Update vignettes to use ReadMrBayesTrees()

.github/workflows/R-CMD-check.yml

@@ -47,9 +47,9 @@ jobs:
         config:
           - {os: windows-latest, r: 'release'}
           - {os: macOS-latest, r: 'release'}
-          - {os: ubuntu-latest, r: '4.1', rspm: "https://packagemanager.rstudio.com/cran/__linux__/noble/latest"} # Until TreeDist can slough phangorn
-          - {os: ubuntu-latest, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/noble/latest"}
-          - {os: ubuntu-latest, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/noble/latest"}
+          - {os: ubuntu-22.04, r: '4.1', rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"} # Until TreeDist can slough phangorn
+          - {os: ubuntu-24.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/noble/latest"}
+          - {os: ubuntu-24.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/noble/latest"}
 
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true

.github/workflows/memcheck.yml

@@ -24,7 +24,7 @@ name: mem-check
 
 jobs:
   mem-check:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-24.04 # Remember to update RSPM below to match
 
     name: valgrind ${{ matrix.config.test }}
 
@@ -45,58 +45,7 @@ jobs:
       - uses: actions/checkout@v4
         with:
           submodules: true
-
-      - uses: r-lib/actions/setup-r@v2
-        with:
-          r-version: release # CRAN uses devel, but takes ages to load deps.
-
-      - name: Install apt packages
-        run: |
-          sudo apt-get install valgrind texlive-latex-base
-
-      - uses: r-lib/actions/setup-pandoc@v2
-
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = c("soft",
-              "Config/Needs/github-actions", "Config/Needs/memcheck")),
-            ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
-
-      - name: Cache R packages
-        uses: actions/cache@v4
+
+      - uses: ms609/actions/memcheck@main
         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
-        run: |
-          while read -r cmd
-          do
-            eval sudo $cmd
-          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
-
-      - name: Install dependencies
-        run: |
-          remotes::install_github('emmanuelparadis/ape')
-          if ("${{ matrix.config.test }}" == 'tests') {
-            remotes::install_github('r-lib/brio#20') # brio mem leak
-          }
-          remotes::install_deps(dependencies = c("soft", "Config/Needs/github-actions", "Config/Needs/memcheck"))
-        shell: Rscript {0}
-
-      - name: Install this package
-        run: |
-          cd ..
-          R CMD build --no-manual --no-resave-data Rogue
-          R CMD INSTALL Rogue*.tar.gz
-          cd Rogue
-
-      - name: valgrind - memcheck ${{ matrix.config.test }}
-        run: |
-          R -d "valgrind --tool=memcheck --leak-check=full \
-          --errors-for-leak-kinds=definite --error-exitcode=1" \
-          --vanilla < memcheck/${{ matrix.config.test }}.R
+          test: ${{ matrix.config.test}}

.github/workflows/pkgdown.yml

@@ -15,7 +15,7 @@ name: pkgdown
 
 jobs:
   pkgdown:
-    runs-on: macOS-latest
+    runs-on: ubuntu-latest
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
@@ -26,38 +26,5 @@ jobs:
         with:
           submodules: true
 
-      - uses: r-lib/actions/setup-r@v2
-
-      - uses: r-lib/actions/setup-pandoc@v2
-
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = c('soft', 'Config/Needs/website')), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
-
-      - 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 Mac OS dependencies
-        run: |
-          brew install libgit2
-
-      - name: Install dependencies
-        run: |
-          remotes::install_deps(dependencies = c('soft', 'Config/Needs/website'))
-        shell: Rscript {0}
-
-      - name: Install package
-        run: R CMD INSTALL .
-
-      - name: Deploy package
-        run: |
-          git config --local user.email "actions@github.com"
-          git config --local user.name "GitHub Actions"
-          Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)'
+    steps:
+      - uses: ms609/actions/pkgdown@main

DESCRIPTION

@@ -37,12 +37,15 @@ Imports:
   Rfast,
   stats,
   TreeDist (> 2.2.0),
-  TreeTools (>= 1.9.1.9003),
+  TreeTools (>= 1.10.0),
   utils,
+Remotes:
+  ms609/TreeTools,
 Suggests:
   knitr,
   PlotTools,
   rmarkdown,
+  RCurl,
   spelling,
   testthat,
 Config/Needs/github-actions:

NEWS.md

@@ -1,5 +1,7 @@
 # Rogue v2.1.7 (2025-07-01)
 
+- Simplify vignette with new `TreeTools::ReadMrBayesTrees()`.
+
 - Improve tip instability calculation in identical tree sets
   ([#29](https://github.com/ms609/Rogue/issues/29)).
 - Improve variable protection.

vignettes/Bayesian.Rmd

@@ -37,10 +37,7 @@ library("Rogue") # Find rogue taxa
 ```
 
 ```{r test-connection, echo = FALSE}
-online <- tryCatch({
-    read.csv("https://raw.githubusercontent.com/ms609/hyoliths/master/MrBayes/hyo.nex.pstat")
-    TRUE
-  },
+online <- tryCatch(RCurl::url.exists("https://raw.githubusercontent.com/"),
   warning = function(w) invokeRestart(""),
   error = function(e) FALSE
 )
@@ -51,63 +48,25 @@ analysis of early brachiopods [@Sun2018] using
 [MrBayes](https://nbisweden.github.io/MrBayes/) [@Hulsenbeck2001].
 Our data files are stored on
 [GitHub](https://github.com/ms609/hyoliths/tree/master/MrBayes).
-Let's load the results of run 1:
+Let's sample 100 trees from the posterior (after discarding a 25% burn-in):
 
 ```{R load-trees}
 if (online) {
-  dataFolder <- "https://raw.githubusercontent.com/ms609/hyoliths/master/MrBayes/"
-  run1.t <- paste0(dataFolder, "hyo.nex.run1.t")
-  # Reading 10k trees takes a second or two...
-  run1Trees <- ape::read.nexus(run1.t)
-  if (packageVersion('ape') <= "5.6.1") {
-    # Workaround for a bug in ape, hopefully fixed in v5.6.2
-    run1Trees <- structure(lapply(run1Trees, function(tr) {
-      tr$tip.label <- attr(run1Trees, 'TipLabel')
-      tr
-    }), class = 'multiPhylo')
-  }
+  # Downloading all trees takes a second or two...
+  trees <- ReadMrBayesTrees(
+    "https://raw.githubusercontent.com/ms609/hyoliths/master/MrBayes/hyo.nex",
+    n = 100,
+    burninFrac = 0.25
+  )
 } else {
   # If no internet connection, we can generate some example trees instead
-  run1Trees <- structure(unlist(lapply(0:21, function(backbone) {
-    AddTipEverywhere(ape::as.phylo(0, nTip = 12), 'ROGUE')
-  }), recursive = FALSE), class = 'multiPhylo')
+  trees <- structure(unlist(lapply(0:21, function(backbone) {
+    AddTipEverywhere(ape::as.phylo(0, nTip = 12), "ROGUE")
+  }), recursive = FALSE), class = "multiPhylo")
 }
 ```
 
 
-## Select trees to analyse
-
-Our tree file contains all trees generated.  We typically want to discard 
-a proportion of trees as burn-in:
-
-```{R discard-burnin}
-burninFrac <- 0.25
-nTrees <- length(run1Trees)
-trees <- run1Trees[seq(from = burninFrac * nTrees, to = nTrees)]
-```
-
-This is a large number of trees to analyse.  We could save time for an initial
-analysis by thinning our sample somewhat.
-
-```{R thin-trees}
-sampleSize <- 100
-trees <- run1Trees[seq(from = burninFrac * nTrees, to = nTrees,
-                       length.out = sampleSize)]
-```
-
-For a full analysis, we ought to consider the output from the other runs of our
-analysis, perhaps with
-
-```r
-nRuns <- 4
-allTrees <- lapply(seq_len(nRuns), function(run) {
-  runTrees <- ape::read.nexus(paste0(dataFolder, 'hyo.nex.run', run, .'t'))
-  runTrees <- runTrees[seq(from = burninFrac * nTrees, to = nTrees,
-                           length.out = sampleSize / nRuns)]
-})
-trees <- structure(unlist(allTrees, recursive = FALSE), class = 'multiPhylo')
-```
-
 ## Initial appraisal
 
 Let's start by looking at the majority rule consensus tree.
@@ -122,7 +81,7 @@ plenary <- Consensus(trees, p = 0.5)
 par(mar = rep(0, 4), cex = 0.85)
 plot(plenary, tip.color = ColByStability(trees))
 PlotTools::SpectrumLegend(
-  "bottomright", legend = c("Stable", "Unstable"),
+  "bottomright", legend = c("Stable", " ", "Unstable"),
   palette = hcl.colors(131, 'inferno')[1:101]
 )
 ```