Changelog
Source:NEWS.md
Quartet v1.2.6.9001 (development, 2024-04-16)
-
VizualizeQuartet()
now returns calculation results. - Use spectrum legend in
VisualizeQuartet()
.
Quartet v1.2.6 (2024-02-08)
CRAN release: 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 v1.2.4 (2022-05-02)
CRAN release: 2022-05-02
-
QuartetStates()
handles absent leaves gracefully. - Copy-edit documentation.
Quartet v1.2.3
- Replace deprecated function
TreeTools::in.Splits()
. - Update test cases in readiness for TreeTools v1.7.0.
Quartet v1.2.0 (2020-10-22)
CRAN release: 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 toRawSymmetricDifference()
. -
QuartetState[s]()
now uses sister-of-4 notation, rather than sister-of-1, to give values within [0, 3]. -
ManyToManyQuartetAgreement()
now returns entries forN
andQ
.
Improvements
- Faster C++ implementation of
AllQuartets()
andQuartetStates()
. -
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 v1.1.0 (2020-01-29)
CRAN release: 2020-01-28
- Pass trees directly to C, without writing to temporary intermediate file.
- Use
TreeTools
in place ofTreeSearch
, supporting newSplits
class. - Facilitate comparison between lists of multiple trees.
- Fix Latex error in vignettes.
Quartet v1.0.3
CRAN release: 2019-12-30
- Remove deprecated C function
ptr_fun
. - Clarify some documentation pages.
Quartet v1.0.2
CRAN release: 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 v1.0.0 (2019-01-09)
CRAN release: 2019-01-16
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 ofQuartetStatus(trees)
, rather than a list of trees. - Function
SplitStatus
now returns output using the same column headers asQuartetStatus
- Column
N
added toQuartetStatus
output. - Function names changed, to become more precise:
-
QuartetMetrics
→SimilarityMetrics
-
MatchingSplits
→SplitStatus
-
MatchingQuartets
→QuartetStatus
-
Choices
→AllQuartets
-