## The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
-## which was just loaded, will retire in October 2023.
-## Please refer to R-spatial evolution reports for details, especially
-## https://r-spatial.org/r/2023/05/15/evolution4.html.
-## It may be desirable to make the sf package available;
-## package maintainers should consider adding sf to Suggests:.
-## The sp package is now running under evolution status 2
-## (status 2 uses the sf package in place of rgdal)
-expectedQD <- 2 / 3
+library("Quartet", exclude = "RobinsonFoulds")
+expectedQD <- 2 / 3
normalizedQD <- QuartetDivergence(QuartetStatus(tree1, tree2),
similarity = FALSE) / expectedQDThe expected distance is more difficult to calculate for other @@ -274,7 +265,7 @@
Normalizing to random similarityTreeDistData’. We can
view (normalized) distances for a selection of methods:
-
+
if (requireNamespace("TreeDistData", quietly = TRUE)) {
library("TreeDistData", exclude = "PairwiseDistances")
data("randomTreeDistances", package = "TreeDistData")
@@ -308,7 +299,7 @@ Normalizing to random similarity}
or use these calculated values to normalize our tree distance:
-
+
expectedCID <- randomTreeDistances["cid", "mean", "9"]
ClusteringInfoDistance(tree1, tree2, normalize = TRUE) / expectedCID
@@ -331,7 +322,7 @@ Testing similarity to a known tree
Ternary diagrams allow us to visualise the quality of a reconstructed
tree with reference to a known “true” tree:
-
+
testTrees <- list(
trueTree = ape::read.tree(text = '(a, (b, (c, (d, (e, (f, (g, h)))))));'),
lackRes = ape::read.tree(text = '(a, (b, c, (d, e, (f, g, h))));'),
@@ -341,11 +332,11 @@ Testing similarity to a known treeVisualizeMatching(MutualClusteringInfo, testTrees$trueTree, testTrees$lackRes)
points(4, 7.5, pch = 2, cex = 3, col = "#E69F00")
-
+
VisualizeMatching(MutualClusteringInfo, testTrees$trueTree, testTrees$smallErr)
points(4, 7.5, pch = 3, cex = 3, col = "#56B4E9")
-
+
VisualizeMatching(MutualClusteringInfo, testTrees$trueTree, testTrees$bigErr)
points(4, 7.5, pch = 4, cex = 3, col = "#009E73")
@@ -353,7 +344,7 @@ Testing similarity to a known tree
-
+
if (requireNamespace("Ternary", quietly = TRUE)) {
library("Ternary")
oldPar <- par(mar = rep(0.1, 4))
@@ -381,14 +372,14 @@ Example
First, let’s generate a starting tree, which will represent our
reference topology:
-
+
set.seed(0)
trueTree <- TreeTools::RandomTree(20, root = TRUE)
Then, let’s generate 200 degraded trees. We’ll move away from the
true tree by making a TBR move, then reduce resolution by taking the
consensus of this tree and three trees from its immediate neighbourhood
(one NNI move away).
-
+
treeSearchInstalled <- requireNamespace("TreeSearch", quietly = TRUE)
if (treeSearchInstalled) {
library("TreeSearch", quietly = TRUE) # for TBR, NNI
@@ -406,7 +397,7 @@ Example
-
+
if (treeSearchInstalled) {
threeAway <- structure(lapply(seq_len(200), function(x) {
tbrTree <- TBR(TBR(TBR(trueTree)))
@@ -419,33 +410,33 @@ ExampleNow let’s calculate their tree similarity scores. We need to
calculate the amount of information each tree has in common with the
true tree:
-
+
if (treeSearchInstalled) {
correct1 <- MutualClusteringInfo(trueTree, oneAway)
correct3 <- MutualClusteringInfo(trueTree, threeAway)
}
The amount of information in each degraded tree:
-
+
if (treeSearchInstalled) {
infoInTree1 <- ClusteringEntropy(oneAway)
infoInTree3 <- ClusteringEntropy(threeAway)
}
The amount of information that could have been resolved, but was
not:
-
+
if (treeSearchInstalled) {
unresolved1 <- ClusteringEntropy(trueTree) - infoInTree1
unresolved3 <- ClusteringEntropy(trueTree) - infoInTree3
}
And the amount of information incorrectly resolved:
-
+
if (treeSearchInstalled) {
incorrect1 <- infoInTree1 - correct1
incorrect3 <- infoInTree3 - correct3
}
In preparation for our plot, let’s colour our one-away trees orange , and our three-away
trees blue :
-
+
col1 <- hcl(200, alpha = 0.9)
col3 <- hcl(40, alpha = 0.9)
spec1 <- matrix(col2rgb(col1, alpha = TRUE), nrow = 4, ncol = 181)
@@ -455,7 +446,7 @@ Examplespec1 <- apply(spec1, 2, ColToHex)
spec3 <- apply(spec3, 2, ColToHex)
Now we can plot this information on a ternary diagram.
-
+
if (treeSearchInstalled && requireNamespace("Ternary", quietly = TRUE)) {
layout(matrix(c(1, 2), ncol = 2), widths = c(5, 2))
oldPar <- par(mar = rep(0, 4))
diff --git a/authors.html b/authors.html
index b46f8c95..1c09046b 100644
--- a/authors.html
+++ b/authors.html
@@ -23,7 +23,7 @@
@@ -155,9 +155,9 @@ Citation
pages = {1255-1270},
year = {2022},
}
- Smith, M.R. (2020b). TreeDist: Distances between Phylogenetic Trees. R package version 2.6.3. Comprehensive R Archive Network. doi:10.5281/zenodo.3528124
+ Smith, M.R. (2020b). TreeDist: Distances between Phylogenetic Trees. R package version 2.7.0. Comprehensive R Archive Network. doi:10.5281/zenodo.3528124
@Manual{TreeDist,
- title = {TreeDist: Distances between Phylogenetic Trees. R package version 2.6.3},
+ title = {TreeDist: Distances between Phylogenetic Trees. R package version 2.7.0},
author = {Martin R. Smith},
doi = {10.5281/zenodo.3528124},
journal = {Comprehensive R Archive Network},
diff --git a/index.html b/index.html
index 63a64d62..f061caf8 100644
--- a/index.html
+++ b/index.html
@@ -58,7 +58,7 @@
diff --git a/news/index.html b/news/index.html
index e62bd1c7..5233dfb9 100644
--- a/news/index.html
+++ b/news/index.html
@@ -23,7 +23,7 @@
@@ -107,6 +107,13 @@ Changelog
Source: NEWS.md
+
+TreeDist 2.7.0 (2023-10-25)
+Fix calculation error in StrainCol().
App: Display strain in 3D tree space viewer.
Support for distances between larger trees.
Support unrooted trees in VisualizeMatching() (#103).
TreeDist 2.6.3 (2023-08-25)2023-08-25
Fix bug when comparing a “multiPhylo” object containing a single tree.
diff --git a/reference/CalculateTreeDistance.html b/reference/CalculateTreeDistance.html
index 99e79153..7fa2e8fb 100644
--- a/reference/CalculateTreeDistance.html
+++ b/reference/CalculateTreeDistance.html
@@ -23,7 +23,7 @@
diff --git a/reference/CompareAll.html b/reference/CompareAll.html
index 8555eb8d..039422e3 100644
--- a/reference/CompareAll.html
+++ b/reference/CompareAll.html
@@ -24,7 +24,7 @@
diff --git a/reference/Entropy.html b/reference/Entropy.html
index bf8e08c1..d96affd4 100644
--- a/reference/Entropy.html
+++ b/reference/Entropy.html
@@ -25,7 +25,7 @@
diff --git a/reference/GeneralizedRF.html b/reference/GeneralizedRF.html
index 67a6395d..29d5ae56 100644
--- a/reference/GeneralizedRF.html
+++ b/reference/GeneralizedRF.html
@@ -24,7 +24,7 @@
diff --git a/reference/JaccardRobinsonFoulds.html b/reference/JaccardRobinsonFoulds.html
index 0cc1ba05..09be2091 100644
--- a/reference/JaccardRobinsonFoulds.html
+++ b/reference/JaccardRobinsonFoulds.html
@@ -27,7 +27,7 @@
diff --git a/reference/KendallColijn.html b/reference/KendallColijn.html
index ab03d158..e443f10f 100644
--- a/reference/KendallColijn.html
+++ b/reference/KendallColijn.html
@@ -24,7 +24,7 @@
diff --git a/reference/LAPJV.html b/reference/LAPJV.html
index 014965a7..9ed5456e 100644
--- a/reference/LAPJV.html
+++ b/reference/LAPJV.html
@@ -25,7 +25,7 @@
diff --git a/reference/MASTSize.html b/reference/MASTSize.html
index 0fcbf448..4fbc3dc3 100644
--- a/reference/MASTSize.html
+++ b/reference/MASTSize.html
@@ -30,7 +30,7 @@
diff --git a/reference/MSTSegments-1.png b/reference/MSTSegments-1.png
index 51d2519a..ba2f9aed 100644
Binary files a/reference/MSTSegments-1.png and b/reference/MSTSegments-1.png differ
diff --git a/reference/MSTSegments.html b/reference/MSTSegments.html
index c1943063..caa81d8c 100644
--- a/reference/MSTSegments.html
+++ b/reference/MSTSegments.html
@@ -28,7 +28,7 @@
@@ -109,7 +109,7 @@
Add minimum spanning tree to plot, colouring by stress
- Source: R/plot.R
+ Source: R/MSTSegments.R
MSTSegments.Rd
diff --git a/reference/MapTrees.html b/reference/MapTrees.html
index eff612ca..f9b72c99 100644
--- a/reference/MapTrees.html
+++ b/reference/MapTrees.html
@@ -26,7 +26,7 @@
diff --git a/reference/MappingQuality.html b/reference/MappingQuality.html
index dbf7a66f..4315d13c 100644
--- a/reference/MappingQuality.html
+++ b/reference/MappingQuality.html
@@ -29,7 +29,7 @@
diff --git a/reference/MatchingSplitDistance.html b/reference/MatchingSplitDistance.html
index bf9ff66a..b2c56c1d 100644
--- a/reference/MatchingSplitDistance.html
+++ b/reference/MatchingSplitDistance.html
@@ -26,7 +26,7 @@
diff --git a/reference/MeilaVariationOfInformation.html b/reference/MeilaVariationOfInformation.html
index bb6f8354..6536f594 100644
--- a/reference/MeilaVariationOfInformation.html
+++ b/reference/MeilaVariationOfInformation.html
@@ -25,7 +25,7 @@
diff --git a/reference/NNIDist.html b/reference/NNIDist.html
index 19be5919..cc7573f6 100644
--- a/reference/NNIDist.html
+++ b/reference/NNIDist.html
@@ -27,7 +27,7 @@
diff --git a/reference/NormalizeInfo.html b/reference/NormalizeInfo.html
index c6099a6c..5c60e5dc 100644
--- a/reference/NormalizeInfo.html
+++ b/reference/NormalizeInfo.html
@@ -23,7 +23,7 @@
diff --git a/reference/NyeSimilarity.html b/reference/NyeSimilarity.html
index 9176588c..8c082666 100644
--- a/reference/NyeSimilarity.html
+++ b/reference/NyeSimilarity.html
@@ -32,7 +32,7 @@
diff --git a/reference/PathDist.html b/reference/PathDist.html
index 48b44db6..0e996300 100644
--- a/reference/PathDist.html
+++ b/reference/PathDist.html
@@ -23,7 +23,7 @@
diff --git a/reference/Plot3.html b/reference/Plot3.html
index 255ccd7c..8d0acab6 100644
--- a/reference/Plot3.html
+++ b/reference/Plot3.html
@@ -26,7 +26,7 @@
diff --git a/reference/ReportMatching.html b/reference/ReportMatching.html
index 61eb1f43..5f14d656 100644
--- a/reference/ReportMatching.html
+++ b/reference/ReportMatching.html
@@ -23,7 +23,7 @@
diff --git a/reference/Robinson-Foulds.html b/reference/Robinson-Foulds.html
index 0cf910f9..36e15367 100644
--- a/reference/Robinson-Foulds.html
+++ b/reference/Robinson-Foulds.html
@@ -37,7 +37,7 @@
diff --git a/reference/SPRDist.html b/reference/SPRDist.html
index dfbbe2b8..ccb4cdb7 100644
--- a/reference/SPRDist.html
+++ b/reference/SPRDist.html
@@ -23,7 +23,7 @@
diff --git a/reference/SpectralEigens.html b/reference/SpectralEigens.html
index 50021dd9..3b2442a5 100644
--- a/reference/SpectralEigens.html
+++ b/reference/SpectralEigens.html
@@ -25,7 +25,7 @@
diff --git a/reference/SplitEntropy.html b/reference/SplitEntropy.html
index d12a7335..7b9537f3 100644
--- a/reference/SplitEntropy.html
+++ b/reference/SplitEntropy.html
@@ -31,7 +31,7 @@
diff --git a/reference/SplitSharedInformation.html b/reference/SplitSharedInformation.html
index 3c49b85f..eb018a79 100644
--- a/reference/SplitSharedInformation.html
+++ b/reference/SplitSharedInformation.html
@@ -26,7 +26,7 @@
diff --git a/reference/SplitsCompatible.html b/reference/SplitsCompatible.html
index 927f4521..d493ac80 100644
--- a/reference/SplitsCompatible.html
+++ b/reference/SplitsCompatible.html
@@ -24,7 +24,7 @@
diff --git a/reference/StartParallel.html b/reference/StartParallel.html
index eed18f1e..f38d19cd 100644
--- a/reference/StartParallel.html
+++ b/reference/StartParallel.html
@@ -23,7 +23,7 @@
diff --git a/reference/TreeDist-package.html b/reference/TreeDist-package.html
index 2306ee8d..81eb85e2 100644
--- a/reference/TreeDist-package.html
+++ b/reference/TreeDist-package.html
@@ -27,7 +27,7 @@
diff --git a/reference/TreeDistPlot.html b/reference/TreeDistPlot.html
index 272ae03c..42b74306 100644
--- a/reference/TreeDistPlot.html
+++ b/reference/TreeDistPlot.html
@@ -23,7 +23,7 @@
diff --git a/reference/TreeDistance.html b/reference/TreeDistance.html
index bb2effb3..0e7e5871 100644
--- a/reference/TreeDistance.html
+++ b/reference/TreeDistance.html
@@ -25,7 +25,7 @@
@@ -338,6 +338,23 @@ Normalization
To calculate the relative similarity against a reference tree that is known
to be "correct", use normalize = SplitwiseInfo(trueTree) (SPI, MSI) or
ClusteringEntropy(trueTree) (MCI).
+
+
+ Distances between large trees
+ To balance memory demands and runtime with flexibility, these functions are
+implemented for trees with up to 2048 leaves.
+To analyse trees with up to 8192 leaves, you will need to a modified version
+of TreeTools.
+First uninstall TreeDist and TreeTools using remove.packages().
+Then use devtools::install_github("ms609/TreeTools", ref = "more-leaves")
+to install the modified TreeTools package.
+Finally, install TreeDist using
+devtools::install_github("ms609/TreeDist").
+(TreeDist will need building from source after the modified
+TreeTools package has been installed, as its code links to values
+set in the TreeTools source code.)
+Trees with over 8192 leaves require further modification of the source code,
+which the maintainer will attempt on demand; please comment on GitHub if you would find this useful.
References
diff --git a/reference/TreeInfo.html b/reference/TreeInfo.html
index 611e037f..9ccdb849 100644
--- a/reference/TreeInfo.html
+++ b/reference/TreeInfo.html
@@ -30,7 +30,7 @@
diff --git a/reference/VisualizeMatching.html b/reference/VisualizeMatching.html
index c48c63fc..d079e3d9 100644
--- a/reference/VisualizeMatching.html
+++ b/reference/VisualizeMatching.html
@@ -25,7 +25,7 @@
@@ -106,7 +106,7 @@
diff --git a/reference/cluster-statistics.html b/reference/cluster-statistics.html
index d968ed3d..02861d56 100644
--- a/reference/cluster-statistics.html
+++ b/reference/cluster-statistics.html
@@ -23,7 +23,7 @@
diff --git a/reference/dot-MASTSizeEdges.html b/reference/dot-MASTSizeEdges.html
index 41d7b9b3..d7548119 100644
--- a/reference/dot-MASTSizeEdges.html
+++ b/reference/dot-MASTSizeEdges.html
@@ -23,7 +23,7 @@
diff --git a/reference/dot-PairMean.html b/reference/dot-PairMean.html
index d8023690..d3ac8712 100644
--- a/reference/dot-PairMean.html
+++ b/reference/dot-PairMean.html
@@ -23,7 +23,7 @@
diff --git a/reference/dot-TreeDistance.html b/reference/dot-TreeDistance.html
index 6eb10cad..6a320965 100644
--- a/reference/dot-TreeDistance.html
+++ b/reference/dot-TreeDistance.html
@@ -23,7 +23,7 @@
diff --git a/reference/index.html b/reference/index.html
index 761a98a7..93388cf9 100644
--- a/reference/index.html
+++ b/reference/index.html
@@ -23,7 +23,7 @@
diff --git a/reference/kmeanspp.html b/reference/kmeanspp.html
index 9c81f8c6..8c75c18c 100644
--- a/reference/kmeanspp.html
+++ b/reference/kmeanspp.html
@@ -31,7 +31,7 @@
diff --git a/reference/median.multiPhylo.html b/reference/median.multiPhylo.html
index 576ce6eb..27fc9f98 100644
--- a/reference/median.multiPhylo.html
+++ b/reference/median.multiPhylo.html
@@ -24,7 +24,7 @@
+if (requireNamespace("TreeDistData", quietly = TRUE)) { library("TreeDistData", exclude = "PairwiseDistances") data("randomTreeDistances", package = "TreeDistData") @@ -308,7 +299,7 @@Normalizing to random similarity}
or use these calculated values to normalize our tree distance:
-@@ -331,7 +322,7 @@+expectedCID <- randomTreeDistances["cid", "mean", "9"] ClusteringInfoDistance(tree1, tree2, normalize = TRUE) / expectedCIDTesting similarity to a known tree
Ternary diagrams allow us to visualise the quality of a reconstructed tree with reference to a known “true” tree:
-diff --git a/reference/NormalizeInfo.html b/reference/NormalizeInfo.html index c6099a6c..5c60e5dc 100644 --- a/reference/NormalizeInfo.html +++ b/reference/NormalizeInfo.html @@ -23,7 +23,7 @@+testTrees <- list( trueTree = ape::read.tree(text = '(a, (b, (c, (d, (e, (f, (g, h)))))));'), lackRes = ape::read.tree(text = '(a, (b, c, (d, e, (f, g, h))));'), @@ -341,11 +332,11 @@Testing similarity to a known treeVisualizeMatching(MutualClusteringInfo, testTrees$trueTree, testTrees$lackRes) points(4, 7.5, pch = 2, cex = 3, col = "#E69F00")
-
diff --git a/reference/NNIDist.html b/reference/NNIDist.html index 19be5919..cc7573f6 100644 --- a/reference/NNIDist.html +++ b/reference/NNIDist.html @@ -27,7 +27,7 @@+VisualizeMatching(MutualClusteringInfo, testTrees$trueTree, testTrees$smallErr) points(4, 7.5, pch = 3, cex = 3, col = "#56B4E9")-
diff --git a/reference/MeilaVariationOfInformation.html b/reference/MeilaVariationOfInformation.html index bb6f8354..6536f594 100644 --- a/reference/MeilaVariationOfInformation.html +++ b/reference/MeilaVariationOfInformation.html @@ -25,7 +25,7 @@+VisualizeMatching(MutualClusteringInfo, testTrees$trueTree, testTrees$bigErr) points(4, 7.5, pch = 4, cex = 3, col = "#009E73")@@ -353,7 +344,7 @@
Testing similarity to a known tree -
diff --git a/reference/MatchingSplitDistance.html b/reference/MatchingSplitDistance.html index bf9ff66a..b2c56c1d 100644 --- a/reference/MatchingSplitDistance.html +++ b/reference/MatchingSplitDistance.html @@ -26,7 +26,7 @@+@@ -109,7 +109,7 @@if (requireNamespace("Ternary", quietly = TRUE)) { library("Ternary") oldPar <- par(mar = rep(0.1, 4)) @@ -381,14 +372,14 @@Example
First, let’s generate a starting tree, which will represent our reference topology:
-diff --git a/reference/MSTSegments-1.png b/reference/MSTSegments-1.png index 51d2519a..ba2f9aed 100644 Binary files a/reference/MSTSegments-1.png and b/reference/MSTSegments-1.png differ diff --git a/reference/MSTSegments.html b/reference/MSTSegments.html index c1943063..caa81d8c 100644 --- a/reference/MSTSegments.html +++ b/reference/MSTSegments.html @@ -28,7 +28,7 @@+set.seed(0) trueTree <- TreeTools::RandomTree(20, root = TRUE)Then, let’s generate 200 degraded trees. We’ll move away from the true tree by making a TBR move, then reduce resolution by taking the consensus of this tree and three trees from its immediate neighbourhood (one NNI move away).
-diff --git a/reference/MASTSize.html b/reference/MASTSize.html index 0fcbf448..4fbc3dc3 100644 --- a/reference/MASTSize.html +++ b/reference/MASTSize.html @@ -30,7 +30,7 @@+diff --git a/reference/LAPJV.html b/reference/LAPJV.html index 014965a7..9ed5456e 100644 --- a/reference/LAPJV.html +++ b/reference/LAPJV.html @@ -25,7 +25,7 @@treeSearchInstalled <- requireNamespace("TreeSearch", quietly = TRUE) if (treeSearchInstalled) { library("TreeSearch", quietly = TRUE) # for TBR, NNI @@ -406,7 +397,7 @@Example -
diff --git a/reference/KendallColijn.html b/reference/KendallColijn.html index ab03d158..e443f10f 100644 --- a/reference/KendallColijn.html +++ b/reference/KendallColijn.html @@ -24,7 +24,7 @@+diff --git a/reference/JaccardRobinsonFoulds.html b/reference/JaccardRobinsonFoulds.html index 0cc1ba05..09be2091 100644 --- a/reference/JaccardRobinsonFoulds.html +++ b/reference/JaccardRobinsonFoulds.html @@ -27,7 +27,7 @@if (treeSearchInstalled) { threeAway <- structure(lapply(seq_len(200), function(x) { tbrTree <- TBR(TBR(TBR(trueTree))) @@ -419,33 +410,33 @@ExampleNow let’s calculate their tree similarity scores. We need to calculate the amount of information each tree has in common with the true tree: -
diff --git a/reference/GeneralizedRF.html b/reference/GeneralizedRF.html index 67a6395d..29d5ae56 100644 --- a/reference/GeneralizedRF.html +++ b/reference/GeneralizedRF.html @@ -24,7 +24,7 @@+if (treeSearchInstalled) { correct1 <- MutualClusteringInfo(trueTree, oneAway) correct3 <- MutualClusteringInfo(trueTree, threeAway) }The amount of information in each degraded tree:
-diff --git a/reference/Entropy.html b/reference/Entropy.html index bf8e08c1..d96affd4 100644 --- a/reference/Entropy.html +++ b/reference/Entropy.html @@ -25,7 +25,7 @@+if (treeSearchInstalled) { infoInTree1 <- ClusteringEntropy(oneAway) infoInTree3 <- ClusteringEntropy(threeAway) }The amount of information that could have been resolved, but was not:
-diff --git a/reference/CompareAll.html b/reference/CompareAll.html index 8555eb8d..039422e3 100644 --- a/reference/CompareAll.html +++ b/reference/CompareAll.html @@ -24,7 +24,7 @@+if (treeSearchInstalled) { unresolved1 <- ClusteringEntropy(trueTree) - infoInTree1 unresolved3 <- ClusteringEntropy(trueTree) - infoInTree3 }And the amount of information incorrectly resolved:
-++if (treeSearchInstalled) { incorrect1 <- infoInTree1 - correct1 incorrect3 <- infoInTree3 - correct3 }In preparation for our plot, let’s colour our one-away trees orange , and our three-away trees blue :
-@@ -107,6 +107,13 @@+col1 <- hcl(200, alpha = 0.9) col3 <- hcl(40, alpha = 0.9) spec1 <- matrix(col2rgb(col1, alpha = TRUE), nrow = 4, ncol = 181) @@ -455,7 +446,7 @@Examplespec1 <- apply(spec1, 2, ColToHex) spec3 <- apply(spec3, 2, ColToHex)
Now we can plot this information on a ternary diagram.
-diff --git a/news/index.html b/news/index.html index e62bd1c7..5233dfb9 100644 --- a/news/index.html +++ b/news/index.html @@ -23,7 +23,7 @@+-@@ -155,9 +155,9 @@if (treeSearchInstalled && requireNamespace("Ternary", quietly = TRUE)) { layout(matrix(c(1, 2), ncol = 2), widths = c(5, 2)) oldPar <- par(mar = rep(0, 4)) diff --git a/authors.html b/authors.html index b46f8c95..1c09046b 100644 --- a/authors.html +++ b/authors.html @@ -23,7 +23,7 @@Citation
pages = {1255-1270}, year = {2022}, }Smith, M.R. (2020b). TreeDist: Distances between Phylogenetic Trees. R package version 2.6.3. Comprehensive R Archive Network. doi:10.5281/zenodo.3528124
+Smith, M.R. (2020b). TreeDist: Distances between Phylogenetic Trees. R package version 2.7.0. Comprehensive R Archive Network. doi:10.5281/zenodo.3528124
@Manual{TreeDist, - title = {TreeDist: Distances between Phylogenetic Trees. R package version 2.6.3}, + title = {TreeDist: Distances between Phylogenetic Trees. R package version 2.7.0}, author = {Martin R. Smith}, doi = {10.5281/zenodo.3528124}, journal = {Comprehensive R Archive Network}, diff --git a/index.html b/index.html index 63a64d62..f061caf8 100644 --- a/index.html +++ b/index.html @@ -58,7 +58,7 @@Changelog
Source:NEWS.md+TreeDist 2.7.0 (2023-10-25)
+
- +
Fix calculation error in
StrainCol().- +
App: Display strain in 3D tree space viewer.
- +
Support for distances between larger trees.
- +
Support unrooted trees in
VisualizeMatching()(#103).diff --git a/reference/CalculateTreeDistance.html b/reference/CalculateTreeDistance.html index 99e79153..7fa2e8fb 100644 --- a/reference/CalculateTreeDistance.html +++ b/reference/CalculateTreeDistance.html @@ -23,7 +23,7 @@TreeDist 2.6.3 (2023-08-25)2023-08-25
- diff --git a/pkgdown.yml b/pkgdown.yml index 8a7aa38f..274db843 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -11,7 +11,7 @@ articles: landscapes: landscapes.html treespace: treespace.html using-distances: using-distances.html -last_built: 2023-08-27T00:45Z +last_built: 2023-10-25T16:24Z urls: reference: https://ms609.github.io/TreeDist/reference article: https://ms609.github.io/TreeDist/articles diff --git a/reference/AllSplitPairings.html b/reference/AllSplitPairings.html index 18d70600..e71c8367 100644 --- a/reference/AllSplitPairings.html +++ b/reference/AllSplitPairings.html @@ -28,7 +28,7 @@
Fix bug when comparing a “multiPhylo” object containing a single tree.
diff --git a/reference/MappingQuality.html b/reference/MappingQuality.html index dbf7a66f..4315d13c 100644 --- a/reference/MappingQuality.html +++ b/reference/MappingQuality.html @@ -29,7 +29,7 @@diff --git a/reference/MapTrees.html b/reference/MapTrees.html index eff612ca..f9b72c99 100644 --- a/reference/MapTrees.html +++ b/reference/MapTrees.html @@ -26,7 +26,7 @@Add minimum spanning tree to plot, colouring by stress
- Source:R/plot.R+ Source:R/MSTSegments.RMSTSegments.Rd
Distances between large trees
+To balance memory demands and runtime with flexibility, these functions are
+implemented for trees with up to 2048 leaves.
+To analyse trees with up to 8192 leaves, you will need to a modified version
+of TreeTools.
+First uninstall TreeDist and TreeTools using remove.packages().
+Then use devtools::install_github("ms609/TreeTools", ref = "more-leaves")
+to install the modified TreeTools package.
+Finally, install TreeDist using
+devtools::install_github("ms609/TreeDist").
+(TreeDist will need building from source after the modified
+TreeTools package has been installed, as its code links to values
+set in the TreeTools source code.)
Trees with over 8192 leaves require further modification of the source code, +which the maintainer will attempt on demand; please comment on GitHub if you would find this useful.