Martin R. Smith, Durham UniversityMartin R. Smith, Durham Universityvignettes/Bayesian.Rmd
Bayesian.RmdCRAN release: 2023-11-29
TipInstability(), adding parallel parameter to allow user to override.rawImprovement: Improvement in score obtained by this operation
IC: Information content of tree after dropping all leaves so far,
by the measure indicated by info.
C_RogueNaRok() returns 0 if successful; -1 on error.
QuickRogue() returns a data.frame in the same format as
+RogueTaxa().
C_RogueNaRok() returns 0 if successful; -1 on error.
reduced <- RogueTaxa(trees, info = "phylogenetic", ret = "tree")
-#> ✔ 2023-11-29 10:05:42.824518: Dropped 2 leaves, rendering 17.0678 bits.
+#> ✔ 2024-02-23 14:46:10.014404: Dropped 2 leaves, rendering 17.0678 bits.
plot(reduced)
LabelSplits(reduced, SplitFrequency(reduced, trees) / length(trees))
diff --git a/search.json b/search.json
index f3b922f..1120b8f 100644
--- a/search.json
+++ b/search.json
@@ -1 +1 @@
-[{"path":"https://ms609.github.io/Rogue/CODE_OF_CONDUCT.html","id":null,"dir":"","previous_headings":"","what":"Contributor Code of Conduct","title":"Contributor Code of Conduct","text":"contributors maintainers project, pledge respect people contribute reporting issues, posting feature requests, updating documentation, submitting pull requests patches, activities. committed making participation project harassment-free experience everyone, regardless level experience, gender, gender identity expression, sexual orientation, disability, personal appearance, body size, race, ethnicity, age, religion. Examples unacceptable behavior participants include use sexual language imagery, derogatory comments personal attacks, trolling, public private harassment, insults, unprofessional conduct. Project maintainers right responsibility remove, edit, reject comments, commits, code, wiki edits, issues, contributions aligned Code Conduct. Project maintainers follow Code Conduct may removed project team. Instances abusive, harassing, otherwise unacceptable behavior may reported opening issue contacting one project maintainers. Code Conduct adapted Contributor Covenant (https://www.contributor-covenant.org), version 1.0.0, available https://contributor-covenant.org/version/1/0/0/.","code":""},{"path":[]},{"path":"https://ms609.github.io/Rogue/CONTRIBUTING.html","id":"fixing-typos","dir":"","previous_headings":"","what":"Fixing typos","title":"CONTRIBUTING","text":"Small typos grammatical errors documentation may edited directly using GitHub web interface, long changes made source file. : edit roxygen comment .R file R/. DON’T: edit .Rd file man/.","code":""},{"path":"https://ms609.github.io/Rogue/CONTRIBUTING.html","id":"prerequisites","dir":"","previous_headings":"","what":"Prerequisites","title":"CONTRIBUTING","text":"make substantial pull request, always file issue make sure someone team agrees ’s problem. ’ve found bug, create associated issue illustrate bug minimal reprex.","code":""},{"path":"https://ms609.github.io/Rogue/CONTRIBUTING.html","id":"pull-request-process","dir":"","previous_headings":"","what":"Pull request process","title":"CONTRIBUTING","text":"recommend create Git branch pull request (PR). Look GitHub actions CodeCovr build status making changes. follow Google’s R style guide use camelCase variable names, TitleCase function names. use Oxford ending ‘ize’ (‘ise’), UK spelling (e.g. ‘colour’) possible avoid distinction (e.g. shortening ‘col’) use roxygen2 build documentation. use testthat. Contributions test cases included easier accept. user-facing changes, add bullet top NEWS.md current development version header describing changes made followed GitHub username, links relevant issue(s)/PR(s).","code":""},{"path":"https://ms609.github.io/Rogue/CONTRIBUTING.html","id":"code-of-conduct","dir":"","previous_headings":"","what":"Code of Conduct","title":"CONTRIBUTING","text":"Please note project released Contributor Code Conduct. contributing project agree abide terms.","code":""},{"path":"https://ms609.github.io/Rogue/CONTRIBUTING.html","id":"prefer-to-e-mail","dir":"","previous_headings":"","what":"Prefer to e-mail?","title":"CONTRIBUTING","text":"E-mail person listed maintainer DESCRIPTION file repo. Private discussions email don’t help others - course email totally warranted sensitive problems.","code":""},{"path":"https://ms609.github.io/Rogue/CONTRIBUTING.html","id":"thanks-for-contributing","dir":"","previous_headings":"","what":"Thanks for contributing!","title":"CONTRIBUTING","text":"document adapted tidyverse contributing guide.","code":""},{"path":"https://ms609.github.io/Rogue/articles/Bayesian.html","id":"set-up","dir":"Articles","previous_headings":"","what":"Set up","title":"Detecting rogue taxa in Bayesian posterior tree sets","text":"Let’s start loading packages ’ll need: ’ll work example data generated morphological analysis early brachiopods (Sun et al., 2018) using MrBayes (Hulsenbeck & Ronquist, 2001). data files stored GitHub. Let’s load results run 1:","code":"library(\"TreeTools\") # Read and plot trees library(\"Rogue\") # Find rogue taxa 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') } } 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') }"},{"path":"https://ms609.github.io/Rogue/articles/Bayesian.html","id":"select-trees-to-analyse","dir":"Articles","previous_headings":"","what":"Select trees to analyse","title":"Detecting rogue taxa in Bayesian posterior tree sets","text":"tree file contains trees generated. typically want discard proportion trees burn-: large number trees analyse. save time initial analysis thinning sample somewhat. full analysis, consider output runs analysis, perhaps ","code":"burninFrac <- 0.25 nTrees <- length(run1Trees) trees <- run1Trees[seq(from = burninFrac * nTrees, to = nTrees)] sampleSize <- 100 trees <- run1Trees[seq(from = burninFrac * nTrees, to = nTrees, length.out = sampleSize)] 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')"},{"path":"https://ms609.github.io/Rogue/articles/Bayesian.html","id":"initial-appraisal","dir":"Articles","previous_headings":"","what":"Initial appraisal","title":"Detecting rogue taxa in Bayesian posterior tree sets","text":"Let’s start looking majority rule consensus tree. can instructive colour leaves instability; use ad hoc approach Smith (2022). First let’s define function plot gradient legend: taxa stand less stable position tree others. removing taxa reveal enough additional information remaining taxa compensate loss information taxa plot?","code":"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\"), palette = hcl.colors(131, 'inferno')[1:101] )"},{"path":"https://ms609.github.io/Rogue/articles/Bayesian.html","id":"detect-rogue-taxa","dir":"Articles","previous_headings":"","what":"Detect rogue taxa","title":"Detecting rogue taxa in Bayesian posterior tree sets","text":"options evaluate negative impact retaining rogue taxa consensus tree. QuickRogue() uses quick heuristic method Smith (2022); RogueTaxa() supports Smith’s slower heuristic, might find set rogue taxa yield slightly improvement consensus tree; can also configured employ RogueNaRok approach (Aberer, Krompass, & Stamatakis, 2013).","code":"rogues <- QuickRogue(trees) # rogues <- RogueTaxa(trees) might do a better job, much more slowly rogues ## num taxNum taxon rawImprovement IC ## 1 0