From 5d778159e81cb7e8dc2e80a2cec41f7239a40c6e Mon Sep 17 00:00:00 2001 From: GitHub Actions Date: Wed, 3 Apr 2024 06:56:44 +0000 Subject: [PATCH] Built site for TreeSearch: 1.4.0.9000@4615aca --- dev/articles/custom.html | 4 ++-- .../custom_files/figure-html/cid-1.png | Bin 13739 -> 14871 bytes .../custom_files/figure-html/tci-search-1.png | Bin 11913 -> 11863 bytes dev/articles/getting-started.html | 2 +- dev/articles/profile-scores.html | 2 +- dev/articles/profile.html | 2 +- dev/articles/tree-search.html | 2 +- dev/articles/tree-space.html | 2 +- dev/pkgdown.yml | 2 +- dev/reference/DoubleNNI.html | 2 +- dev/reference/MaximizeParsimony.html | 6 +++--- dev/reference/TaxonInfluence.html | 4 ++-- 12 files changed, 14 insertions(+), 14 deletions(-) diff --git a/dev/articles/custom.html b/dev/articles/custom.html index 0a18820f8..23904be80 100644 --- a/dev/articles/custom.html +++ b/dev/articles/custom.html @@ -118,7 +118,7 @@

Tree search with custom optimality criteria

Martin R. Smith

-

2024-04-02

+

2024-04-03

Source: vignettes/custom.Rmd @@ -218,7 +218,7 @@

Maximizing tree distance TreeScorer = DistanceScore, maxIter = 50L, maxHits = 10L, verbosity = 1L) -
##   - Performing tree search.  Initial score: -7.46857574523181
+
##   - Performing tree search.  Initial score: -6.15729762077267
##   - Final score -7.87744375108174 found 1 times after 50 rearrangements.
 par(mfrow = c(1, 2))
diff --git a/dev/articles/custom_files/figure-html/cid-1.png b/dev/articles/custom_files/figure-html/cid-1.png
index 84045dd67865912310f650bd6c583af2a2a18763..8e5fac98e9224387bc4277c67a4d9abeb4b7377f 100644
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diff --git a/dev/articles/getting-started.html b/dev/articles/getting-started.html
index e00108330..33b776f28 100644
--- a/dev/articles/getting-started.html
+++ b/dev/articles/getting-started.html
@@ -119,7 +119,7 @@ 

Getting started: Installing R and

Martin R. Smith

-

2024-04-02

+

2024-04-03

Source:
vignettes/getting-started.Rmd diff --git a/dev/articles/profile-scores.html b/dev/articles/profile-scores.html index 130d9e25f..65bd47cec 100644 --- a/dev/articles/profile-scores.html +++ b/dev/articles/profile-scores.html @@ -118,7 +118,7 @@

Profile parsimony

Martin R. Smith

-

2024-04-02

+

2024-04-03

Source: vignettes/profile-scores.Rmd diff --git a/dev/articles/profile.html b/dev/articles/profile.html index 627274ac8..54407ac3c 100644 --- a/dev/articles/profile.html +++ b/dev/articles/profile.html @@ -118,7 +118,7 @@

Tree search with Profile parsimony

Martin R. Smith

-

2024-04-02

+

2024-04-03

Source: vignettes/profile.Rmd diff --git a/dev/articles/tree-search.html b/dev/articles/tree-search.html index 631e9f87a..5e24fff79 100644 --- a/dev/articles/tree-search.html +++ b/dev/articles/tree-search.html @@ -118,7 +118,7 @@

Getting started: Simple tree searches

Martin R. Smith

-

2024-04-02

+

2024-04-03

Source: vignettes/tree-search.Rmd diff --git a/dev/articles/tree-space.html b/dev/articles/tree-space.html index 7deb880f5..3899c374f 100644 --- a/dev/articles/tree-space.html +++ b/dev/articles/tree-space.html @@ -118,7 +118,7 @@

Getting started: Exploring tree space

Martin R. Smith

-

2024-04-02

+

2024-04-03

Source: vignettes/tree-space.Rmd diff --git a/dev/pkgdown.yml b/dev/pkgdown.yml index e37133f0b..d24c4ed93 100644 --- a/dev/pkgdown.yml +++ b/dev/pkgdown.yml @@ -8,7 +8,7 @@ articles: profile: profile.html tree-search: tree-search.html tree-space: tree-space.html -last_built: 2024-04-02T18:47Z +last_built: 2024-04-03T06:55Z urls: reference: https://ms609.github.io/TreeSearch/reference article: https://ms609.github.io/TreeSearch/articles diff --git a/dev/reference/DoubleNNI.html b/dev/reference/DoubleNNI.html index 794b332f0..7455308e7 100644 --- a/dev/reference/DoubleNNI.html +++ b/dev/reference/DoubleNNI.html @@ -119,7 +119,7 @@

Arguments

Value

-

the tree$edge parameter of the two trees consistent with the specified rearrangement

+

the tree[["edge"]] parameter of the two trees consistent with the specified rearrangement

Author

diff --git a/dev/reference/MaximizeParsimony.html b/dev/reference/MaximizeParsimony.html index 4385c6945..7b2bcc231 100644 --- a/dev/reference/MaximizeParsimony.html +++ b/dev/reference/MaximizeParsimony.html @@ -129,7 +129,7 @@

Find most parsimonious trees

quickHits = 1/3, concavity = Inf, ratchEW = TRUE, - tolerance = sqrt(.Machine$double.eps), + tolerance = sqrt(.Machine[["double.eps"]]), constraint, verbosity = 3L ) @@ -447,8 +447,8 @@

Examples

#> #> ── Sample local optimum ──────────────────────────────────────────────────────── #> → TBR depth 1; keeping 4 trees; k = 10 -#> 2024-04-02 18:48:01: Score: 12.6384 -#> 2024-04-02 18:48:02: Tree search terminated with score 12.1193 +#> 2024-04-03 06:55:30: Score: 12.6384 +#> 2024-04-03 06:55:31: Tree search terminated with score 12.1193 names(trees) #> [1] "final_1" diff --git a/dev/reference/TaxonInfluence.html b/dev/reference/TaxonInfluence.html index 09b3742ef..71f093609 100644 --- a/dev/reference/TaxonInfluence.html +++ b/dev/reference/TaxonInfluence.html @@ -251,8 +251,8 @@

Examples

#> #> ── Sample local optimum ──────────────────────────────────────────────────────── #> → TBR depth 2; keeping 14.4 trees; k = Inf -#> 2024-04-02 18:48:09: Score: 86 -#> 2024-04-02 18:48:09: Tree search terminated with score 82 +#> 2024-04-03 06:55:38: Score: 86 +#> 2024-04-03 06:55:38: Tree search terminated with score 82 # Colour tip labels according to their influence upperBound <- 2 * TreeDist::ClusteringEntropy(