MatchingSplits
→ SplitStatus
MatchingQuartets
→ QuartetStatus
Choices
→ AllQuartets
Quartet 0.2.0
Modifications
- Add
MatchingSplits
function to calculate number of splits contradicted / unresolved.
- Add vignettes to document when the quartet metric may be preferable to other tree distance metrics.