References
-
+
What next?
Shiny appAdd batch to existing
-
diff --git a/dev/reference/LAPJV.html b/dev/reference/LAPJV.html
index 51b3f8c0..6ef7bc3d 100644
--- a/dev/reference/LAPJV.html
+++ b/dev/reference/LAPJV.html
@@ -25,7 +25,7 @@
diff --git a/dev/reference/MASTSize.html b/dev/reference/MASTSize.html
index 8c3f9060..9abc4a24 100644
--- a/dev/reference/MASTSize.html
+++ b/dev/reference/MASTSize.html
@@ -30,7 +30,7 @@
diff --git a/dev/reference/MSTSegments.html b/dev/reference/MSTSegments.html
index 2cffab7c..ce9a599c 100644
--- a/dev/reference/MSTSegments.html
+++ b/dev/reference/MSTSegments.html
@@ -28,7 +28,7 @@
diff --git a/dev/reference/MapTrees.html b/dev/reference/MapTrees.html
index 76f97514..5bee900b 100644
--- a/dev/reference/MapTrees.html
+++ b/dev/reference/MapTrees.html
@@ -26,7 +26,7 @@
diff --git a/dev/reference/MappingQuality.html b/dev/reference/MappingQuality.html
index 4b092454..8fd63ca5 100644
--- a/dev/reference/MappingQuality.html
+++ b/dev/reference/MappingQuality.html
@@ -29,7 +29,7 @@
diff --git a/dev/reference/MatchingSplitDistance.html b/dev/reference/MatchingSplitDistance.html
index 70990261..e036dd7f 100644
--- a/dev/reference/MatchingSplitDistance.html
+++ b/dev/reference/MatchingSplitDistance.html
@@ -26,7 +26,7 @@
diff --git a/dev/reference/MeilaVariationOfInformation.html b/dev/reference/MeilaVariationOfInformation.html
index 9dad5107..3de5765c 100644
--- a/dev/reference/MeilaVariationOfInformation.html
+++ b/dev/reference/MeilaVariationOfInformation.html
@@ -25,7 +25,7 @@
diff --git a/dev/reference/NNIDist.html b/dev/reference/NNIDist.html
index 1aa165b6..8bf6bc8b 100644
--- a/dev/reference/NNIDist.html
+++ b/dev/reference/NNIDist.html
@@ -27,7 +27,7 @@
diff --git a/dev/reference/NormalizeInfo.html b/dev/reference/NormalizeInfo.html
index d57f01ed..dc28f9f4 100644
--- a/dev/reference/NormalizeInfo.html
+++ b/dev/reference/NormalizeInfo.html
@@ -23,7 +23,7 @@
diff --git a/dev/reference/NyeSimilarity.html b/dev/reference/NyeSimilarity.html
index 556e6735..338f6535 100644
--- a/dev/reference/NyeSimilarity.html
+++ b/dev/reference/NyeSimilarity.html
@@ -32,7 +32,7 @@
diff --git a/dev/reference/PathDist.html b/dev/reference/PathDist.html
index 9c69948d..17af638b 100644
--- a/dev/reference/PathDist.html
+++ b/dev/reference/PathDist.html
@@ -23,7 +23,7 @@
diff --git a/dev/reference/Plot3.html b/dev/reference/Plot3.html
index a2fcaf05..57983756 100644
--- a/dev/reference/Plot3.html
+++ b/dev/reference/Plot3.html
@@ -26,7 +26,7 @@
diff --git a/dev/reference/ReportMatching.html b/dev/reference/ReportMatching.html
index 73be1e94..ebbd4311 100644
--- a/dev/reference/ReportMatching.html
+++ b/dev/reference/ReportMatching.html
@@ -23,7 +23,7 @@
diff --git a/dev/reference/Robinson-Foulds.html b/dev/reference/Robinson-Foulds.html
index aa294c2e..ccef085f 100644
--- a/dev/reference/Robinson-Foulds.html
+++ b/dev/reference/Robinson-Foulds.html
@@ -37,7 +37,7 @@
diff --git a/dev/reference/SPRDist.html b/dev/reference/SPRDist.html
index f510c18c..fa1d1838 100644
--- a/dev/reference/SPRDist.html
+++ b/dev/reference/SPRDist.html
@@ -23,7 +23,7 @@
diff --git a/dev/reference/SpectralEigens.html b/dev/reference/SpectralEigens.html
index 5470c66d..d9181925 100644
--- a/dev/reference/SpectralEigens.html
+++ b/dev/reference/SpectralEigens.html
@@ -25,7 +25,7 @@
diff --git a/dev/reference/SplitEntropy.html b/dev/reference/SplitEntropy.html
index 76526aa9..dfdfa516 100644
--- a/dev/reference/SplitEntropy.html
+++ b/dev/reference/SplitEntropy.html
@@ -31,7 +31,7 @@
diff --git a/dev/reference/SplitSharedInformation.html b/dev/reference/SplitSharedInformation.html
index 4645d986..bc1b191c 100644
--- a/dev/reference/SplitSharedInformation.html
+++ b/dev/reference/SplitSharedInformation.html
@@ -26,7 +26,7 @@
diff --git a/dev/reference/SplitsCompatible.html b/dev/reference/SplitsCompatible.html
index e97ac9eb..b1c6a88f 100644
--- a/dev/reference/SplitsCompatible.html
+++ b/dev/reference/SplitsCompatible.html
@@ -24,7 +24,7 @@
diff --git a/dev/reference/StartParallel.html b/dev/reference/StartParallel.html
index d52249f8..3b91b103 100644
--- a/dev/reference/StartParallel.html
+++ b/dev/reference/StartParallel.html
@@ -23,7 +23,7 @@
@@ -171,7 +171,7 @@
Böcker, S., Canzar, S., & Klau, G. W. (2013). The generalized
Robinson-Foulds metric. In A. Darling & J.
diff --git a/dev/articles/Robinson-Foulds.html b/dev/articles/Robinson-Foulds.html
index beb6c5bc..0b7c7467 100644
--- a/dev/articles/Robinson-Foulds.html
+++ b/dev/articles/Robinson-Foulds.html
@@ -42,7 +42,7 @@
@@ -406,7 +406,7 @@ What next?
References
-
+
Böcker, S., Canzar, S., & Klau, G. W. (2013). The generalized
Robinson-Foulds metric. In A. Darling & J.
diff --git a/dev/articles/Using-TreeDist.html b/dev/articles/Using-TreeDist.html
index 7409b5ae..0d75af61 100644
--- a/dev/articles/Using-TreeDist.html
+++ b/dev/articles/Using-TreeDist.html
@@ -42,7 +42,7 @@
@@ -204,12 +204,12 @@ Multiple comparisonsTreeDistance(oneTree, twoTrees)
## one two
-## 0.8258625 0.8651397
+## 0.7038526 0.8226153
TreeDistance(twoTrees, threeTrees)
## a b c
-## one 0.6583478 0.4713275 0.7178246
-## two 0.7065470 0.7923405 0.7596224
+## one 0.6519454 0.7102915 0.7918863
+## two 0.8058111 0.7890746 0.8282341
Böcker, S., Canzar, S., & Klau, G. W. (2013). The generalized
Robinson-Foulds metric. In A. Darling & J.
diff --git a/dev/articles/Using-TreeDist.html b/dev/articles/Using-TreeDist.html
index 7409b5ae..0d75af61 100644
--- a/dev/articles/Using-TreeDist.html
+++ b/dev/articles/Using-TreeDist.html
@@ -42,7 +42,7 @@
@@ -204,12 +204,12 @@ Multiple comparisonsTreeDistance(oneTree, twoTrees)
## one two
-## 0.8258625 0.8651397
TreeDistance(twoTrees, threeTrees)## a b c
-## one 0.6583478 0.4713275 0.7178246
-## two 0.7065470 0.7923405 0.7596224
diff --git a/dev/articles/compare-treesets.html b/dev/articles/compare-treesets.html
index 45b37488..44320422 100644
--- a/dev/articles/compare-treesets.html
+++ b/dev/articles/compare-treesets.html
@@ -42,7 +42,7 @@
@@ -164,8 +164,8 @@ Shiny appAdd batch to existing
-
-
Load tree batches
+
+Load tree batches
- On the Display tab,
@@ -174,8 +174,8 @@
Shiny app
-
Tree batch styles
+
+Tree batch styles
@@ -219,8 +219,8 @@ Comparing trees’ dispersal / hy
Interpreting and comparing the areas of tree space from a projection
can be misleading – the expanded apparent area of Greenland under the
Mercator projection being a familiar example.
-
-
Mapping can introduce distortion
+
+Mapping can introduce distortion
As such, it is always best to work with original distances when
interpreting whether sets of trees occupy larger or smaller regions of
@@ -311,7 +311,7 @@
Consensus resolution
References
-
+
Smith, M. R. (2022a). Robust analysis of phylogenetic tree space.
Systematic Biology, 71(5), 1255–1270. doi: 10.1093/sysbio/syab100
diff --git a/dev/articles/different-leaves.html b/dev/articles/different-leaves.html
index eb19d25d..c42a702b 100644
--- a/dev/articles/different-leaves.html
+++ b/dev/articles/different-leaves.html
@@ -42,7 +42,7 @@
diff --git a/dev/articles/index.html b/dev/articles/index.html
index 8881b823..3f857641 100644
--- a/dev/articles/index.html
+++ b/dev/articles/index.html
@@ -23,7 +23,7 @@
diff --git a/dev/articles/information.html b/dev/articles/information.html
index 2d85bbd5..f319f8dd 100644
--- a/dev/articles/information.html
+++ b/dev/articles/information.html
@@ -42,7 +42,7 @@
@@ -198,10 +198,9 @@ Application to splitsThe split \(S_1 =\)
AB|CDEF is found in 15 of the 105 six-leaf trees; as such,
the probability that a randomly drawn tree contains \(S_1\) is \(P(S_1)
-= \frac{15}{105}\), and the information content \(h(S_1) = -\log_2{\frac{15}{105}} \approx
-2.81\textrm{ bits}\). Steel & Penny
-(2006) dub this quantity the phylogenetic information
-content.
+= \frac{15}{105}\), and the information content \(h(S_1) =
+-\log_2{\frac{15}{105}} \approx 2.81\textrm{ bits}\). Steel & Penny (2006) dub this quantity the
+phylogenetic information content.
Likewise, the split \(S_2 =\)
ABC|DEF occurs in nine of the 105 six-leaf trees, so \(h(S_2) = -\log_2{\frac{9}{105}} \approx
3.54\textrm{ bits}\). Three six-leaf trees contain both splits,
@@ -209,10 +208,10 @@
Application to splits of information.
Because \(h(S_1,S_2) < h(S_1) +
h(S_2)\), some of the information in \(S_1\) is also present in \(S_2\). The information in common between
-\(S_1\) and \(S_2\) is \(h_{shared}(S_1, S_2) = h(S_1) + h(S_2) -
-h(S_1,S_2) \approx 1.22\textrm{ bits}\). The information unique
-to \(S_1\) and \(S_2\) is \(h_{different}(S_1,S_2) = 2h(S_1,S_2) - h(S_1) -
-h(S_2) \approx 3.91\textrm{ bits}\).
+\(S_1\) and \(S_2\) is \(h_{shared}(S_1, S_2) =
+h(S_1) + h(S_2) - h(S_1,S_2) \approx 1.22\textrm{ bits}\). The
+information unique to \(S_1\) and \(S_2\) is \(h_{different}(S_1,S_2) =
+2h(S_1,S_2) - h(S_1) - h(S_2) \approx 3.91\textrm{ bits}\).
These quantities can be calculated using functions in the ‘TreeTools’ package.
library("TreeTools", quietly = TRUE)
@@ -304,10 +303,12 @@ Entropy
-\(\begin{aligned} H(S_1, S_2) =
-\frac{2}{3}\log_2{\frac{2}{3}} + \frac{1}{3}\log_2{\frac{1}{3}} +
-\frac{1}{3}\log_2{\frac{1}{3}} + \frac{2}{3}\log_2{\frac{2}{3}} \approx
-1.84 \textrm{ bits} \end{aligned}\)
+\(\begin{aligned}
+H(S_1, S_2) = \frac{2}{3}\log_2{\frac{2}{3}} +
+\frac{1}{3}\log_2{\frac{1}{3}} + \frac{1}{3}\log_2{\frac{1}{3}} +
+\frac{2}{3}\log_2{\frac{2}{3}} \approx
+1.84 \textrm{ bits}
+\end{aligned}\)
Note that this less than the \(\log_2{6}
\approx 2.58\textrm{ bits}\) we require to determine the exact
value of the roll: knowledge of \(S_1\)
@@ -395,22 +396,23 @@
Application to splits
\(S_2: x \in A_2\)
-\(P(A_1,A_2) = \frac{|A_1 \cap
-A_2|}{n}\)
+\(P(A_1,A_2) =
+\frac{|A_1 \cap A_2|}{n}\)
\(P(B_1,A_2) = \frac{|B_1 \cap
A_2|}{n}\)
\(S_2: x \in B_2\)
-\(P(A_1,B_2) = \frac{|A_1 \cap
-B_2|}{n}\)
+\(P(A_1,B_2) =
+\frac{|A_1 \cap B_2|}{n}\)
\(P(B_1,B_2) = \frac{|B_1 \cap
B_2|}{n}\)
-\(H(S_1, S_2) = P(A_1,A_2) \log_2
-{P(A_1,A_2)} + P(B_1,A_2) \log_2 {P(B_1,A_2)}\)
+\(H(S_1, S_2) =
+P(A_1,A_2) \log_2 {P(A_1,A_2)} +
+P(B_1,A_2) \log_2 {P(B_1,A_2)}\)
\(+ P(A_1,B_2)\log_2{P(A_1,B_2)} +
P(B_1,B_2)\log_2{P(B_1,B_2)}\)
These values can then be substituted into the definitions of mutual
@@ -424,7 +426,7 @@
Application to splits
References
-
+
MacKay, D. J. C. (2003). Information theory, inference, and learning
algorithms. Cambridge: Cambridge University Press. Retrieved from
diff --git a/dev/articles/landscapes.html b/dev/articles/landscapes.html
index 61497cfa..5374486f 100644
--- a/dev/articles/landscapes.html
+++ b/dev/articles/landscapes.html
@@ -42,7 +42,7 @@
@@ -254,12 +254,12 @@ } else {
print("Run `install.packages('plotly')` to view this output")
}
-
-(Use the mouse to reorient)
+
+(Use the mouse to reorient)
References
-
+
Bastert, O., Rockmore, D., Stadler, P. F., & Tinhofer, G. (2002).
Landscapes on spaces of trees. Applied Mathematics and
diff --git a/dev/articles/treespace.html b/dev/articles/treespace.html
index fd306ae1..2b1f125c 100644
--- a/dev/articles/treespace.html
+++ b/dev/articles/treespace.html
@@ -42,7 +42,7 @@
@@ -514,7 +514,7 @@ What next?
References
-
+
Arthur, D., & Vassilvitskii, S. (2007). K-means++: The advantages of
careful seeding. Proceedings of the Eighteenth Annual
diff --git a/dev/articles/treespace_files/figure-html/umatrix-1.png b/dev/articles/treespace_files/figure-html/umatrix-1.png
index f8b3613e..60d1f935 100644
Binary files a/dev/articles/treespace_files/figure-html/umatrix-1.png and b/dev/articles/treespace_files/figure-html/umatrix-1.png differ
diff --git a/dev/articles/using-distances.html b/dev/articles/using-distances.html
index 719e74fc..335f61a0 100644
--- a/dev/articles/using-distances.html
+++ b/dev/articles/using-distances.html
@@ -42,7 +42,7 @@
@@ -519,7 +519,7 @@ What next?
References
-
+
Nye, T. M. W., Liò, P., & Gilks, W. R. (2006). A novel algorithm and web-based tool for comparing two
alternative phylogenetic trees. Bioinformatics,
diff --git a/dev/authors.html b/dev/authors.html
index f4a01a97..419c5187 100644
--- a/dev/authors.html
+++ b/dev/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 2.7.0.9000. Comprehensive R Archive Network. doi:10.5281/zenodo.3528124
+ Smith, M.R. (2020b). TreeDist: Distances between Phylogenetic Trees. R package version 2.7.0.9001. Comprehensive R Archive Network. doi:10.5281/zenodo.3528124
@Manual{TreeDist,
- title = {TreeDist: Distances between Phylogenetic Trees. R package version 2.7.0.9000},
+ title = {TreeDist: Distances between Phylogenetic Trees. R package version 2.7.0.9001},
author = {Martin R. Smith},
doi = {10.5281/zenodo.3528124},
journal = {Comprehensive R Archive Network},
diff --git a/dev/index.html b/dev/index.html
index 61d48be5..361c5ce7 100644
--- a/dev/index.html
+++ b/dev/index.html
@@ -59,7 +59,7 @@
@@ -202,8 +202,8 @@ Tree space analysis
TreeDist::MapTrees()
-
diff --git a/dev/news/index.html b/dev/news/index.html
index 6384873a..3434ad0a 100644
--- a/dev/news/index.html
+++ b/dev/news/index.html
@@ -23,7 +23,7 @@
@@ -108,8 +108,9 @@ Changelog
TreeDist 2.7.0 (2023-10-25)2023-10-25
diff --git a/dev/pkgdown.yml b/dev/pkgdown.yml
index 952d9b38..a6ef3bc5 100644
--- a/dev/pkgdown.yml
+++ b/dev/pkgdown.yml
@@ -1,4 +1,4 @@
-pandoc: 2.19.2
+pandoc: 3.1.11
pkgdown: 2.0.7
pkgdown_sha: ~
articles:
@@ -11,7 +11,7 @@ articles:
landscapes: landscapes.html
treespace: treespace.html
using-distances: using-distances.html
-last_built: 2024-02-23T15:03Z
+last_built: 2024-02-29T08:01Z
urls:
reference: https://ms609.github.io/TreeDist/reference
article: https://ms609.github.io/TreeDist/articles
diff --git a/dev/reference/AllSplitPairings.html b/dev/reference/AllSplitPairings.html
index 381eb3eb..c9ae9ab8 100644
--- a/dev/reference/AllSplitPairings.html
+++ b/dev/reference/AllSplitPairings.html
@@ -28,7 +28,7 @@
diff --git a/dev/reference/CalculateTreeDistance.html b/dev/reference/CalculateTreeDistance.html
index acbac29b..4dbbe45c 100644
--- a/dev/reference/CalculateTreeDistance.html
+++ b/dev/reference/CalculateTreeDistance.html
@@ -23,7 +23,7 @@
diff --git a/dev/reference/CompareAll.html b/dev/reference/CompareAll.html
index 08a7dbed..a092013f 100644
--- a/dev/reference/CompareAll.html
+++ b/dev/reference/CompareAll.html
@@ -24,7 +24,7 @@
diff --git a/dev/reference/Entropy.html b/dev/reference/Entropy.html
index 74123faa..0a18776a 100644
--- a/dev/reference/Entropy.html
+++ b/dev/reference/Entropy.html
@@ -25,7 +25,7 @@
diff --git a/dev/reference/GeneralizedRF.html b/dev/reference/GeneralizedRF.html
index f622fdf5..101daf50 100644
--- a/dev/reference/GeneralizedRF.html
+++ b/dev/reference/GeneralizedRF.html
@@ -24,7 +24,7 @@
diff --git a/dev/reference/JaccardRobinsonFoulds.html b/dev/reference/JaccardRobinsonFoulds.html
index 19a08a67..b3f47090 100644
--- a/dev/reference/JaccardRobinsonFoulds.html
+++ b/dev/reference/JaccardRobinsonFoulds.html
@@ -27,7 +27,7 @@
diff --git a/dev/reference/KendallColijn.html b/dev/reference/KendallColijn.html
index cb2ad3d0..bf7aff00 100644
--- a/dev/reference/KendallColijn.html
+++ b/dev/reference/KendallColijn.html
@@ -24,7 +24,7 @@
@@ -289,12 +289,10 @@ Examples
#> 1 2
#> 2 2.449490
#> 3 2.449490 3.162278
-KCDiameter(trees)
-#> Warning: first element used of 'length.out' argument
-#> Warning: longer object length is not a multiple of shorter object length
-#> [1] 15.87451
KCDiameter(4)
#> [1] 3.162278
+KCDiameter(trees)
+#> [1] 15.87451 15.87451 15.87451
Load tree batches
+
+
Load tree batches
- On the Display tab,
@@ -174,8 +174,8 @@
Shiny app -
Tree batch styles
++Tree batch styles
Comparing trees’ dispersal / hy
Interpreting and comparing the areas of tree space from a projection can be misleading – the expanded apparent area of Greenland under the Mercator projection being a familiar example.
-
-Consensus resolution
@@ -289,12 +289,10 @@ Mapping can introduce distortion
+
+
Mapping can introduce distortion
As such, it is always best to work with original distances when interpreting whether sets of trees occupy larger or smaller regions of @@ -311,7 +311,7 @@
Consensus resolution
References
-
+
Smith, M. R. (2022a). Robust analysis of phylogenetic tree space.
Systematic Biology, 71(5), 1255–1270. doi: 10.1093/sysbio/syab100
diff --git a/dev/articles/different-leaves.html b/dev/articles/different-leaves.html
index eb19d25d..c42a702b 100644
--- a/dev/articles/different-leaves.html
+++ b/dev/articles/different-leaves.html
@@ -42,7 +42,7 @@
diff --git a/dev/articles/index.html b/dev/articles/index.html
index 8881b823..3f857641 100644
--- a/dev/articles/index.html
+++ b/dev/articles/index.html
@@ -23,7 +23,7 @@
diff --git a/dev/articles/information.html b/dev/articles/information.html
index 2d85bbd5..f319f8dd 100644
--- a/dev/articles/information.html
+++ b/dev/articles/information.html
@@ -42,7 +42,7 @@
@@ -198,10 +198,9 @@ Application to splitsThe split \(S_1 =\)
AB|CDEF is found in 15 of the 105 six-leaf trees; as such,
the probability that a randomly drawn tree contains \(S_1\) is \(P(S_1)
-= \frac{15}{105}\), and the information content \(h(S_1) = -\log_2{\frac{15}{105}} \approx
-2.81\textrm{ bits}\). Steel & Penny
-(2006) dub this quantity the phylogenetic information
-content.
+= \frac{15}{105}\), and the information content \(h(S_1) =
+-\log_2{\frac{15}{105}} \approx 2.81\textrm{ bits}\). Steel & Penny (2006) dub this quantity the
+phylogenetic information content.
Likewise, the split \(S_2 =\)
ABC|DEF occurs in nine of the 105 six-leaf trees, so \(h(S_2) = -\log_2{\frac{9}{105}} \approx
3.54\textrm{ bits}\). Three six-leaf trees contain both splits,
@@ -209,10 +208,10 @@
Application to splits of information.
Because \(h(S_1,S_2) < h(S_1) +
h(S_2)\), some of the information in \(S_1\) is also present in \(S_2\). The information in common between
-\(S_1\) and \(S_2\) is \(h_{shared}(S_1, S_2) = h(S_1) + h(S_2) -
-h(S_1,S_2) \approx 1.22\textrm{ bits}\). The information unique
-to \(S_1\) and \(S_2\) is \(h_{different}(S_1,S_2) = 2h(S_1,S_2) - h(S_1) -
-h(S_2) \approx 3.91\textrm{ bits}\).
+\(S_1\) and \(S_2\) is \(h_{shared}(S_1, S_2) =
+h(S_1) + h(S_2) - h(S_1,S_2) \approx 1.22\textrm{ bits}\). The
+information unique to \(S_1\) and \(S_2\) is \(h_{different}(S_1,S_2) =
+2h(S_1,S_2) - h(S_1) - h(S_2) \approx 3.91\textrm{ bits}\).
These quantities can be calculated using functions in the ‘TreeTools’ package.
library("TreeTools", quietly = TRUE)
@@ -304,10 +303,12 @@ Entropy
-\(\begin{aligned} H(S_1, S_2) =
-\frac{2}{3}\log_2{\frac{2}{3}} + \frac{1}{3}\log_2{\frac{1}{3}} +
-\frac{1}{3}\log_2{\frac{1}{3}} + \frac{2}{3}\log_2{\frac{2}{3}} \approx
-1.84 \textrm{ bits} \end{aligned}\)
+\(\begin{aligned}
+H(S_1, S_2) = \frac{2}{3}\log_2{\frac{2}{3}} +
+\frac{1}{3}\log_2{\frac{1}{3}} + \frac{1}{3}\log_2{\frac{1}{3}} +
+\frac{2}{3}\log_2{\frac{2}{3}} \approx
+1.84 \textrm{ bits}
+\end{aligned}\)
Note that this less than the \(\log_2{6}
\approx 2.58\textrm{ bits}\) we require to determine the exact
value of the roll: knowledge of \(S_1\)
@@ -395,22 +396,23 @@
Application to splits
\(S_2: x \in A_2\)
-\(P(A_1,A_2) = \frac{|A_1 \cap
-A_2|}{n}\)
+\(P(A_1,A_2) =
+\frac{|A_1 \cap A_2|}{n}\)
\(P(B_1,A_2) = \frac{|B_1 \cap
A_2|}{n}\)
\(S_2: x \in B_2\)
-\(P(A_1,B_2) = \frac{|A_1 \cap
-B_2|}{n}\)
+\(P(A_1,B_2) =
+\frac{|A_1 \cap B_2|}{n}\)
\(P(B_1,B_2) = \frac{|B_1 \cap
B_2|}{n}\)
-\(H(S_1, S_2) = P(A_1,A_2) \log_2
-{P(A_1,A_2)} + P(B_1,A_2) \log_2 {P(B_1,A_2)}\)
+\(H(S_1, S_2) =
+P(A_1,A_2) \log_2 {P(A_1,A_2)} +
+P(B_1,A_2) \log_2 {P(B_1,A_2)}\)
\(+ P(A_1,B_2)\log_2{P(A_1,B_2)} +
P(B_1,B_2)\log_2{P(B_1,B_2)}\)
These values can then be substituted into the definitions of mutual
@@ -424,7 +426,7 @@
Application to splits
References
-
+
MacKay, D. J. C. (2003). Information theory, inference, and learning
algorithms. Cambridge: Cambridge University Press. Retrieved from
diff --git a/dev/articles/landscapes.html b/dev/articles/landscapes.html
index 61497cfa..5374486f 100644
--- a/dev/articles/landscapes.html
+++ b/dev/articles/landscapes.html
@@ -42,7 +42,7 @@
@@ -254,12 +254,12 @@ } else {
print("Run `install.packages('plotly')` to view this output")
}
-
-(Use the mouse to reorient)
+
+(Use the mouse to reorient)
References
-
+
Bastert, O., Rockmore, D., Stadler, P. F., & Tinhofer, G. (2002).
Landscapes on spaces of trees. Applied Mathematics and
diff --git a/dev/articles/treespace.html b/dev/articles/treespace.html
index fd306ae1..2b1f125c 100644
--- a/dev/articles/treespace.html
+++ b/dev/articles/treespace.html
@@ -42,7 +42,7 @@
@@ -514,7 +514,7 @@ What next?
References
-
+
Arthur, D., & Vassilvitskii, S. (2007). K-means++: The advantages of
careful seeding. Proceedings of the Eighteenth Annual
diff --git a/dev/articles/treespace_files/figure-html/umatrix-1.png b/dev/articles/treespace_files/figure-html/umatrix-1.png
index f8b3613e..60d1f935 100644
Binary files a/dev/articles/treespace_files/figure-html/umatrix-1.png and b/dev/articles/treespace_files/figure-html/umatrix-1.png differ
diff --git a/dev/articles/using-distances.html b/dev/articles/using-distances.html
index 719e74fc..335f61a0 100644
--- a/dev/articles/using-distances.html
+++ b/dev/articles/using-distances.html
@@ -42,7 +42,7 @@
@@ -519,7 +519,7 @@ What next?
References
-
+
Nye, T. M. W., Liò, P., & Gilks, W. R. (2006). A novel algorithm and web-based tool for comparing two
alternative phylogenetic trees. Bioinformatics,
diff --git a/dev/authors.html b/dev/authors.html
index f4a01a97..419c5187 100644
--- a/dev/authors.html
+++ b/dev/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 2.7.0.9000. Comprehensive R Archive Network. doi:10.5281/zenodo.3528124
+ Smith, M.R. (2020b). TreeDist: Distances between Phylogenetic Trees. R package version 2.7.0.9001. Comprehensive R Archive Network. doi:10.5281/zenodo.3528124
@Manual{TreeDist,
- title = {TreeDist: Distances between Phylogenetic Trees. R package version 2.7.0.9000},
+ title = {TreeDist: Distances between Phylogenetic Trees. R package version 2.7.0.9001},
author = {Martin R. Smith},
doi = {10.5281/zenodo.3528124},
journal = {Comprehensive R Archive Network},
diff --git a/dev/index.html b/dev/index.html
index 61d48be5..361c5ce7 100644
--- a/dev/index.html
+++ b/dev/index.html
@@ -59,7 +59,7 @@
@@ -202,8 +202,8 @@ Tree space analysis
TreeDist::MapTrees()
-
diff --git a/dev/news/index.html b/dev/news/index.html
index 6384873a..3434ad0a 100644
--- a/dev/news/index.html
+++ b/dev/news/index.html
@@ -23,7 +23,7 @@
@@ -108,8 +108,9 @@ Changelog
TreeDist 2.7.0 (2023-10-25)2023-10-25
diff --git a/dev/pkgdown.yml b/dev/pkgdown.yml
index 952d9b38..a6ef3bc5 100644
--- a/dev/pkgdown.yml
+++ b/dev/pkgdown.yml
@@ -1,4 +1,4 @@
-pandoc: 2.19.2
+pandoc: 3.1.11
pkgdown: 2.0.7
pkgdown_sha: ~
articles:
@@ -11,7 +11,7 @@ articles:
landscapes: landscapes.html
treespace: treespace.html
using-distances: using-distances.html
-last_built: 2024-02-23T15:03Z
+last_built: 2024-02-29T08:01Z
urls:
reference: https://ms609.github.io/TreeDist/reference
article: https://ms609.github.io/TreeDist/articles
diff --git a/dev/reference/AllSplitPairings.html b/dev/reference/AllSplitPairings.html
index 381eb3eb..c9ae9ab8 100644
--- a/dev/reference/AllSplitPairings.html
+++ b/dev/reference/AllSplitPairings.html
@@ -28,7 +28,7 @@
diff --git a/dev/reference/CalculateTreeDistance.html b/dev/reference/CalculateTreeDistance.html
index acbac29b..4dbbe45c 100644
--- a/dev/reference/CalculateTreeDistance.html
+++ b/dev/reference/CalculateTreeDistance.html
@@ -23,7 +23,7 @@
diff --git a/dev/reference/CompareAll.html b/dev/reference/CompareAll.html
index 08a7dbed..a092013f 100644
--- a/dev/reference/CompareAll.html
+++ b/dev/reference/CompareAll.html
@@ -24,7 +24,7 @@
diff --git a/dev/reference/Entropy.html b/dev/reference/Entropy.html
index 74123faa..0a18776a 100644
--- a/dev/reference/Entropy.html
+++ b/dev/reference/Entropy.html
@@ -25,7 +25,7 @@
diff --git a/dev/reference/GeneralizedRF.html b/dev/reference/GeneralizedRF.html
index f622fdf5..101daf50 100644
--- a/dev/reference/GeneralizedRF.html
+++ b/dev/reference/GeneralizedRF.html
@@ -24,7 +24,7 @@
diff --git a/dev/reference/JaccardRobinsonFoulds.html b/dev/reference/JaccardRobinsonFoulds.html
index 19a08a67..b3f47090 100644
--- a/dev/reference/JaccardRobinsonFoulds.html
+++ b/dev/reference/JaccardRobinsonFoulds.html
@@ -27,7 +27,7 @@
diff --git a/dev/reference/KendallColijn.html b/dev/reference/KendallColijn.html
index cb2ad3d0..bf7aff00 100644
--- a/dev/reference/KendallColijn.html
+++ b/dev/reference/KendallColijn.html
@@ -24,7 +24,7 @@
Smith, M. R. (2022a). Robust analysis of phylogenetic tree space.
Systematic Biology, 71(5), 1255–1270. doi: 10.1093/sysbio/syab100
diff --git a/dev/articles/different-leaves.html b/dev/articles/different-leaves.html
index eb19d25d..c42a702b 100644
--- a/dev/articles/different-leaves.html
+++ b/dev/articles/different-leaves.html
@@ -42,7 +42,7 @@
diff --git a/dev/articles/index.html b/dev/articles/index.html
index 8881b823..3f857641 100644
--- a/dev/articles/index.html
+++ b/dev/articles/index.html
@@ -23,7 +23,7 @@
AB|CDEF is found in 15 of the 105 six-leaf trees; as such,
the probability that a randomly drawn tree contains \(S_1\) is \(P(S_1)
-= \frac{15}{105}\), and the information content \(h(S_1) = -\log_2{\frac{15}{105}} \approx
-2.81\textrm{ bits}\). Steel & Penny
-(2006) dub this quantity the phylogenetic information
-content.
+= \frac{15}{105}\), and the information content \(h(S_1) =
+-\log_2{\frac{15}{105}} \approx 2.81\textrm{ bits}\). Steel & Penny (2006) dub this quantity the
+phylogenetic information content.
Likewise, the split \(S_2 =\)
ABC|DEF occurs in nine of the 105 six-leaf trees, so \(h(S_2) = -\log_2{\frac{9}{105}} \approx
3.54\textrm{ bits}\). Three six-leaf trees contain both splits,
@@ -209,10 +208,10 @@
Application to splits of information.
Because \(h(S_1,S_2) < h(S_1) +
h(S_2)\), some of the information in \(S_1\) is also present in \(S_2\). The information in common between
-\(S_1\) and \(S_2\) is \(h_{shared}(S_1, S_2) = h(S_1) + h(S_2) -
-h(S_1,S_2) \approx 1.22\textrm{ bits}\). The information unique
-to \(S_1\) and \(S_2\) is \(h_{different}(S_1,S_2) = 2h(S_1,S_2) - h(S_1) -
-h(S_2) \approx 3.91\textrm{ bits}\).
+\(S_1\) and \(S_2\) is \(h_{shared}(S_1, S_2) =
+h(S_1) + h(S_2) - h(S_1,S_2) \approx 1.22\textrm{ bits}\). The
+information unique to \(S_1\) and \(S_2\) is \(h_{different}(S_1,S_2) =
+2h(S_1,S_2) - h(S_1) - h(S_2) \approx 3.91\textrm{ bits}\).
These quantities can be calculated using functions in the ‘TreeTools’ package.
library("TreeTools", quietly = TRUE)
@@ -304,10 +303,12 @@ Entropy
-\(\begin{aligned} H(S_1, S_2) =
-\frac{2}{3}\log_2{\frac{2}{3}} + \frac{1}{3}\log_2{\frac{1}{3}} +
-\frac{1}{3}\log_2{\frac{1}{3}} + \frac{2}{3}\log_2{\frac{2}{3}} \approx
-1.84 \textrm{ bits} \end{aligned}\)
+\(\begin{aligned}
+H(S_1, S_2) = \frac{2}{3}\log_2{\frac{2}{3}} +
+\frac{1}{3}\log_2{\frac{1}{3}} + \frac{1}{3}\log_2{\frac{1}{3}} +
+\frac{2}{3}\log_2{\frac{2}{3}} \approx
+1.84 \textrm{ bits}
+\end{aligned}\)
Note that this less than the \(\log_2{6}
\approx 2.58\textrm{ bits}\) we require to determine the exact
value of the roll: knowledge of \(S_1\)
@@ -395,22 +396,23 @@
Application to splits
\(S_2: x \in A_2\)
-\(P(A_1,A_2) = \frac{|A_1 \cap
-A_2|}{n}\)
+\(P(A_1,A_2) =
+\frac{|A_1 \cap A_2|}{n}\)
\(P(B_1,A_2) = \frac{|B_1 \cap
A_2|}{n}\)
\(S_2: x \in B_2\)
-\(P(A_1,B_2) = \frac{|A_1 \cap
-B_2|}{n}\)
+\(P(A_1,B_2) =
+\frac{|A_1 \cap B_2|}{n}\)
\(P(B_1,B_2) = \frac{|B_1 \cap
B_2|}{n}\)
-\(H(S_1, S_2) = P(A_1,A_2) \log_2
-{P(A_1,A_2)} + P(B_1,A_2) \log_2 {P(B_1,A_2)}\)
+\(H(S_1, S_2) =
+P(A_1,A_2) \log_2 {P(A_1,A_2)} +
+P(B_1,A_2) \log_2 {P(B_1,A_2)}\)
\(+ P(A_1,B_2)\log_2{P(A_1,B_2)} +
P(B_1,B_2)\log_2{P(B_1,B_2)}\)
These values can then be substituted into the definitions of mutual
@@ -424,7 +426,7 @@
Application to splits
References
-
+
MacKay, D. J. C. (2003). Information theory, inference, and learning
algorithms. Cambridge: Cambridge University Press. Retrieved from
diff --git a/dev/articles/landscapes.html b/dev/articles/landscapes.html
index 61497cfa..5374486f 100644
--- a/dev/articles/landscapes.html
+++ b/dev/articles/landscapes.html
@@ -42,7 +42,7 @@
@@ -254,12 +254,12 @@ } else {
print("Run `install.packages('plotly')` to view this output")
}
-
-(Use the mouse to reorient)
+
+(Use the mouse to reorient)
References
-
+
Bastert, O., Rockmore, D., Stadler, P. F., & Tinhofer, G. (2002).
Landscapes on spaces of trees. Applied Mathematics and
diff --git a/dev/articles/treespace.html b/dev/articles/treespace.html
index fd306ae1..2b1f125c 100644
--- a/dev/articles/treespace.html
+++ b/dev/articles/treespace.html
@@ -42,7 +42,7 @@
@@ -514,7 +514,7 @@ What next?
References
-
+
Arthur, D., & Vassilvitskii, S. (2007). K-means++: The advantages of
careful seeding. Proceedings of the Eighteenth Annual
diff --git a/dev/articles/treespace_files/figure-html/umatrix-1.png b/dev/articles/treespace_files/figure-html/umatrix-1.png
index f8b3613e..60d1f935 100644
Binary files a/dev/articles/treespace_files/figure-html/umatrix-1.png and b/dev/articles/treespace_files/figure-html/umatrix-1.png differ
diff --git a/dev/articles/using-distances.html b/dev/articles/using-distances.html
index 719e74fc..335f61a0 100644
--- a/dev/articles/using-distances.html
+++ b/dev/articles/using-distances.html
@@ -42,7 +42,7 @@
@@ -519,7 +519,7 @@ What next?
References
-
+
Nye, T. M. W., Liò, P., & Gilks, W. R. (2006). A novel algorithm and web-based tool for comparing two
alternative phylogenetic trees. Bioinformatics,
diff --git a/dev/authors.html b/dev/authors.html
index f4a01a97..419c5187 100644
--- a/dev/authors.html
+++ b/dev/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 2.7.0.9000. Comprehensive R Archive Network. doi:10.5281/zenodo.3528124
+ Smith, M.R. (2020b). TreeDist: Distances between Phylogenetic Trees. R package version 2.7.0.9001. Comprehensive R Archive Network. doi:10.5281/zenodo.3528124
@Manual{TreeDist,
- title = {TreeDist: Distances between Phylogenetic Trees. R package version 2.7.0.9000},
+ title = {TreeDist: Distances between Phylogenetic Trees. R package version 2.7.0.9001},
author = {Martin R. Smith},
doi = {10.5281/zenodo.3528124},
journal = {Comprehensive R Archive Network},
diff --git a/dev/index.html b/dev/index.html
index 61d48be5..361c5ce7 100644
--- a/dev/index.html
+++ b/dev/index.html
@@ -59,7 +59,7 @@
@@ -202,8 +202,8 @@ Tree space analysis
TreeDist::MapTrees()
-
diff --git a/dev/news/index.html b/dev/news/index.html
index 6384873a..3434ad0a 100644
--- a/dev/news/index.html
+++ b/dev/news/index.html
@@ -23,7 +23,7 @@
@@ -108,8 +108,9 @@ Changelog
TreeDist 2.7.0 (2023-10-25)2023-10-25
diff --git a/dev/pkgdown.yml b/dev/pkgdown.yml
index 952d9b38..a6ef3bc5 100644
--- a/dev/pkgdown.yml
+++ b/dev/pkgdown.yml
@@ -1,4 +1,4 @@
-pandoc: 2.19.2
+pandoc: 3.1.11
pkgdown: 2.0.7
pkgdown_sha: ~
articles:
@@ -11,7 +11,7 @@ articles:
landscapes: landscapes.html
treespace: treespace.html
using-distances: using-distances.html
-last_built: 2024-02-23T15:03Z
+last_built: 2024-02-29T08:01Z
urls:
reference: https://ms609.github.io/TreeDist/reference
article: https://ms609.github.io/TreeDist/articles
diff --git a/dev/reference/AllSplitPairings.html b/dev/reference/AllSplitPairings.html
index 381eb3eb..c9ae9ab8 100644
--- a/dev/reference/AllSplitPairings.html
+++ b/dev/reference/AllSplitPairings.html
@@ -28,7 +28,7 @@
diff --git a/dev/reference/CalculateTreeDistance.html b/dev/reference/CalculateTreeDistance.html
index acbac29b..4dbbe45c 100644
--- a/dev/reference/CalculateTreeDistance.html
+++ b/dev/reference/CalculateTreeDistance.html
@@ -23,7 +23,7 @@
diff --git a/dev/reference/CompareAll.html b/dev/reference/CompareAll.html
index 08a7dbed..a092013f 100644
--- a/dev/reference/CompareAll.html
+++ b/dev/reference/CompareAll.html
@@ -24,7 +24,7 @@
diff --git a/dev/reference/Entropy.html b/dev/reference/Entropy.html
index 74123faa..0a18776a 100644
--- a/dev/reference/Entropy.html
+++ b/dev/reference/Entropy.html
@@ -25,7 +25,7 @@
diff --git a/dev/reference/GeneralizedRF.html b/dev/reference/GeneralizedRF.html
index f622fdf5..101daf50 100644
--- a/dev/reference/GeneralizedRF.html
+++ b/dev/reference/GeneralizedRF.html
@@ -24,7 +24,7 @@
diff --git a/dev/reference/JaccardRobinsonFoulds.html b/dev/reference/JaccardRobinsonFoulds.html
index 19a08a67..b3f47090 100644
--- a/dev/reference/JaccardRobinsonFoulds.html
+++ b/dev/reference/JaccardRobinsonFoulds.html
@@ -27,7 +27,7 @@
diff --git a/dev/reference/KendallColijn.html b/dev/reference/KendallColijn.html
index cb2ad3d0..bf7aff00 100644
--- a/dev/reference/KendallColijn.html
+++ b/dev/reference/KendallColijn.html
@@ -24,7 +24,7 @@
library("TreeTools", quietly = TRUE)
@@ -304,10 +303,12 @@ Entropy
-\(\begin{aligned} H(S_1, S_2) =
-\frac{2}{3}\log_2{\frac{2}{3}} + \frac{1}{3}\log_2{\frac{1}{3}} +
-\frac{1}{3}\log_2{\frac{1}{3}} + \frac{2}{3}\log_2{\frac{2}{3}} \approx
-1.84 \textrm{ bits} \end{aligned}\)
+\(\begin{aligned}
+H(S_1, S_2) = \frac{2}{3}\log_2{\frac{2}{3}} +
+\frac{1}{3}\log_2{\frac{1}{3}} + \frac{1}{3}\log_2{\frac{1}{3}} +
+\frac{2}{3}\log_2{\frac{2}{3}} \approx
+1.84 \textrm{ bits}
+\end{aligned}\)
Note that this less than the \(\log_2{6}
\approx 2.58\textrm{ bits}\) we require to determine the exact
value of the roll: knowledge of \(S_1\)
@@ -395,22 +396,23 @@
Application to splits
\(S_2: x \in A_2\)
-\(P(A_1,A_2) = \frac{|A_1 \cap
-A_2|}{n}\)
+\(P(A_1,A_2) =
+\frac{|A_1 \cap A_2|}{n}\)
\(P(B_1,A_2) = \frac{|B_1 \cap
A_2|}{n}\)
\(S_2: x \in B_2\)
-\(P(A_1,B_2) = \frac{|A_1 \cap
-B_2|}{n}\)
+\(P(A_1,B_2) =
+\frac{|A_1 \cap B_2|}{n}\)
\(P(B_1,B_2) = \frac{|B_1 \cap
B_2|}{n}\)
-\(H(S_1, S_2) = P(A_1,A_2) \log_2
-{P(A_1,A_2)} + P(B_1,A_2) \log_2 {P(B_1,A_2)}\)
+\(H(S_1, S_2) =
+P(A_1,A_2) \log_2 {P(A_1,A_2)} +
+P(B_1,A_2) \log_2 {P(B_1,A_2)}\)
\(+ P(A_1,B_2)\log_2{P(A_1,B_2)} +
P(B_1,B_2)\log_2{P(B_1,B_2)}\)
These values can then be substituted into the definitions of mutual
@@ -424,7 +426,7 @@
Application to splits
References
-
+
MacKay, D. J. C. (2003). Information theory, inference, and learning
algorithms. Cambridge: Cambridge University Press. Retrieved from
diff --git a/dev/articles/landscapes.html b/dev/articles/landscapes.html
index 61497cfa..5374486f 100644
--- a/dev/articles/landscapes.html
+++ b/dev/articles/landscapes.html
@@ -42,7 +42,7 @@
@@ -254,12 +254,12 @@ } else {
print("Run `install.packages('plotly')` to view this output")
}
-
-(Use the mouse to reorient)
+
+(Use the mouse to reorient)
References
-
+
Bastert, O., Rockmore, D., Stadler, P. F., & Tinhofer, G. (2002).
Landscapes on spaces of trees. Applied Mathematics and
diff --git a/dev/articles/treespace.html b/dev/articles/treespace.html
index fd306ae1..2b1f125c 100644
--- a/dev/articles/treespace.html
+++ b/dev/articles/treespace.html
@@ -42,7 +42,7 @@
@@ -514,7 +514,7 @@ What next?
References
-
+
Arthur, D., & Vassilvitskii, S. (2007). K-means++: The advantages of
careful seeding. Proceedings of the Eighteenth Annual
diff --git a/dev/articles/treespace_files/figure-html/umatrix-1.png b/dev/articles/treespace_files/figure-html/umatrix-1.png
index f8b3613e..60d1f935 100644
Binary files a/dev/articles/treespace_files/figure-html/umatrix-1.png and b/dev/articles/treespace_files/figure-html/umatrix-1.png differ
diff --git a/dev/articles/using-distances.html b/dev/articles/using-distances.html
index 719e74fc..335f61a0 100644
--- a/dev/articles/using-distances.html
+++ b/dev/articles/using-distances.html
@@ -42,7 +42,7 @@
@@ -519,7 +519,7 @@ What next?
References
-
+
Nye, T. M. W., Liò, P., & Gilks, W. R. (2006). A novel algorithm and web-based tool for comparing two
alternative phylogenetic trees. Bioinformatics,
diff --git a/dev/authors.html b/dev/authors.html
index f4a01a97..419c5187 100644
--- a/dev/authors.html
+++ b/dev/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 2.7.0.9000. Comprehensive R Archive Network. doi:10.5281/zenodo.3528124
+ Smith, M.R. (2020b). TreeDist: Distances between Phylogenetic Trees. R package version 2.7.0.9001. Comprehensive R Archive Network. doi:10.5281/zenodo.3528124
@Manual{TreeDist,
- title = {TreeDist: Distances between Phylogenetic Trees. R package version 2.7.0.9000},
+ title = {TreeDist: Distances between Phylogenetic Trees. R package version 2.7.0.9001},
author = {Martin R. Smith},
doi = {10.5281/zenodo.3528124},
journal = {Comprehensive R Archive Network},
diff --git a/dev/index.html b/dev/index.html
index 61d48be5..361c5ce7 100644
--- a/dev/index.html
+++ b/dev/index.html
@@ -59,7 +59,7 @@
@@ -202,8 +202,8 @@ Tree space analysis
TreeDist::MapTrees()
-
diff --git a/dev/news/index.html b/dev/news/index.html
index 6384873a..3434ad0a 100644
--- a/dev/news/index.html
+++ b/dev/news/index.html
@@ -23,7 +23,7 @@
@@ -108,8 +108,9 @@ Changelog
TreeDist 2.7.0 (2023-10-25)2023-10-25
diff --git a/dev/pkgdown.yml b/dev/pkgdown.yml
index 952d9b38..a6ef3bc5 100644
--- a/dev/pkgdown.yml
+++ b/dev/pkgdown.yml
@@ -1,4 +1,4 @@
-pandoc: 2.19.2
+pandoc: 3.1.11
pkgdown: 2.0.7
pkgdown_sha: ~
articles:
@@ -11,7 +11,7 @@ articles:
landscapes: landscapes.html
treespace: treespace.html
using-distances: using-distances.html
-last_built: 2024-02-23T15:03Z
+last_built: 2024-02-29T08:01Z
urls:
reference: https://ms609.github.io/TreeDist/reference
article: https://ms609.github.io/TreeDist/articles
diff --git a/dev/reference/AllSplitPairings.html b/dev/reference/AllSplitPairings.html
index 381eb3eb..c9ae9ab8 100644
--- a/dev/reference/AllSplitPairings.html
+++ b/dev/reference/AllSplitPairings.html
@@ -28,7 +28,7 @@
diff --git a/dev/reference/CalculateTreeDistance.html b/dev/reference/CalculateTreeDistance.html
index acbac29b..4dbbe45c 100644
--- a/dev/reference/CalculateTreeDistance.html
+++ b/dev/reference/CalculateTreeDistance.html
@@ -23,7 +23,7 @@
diff --git a/dev/reference/CompareAll.html b/dev/reference/CompareAll.html
index 08a7dbed..a092013f 100644
--- a/dev/reference/CompareAll.html
+++ b/dev/reference/CompareAll.html
@@ -24,7 +24,7 @@
diff --git a/dev/reference/Entropy.html b/dev/reference/Entropy.html
index 74123faa..0a18776a 100644
--- a/dev/reference/Entropy.html
+++ b/dev/reference/Entropy.html
@@ -25,7 +25,7 @@
diff --git a/dev/reference/GeneralizedRF.html b/dev/reference/GeneralizedRF.html
index f622fdf5..101daf50 100644
--- a/dev/reference/GeneralizedRF.html
+++ b/dev/reference/GeneralizedRF.html
@@ -24,7 +24,7 @@
diff --git a/dev/reference/JaccardRobinsonFoulds.html b/dev/reference/JaccardRobinsonFoulds.html
index 19a08a67..b3f47090 100644
--- a/dev/reference/JaccardRobinsonFoulds.html
+++ b/dev/reference/JaccardRobinsonFoulds.html
@@ -27,7 +27,7 @@
Examples
#> 1 2 #> 2 2.449490 #> 3 2.449490 3.162278 -KCDiameter(trees) -#> Warning: first element used of 'length.out' argument -#> Warning: longer object length is not a multiple of shorter object length -#> [1] 15.87451 KCDiameter(4) #> [1] 3.162278 +KCDiameter(trees) +#> [1] 15.87451 15.87451 15.87451Author
Examples
if (interactive()) { # Only run in terminal
library("TreeTools", quietly = TRUE)
- nCores <- ceiling(detectCores() / 2)
+ nCores <- ceiling(parallel::detectCores() / 2)
StartParallel(nCores) # Takes a few seconds to set up processes
GetParallel()
ClusteringInfoDistance(as.phylo(0:6, 100))
diff --git a/dev/reference/TreeDist-package.html b/dev/reference/TreeDist-package.html
index 846d2376..7ece2ac2 100644
--- a/dev/reference/TreeDist-package.html
+++ b/dev/reference/TreeDist-package.html
@@ -27,7 +27,7 @@