From 09502602c58418e779c25402bda776bc2d04ccbe Mon Sep 17 00:00:00 2001 From: GitHub Actions Date: Tue, 23 Apr 2024 09:15:26 +0000 Subject: [PATCH] cli-147-856 --- dev/CODE_OF_CONDUCT.html | 6 +- dev/CONTRIBUTING.html | 6 +- dev/articles/Generalized-RF.html | 6 +- dev/articles/Robinson-Foulds.html | 6 +- dev/articles/Using-TreeDist.html | 12 ++-- dev/articles/compare-treesets.html | 6 +- dev/articles/different-leaves.html | 6 +- dev/articles/index.html | 6 +- dev/articles/information.html | 6 +- dev/articles/landscapes.html | 12 ++-- .../fill.css | 0 dev/articles/treespace.html | 6 +- dev/articles/using-distances.html | 6 +- dev/authors.html | 12 ++-- dev/index.html | 25 ++----- dev/news/index.html | 11 +-- dev/pkgdown.yml | 10 +-- dev/reference/AllSplitPairings.html | 6 +- dev/reference/CalculateTreeDistance.html | 6 +- dev/reference/CompareAll.html | 6 +- dev/reference/Entropy.html | 6 +- dev/reference/GeneralizedRF.html | 6 +- dev/reference/JaccardRobinsonFoulds.html | 6 +- dev/reference/KendallColijn.html | 6 +- dev/reference/LAPJV.html | 6 +- dev/reference/MASTSize.html | 6 +- dev/reference/MSTSegments.html | 6 +- dev/reference/MapTrees.html | 11 ++- dev/reference/MappingQuality.html | 6 +- dev/reference/MatchingSplitDistance.html | 6 +- .../MeilaVariationOfInformation.html | 6 +- dev/reference/NNIDist.html | 6 +- dev/reference/NormalizeInfo.html | 69 ++++++++++++++++++- dev/reference/NyeSimilarity.html | 6 +- dev/reference/PathDist.html | 6 +- dev/reference/Plot3.html | 6 +- dev/reference/ReportMatching.html | 6 +- dev/reference/Robinson-Foulds.html | 11 ++- dev/reference/SPRDist.html | 6 +- dev/reference/SpectralEigens.html | 6 +- dev/reference/SplitEntropy.html | 6 +- dev/reference/SplitSharedInformation.html | 6 +- dev/reference/SplitsCompatible.html | 6 +- dev/reference/StartParallel.html | 6 +- dev/reference/TreeDist-package.html | 6 +- dev/reference/TreeDistPlot.html | 6 +- dev/reference/TreeDistance.html | 21 +++--- dev/reference/TreeInfo.html | 6 +- dev/reference/VisualizeMatching.html | 6 +- dev/reference/cluster-statistics.html | 6 +- dev/reference/dot-MASTSizeEdges.html | 6 +- dev/reference/dot-PairMean.html | 6 +- dev/reference/dot-TreeDistance.html | 6 +- dev/reference/index.html | 14 ++-- dev/reference/kmeanspp.html | 6 +- dev/reference/median.multiPhylo.html | 6 +- 56 files changed, 258 insertions(+), 214 deletions(-) rename dev/articles/landscapes_files/{htmltools-fill-0.5.8 => htmltools-fill-0.5.8.1}/fill.css (100%) diff --git a/dev/CODE_OF_CONDUCT.html b/dev/CODE_OF_CONDUCT.html index b2c3f1eb9..971730a6e 100644 --- a/dev/CODE_OF_CONDUCT.html +++ b/dev/CODE_OF_CONDUCT.html @@ -1,5 +1,5 @@ -Contributor Code of Conduct • TreeDistContributor Code of Conduct • TreeDistCONTRIBUTING • TreeDist + @@ -42,7 +42,7 @@ TreeDist - 2.7.0.9001 + 2.7.0.9002 @@ -432,7 +432,7 @@

References

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/dev/articles/Robinson-Foulds.html b/dev/articles/Robinson-Foulds.html index 0b7c74677..d28854842 100644 --- a/dev/articles/Robinson-Foulds.html +++ b/dev/articles/Robinson-Foulds.html @@ -6,7 +6,7 @@ Extending the Robinson-Foulds metric • TreeDist - + @@ -42,7 +42,7 @@ TreeDist - 2.7.0.9001 + 2.7.0.9002 @@ -458,7 +458,7 @@

References

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/dev/articles/Using-TreeDist.html b/dev/articles/Using-TreeDist.html index a53d260b6..d3faa801f 100644 --- a/dev/articles/Using-TreeDist.html +++ b/dev/articles/Using-TreeDist.html @@ -6,7 +6,7 @@ Calculate tree similarity with 'TreeDist' • TreeDist - + @@ -42,7 +42,7 @@ TreeDist - 2.7.0.9001 + 2.7.0.9002 @@ -204,12 +204,12 @@

Multiple comparisonsTreeDistance(oneTree, twoTrees) 
##       one       two 
-## 0.8390473 0.8386626
+## 0.7826864 0.6856279 
 TreeDistance(twoTrees, threeTrees)
##             a         b         c
-## one 0.8277881 0.6278379 0.7178329
-## two 0.8094458 0.7718845 0.7914965
+## one 0.8620894 0.7514794 0.7861809 +## two 0.8556624 0.7150163 0.7658788
@@ -308,7 +308,7 @@

What next?

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/dev/articles/compare-treesets.html b/dev/articles/compare-treesets.html index 44320422a..482d92a85 100644 --- a/dev/articles/compare-treesets.html +++ b/dev/articles/compare-treesets.html @@ -6,7 +6,7 @@ Comparing sets of trees from different analyses • TreeDist - + @@ -42,7 +42,7 @@ TreeDist - 2.7.0.9001 + 2.7.0.9002 @@ -342,7 +342,7 @@

References

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/dev/articles/different-leaves.html b/dev/articles/different-leaves.html index c42a702b7..42af4850a 100644 --- a/dev/articles/different-leaves.html +++ b/dev/articles/different-leaves.html @@ -6,7 +6,7 @@ Trees with different leaves • TreeDist - + @@ -42,7 +42,7 @@ TreeDist - 2.7.0.9001 + 2.7.0.9002 @@ -244,7 +244,7 @@

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/dev/articles/index.html b/dev/articles/index.html index 3f8576416..dc3f1ac22 100644 --- a/dev/articles/index.html +++ b/dev/articles/index.html @@ -1,5 +1,5 @@ -Articles • TreeDistArticles • TreeDist + @@ -42,7 +42,7 @@ TreeDist - 2.7.0.9001 + 2.7.0.9002 @@ -468,7 +468,7 @@

References

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/dev/articles/landscapes.html b/dev/articles/landscapes.html index 033d8ffa6..9b5825634 100644 --- a/dev/articles/landscapes.html +++ b/dev/articles/landscapes.html @@ -6,7 +6,7 @@ Analysing landscapes of phylogenetic trees • TreeDist - + @@ -42,7 +42,7 @@ TreeDist - 2.7.0.9001 + 2.7.0.9002 @@ -132,7 +132,7 @@ - +
@@ -255,8 +255,8 @@

} else { print("Run `install.packages('plotly')` to view this output") }

-
-

(Use the mouse to reorient)

+
+

(Use the mouse to reorient)

References

@@ -310,7 +310,7 @@

References

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/dev/articles/landscapes_files/htmltools-fill-0.5.8/fill.css b/dev/articles/landscapes_files/htmltools-fill-0.5.8.1/fill.css similarity index 100% rename from dev/articles/landscapes_files/htmltools-fill-0.5.8/fill.css rename to dev/articles/landscapes_files/htmltools-fill-0.5.8.1/fill.css diff --git a/dev/articles/treespace.html b/dev/articles/treespace.html index 2b1f125c9..c5febdeaa 100644 --- a/dev/articles/treespace.html +++ b/dev/articles/treespace.html @@ -6,7 +6,7 @@ Tree space analysis • TreeDist - + @@ -42,7 +42,7 @@ TreeDist - 2.7.0.9001 + 2.7.0.9002 @@ -604,7 +604,7 @@

References

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/dev/articles/using-distances.html b/dev/articles/using-distances.html index 335f61a0d..64ac757a6 100644 --- a/dev/articles/using-distances.html +++ b/dev/articles/using-distances.html @@ -6,7 +6,7 @@ Contextualizing tree distances • TreeDist - + @@ -42,7 +42,7 @@ TreeDist - 2.7.0.9001 + 2.7.0.9002 @@ -562,7 +562,7 @@

References

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/dev/authors.html b/dev/authors.html index 419c51879..b1e8cb5ed 100644 --- a/dev/authors.html +++ b/dev/authors.html @@ -1,5 +1,5 @@ -Authors and Citation • TreeDistAuthors and Citation • TreeDist + @@ -14,24 +14,7 @@ - + Changelog • TreeDistChangelog • TreeDistVariation of information for all split pairings — AllSplitPairings • TreeDist TreeDist - 2.7.0.9001 + 2.7.0.9002 @@ -189,7 +189,7 @@

Examples

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/dev/reference/CalculateTreeDistance.html b/dev/reference/CalculateTreeDistance.html index 4dbbe45cd..4ef1246d6 100644 --- a/dev/reference/CalculateTreeDistance.html +++ b/dev/reference/CalculateTreeDistance.html @@ -1,5 +1,5 @@ -Wrapper for tree distance calculations — CalculateTreeDistance • TreeDistWrapper for tree distance calculations — CalculateTreeDistance • TreeDistDistances between each pair of trees — CompareAll • TreeDistEntropy in bits — Entropy • TreeDistEntropy in bits — Entropy • TreeDistGeneralized Robinson–Foulds distance — GeneralizedRF • TreeDistGeneralized Robinson–Foulds distance — GeneralizedRF • TreeDistJaccard–Robinson–Foulds metric — JaccardRobinsonFoulds • TreeDistJaccard–Robinson–Foulds metric — JaccardRobinsonFoulds • TreeDist TreeDist - 2.7.0.9001 + 2.7.0.9002 @@ -299,7 +299,7 @@

Examples

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/dev/reference/KendallColijn.html b/dev/reference/KendallColijn.html index bf7aff009..98221ed34 100644 --- a/dev/reference/KendallColijn.html +++ b/dev/reference/KendallColijn.html @@ -1,5 +1,5 @@ -Kendall–Colijn distance — KendallColijn • TreeDistKendall–Colijn distance — KendallColijn • TreeDistSolve linear assignment problem using LAPJV — LAPJV • TreeDistSolve linear assignment problem using LAPJV — LAPJV • TreeDistMaximum Agreement Subtree size — MASTSize • TreeDistMaximum Agreement Subtree size — MASTSize • TreeDist TreeDist - 2.7.0.9001 + 2.7.0.9002 @@ -248,7 +248,7 @@

Examples

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/dev/reference/MSTSegments.html b/dev/reference/MSTSegments.html index ce9a599cc..9359dd180 100644 --- a/dev/reference/MSTSegments.html +++ b/dev/reference/MSTSegments.html @@ -1,5 +1,5 @@ -Add minimum spanning tree to plot, colouring by stress — MSTSegments • TreeDistAdd minimum spanning tree to plot, colouring by stress — MSTSegments • TreeDist TreeDist - 2.7.0.9001 + 2.7.0.9002 @@ -234,7 +234,7 @@

Examples

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/dev/reference/MapTrees.html b/dev/reference/MapTrees.html index 5bee900b7..f7a867413 100644 --- a/dev/reference/MapTrees.html +++ b/dev/reference/MapTrees.html @@ -1,7 +1,5 @@ -Graphical user interface for mapping distances and analysing -tree space — MapTrees • TreeDistFaithfulness of mapped distances — MappingQuality • TreeDistFaithfulness of mapped distances — MappingQuality • TreeDist TreeDist - 2.7.0.9001 + 2.7.0.9002 @@ -203,7 +203,7 @@

Examples

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/dev/reference/MatchingSplitDistance.html b/dev/reference/MatchingSplitDistance.html index e036dd7f3..2fb316f0e 100644 --- a/dev/reference/MatchingSplitDistance.html +++ b/dev/reference/MatchingSplitDistance.html @@ -1,5 +1,5 @@ -Matching Split Distance — MatchingSplitDistance • TreeDistMatching Split Distance — MatchingSplitDistance • TreeDistUse variation of clustering information to compare pairs of splits — MeilaVariationOfInformation • TreeDistUse variation of clustering information to compare pairs of splits — MeilaVariationOfInformation • TreeDistApproximate Nearest Neighbour Interchange distance — NNIDist • TreeDistApproximate Nearest Neighbour Interchange distance — NNIDist • TreeDist TreeDist - 2.7.0.9001 + 2.7.0.9002 @@ -361,7 +361,7 @@

Examples

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/dev/reference/NormalizeInfo.html b/dev/reference/NormalizeInfo.html index dc28f9f48..3b9dda321 100644 --- a/dev/reference/NormalizeInfo.html +++ b/dev/reference/NormalizeInfo.html @@ -1,5 +1,5 @@ -Normalize information against total present in both starting trees — NormalizeInfo • TreeDistNormalize information against total present in both starting trees — NormalizeInfo • TreeDistNye et al. (2006) tree comparison — NyeSimilarity • TreeDist TreeDist - 2.7.0.9001 + 2.7.0.9002 @@ -300,7 +300,7 @@

Examples

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/dev/reference/PathDist.html b/dev/reference/PathDist.html index 17af638b7..e55d0f774 100644 --- a/dev/reference/PathDist.html +++ b/dev/reference/PathDist.html @@ -1,5 +1,5 @@ -Path distance — PathDist • TreeDistPath distance — PathDist • TreeDistPseudo-3D plotting — Plot3 • TreeDistList clades as text — ReportMatching • TreeDistList clades as text — ReportMatching • TreeDistRobinson–Foulds distances, with adjustments for phylogenetic information content — Robinson-Foulds • TreeDist TreeDist - 2.7.0.9001 + 2.7.0.9002 @@ -117,8 +115,7 @@
-

Robinson–Foulds distances, with adjustments for phylogenetic information -content

+

Robinson–Foulds distances, with adjustments for phylogenetic information content

Source: R/tree_distance_rf.R
@@ -330,7 +327,7 @@

Examples

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/dev/reference/SPRDist.html b/dev/reference/SPRDist.html index fa1d18388..18b295389 100644 --- a/dev/reference/SPRDist.html +++ b/dev/reference/SPRDist.html @@ -1,5 +1,5 @@ -Approximate Subtree Prune and Regraft distance — SPRDist • TreeDistApproximate Subtree Prune and Regraft distance — SPRDist • TreeDistEigenvalues for spectral clustering — SpectralEigens • TreeDistEntropy of two splits — SplitEntropy • TreeDistEntropy of two splits — SplitEntropy • TreeDist TreeDist - 2.7.0.9001 + 2.7.0.9002 @@ -194,7 +194,7 @@

Examples

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/dev/reference/SplitSharedInformation.html b/dev/reference/SplitSharedInformation.html index bc1b191c0..ebc8c5473 100644 --- a/dev/reference/SplitSharedInformation.html +++ b/dev/reference/SplitSharedInformation.html @@ -1,5 +1,5 @@ -Shared information content of two splits — SplitSharedInformation • TreeDistShared information content of two splits — SplitSharedInformation • TreeDistAre splits compatible? — SplitsCompatible • TreeDistAre splits compatible? — SplitsCompatible • TreeDistCalculate distances in parallel — StartParallel • TreeDistCalculate distances in parallel — StartParallel • TreeDistTreeDist: Distances between Phylogenetic Trees — TreeDist-package • TreeDist TreeDist - 2.7.0.9001 + 2.7.0.9002 @@ -274,7 +274,7 @@

Author

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/dev/reference/TreeDistPlot.html b/dev/reference/TreeDistPlot.html index 10f53e8a2..5b6cc7796 100644 --- a/dev/reference/TreeDistPlot.html +++ b/dev/reference/TreeDistPlot.html @@ -1,5 +1,5 @@ -Plot a simple tree — TreeDistPlot • TreeDistPlot a simple tree — TreeDistPlot • TreeDistInformation-based generalized Robinson–Foulds distances — TreeDistance • TreeDistInformation content of splits within a tree — TreeInfo • TreeDistInformation content of splits within a tree — TreeInfo • TreeDist TreeDist - 2.7.0.9001 + 2.7.0.9002 @@ -381,7 +381,7 @@

Examples

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/dev/reference/VisualizeMatching.html b/dev/reference/VisualizeMatching.html index 0d318ecd2..b122e14b0 100644 --- a/dev/reference/VisualizeMatching.html +++ b/dev/reference/VisualizeMatching.html @@ -1,5 +1,5 @@ -Visualise a matching — VisualizeMatching • TreeDistVisualise a matching — VisualizeMatching • TreeDistCluster size statistics — cluster-statistics • TreeDistCluster size statistics — cluster-statistics • TreeDistCalculate MAST size from edge matrices. — .MASTSizeEdges • TreeDistMean of two numbers — .PairMean • TreeDistCalculate distance between trees, or lists of trees — .TreeDistance • TreeDistFunction reference • TreeDistk-means++ clustering — KMeansPP • TreeDist TreeDist - 2.7.0.9001 + 2.7.0.9002 @@ -208,7 +208,7 @@

Examples

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/dev/reference/median.multiPhylo.html b/dev/reference/median.multiPhylo.html index 9d226b5f1..42a4a6980 100644 --- a/dev/reference/median.multiPhylo.html +++ b/dev/reference/median.multiPhylo.html @@ -1,5 +1,5 @@ -Median of a set of trees — median.multiPhylo • TreeDist