From 5f44b9f79daf7ba4564f36683e01ac91b2dc5ae8 Mon Sep 17 00:00:00 2001
From: "Martin R. Smith" <1695515+ms609@users.noreply.github.com>
Date: Mon, 26 Aug 2024 11:10:01 +0100
Subject: [PATCH 01/30] Require R3.6

---
 .github/workflows/R-CMD-check.yml        | 15 ++++++++++++++-
 DESCRIPTION                              |  4 ++--
 NEWS.md                                  |  6 ++++++
 tests/testthat/test-CustomSearch.R       |  2 --
 tests/testthat/test-Jackknife.R          |  1 -
 tests/testthat/test-pp-random-tree.R     |  3 ---
 tests/testthat/test-zzz-tree-rearrange.R |  2 --
 vignettes/profile.Rmd                    |  1 -
 vignettes/tree-search.Rmd                |  1 -
 9 files changed, 22 insertions(+), 13 deletions(-)

diff --git a/.github/workflows/R-CMD-check.yml b/.github/workflows/R-CMD-check.yml
index 3935d785b..a523a6b71 100644
--- a/.github/workflows/R-CMD-check.yml
+++ b/.github/workflows/R-CMD-check.yml
@@ -47,8 +47,8 @@ jobs:
         config:
           - {os: windows-latest, r: 'release'}
           - {os: macOS-latest, r: 'release'}
+          - {os: ubuntu-20.04, r: '3.6', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
           - {os: ubuntu-20.04, r: '4.1', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} # Until TreeDist can slough phangorn
-          #- {os: ubuntu-20.04, r: '3.6', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
           - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
           - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
 
@@ -79,8 +79,21 @@ jobs:
         if: runner.os == 'macOS'
         run: |
           brew install libgit2 xquartz ghostscript
+                  
+      - name: Set up R dependencies (R 3.6)
+        if: matrix.config.r == '3.6'
+        uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: |
+            evaluate@0.23
+            knitr@1.45
+            rjson@0.2.20
+            XML@3.99-0.3
+          needs: |
+            check
       
       - name: Set up R dependencies
+        if: matrix.config.r != '3.6'
         uses: r-lib/actions/setup-r-dependencies@v2
         with:
           needs: |
diff --git a/DESCRIPTION b/DESCRIPTION
index 7877fd1dc..e4771c456 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: TreeSearch
 Title: Phylogenetic Analysis with Discrete Character Data
-Version: 1.5.1
+Version: 1.5.1.9000
 Authors@R: c(
     person(
       "Martin R.", 'Smith',
@@ -32,7 +32,7 @@ Description: Reconstruct phylogenetic trees from discrete data.
 URL: https://ms609.github.io/TreeSearch/ (doc),
   https://github.com/ms609/TreeSearch/ (devel)
 BugReports: https://github.com/ms609/TreeSearch/issues/
-Depends: R (>= 3.5.0)
+Depends: R (>= 3.6.0)
 Imports: 
   ape (>= 5.6),
   cli (>= 3.0),
diff --git a/NEWS.md b/NEWS.md
index 01a62acf5..92863ea3f 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,9 @@
+# TreeSearch 1.5.1.9000 (2024-08)
+
+- Support for ordered (additive) characters
+- Require R 3.6 (to simplify maintenance)
+
+
 # TreeSearch 1.5.1 (2024-05-23)
 
 - Fix calls to `DescendantEdges()`
diff --git a/tests/testthat/test-CustomSearch.R b/tests/testthat/test-CustomSearch.R
index 71fb5995b..fde6520d7 100644
--- a/tests/testthat/test-CustomSearch.R
+++ b/tests/testthat/test-CustomSearch.R
@@ -10,7 +10,6 @@ RootySwappers <- list(RootedTBRSwap, RootedSPRSwap, RootedNNISwap)
 test_that("Tree can be found", {
   skip_if_not_installed("phangorn")
   phy11 <- phangorn::phyDat(data11, type = "USER", levels = c(FALSE, TRUE))
-  suppressWarnings(RNGversion("3.5.0")) # Until we can require R3.6.0
   set.seed(1)
   random11 <- as.phylo(17905853L, 11, letters[1:11])
   expect_error(TreeSearch(unrooted11, dataset = phy11))
@@ -110,7 +109,6 @@ test_that("Profile parsimony works in tree search", {
   dataset <- TreeTools::PhyDat(sillyData)
   readyData <- PrepareDataProfile(dataset)
   
-  suppressWarnings(RNGversion("3.5.0")) # Until we can require R3.6.0
   set.seed(0)
   
   rTree <- randomTree <- RandomTree(dataset, "1")
diff --git a/tests/testthat/test-Jackknife.R b/tests/testthat/test-Jackknife.R
index 85fed2a5a..8771cc42d 100644
--- a/tests/testthat/test-Jackknife.R
+++ b/tests/testthat/test-Jackknife.R
@@ -11,7 +11,6 @@ test_that("Jackknife supports are correct", {
   expect_error(Jackknife(start_tree, dataset, resampleFreq = 0))
   expect_error(Jackknife(start_tree, dataset, resampleFreq = 9/10))
   
-  suppressWarnings(RNGversion("3.5.0")) # Until we can require R3.6.0
   set.seed(0)
   
   strict <- TreeSearch(start_tree, dataset, verbosity = 0)
diff --git a/tests/testthat/test-pp-random-tree.R b/tests/testthat/test-pp-random-tree.R
index e1d93fdf2..385003335 100644
--- a/tests/testthat/test-pp-random-tree.R
+++ b/tests/testthat/test-pp-random-tree.R
@@ -38,7 +38,6 @@ test_that("four-tip trees are randomly distributed", {
 })
 
 test_that("four-tip trees are randomly scored", {
-  suppressWarnings(RNGversion("3.5.0")) # Until we can require R3.6.0
   set.seed(0)
   
   nTrees <- 6000
@@ -57,7 +56,6 @@ test_that("four-tip trees are randomly scored", {
 })
 
 test_that("five-tip trees are randomly scored", {
-  suppressWarnings(RNGversion("3.5.0")) # Until we can require R3.6.0
   set.seed(0)
   nTrees <- 6000
   stringency <- 0.005
@@ -75,7 +73,6 @@ test_that("five-tip trees are randomly scored", {
 
 
 test_that("six-tip trees are randomly scored", {
-  suppressWarnings(RNGversion("3.5.0")) # Until we can require R3.6.0
   set.seed(0)
   
   nTrees <- 6000
diff --git a/tests/testthat/test-zzz-tree-rearrange.R b/tests/testthat/test-zzz-tree-rearrange.R
index 0cf235f99..447026f23 100644
--- a/tests/testthat/test-zzz-tree-rearrange.R
+++ b/tests/testthat/test-zzz-tree-rearrange.R
@@ -46,7 +46,6 @@ test_that("NNI works", {
   Test(2, 0, 3, 9)
   Test(2, 1, 8, 9)
   
-  suppressWarnings(RNGversion("3.5.0")) # Until we can require R3.6.0
   set.seed(0)
   nniComb <- NNI(trComb)
   expect_equal(nniComb$tip.label, trComb$tip.label)
@@ -252,7 +251,6 @@ CheckTreeSanity <- function (tree) {
   expect_true(all(child[!tips] > parent[!tips]), info="Parent nodes must be > child nodes")
 }
 
-suppressWarnings(RNGversion("3.5.0")) # Until we can require R3.6.0
 set.seed(0)
 small_tree <- rtree(8)
 large_tree <- rtree(80)  
diff --git a/vignettes/profile.Rmd b/vignettes/profile.Rmd
index b30b76acf..f8469d22d 100644
--- a/vignettes/profile.Rmd
+++ b/vignettes/profile.Rmd
@@ -42,7 +42,6 @@ In order to reproduce the random elements of this document, set a random seed:
 
 ```{R rng-version}
 # Set a random seed so that random functions in this document are reproducible
-suppressWarnings(RNGversion("3.5.0")) # Until we can require R3.6.0
 set.seed(888)
 ```
 
diff --git a/vignettes/tree-search.Rmd b/vignettes/tree-search.Rmd
index 5bf02b4a5..1456f15aa 100644
--- a/vignettes/tree-search.Rmd
+++ b/vignettes/tree-search.Rmd
@@ -75,7 +75,6 @@ vinther <- TreeSearch::inapplicable.phyData[["Vinther2008"]]
 
 ```{R RNG-version}
 # Set a random seed so that random functions in this document are reproducible
-suppressWarnings(RNGversion("3.5.0")) # Until we require R v3.6.0
 set.seed(0)
 ```
 

From 2d534122048ad8c89ba8c1e3245d124d52f74faf Mon Sep 17 00:00:00 2001
From: "Martin R. Smith" <1695515+ms609@users.noreply.github.com>
Date: Mon, 26 Aug 2024 11:16:33 +0100
Subject: [PATCH 02/30] dataset via ReadCharacters()

---
 man-roxygen/datasetParam.r      | 1 +
 man/AdditionTree.Rd             | 3 ++-
 man/CharacterLength.Rd          | 3 ++-
 man/ConcordantInformation.Rd    | 3 ++-
 man/Consistency.Rd              | 3 ++-
 man/MaximizeParsimony.Rd        | 3 ++-
 man/PlotCharacter.Rd            | 3 ++-
 man/SiteConcordance.Rd          | 3 ++-
 man/SuccessiveApproximations.Rd | 3 ++-
 man/TaxonInfluence.Rd           | 3 ++-
 man/TreeLength.Rd               | 3 ++-
 man/TreeSearch.Rd               | 3 ++-
 12 files changed, 23 insertions(+), 11 deletions(-)

diff --git a/man-roxygen/datasetParam.r b/man-roxygen/datasetParam.r
index a2c73a71a..5038c6a27 100644
--- a/man-roxygen/datasetParam.r
+++ b/man-roxygen/datasetParam.r
@@ -1,3 +1,4 @@
 #' @param dataset A phylogenetic data matrix of \pkg{phangorn} class
 #' \code{phyDat}, whose names correspond to the labels of any accompanying tree.
+#' Perhaps load into R using \code{\link[TreeTools]{ReadCharacters}}.
 # Defined in TreeTools.  Please propagate any changes there.
diff --git a/man/AdditionTree.Rd b/man/AdditionTree.Rd
index f212a690f..88fe9b76c 100644
--- a/man/AdditionTree.Rd
+++ b/man/AdditionTree.Rd
@@ -8,7 +8,8 @@ AdditionTree(dataset, concavity = Inf, constraint, sequence)
 }
 \arguments{
 \item{dataset}{A phylogenetic data matrix of \pkg{phangorn} class
-\code{phyDat}, whose names correspond to the labels of any accompanying tree.}
+\code{phyDat}, whose names correspond to the labels of any accompanying tree.
+Perhaps load into R using \code{\link[TreeTools]{ReadCharacters}}.}
 
 \item{concavity}{Numeric specifying concavity constant for implied step
 weighting.
diff --git a/man/CharacterLength.Rd b/man/CharacterLength.Rd
index 1e318e990..5f217f6c5 100644
--- a/man/CharacterLength.Rd
+++ b/man/CharacterLength.Rd
@@ -16,7 +16,8 @@ FastCharacterLength(tree, dataset)
 \item{tree}{A tree of class \code{\link{phylo}}.}
 
 \item{dataset}{A phylogenetic data matrix of \pkg{phangorn} class
-\code{phyDat}, whose names correspond to the labels of any accompanying tree.}
+\code{phyDat}, whose names correspond to the labels of any accompanying tree.
+Perhaps load into R using \code{\link[TreeTools]{ReadCharacters}}.}
 
 \item{compress}{Logical specifying whether to retain the compression of a
 \code{phyDat} object or to return a vector specifying to each individual
diff --git a/man/ConcordantInformation.Rd b/man/ConcordantInformation.Rd
index c0699961c..b1d10935d 100644
--- a/man/ConcordantInformation.Rd
+++ b/man/ConcordantInformation.Rd
@@ -16,7 +16,8 @@ ConcordantInfo(tree, dataset)
 \item{tree}{A tree of class \code{\link{phylo}}.}
 
 \item{dataset}{A phylogenetic data matrix of \pkg{phangorn} class
-\code{phyDat}, whose names correspond to the labels of any accompanying tree.}
+\code{phyDat}, whose names correspond to the labels of any accompanying tree.
+Perhaps load into R using \code{\link[TreeTools]{ReadCharacters}}.}
 }
 \value{
 \code{ConcordantInformation()} returns a named vector with elements:
diff --git a/man/Consistency.Rd b/man/Consistency.Rd
index 3bd55a753..2af757710 100644
--- a/man/Consistency.Rd
+++ b/man/Consistency.Rd
@@ -8,7 +8,8 @@ Consistency(dataset, tree, compress = FALSE)
 }
 \arguments{
 \item{dataset}{A phylogenetic data matrix of \pkg{phangorn} class
-\code{phyDat}, whose names correspond to the labels of any accompanying tree.}
+\code{phyDat}, whose names correspond to the labels of any accompanying tree.
+Perhaps load into R using \code{\link[TreeTools]{ReadCharacters}}.}
 
 \item{tree}{A tree of class \code{\link{phylo}}.}
 
diff --git a/man/MaximizeParsimony.Rd b/man/MaximizeParsimony.Rd
index a3fa74c8c..8de3f5d24 100644
--- a/man/MaximizeParsimony.Rd
+++ b/man/MaximizeParsimony.Rd
@@ -47,7 +47,8 @@ EasyTreesy()
 }
 \arguments{
 \item{dataset}{A phylogenetic data matrix of \pkg{phangorn} class
-\code{phyDat}, whose names correspond to the labels of any accompanying tree.}
+\code{phyDat}, whose names correspond to the labels of any accompanying tree.
+Perhaps load into R using \code{\link[TreeTools]{ReadCharacters}}.}
 
 \item{tree}{(optional) A bifurcating tree of class \code{\link{phylo}},
 containing only the tips listed in \code{dataset}, from which the search
diff --git a/man/PlotCharacter.Rd b/man/PlotCharacter.Rd
index fe4494386..094859f81 100644
--- a/man/PlotCharacter.Rd
+++ b/man/PlotCharacter.Rd
@@ -25,7 +25,8 @@ PlotCharacter(
 \item{tree}{A tree of class \code{\link{phylo}}.}
 
 \item{dataset}{A phylogenetic data matrix of \pkg{phangorn} class
-\code{phyDat}, whose names correspond to the labels of any accompanying tree.}
+\code{phyDat}, whose names correspond to the labels of any accompanying tree.
+Perhaps load into R using \code{\link[TreeTools]{ReadCharacters}}.}
 
 \item{char}{Index of character to plot.}
 
diff --git a/man/SiteConcordance.Rd b/man/SiteConcordance.Rd
index 6b627b473..784fe6317 100644
--- a/man/SiteConcordance.Rd
+++ b/man/SiteConcordance.Rd
@@ -23,7 +23,8 @@ SharedPhylogeneticConcordance(tree, dataset)
 \item{tree}{A tree of class \code{\link{phylo}}.}
 
 \item{dataset}{A phylogenetic data matrix of \pkg{phangorn} class
-\code{phyDat}, whose names correspond to the labels of any accompanying tree.}
+\code{phyDat}, whose names correspond to the labels of any accompanying tree.
+Perhaps load into R using \code{\link[TreeTools]{ReadCharacters}}.}
 }
 \description{
 The site concordance factor \insertCite{Minh2020}{TreeSearch} is a measure
diff --git a/man/SuccessiveApproximations.Rd b/man/SuccessiveApproximations.Rd
index 100873516..774dc45b7 100644
--- a/man/SuccessiveApproximations.Rd
+++ b/man/SuccessiveApproximations.Rd
@@ -25,7 +25,8 @@ SuccessiveWeights(tree, dataset)
 \item{tree}{A tree of class \code{\link{phylo}}.}
 
 \item{dataset}{A phylogenetic data matrix of \pkg{phangorn} class
-\code{phyDat}, whose names correspond to the labels of any accompanying tree.}
+\code{phyDat}, whose names correspond to the labels of any accompanying tree.
+Perhaps load into R using \code{\link[TreeTools]{ReadCharacters}}.}
 
 \item{outgroup}{if not NULL, taxa on which the tree should be rooted}
 
diff --git a/man/TaxonInfluence.Rd b/man/TaxonInfluence.Rd
index cee842a94..fdfe41d85 100644
--- a/man/TaxonInfluence.Rd
+++ b/man/TaxonInfluence.Rd
@@ -18,7 +18,8 @@ TaxonInfluence(
 }
 \arguments{
 \item{dataset}{A phylogenetic data matrix of \pkg{phangorn} class
-\code{phyDat}, whose names correspond to the labels of any accompanying tree.}
+\code{phyDat}, whose names correspond to the labels of any accompanying tree.
+Perhaps load into R using \code{\link[TreeTools]{ReadCharacters}}.}
 
 \item{tree}{Optimal tree or summary tree (of class "phylo") or list of trees
 (of class "list" or "multiPhylo") against which results should be evaluated.
diff --git a/man/TreeLength.Rd b/man/TreeLength.Rd
index 59dd07d0a..075a2b63c 100644
--- a/man/TreeLength.Rd
+++ b/man/TreeLength.Rd
@@ -30,7 +30,8 @@ Fitch(tree, dataset)
 uniformly sampled.}
 
 \item{dataset}{A phylogenetic data matrix of \pkg{phangorn} class
-\code{phyDat}, whose names correspond to the labels of any accompanying tree.}
+\code{phyDat}, whose names correspond to the labels of any accompanying tree.
+Perhaps load into R using \code{\link[TreeTools]{ReadCharacters}}.}
 
 \item{concavity}{Determines the degree to which extra steps beyond the first
 are penalized.  Specify a numeric value to use implied weighting
diff --git a/man/TreeSearch.Rd b/man/TreeSearch.Rd
index aec08cdc2..f6467e55e 100644
--- a/man/TreeSearch.Rd
+++ b/man/TreeSearch.Rd
@@ -53,7 +53,8 @@ DoNothing(...)
 - (optionally, if score provided) number of times this score has been hit}
 
 \item{dataset}{A phylogenetic data matrix of \pkg{phangorn} class
-\code{phyDat}, whose names correspond to the labels of any accompanying tree.}
+\code{phyDat}, whose names correspond to the labels of any accompanying tree.
+Perhaps load into R using \code{\link[TreeTools]{ReadCharacters}}.}
 
 \item{TreeScorer}{function to score a given tree.
 The function will be passed three parameters, corresponding to the

From 3c3d41fabe9c81d3193916f5164d54dd8ceca8c9 Mon Sep 17 00:00:00 2001
From: "Martin R. Smith" <1695515+ms609@users.noreply.github.com>
Date: Mon, 26 Aug 2024 14:31:22 +0100
Subject: [PATCH 03/30] Still use RNGVersion

Could in future re-seed.
---
 tests/testthat/test-CustomSearch.R       | 2 ++
 tests/testthat/test-Jackknife.R          | 1 +
 tests/testthat/test-pp-random-tree.R     | 4 +++-
 tests/testthat/test-zzz-tree-rearrange.R | 6 ++++--
 vignettes/profile.Rmd                    | 1 +
 vignettes/tree-search.Rmd                | 3 ++-
 6 files changed, 13 insertions(+), 4 deletions(-)

diff --git a/tests/testthat/test-CustomSearch.R b/tests/testthat/test-CustomSearch.R
index fde6520d7..fe2d418da 100644
--- a/tests/testthat/test-CustomSearch.R
+++ b/tests/testthat/test-CustomSearch.R
@@ -10,6 +10,7 @@ RootySwappers <- list(RootedTBRSwap, RootedSPRSwap, RootedNNISwap)
 test_that("Tree can be found", {
   skip_if_not_installed("phangorn")
   phy11 <- phangorn::phyDat(data11, type = "USER", levels = c(FALSE, TRUE))
+  RNGversion("3.5.0")
   set.seed(1)
   random11 <- as.phylo(17905853L, 11, letters[1:11])
   expect_error(TreeSearch(unrooted11, dataset = phy11))
@@ -109,6 +110,7 @@ test_that("Profile parsimony works in tree search", {
   dataset <- TreeTools::PhyDat(sillyData)
   readyData <- PrepareDataProfile(dataset)
   
+  RNGversion("3.5.0")
   set.seed(0)
   
   rTree <- randomTree <- RandomTree(dataset, "1")
diff --git a/tests/testthat/test-Jackknife.R b/tests/testthat/test-Jackknife.R
index 8771cc42d..aa198d39c 100644
--- a/tests/testthat/test-Jackknife.R
+++ b/tests/testthat/test-Jackknife.R
@@ -11,6 +11,7 @@ test_that("Jackknife supports are correct", {
   expect_error(Jackknife(start_tree, dataset, resampleFreq = 0))
   expect_error(Jackknife(start_tree, dataset, resampleFreq = 9/10))
   
+  RNGversion("3.5.0")
   set.seed(0)
   
   strict <- TreeSearch(start_tree, dataset, verbosity = 0)
diff --git a/tests/testthat/test-pp-random-tree.R b/tests/testthat/test-pp-random-tree.R
index 385003335..f210bacc3 100644
--- a/tests/testthat/test-pp-random-tree.R
+++ b/tests/testthat/test-pp-random-tree.R
@@ -38,7 +38,7 @@ test_that("four-tip trees are randomly distributed", {
 })
 
 test_that("four-tip trees are randomly scored", {
-  set.seed(0)
+  RNGversion("3.5.0")set.seed(0)
   
   nTrees <- 6000
   stringency <- 0.005
@@ -56,6 +56,7 @@ test_that("four-tip trees are randomly scored", {
 })
 
 test_that("five-tip trees are randomly scored", {
+  RNGversion("3.5.0")
   set.seed(0)
   nTrees <- 6000
   stringency <- 0.005
@@ -73,6 +74,7 @@ test_that("five-tip trees are randomly scored", {
 
 
 test_that("six-tip trees are randomly scored", {
+  RNGversion("3.5.0")
   set.seed(0)
   
   nTrees <- 6000
diff --git a/tests/testthat/test-zzz-tree-rearrange.R b/tests/testthat/test-zzz-tree-rearrange.R
index 447026f23..432707315 100644
--- a/tests/testthat/test-zzz-tree-rearrange.R
+++ b/tests/testthat/test-zzz-tree-rearrange.R
@@ -46,6 +46,7 @@ test_that("NNI works", {
   Test(2, 0, 3, 9)
   Test(2, 1, 8, 9)
   
+  RNGversion("3.5.0")
   set.seed(0)
   nniComb <- NNI(trComb)
   expect_equal(nniComb$tip.label, trComb$tip.label)
@@ -56,7 +57,7 @@ test_that("NNI works", {
 
 test_that("SPR works", {
   testTree <- Preorder(root(BalancedTree(7), 1, resolve.root = TRUE))
-  edge <- testTree$edge
+  edge <- testTree[["edge"]]
   expect_equal(spr(edge, 66), cSPR(testTree, 66)$edge)
   
   Test <- function (m, p1, r1) {
@@ -242,7 +243,7 @@ CheckTreeSanity <- function (tree) {
                info=paste0("Root is numbered ", min(parent), "; expecting ", nTip + 1)
   )
   expect_false(min(parent) %in% child, 
-               info=paste0("Root node (", min(parent), ") is child of edge ", paste0(which(min(parent) == child), collapse=', '))
+               info=paste0("Root node (", min(parent), ") is child of edge ", paste0(which(min(parent) == child), collapse = ", "))
   )
   expect_true(all(seq_len(nTip) %in% child)) # No missing tips
   expect_equal(max(parent), nTip + nNode)
@@ -251,6 +252,7 @@ CheckTreeSanity <- function (tree) {
   expect_true(all(child[!tips] > parent[!tips]), info="Parent nodes must be > child nodes")
 }
 
+RNGversion("3.5.0")
 set.seed(0)
 small_tree <- rtree(8)
 large_tree <- rtree(80)  
diff --git a/vignettes/profile.Rmd b/vignettes/profile.Rmd
index f8469d22d..ef2fd1389 100644
--- a/vignettes/profile.Rmd
+++ b/vignettes/profile.Rmd
@@ -42,6 +42,7 @@ In order to reproduce the random elements of this document, set a random seed:
 
 ```{R rng-version}
 # Set a random seed so that random functions in this document are reproducible
+RNGversion("3.5.0")
 set.seed(888)
 ```
 
diff --git a/vignettes/tree-search.Rmd b/vignettes/tree-search.Rmd
index 1456f15aa..4a85b19d7 100644
--- a/vignettes/tree-search.Rmd
+++ b/vignettes/tree-search.Rmd
@@ -73,8 +73,9 @@ escape from local optima.
 vinther <- TreeSearch::inapplicable.phyData[["Vinther2008"]]
 ```
 
-```{R RNG-version}
+```{R RNG-version, warn = FALSE}
 # Set a random seed so that random functions in this document are reproducible
+RNGversion("3.5.0")
 set.seed(0)
 ```
 

From b49059941726c3df78a515805be52abd30eeb6ca Mon Sep 17 00:00:00 2001
From: "Martin R. Smith" <1695515+ms609@users.noreply.github.com>
Date: Mon, 26 Aug 2024 14:31:49 +0100
Subject: [PATCH 04/30] ignore phangorn

---
 .github/workflows/R-CMD-check.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/R-CMD-check.yml b/.github/workflows/R-CMD-check.yml
index a523a6b71..d40ea630c 100644
--- a/.github/workflows/R-CMD-check.yml
+++ b/.github/workflows/R-CMD-check.yml
@@ -87,6 +87,7 @@ jobs:
           extra-packages: |
             evaluate@0.23
             knitr@1.45
+            phangorn=?ignore-before-r=4.1.0
             rjson@0.2.20
             XML@3.99-0.3
           needs: |

From 6f7c21efb21548dae7b2dfd5842cdc7177177377 Mon Sep 17 00:00:00 2001
From: "Martin R. Smith" <1695515+ms609@users.noreply.github.com>
Date: Mon, 26 Aug 2024 14:34:59 +0100
Subject: [PATCH 05/30] phangorn@2.7.1

---
 .github/workflows/R-CMD-check.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/R-CMD-check.yml b/.github/workflows/R-CMD-check.yml
index d40ea630c..2dca1b431 100644
--- a/.github/workflows/R-CMD-check.yml
+++ b/.github/workflows/R-CMD-check.yml
@@ -87,7 +87,7 @@ jobs:
           extra-packages: |
             evaluate@0.23
             knitr@1.45
-            phangorn=?ignore-before-r=4.1.0
+            phangorn@2.7.1
             rjson@0.2.20
             XML@3.99-0.3
           needs: |

From 96c130b84685be088838bd14461d0c6ed44312ef Mon Sep 17 00:00:00 2001
From: "Martin R. Smith" <1695515+ms609@users.noreply.github.com>
Date: Mon, 26 Aug 2024 14:36:03 +0100
Subject: [PATCH 06/30] pandoc v2

---
 .github/workflows/gcc-ASAN.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/gcc-ASAN.yml b/.github/workflows/gcc-ASAN.yml
index 61390a044..46245981d 100644
--- a/.github/workflows/gcc-ASAN.yml
+++ b/.github/workflows/gcc-ASAN.yml
@@ -66,7 +66,7 @@ jobs:
 
       - name: Setup pandoc
         if: ${{ matrix.config.test }} == 'vignettes'
-        uses: r-lib/actions/setup-pandoc@master
+        uses: r-lib/actions/setup-pandoc@v2
 
       - name: Query dependencies
         run: |

From 0e8cbfb310850161a6738fede02122c9497ed8af Mon Sep 17 00:00:00 2001
From: "Martin R. Smith" <1695515+ms609@users.noreply.github.com>
Date: Mon, 26 Aug 2024 14:37:16 +0100
Subject: [PATCH 07/30] rm dead link

---
 vignettes/getting-started.Rmd | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/vignettes/getting-started.Rmd b/vignettes/getting-started.Rmd
index c1fdf5bb0..39c333b52 100644
--- a/vignettes/getting-started.Rmd
+++ b/vignettes/getting-started.Rmd
@@ -18,9 +18,8 @@ datasets.
 ### Simple installation
 
 To use "TreeSearch" you will first need to [install R](https://CRAN.R-project.org/). 
-[RStudio](https://posit.co/)
-([overview](https://dss.princeton.edu/training/RStudio101.pdf)) is a popular
-front-end that makes several of R's features easier to use.
+[RStudio](https://posit.co/) is a popular front-end that makes several of R's
+features easier to use.
 
 The "TreeSearch" package can be installed as any other package. 
 To get the latest stable version from CRAN, type

From 77dd2a9bc7c56a1f955d20fb6a6604c7b4e0f334 Mon Sep 17 00:00:00 2001
From: "Martin R. Smith" <1695515+ms609@users.noreply.github.com>
Date: Mon, 26 Aug 2024 14:39:04 +0100
Subject: [PATCH 08/30] \r\n

---
 tests/testthat/test-pp-random-tree.R | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/tests/testthat/test-pp-random-tree.R b/tests/testthat/test-pp-random-tree.R
index f210bacc3..9272e563e 100644
--- a/tests/testthat/test-pp-random-tree.R
+++ b/tests/testthat/test-pp-random-tree.R
@@ -38,7 +38,8 @@ test_that("four-tip trees are randomly distributed", {
 })
 
 test_that("four-tip trees are randomly scored", {
-  RNGversion("3.5.0")set.seed(0)
+  RNGversion("3.5.0")
+  set.seed(0)
   
   nTrees <- 6000
   stringency <- 0.005

From 88c1477521c0bd2169a4a8b48a1814bd2eb5a4d0 Mon Sep 17 00:00:00 2001
From: "Martin R. Smith" <1695515+ms609@users.noreply.github.com>
Date: Mon, 26 Aug 2024 15:01:54 +0100
Subject: [PATCH 09/30]   Rfast@2.0.8

---
 .github/workflows/R-CMD-check.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/R-CMD-check.yml b/.github/workflows/R-CMD-check.yml
index 2dca1b431..c851917f9 100644
--- a/.github/workflows/R-CMD-check.yml
+++ b/.github/workflows/R-CMD-check.yml
@@ -88,6 +88,7 @@ jobs:
             evaluate@0.23
             knitr@1.45
             phangorn@2.7.1
+            Rfast@2.0.8
             rjson@0.2.20
             XML@3.99-0.3
           needs: |

From 522d02b63b8a19656f9534cedc4529bd9c9f74ea Mon Sep 17 00:00:00 2001
From: "Martin R. Smith" <1695515+ms609@users.noreply.github.com>
Date: Mon, 26 Aug 2024 15:25:45 +0100
Subject: [PATCH 10/30] Try RFast 1.9.8

---
 .github/workflows/R-CMD-check.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/R-CMD-check.yml b/.github/workflows/R-CMD-check.yml
index c851917f9..0cefdaedd 100644
--- a/.github/workflows/R-CMD-check.yml
+++ b/.github/workflows/R-CMD-check.yml
@@ -88,7 +88,7 @@ jobs:
             evaluate@0.23
             knitr@1.45
             phangorn@2.7.1
-            Rfast@2.0.8
+            Rfast@1.9.8
             rjson@0.2.20
             XML@3.99-0.3
           needs: |

From 269e2f589c874e9fad1ee585d7900ef3f0eb266c Mon Sep 17 00:00:00 2001
From: "Martin R. Smith" <1695515+ms609@users.noreply.github.com>
Date: Mon, 26 Aug 2024 15:49:05 +0100
Subject: [PATCH 11/30] Crass manual implementation of palette.cols

---
 vignettes/tree-space.Rmd | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/vignettes/tree-space.Rmd b/vignettes/tree-space.Rmd
index 76ad58b86..3d55d9fcd 100644
--- a/vignettes/tree-space.Rmd
+++ b/vignettes/tree-space.Rmd
@@ -259,6 +259,12 @@ nClusters <- length(unique(clustering))
 
 Now we can map tree space into a few dimensions and visualise the distribution
 of trees:
+```{r palette.colors, echo = FALSE}
+if (packageVersion("base") < "4.0.0") {
+  # TODO delete when require R4.0
+  palette.colors <- function(x) paste0(palette()[2:(x - 1)], "CC")
+}
+```
 
 ```{r map-space, fig.keep = "none"}
 nDim <- 3 # Number of dimensions to plot

From 9d4132232d133369423012139396dbd71a43b63e Mon Sep 17 00:00:00 2001
From: "Martin R. Smith" <1695515+ms609@users.noreply.github.com>
Date: Mon, 26 Aug 2024 15:49:56 +0100
Subject: [PATCH 12/30] Alphabet

---
 vignettes/tree-space.Rmd | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/vignettes/tree-space.Rmd b/vignettes/tree-space.Rmd
index 3d55d9fcd..d0aa882bc 100644
--- a/vignettes/tree-space.Rmd
+++ b/vignettes/tree-space.Rmd
@@ -262,7 +262,11 @@ of trees:
 ```{r palette.colors, echo = FALSE}
 if (packageVersion("base") < "4.0.0") {
   # TODO delete when require R4.0
-  palette.colors <- function(x) paste0(palette()[2:(x - 1)], "CC")
+  palette.colors <- function(x, ...) {
+    c("#AA0DFECC", "#3283FECC", "#85660DCC", "#782AB6CC", "#565656CC", 
+"#1C8356CC", "#16FF32CC", "#F7E1A0CC", "#E2E2E2CC", "#1CBE4FCC", 
+"#C4451CCC", "#DEA0FDCC")[seq_len(x)]
+  }
 }
 ```
 

From e93926d38df2641297aaf9b7300a6885fb74e6e5 Mon Sep 17 00:00:00 2001
From: "Martin R. Smith" <1695515+ms609@users.noreply.github.com>
Date: Mon, 26 Aug 2024 16:11:30 +0100
Subject: [PATCH 13/30] dx.doi

avoid redirect
---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 474e49992..d1f66f364 100644
--- a/README.md
+++ b/README.md
@@ -106,7 +106,7 @@ Brazeau, M. D., Guillerme, T. and Smith, M. R. (2019).
 Faith D. P., Trueman J. W. H. (2001).
   Towards an inclusive philosophy for phylogenetic inference.
   Systematic Biology, 50(3), 331–350. 
-  doi: [10.1080/10635150118627](https://doi.org/10.1080/10635150118627).
+  doi: [10.1080/10635150118627](https://dx.doi.org/10.1080/10635150118627).
 
 Farris, J. S. (1969). A successive approximations approach to character weighting. 
   Systematic Biology, 18(4), 374–385.

From d939c4b6f9fb7aa7ffd0c7650e9aa3f07c69f98b Mon Sep 17 00:00:00 2001
From: "Martin R. Smith" <1695515+ms609@users.noreply.github.com>
Date: Mon, 26 Aug 2024 16:14:20 +0100
Subject: [PATCH 14/30]  RNGversion("3.6.0")

---
 tests/testthat/test-Jackknife.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/testthat/test-Jackknife.R b/tests/testthat/test-Jackknife.R
index aa198d39c..b2058710b 100644
--- a/tests/testthat/test-Jackknife.R
+++ b/tests/testthat/test-Jackknife.R
@@ -11,7 +11,7 @@ test_that("Jackknife supports are correct", {
   expect_error(Jackknife(start_tree, dataset, resampleFreq = 0))
   expect_error(Jackknife(start_tree, dataset, resampleFreq = 9/10))
   
-  RNGversion("3.5.0")
+  RNGversion("3.6.0")
   set.seed(0)
   
   strict <- TreeSearch(start_tree, dataset, verbosity = 0)

From e81d385bc54cc502cd53556d58eb5dd0249e99de Mon Sep 17 00:00:00 2001
From: "Martin R. Smith" <1695515+ms609@users.noreply.github.com>
Date: Mon, 26 Aug 2024 16:15:42 +0100
Subject: [PATCH 15/30] RNGVersion unnecessary

---
 tests/testthat/test-pp-random-tree.R | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/tests/testthat/test-pp-random-tree.R b/tests/testthat/test-pp-random-tree.R
index 9272e563e..385003335 100644
--- a/tests/testthat/test-pp-random-tree.R
+++ b/tests/testthat/test-pp-random-tree.R
@@ -38,7 +38,6 @@ test_that("four-tip trees are randomly distributed", {
 })
 
 test_that("four-tip trees are randomly scored", {
-  RNGversion("3.5.0")
   set.seed(0)
   
   nTrees <- 6000
@@ -57,7 +56,6 @@ test_that("four-tip trees are randomly scored", {
 })
 
 test_that("five-tip trees are randomly scored", {
-  RNGversion("3.5.0")
   set.seed(0)
   nTrees <- 6000
   stringency <- 0.005
@@ -75,7 +73,6 @@ test_that("five-tip trees are randomly scored", {
 
 
 test_that("six-tip trees are randomly scored", {
-  RNGversion("3.5.0")
   set.seed(0)
   
   nTrees <- 6000

From a1a78f622c8f04ec2eb6898ee3a3b31c00c4ec37 Mon Sep 17 00:00:00 2001
From: "Martin R. Smith" <1695515+ms609@users.noreply.github.com>
Date: Mon, 26 Aug 2024 16:19:43 +0100
Subject: [PATCH 16/30]    suppressWarnings(RNGversion("3.5.0"))

---
 tests/testthat/test-zzz-tree-rearrange.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/testthat/test-zzz-tree-rearrange.R b/tests/testthat/test-zzz-tree-rearrange.R
index 432707315..566870d8b 100644
--- a/tests/testthat/test-zzz-tree-rearrange.R
+++ b/tests/testthat/test-zzz-tree-rearrange.R
@@ -46,7 +46,7 @@ test_that("NNI works", {
   Test(2, 0, 3, 9)
   Test(2, 1, 8, 9)
   
-  RNGversion("3.5.0")
+  suppressWarnings(RNGversion("3.5.0"))
   set.seed(0)
   nniComb <- NNI(trComb)
   expect_equal(nniComb$tip.label, trComb$tip.label)
@@ -252,7 +252,7 @@ CheckTreeSanity <- function (tree) {
   expect_true(all(child[!tips] > parent[!tips]), info="Parent nodes must be > child nodes")
 }
 
-RNGversion("3.5.0")
+suppressWarnings(RNGversion("3.5.0"))
 set.seed(0)
 small_tree <- rtree(8)
 large_tree <- rtree(80)  

From 72ec9d069d75d686e44d94c6f274affc9820878e Mon Sep 17 00:00:00 2001
From: "Martin R. Smith" <1695515+ms609@users.noreply.github.com>
Date: Mon, 26 Aug 2024 16:19:46 +0100
Subject: [PATCH 17/30] {}

---
 R/NNI.R | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/R/NNI.R b/R/NNI.R
index df79879a5..d4be1bcff 100644
--- a/R/NNI.R
+++ b/R/NNI.R
@@ -93,8 +93,12 @@ NNI <- function (tree, edgeToBreak = NULL) {
 #' @export
 cNNI <- function (tree, edgeToBreak = NULL, whichSwitch = NULL) {
   edge <- tree[["edge"]]
-  if (is.null(edgeToBreak)) edgeToBreak <- sample.int(dim(edge)[1] - NTip(tree) - 1L, 1L)
-  if (is.null(whichSwitch)) whichSwitch <- sample.int(2L, 1L)
+  if (is.null(edgeToBreak)) {
+    edgeToBreak <- sample.int(dim(edge)[[1]] - NTip(tree) - 1L, 1L)
+  }
+  if (is.null(whichSwitch)) {
+    whichSwitch <- sample.int(2L, 1L)
+  }
   tree[["edge"]] <- nni(edge, edgeToBreak, whichSwitch)
   
   # Return:

From 64c76c621ee26da64182c5259b6ae4812da65f65 Mon Sep 17 00:00:00 2001
From: "Martin R. Smith" <1695515+ms609@users.noreply.github.com>
Date: Fri, 30 Aug 2024 09:17:59 +0100
Subject: [PATCH 18/30] RNGversion

---
 tests/testthat/test-Jackknife.R | 2 +-
 vignettes/profile.Rmd           | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/testthat/test-Jackknife.R b/tests/testthat/test-Jackknife.R
index b2058710b..a93d50597 100644
--- a/tests/testthat/test-Jackknife.R
+++ b/tests/testthat/test-Jackknife.R
@@ -11,7 +11,7 @@ test_that("Jackknife supports are correct", {
   expect_error(Jackknife(start_tree, dataset, resampleFreq = 0))
   expect_error(Jackknife(start_tree, dataset, resampleFreq = 9/10))
   
-  RNGversion("3.6.0")
+  suppressWarnings(RNGversion("3.5.0"))
   set.seed(0)
   
   strict <- TreeSearch(start_tree, dataset, verbosity = 0)
diff --git a/vignettes/profile.Rmd b/vignettes/profile.Rmd
index ef2fd1389..3908b4556 100644
--- a/vignettes/profile.Rmd
+++ b/vignettes/profile.Rmd
@@ -40,7 +40,7 @@ library("TreeSearch")
 
 In order to reproduce the random elements of this document, set a random seed:
 
-```{R rng-version}
+```{R rng-version, warn = FALSE}
 # Set a random seed so that random functions in this document are reproducible
 RNGversion("3.5.0")
 set.seed(888)

From 52603ee63c7ae6b4eb79a35a29cbd1dd336c369c Mon Sep 17 00:00:00 2001
From: "Martin R. Smith" <1695515+ms609@users.noreply.github.com>
Date: Fri, 30 Aug 2024 10:25:41 +0100
Subject: [PATCH 19/30] []

---
 R/AdditionTree.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/AdditionTree.R b/R/AdditionTree.R
index 29139ec1d..af09b4bd2 100644
--- a/R/AdditionTree.R
+++ b/R/AdditionTree.R
@@ -31,7 +31,7 @@ AdditionTree <- function (dataset, concavity = Inf, constraint, sequence) {
   # Initialize missing parameters
   taxa <- names(dataset)
   if (missing(sequence)) {
-    sequence <- taxa[1]
+    sequence <- taxa[[1]]
   } else if (is.numeric(sequence)) {
     sequence <- taxa[sequence]
   }

From dc0d8de23151cc6eeae94bc20a80d8e5ccf1cd72 Mon Sep 17 00:00:00 2001
From: "Martin R. Smith" <1695515+ms609@users.noreply.github.com>
Date: Thu, 5 Sep 2024 10:51:13 +0100
Subject: [PATCH 20/30] unset originalIndex attribute

---
 R/AdditionTree.R | 1 +
 1 file changed, 1 insertion(+)

diff --git a/R/AdditionTree.R b/R/AdditionTree.R
index af09b4bd2..bd5b77a01 100644
--- a/R/AdditionTree.R
+++ b/R/AdditionTree.R
@@ -53,6 +53,7 @@ AdditionTree <- function (dataset, concavity = Inf, constraint, sequence) {
   attr(dataset, "info.amounts") <- NULL
   attr(dataset, "min.length") <- NULL
   attr(dataset, "informative") <- NULL
+  attr(dataset, "originalIndex") <- NULL
   
   # Starting tree, rooted on first element in sequence
   tree <- PectinateTree(sequence[1:3])

From a35fde7b101017b64455603bacfadc6082b55db0 Mon Sep 17 00:00:00 2001
From: "Martin R. Smith" <1695515+ms609@users.noreply.github.com>
Date: Thu, 5 Sep 2024 11:06:00 +0100
Subject: [PATCH 21/30] brio 1.1.3 now available

---
 .github/workflows/memcheck.yml | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/.github/workflows/memcheck.yml b/.github/workflows/memcheck.yml
index 170e09f3e..bf14c95f3 100644
--- a/.github/workflows/memcheck.yml
+++ b/.github/workflows/memcheck.yml
@@ -83,9 +83,6 @@ jobs:
 
       - name: Install dependencies
         run: |
-          if ("${{ matrix.config.test }}" == 'tests') {
-            remotes::install_github('r-lib/brio#20') # brio mem leak
-          }
           remotes::install_deps(dependencies = c('soft', 'Config/Needs/memcheck'))
         shell: Rscript {0}
 

From f72f53c60886f8102c5f7e60070950f2650fb541 Mon Sep 17 00:00:00 2001
From: "Martin R. Smith" <1695515+ms609@users.noreply.github.com>
Date: Fri, 11 Oct 2024 12:37:46 +0100
Subject: [PATCH 22/30] Bump version to .9001

---
 DESCRIPTION | 2 +-
 NEWS.md     | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index e4771c456..3d3beb8d2 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: TreeSearch
 Title: Phylogenetic Analysis with Discrete Character Data
-Version: 1.5.1.9000
+Version: 1.5.1.9001
 Authors@R: c(
     person(
       "Martin R.", 'Smith',
diff --git a/NEWS.md b/NEWS.md
index 92863ea3f..687fc4c82 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,4 @@
-# TreeSearch 1.5.1.9000 (2024-08)
+# TreeSearch 1.5.1.9001 (2024-10)
 
 - Support for ordered (additive) characters
 - Require R 3.6 (to simplify maintenance)

From 9f739a45acfa8765d9ecbca5140f667f70c3334e Mon Sep 17 00:00:00 2001
From: RevBayes analysis <1695515+ms609@users.noreply.github.com>
Date: Thu, 31 Oct 2024 09:10:07 +0000
Subject: [PATCH 23/30] Create update-csl.yml

---
 .github/workflows/update-csl.yml | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)
 create mode 100644 .github/workflows/update-csl.yml

diff --git a/.github/workflows/update-csl.yml b/.github/workflows/update-csl.yml
new file mode 100644
index 000000000..0753d13a6
--- /dev/null
+++ b/.github/workflows/update-csl.yml
@@ -0,0 +1,31 @@
+name: Update CSL file
+on:
+  schedule:
+    - cron: '0 0 * * 1'  # Runs weekly on Monday at 00:00 UTC
+  workflow_dispatch:      # Allows manual triggering
+
+jobs:
+  update-csl:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      
+      - name: Download latest CSL file
+        run: |
+          curl -o inst/apa-old-doi-prefix.csl https://raw.githubusercontent.com/citation-style-language/styles/master/apa-old-doi-prefix.csl
+          
+      - name: Check for changes
+        id: changes
+        run: |
+          if git diff --quiet; then
+            echo "No changes to commit"
+            exit 0
+          fi
+          
+      - name: Commit and push if changed
+        run: |
+          git config --local user.email "actions@github.com"
+          git config --local user.name "GitHub Actions"
+          git add inst/apa-old-doi-prefix.csl
+          git commit -m "Update CSL file from upstream"
+          git push

From 4adbc16e15cb1a09ea2a3e1b8c4f2cec11b3a4d3 Mon Sep 17 00:00:00 2001
From: RevBayes analysis <1695515+ms609@users.noreply.github.com>
Date: Thu, 12 Dec 2024 15:17:34 +0000
Subject: [PATCH 24/30] Fixed package versions

---
 .github/workflows/R-CMD-check.yml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/.github/workflows/R-CMD-check.yml b/.github/workflows/R-CMD-check.yml
index 0cefdaedd..49ecd447e 100644
--- a/.github/workflows/R-CMD-check.yml
+++ b/.github/workflows/R-CMD-check.yml
@@ -85,6 +85,10 @@ jobs:
         uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: |
+            downlit@0.4.3
+            pkgdown@2.0.9
+            profvis@0.3.8
+            gtable@0.3.5
             evaluate@0.23
             knitr@1.45
             phangorn@2.7.1

From efa01418c27bfd35bd86b43bf23b82e328c03c97 Mon Sep 17 00:00:00 2001
From: RevBayes analysis <1695515+ms609@users.noreply.github.com>
Date: Thu, 12 Dec 2024 15:38:49 +0000
Subject: [PATCH 25/30] waldo, testthat

---
 .github/workflows/R-CMD-check.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/R-CMD-check.yml b/.github/workflows/R-CMD-check.yml
index 49ecd447e..a518ad8d4 100644
--- a/.github/workflows/R-CMD-check.yml
+++ b/.github/workflows/R-CMD-check.yml
@@ -85,6 +85,8 @@ jobs:
         uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: |
+            waldo@0.5.3
+            testthat@3.2.1
             downlit@0.4.3
             pkgdown@2.0.9
             profvis@0.3.8

From af8c7fb36312a82af287eb9e46d3fbd97aff53c9 Mon Sep 17 00:00:00 2001
From: RevBayes analysis <1695515+ms609@users.noreply.github.com>
Date: Thu, 12 Dec 2024 15:53:36 +0000
Subject: [PATCH 26/30] vdiff, cpp, httr versions

---
 .github/workflows/R-CMD-check.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.github/workflows/R-CMD-check.yml b/.github/workflows/R-CMD-check.yml
index a518ad8d4..ce765887e 100644
--- a/.github/workflows/R-CMD-check.yml
+++ b/.github/workflows/R-CMD-check.yml
@@ -86,6 +86,9 @@ jobs:
         with:
           extra-packages: |
             waldo@0.5.3
+            vdiffr@1.0.7
+            cpp11@0.5.0
+            httr2@1.0.1
             testthat@3.2.1
             downlit@0.4.3
             pkgdown@2.0.9

From 0b260211283b42c79a77062d33c5cb0e9bc61677 Mon Sep 17 00:00:00 2001
From: RevBayes analysis <1695515+ms609@users.noreply.github.com>
Date: Thu, 6 Feb 2025 16:27:20 +0000
Subject: [PATCH 27/30]              bench@1.1.3

---
 .github/workflows/R-CMD-check.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/R-CMD-check.yml b/.github/workflows/R-CMD-check.yml
index ce765887e..0c7642e62 100644
--- a/.github/workflows/R-CMD-check.yml
+++ b/.github/workflows/R-CMD-check.yml
@@ -86,6 +86,7 @@ jobs:
         with:
           extra-packages: |
             waldo@0.5.3
+            bench@1.1.3
             vdiffr@1.0.7
             cpp11@0.5.0
             httr2@1.0.1

From 0ae1e36894d1ff38088bd0ce3ee0d7ba917ace9e Mon Sep 17 00:00:00 2001
From: RevBayes analysis <1695515+ms609@users.noreply.github.com>
Date: Thu, 6 Feb 2025 16:28:48 +0000
Subject: [PATCH 28/30] .9005

---
 DESCRIPTION | 2 +-
 NEWS.md     | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index fd6e04f6f..c3b6c98be 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: TreeSearch
 Title: Phylogenetic Analysis with Discrete Character Data
-Version: 1.5.1.9004
+Version: 1.5.1.9005
 Authors@R: c(
     person(
       "Martin R.", 'Smith',
diff --git a/NEWS.md b/NEWS.md
index 29cdc1404..80ba02969 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,4 @@
-# TreeSearch 1.5.1.9004 (2025-02)
+# TreeSearch 1.5.1.9005 (2025-02)
 
 - Support for ordered (additive) characters
 - Require R 3.6 (to simplify maintenance)

From 63e38d00514a37950e2099e9719139f550d3d819 Mon Sep 17 00:00:00 2001
From: RevBayes analysis <1695515+ms609@users.noreply.github.com>
Date: Thu, 6 Feb 2025 16:38:07 +0000
Subject: [PATCH 29/30] Require R4.0

---
 .github/workflows/R-CMD-check.yml | 29 ++---------------------------
 DESCRIPTION                       |  2 +-
 NEWS.md                           |  2 +-
 vignettes/tree-space.Rmd          | 10 ----------
 4 files changed, 4 insertions(+), 39 deletions(-)

diff --git a/.github/workflows/R-CMD-check.yml b/.github/workflows/R-CMD-check.yml
index 0c7642e62..389663d00 100644
--- a/.github/workflows/R-CMD-check.yml
+++ b/.github/workflows/R-CMD-check.yml
@@ -47,7 +47,7 @@ jobs:
         config:
           - {os: windows-latest, r: 'release'}
           - {os: macOS-latest, r: 'release'}
-          - {os: ubuntu-20.04, r: '3.6', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-20.04, r: '4.0', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
           - {os: ubuntu-20.04, r: '4.1', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} # Until TreeDist can slough phangorn
           - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
           - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
@@ -79,33 +79,8 @@ jobs:
         if: runner.os == 'macOS'
         run: |
           brew install libgit2 xquartz ghostscript
-                  
-      - name: Set up R dependencies (R 3.6)
-        if: matrix.config.r == '3.6'
-        uses: r-lib/actions/setup-r-dependencies@v2
-        with:
-          extra-packages: |
-            waldo@0.5.3
-            bench@1.1.3
-            vdiffr@1.0.7
-            cpp11@0.5.0
-            httr2@1.0.1
-            testthat@3.2.1
-            downlit@0.4.3
-            pkgdown@2.0.9
-            profvis@0.3.8
-            gtable@0.3.5
-            evaluate@0.23
-            knitr@1.45
-            phangorn@2.7.1
-            Rfast@1.9.8
-            rjson@0.2.20
-            XML@3.99-0.3
-          needs: |
-            check
-      
+
       - name: Set up R dependencies
-        if: matrix.config.r != '3.6'
         uses: r-lib/actions/setup-r-dependencies@v2
         with:
           needs: |
diff --git a/DESCRIPTION b/DESCRIPTION
index c3b6c98be..bf99b9165 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -32,7 +32,7 @@ Description: Reconstruct phylogenetic trees from discrete data.
 URL: https://ms609.github.io/TreeSearch/ (doc),
   https://github.com/ms609/TreeSearch/ (devel)
 BugReports: https://github.com/ms609/TreeSearch/issues/
-Depends: R (>= 3.6.0)
+Depends: R (>= 4.0)
 Imports: 
   ape (>= 5.6),
   cli (>= 3.0),
diff --git a/NEWS.md b/NEWS.md
index 80ba02969..4b8fa9af3 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,7 +1,7 @@
 # TreeSearch 1.5.1.9005 (2025-02)
 
 - Support for ordered (additive) characters
-- Require R 3.6 (to simplify maintenance)
+- Require R 4.0 (to simplify maintenance)
 
 # TreeSearch 1.5.1.9003 (2025-02)
 
diff --git a/vignettes/tree-space.Rmd b/vignettes/tree-space.Rmd
index d0aa882bc..76ad58b86 100644
--- a/vignettes/tree-space.Rmd
+++ b/vignettes/tree-space.Rmd
@@ -259,16 +259,6 @@ nClusters <- length(unique(clustering))
 
 Now we can map tree space into a few dimensions and visualise the distribution
 of trees:
-```{r palette.colors, echo = FALSE}
-if (packageVersion("base") < "4.0.0") {
-  # TODO delete when require R4.0
-  palette.colors <- function(x, ...) {
-    c("#AA0DFECC", "#3283FECC", "#85660DCC", "#782AB6CC", "#565656CC", 
-"#1C8356CC", "#16FF32CC", "#F7E1A0CC", "#E2E2E2CC", "#1CBE4FCC", 
-"#C4451CCC", "#DEA0FDCC")[seq_len(x)]
-  }
-}
-```
 
 ```{r map-space, fig.keep = "none"}
 nDim <- 3 # Number of dimensions to plot

From c74e053c0502031b91b09ed5aecd0611af1d5881 Mon Sep 17 00:00:00 2001
From: RevBayes analysis <1695515+ms609@users.noreply.github.com>
Date: Thu, 6 Feb 2025 16:55:27 +0000
Subject: [PATCH 30/30] Rm RNGversion("3.5.0")

---
 tests/testthat/test-CustomSearch.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/testthat/test-CustomSearch.R b/tests/testthat/test-CustomSearch.R
index fe2d418da..9b496184b 100644
--- a/tests/testthat/test-CustomSearch.R
+++ b/tests/testthat/test-CustomSearch.R
@@ -10,7 +10,7 @@ RootySwappers <- list(RootedTBRSwap, RootedSPRSwap, RootedNNISwap)
 test_that("Tree can be found", {
   skip_if_not_installed("phangorn")
   phy11 <- phangorn::phyDat(data11, type = "USER", levels = c(FALSE, TRUE))
-  RNGversion("3.5.0")
+  RNGkind("Mersenne-Twister")
   set.seed(1)
   random11 <- as.phylo(17905853L, 11, letters[1:11])
   expect_error(TreeSearch(unrooted11, dataset = phy11))
@@ -110,7 +110,7 @@ test_that("Profile parsimony works in tree search", {
   dataset <- TreeTools::PhyDat(sillyData)
   readyData <- PrepareDataProfile(dataset)
   
-  RNGversion("3.5.0")
+  RNGkind("Mersenne-Twister")
   set.seed(0)
   
   rTree <- randomTree <- RandomTree(dataset, "1")