From 9418da10712748ecaa36a5e67e6d2a934c68ee49 Mon Sep 17 00:00:00 2001
From: RevBayes analysis <1695515+ms609@users.noreply.github.com>
Date: Mon, 14 Apr 2025 14:54:04 +0100
Subject: [PATCH 01/10] Colours when all leaves stable

---
 R/stability.R | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/R/stability.R b/R/stability.R
index 445c6d8..cf3f9e5 100644
--- a/R/stability.R
+++ b/R/stability.R
@@ -183,7 +183,13 @@ ColByStability <- function(trees, log = TRUE,
     score <- TipInstability(trees, log = log, average = average,
                             deviation = deviation)
     score <- score - min(score)
-    score <- score / max(score)
+    zero <- abs(score) < sqrt(.Machine$double.eps)
+    if (any(!zero)) {
+      score[zero] <- 0
+      score <- score / max(score)
+    } else {
+      score[] <- 0
+    }
   
     # Return:
     setNames(pal[1 + (score * (length(pal) - 1))],

From 665e972c42ff60a825d15bb37acf122c3719e861 Mon Sep 17 00:00:00 2001
From: RevBayes analysis <1695515+ms609@users.noreply.github.com>
Date: Mon, 14 Apr 2025 14:55:05 +0100
Subject: [PATCH 02/10] Test identical trees

---
 tests/testthat/test-stability.R | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/tests/testthat/test-stability.R b/tests/testthat/test-stability.R
index 0437522..ebb645a 100644
--- a/tests/testthat/test-stability.R
+++ b/tests/testthat/test-stability.R
@@ -27,6 +27,9 @@ test_that("GraphGeodesic() works", {
   Test(PectinateTree(7))
   Test(CollapseNode(BalancedTree(101), 104:111))
   Test(as.phylo(201, 1201))
+  
+  expect_equal(GraphGeodesic(BalancedTree(4), log = FALSE),
+               GraphGeodesic(BalancedTree(4), log = 1))
 })
 
 test_that("ColByStability()", {
@@ -38,3 +41,11 @@ test_that("ColByStability()", {
   expect_equal(tipCol["t2"], tipCol["t1"])
 })
 
+test_that("ColByStability() - stable trees", {
+  trees <- c(BalancedTree(4), BalancedTree(4), BalancedTree(4))
+  cons <- Consensus(trees)
+  tipCols <- ColByStability(trees)[cons$tip.label]
+  expect_equal(tipCols, setNames(hcl.colors(131, "inferno")[rep(1, 4)],
+                                 cons[["tip.label"]]))
+})
+

From 08659e35bc31a2b9ffc06273b23cb504b391b8a5 Mon Sep 17 00:00:00 2001
From: RevBayes analysis <1695515+ms609@users.noreply.github.com>
Date: Mon, 14 Apr 2025 15:02:16 +0100
Subject: [PATCH 03/10] 2.1.6.9000

---
 DESCRIPTION |  2 +-
 NEWS.md     | 24 +++++++++++++++---------
 2 files changed, 16 insertions(+), 10 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index def2d22..95db082 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: Rogue
 Title: Identify Rogue Taxa in Sets of Phylogenetic Trees
-Version: 2.1.6
+Version: 2.1.6.9000
 Authors@R: c(person("Martin R.", 'Smith',
                     email = "martin.smith@durham.ac.uk", 
                     role = c("aut", "cre", "cph"), 
diff --git a/NEWS.md b/NEWS.md
index b37ae9c..fa48abd 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,10 @@
-# Rogue v2.1.6
+# Rogue v2.1.6.9000 (2025-04-14)
+
+- Improve tip instability calculation in identical tree sets
+  ([#29](https://github.com/ms609/Rogue/issues/29)).
+
+
+# Rogue v2.1.6 (2023-11-29)
 
 - Legend annotations in documentation.
 - Disable parallel evaluation by default in `TipInstability()`,
@@ -6,37 +12,37 @@
 - Use format string in REprintf().
 
 
-# Rogue v2.1.5
+# Rogue v2.1.5 (2023-03-20)
 
 - Call C functions using symbols, not strings.
 
 
-# Rogue v2.1.4
+# Rogue v2.1.4 (2023-01-16)
 
 - C2X compliant function prototypes.
 
 - Remove unused `sprintf()` calls.
 
 
-# Rogue v2.1.3
+# Rogue v2.1.3 (2022-09-26)
 
 - `ColByStability()` gains `pal` argument to allow specification of custom
   palettes.
 
 
-# Rogue v2.1.2
+# Rogue v2.1.2 (2022-08-16)
 
 - Faster rogue detection when edge lengths provided, per report by Joe Keating.
 
 - Don't list `neverDrop` in `QuickRogue(fullSeq = TRUE)`.
 
 
-# Rogue v2.1.1
+# Rogue v2.1.1 (2022-07-20)
 
 - Handle `ColByStability(trees = NULL)`.
 
 
-# Rogue v2.1.0
+# Rogue v2.1.0 (2022-01-13)
 
 - Early termination of `QuickRogue()` when no further improvement possible.
 
@@ -49,11 +55,11 @@
 - New vignette detailing rogue detection with Bayesian tree samples.
 
 
-# Rogue v2.0.0
+# Rogue v2.0.0 (2021-09-13)
 
 - Information theoretic rogue detection (per Smith, 2022).
 
 
-# Rogue v1.0.0
+# Rogue v1.0.0 (2021-06-28)
 
  - R interface to RogueNaRok.

From 884ce350f73499c6621610ccee2defa8e508239e Mon Sep 17 00:00:00 2001
From: RevBayes analysis <1695515+ms609@users.noreply.github.com>
Date: Mon, 14 Apr 2025 15:19:48 +0100
Subject: [PATCH 04/10] actions@v4

---
 .github/workflows/memcheck.yml    | 4 ++--
 .github/workflows/revdepcheck.yml | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/memcheck.yml b/.github/workflows/memcheck.yml
index 2b961b6..657b0b3 100644
--- a/.github/workflows/memcheck.yml
+++ b/.github/workflows/memcheck.yml
@@ -42,7 +42,7 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           submodules: true
 
@@ -66,7 +66,7 @@ jobs:
         shell: Rscript {0}
 
       - name: Cache R packages
-        uses: actions/cache@v2
+        uses: actions/cache@v4
         with:
           path: ${{ env.R_LIBS_USER }}
           key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
diff --git a/.github/workflows/revdepcheck.yml b/.github/workflows/revdepcheck.yml
index 37ab7c0..4538ad4 100644
--- a/.github/workflows/revdepcheck.yml
+++ b/.github/workflows/revdepcheck.yml
@@ -59,7 +59,7 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:
@@ -76,7 +76,7 @@ jobs:
         shell: Rscript {0}
 
       - name: Cache R packages
-        uses: actions/cache@v2
+        uses: actions/cache@v4
         with:
           path: ${{ env.R_LIBS_USER }}
           key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}

From b695d1b2403bf82b2eeb6f6249405a59d4399ffe Mon Sep 17 00:00:00 2001
From: RevBayes analysis <1695515+ms609@users.noreply.github.com>
Date: Mon, 14 Apr 2025 15:24:16 +0100
Subject: [PATCH 05/10] @v4

---
 .github/workflows/R-CMD-check.yml   | 4 ++--
 .github/workflows/RcppDeepState.yml | 2 +-
 .github/workflows/codemeta.yml      | 4 ++--
 .github/workflows/pkgdown.yml       | 4 ++--
 4 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/R-CMD-check.yml b/.github/workflows/R-CMD-check.yml
index def073c..5a79aaa 100644
--- a/.github/workflows/R-CMD-check.yml
+++ b/.github/workflows/R-CMD-check.yml
@@ -61,7 +61,7 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           submodules: true
 
@@ -96,7 +96,7 @@ jobs:
 
       - name: Cache R packages
         if: runner.os != 'Windows'
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ${{ env.R_LIBS_USER }}
           key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
diff --git a/.github/workflows/RcppDeepState.yml b/.github/workflows/RcppDeepState.yml
index e34a4be..bbac34e 100644
--- a/.github/workflows/RcppDeepState.yml
+++ b/.github/workflows/RcppDeepState.yml
@@ -32,7 +32,7 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps: 
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
         with:
           submodules: true
 
diff --git a/.github/workflows/codemeta.yml b/.github/workflows/codemeta.yml
index 82ee53a..e1ae6e5 100644
--- a/.github/workflows/codemeta.yml
+++ b/.github/workflows/codemeta.yml
@@ -20,7 +20,7 @@ jobs:
       RSPM: ${{ matrix.config.rspm }}
       
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:
@@ -37,7 +37,7 @@ jobs:
         shell: Rscript {0}
 
       - name: Cache R packages
-        uses: actions/cache@v2
+        uses: actions/cache@v4
         with:
           path: ${{ env.R_LIBS_USER }}
           key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
diff --git a/.github/workflows/pkgdown.yml b/.github/workflows/pkgdown.yml
index 985eb5a..9e3ac54 100644
--- a/.github/workflows/pkgdown.yml
+++ b/.github/workflows/pkgdown.yml
@@ -22,7 +22,7 @@ jobs:
       R_COMPILE_AND_INSTALL_PACKAGES: 'never'
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
         with:
           submodules: true
 
@@ -38,7 +38,7 @@ jobs:
         shell: Rscript {0}
 
       - name: Cache R packages
-        uses: actions/cache@v2
+        uses: actions/cache@v4
         with:
           path: ${{ env.R_LIBS_USER }}
           key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}

From 0348a0c7898effec8f9093db39c56e949f159952 Mon Sep 17 00:00:00 2001
From: RevBayes analysis <1695515+ms609@users.noreply.github.com>
Date: Mon, 14 Apr 2025 15:28:52 +0100
Subject: [PATCH 06/10] OS_VERSION

---
 .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 5a79aaa..a297b69 100644
--- a/.github/workflows/R-CMD-check.yml
+++ b/.github/workflows/R-CMD-check.yml
@@ -112,7 +112,7 @@ jobs:
           while read -r cmd
           do
             eval sudo $cmd
-          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
+          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "${OS_VERSION}"))')
 
       - name: Install system dependencies (macOS)
         if: runner.os == 'macOS'

From aea786f1f1a9420595c1872effdb6708432d8174 Mon Sep 17 00:00:00 2001
From: RevBayes analysis <1695515+ms609@users.noreply.github.com>
Date: Mon, 14 Apr 2025 15:38:10 +0100
Subject: [PATCH 07/10] Modernize R CMD Check

---
 .github/workflows/R-CMD-check.yml | 116 ++++++++++++------------------
 1 file changed, 45 insertions(+), 71 deletions(-)

diff --git a/.github/workflows/R-CMD-check.yml b/.github/workflows/R-CMD-check.yml
index a297b69..8e602d2 100644
--- a/.github/workflows/R-CMD-check.yml
+++ b/.github/workflows/R-CMD-check.yml
@@ -64,44 +64,9 @@ jobs:
       - uses: actions/checkout@v4
         with:
           submodules: true
-
-      - uses: r-lib/actions/setup-r@v2
-        with:
-          r-version: ${{ matrix.config.r }}
-
-      - uses: r-lib/actions/setup-pandoc@v2
-
-      - name: Query dependencies
-        if: runner.os != 'macOS'
-        run: |
-          install.packages('remotes')
-          saveRDS(
-            remotes::dev_package_deps(dependencies = c("soft",
-            "Config/Needs/github-actions")), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor),
-            ".github/R-version")
-        shell: Rscript {0}
-
-      - name: Query dependencies (macOS)
-        if: runner.os == 'macOS'
-        run: |
-          install.packages('remotes')
-          saveRDS(
-            remotes::dev_package_deps(dependencies = c("soft",
-            "Config/Needs/coverage", "Config/Needs/github-actions"))
-          , ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor),
-            ".github/R-version")
-        shell: Rscript {0}
-
-      - name: Cache R packages
-        if: runner.os != 'Windows'
-        uses: actions/cache@v4
-        with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
-
+      
+      - uses: actions/cache@v4
+  
       - name: Install system dependencies (Linux)
         if: runner.os == 'Linux'
         run: |
@@ -109,48 +74,57 @@ jobs:
           sudo apt-get install -y libpoppler-glib-dev bwidget libavfilter-dev libtesseract-dev gdal-bin proj-bin libgdal-dev libproj-dev tesseract-ocr-eng libleptonica-dev tcl libgtk2.0-dev libgtk-3-dev
           sudo pkg-config --libs poppler-glib
           sudo pkg-config --cflags poppler-glib
-          while read -r cmd
-          do
-            eval sudo $cmd
-          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "${OS_VERSION}"))')
 
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+      
+      - uses: r-lib/actions/setup-pandoc@v2
+      
       - name: Install system dependencies (macOS)
         if: runner.os == 'macOS'
         run: |
           brew install libgit2 xquartz
 
-      - name: Install callr (Windows)
+      - name: Set up R dependencies (Windows)
         if: runner.os == 'Windows'
-        run: |
-          remotes::install_cran("callr")
-        shell: Rscript {0}
-
-      - name: Install dependencies
-        run: |
-          remotes::install_deps(dependencies = c("soft", "Config/Needs/github-actions"))
-        shell: Rscript {0}
-
-      - name: Install coverage dependencies
-        if: runner.os == 'macOS'
-        run: |
-          remotes::install_deps(dependencies = 'Config/Needs/coverage')
-        shell: Rscript {0}
-
-      - name: Check
-        env:
-          _R_CHECK_CRAN_INCOMING_REMOTE_: false
-        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
-        shell: Rscript {0}
-
-      # - name: Upload check results
-      #   if: failure()
-      #   uses: actions/upload-artifact@main
-      #   with:
-      #     name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-      #     path: check
+        uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: callr
+          needs: |
+            check
+            coverage
+            github-actions
+            
+      - name: Set up R dependencies (Non-Windows)
+        if: runner.os != 'Windows'
+        uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          needs: |
+            check
+            github-actions
+          extra-packages: |
+            phangorn=?ignore-before-r=4.1.0
+            
+      - name: Check package
+        uses: r-lib/actions/check-r-package@v2
 
       - name: Test coverage
-        if: runner.os == 'macOS'
+        if: runner.os == 'Windows'
         run: |
           covr::codecov()
         shell: Rscript {0}
+                
+      - name: Notify on failure
+        if: failure() && github.event_name == 'schedule'
+        uses: actions/github-script@v7
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          script: |
+            github.rest.issues.createComment({
+              owner: context.repo.owner,
+              repo: context.repo.repo,
+              issue_number: 31,
+              body: 'Scheduled workflow has failed: https://github.com/${{ github.repository }}/actions/runs/${{ github.run_id }}'
+            });
+

From ee4383fd709b2aeedc81e352f65ffa66734a6051 Mon Sep 17 00:00:00 2001
From: RevBayes analysis <1695515+ms609@users.noreply.github.com>
Date: Mon, 14 Apr 2025 15:43:59 +0100
Subject: [PATCH 08/10] cache

---
 .github/workflows/R-CMD-check.yml | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/.github/workflows/R-CMD-check.yml b/.github/workflows/R-CMD-check.yml
index 8e602d2..2c3f715 100644
--- a/.github/workflows/R-CMD-check.yml
+++ b/.github/workflows/R-CMD-check.yml
@@ -66,6 +66,11 @@ jobs:
           submodules: true
       
       - uses: actions/cache@v4
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+
   
       - name: Install system dependencies (Linux)
         if: runner.os == 'Linux'

From 2633a98908646ce39c425ec6158d91a21d44ed35 Mon Sep 17 00:00:00 2001
From: RevBayes analysis <1695515+ms609@users.noreply.github.com>
Date: Mon, 14 Apr 2025 15:45:49 +0100
Subject: [PATCH 09/10] Case

---
 .github/workflows/R-CMD-check.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/R-CMD-check.yml b/.github/workflows/R-CMD-check.yml
index 2c3f715..391cd93 100644
--- a/.github/workflows/R-CMD-check.yml
+++ b/.github/workflows/R-CMD-check.yml
@@ -14,7 +14,7 @@ on:
       - "**.json"
       - "**.md"
       - "**.yml"
-      - "!**R-cmd-check.yml"
+      - "!**R-CMD-check.yml"
       - "**.R[dD]ata"
       - "**.Rpro*"
   pull_request:
@@ -29,7 +29,7 @@ on:
       - "**.json"
       - "**.md"
       - "**.yml"
-      - "!**R-cmd-check.yml"
+      - "!**R-CMD-check.yml"
       - "**.R[dD]ata"
       - "**.Rpro*"
 

From 427e71d25a755f983936e78d01979d24eca9dc0d Mon Sep 17 00:00:00 2001
From: RevBayes analysis <1695515+ms609@users.noreply.github.com>
Date: Mon, 14 Apr 2025 15:51:06 +0100
Subject: [PATCH 10/10] Cache in place

---
 .github/workflows/R-CMD-check.yml | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/R-CMD-check.yml b/.github/workflows/R-CMD-check.yml
index 391cd93..5516bf0 100644
--- a/.github/workflows/R-CMD-check.yml
+++ b/.github/workflows/R-CMD-check.yml
@@ -65,13 +65,6 @@ jobs:
         with:
           submodules: true
       
-      - uses: actions/cache@v4
-        with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
-
-  
       - name: Install system dependencies (Linux)
         if: runner.os == 'Linux'
         run: |
@@ -86,6 +79,13 @@ jobs:
       
       - uses: r-lib/actions/setup-pandoc@v2
       
+      - name: Cache R packages
+        uses: actions/cache@v4
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+      
       - name: Install system dependencies (macOS)
         if: runner.os == 'macOS'
         run: |