From de35281f727835479f3b9d4e26bb2c62bcd77c56 Mon Sep 17 00:00:00 2001 From: "Martin R. Smith" <1695515+ms609@users.noreply.github.com> Date: Mon, 13 Sep 2021 19:51:58 +0100 Subject: [PATCH] v2.0.0 (#16) --- DESCRIPTION | 28 ++++++++++++++-------------- NEWS.md | 21 +-------------------- codemeta.json | 12 ++++++------ cran-comments.md | 12 +++++++++--- inst/WORDLIST | 3 +++ 5 files changed, 33 insertions(+), 43 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 865804a..5da3f62 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: Rogue Title: Identify Rogue Taxa in Sets of Phylogenetic Trees -Version: 1.0.0.9005 +Version: 2.0.0 Authors@R: c(person("Martin R.", 'Smith', email = "martin.smith@durham.ac.uk", role = c("aut", "cre", "cph"), @@ -9,15 +9,18 @@ Authors@R: c(person("Martin R.", 'Smith', email = "andre.aberer@googlemail.com") ) License: GPL (>= 3) -Description: Interface to 'RogueNaRok' (Aberer et al. 2013) - . - Rogue taxa are a class of taxa with uncertain position in a - phylogenetic tree. For inference methods that yield a tree set (bootstrapping, - Bayesian tree searches), rogue taxa can assume different positions for each - tree. The presence of rogue taxa in a tree set can potentially remove all - information from a consensus tree. The sum of branch support - values in a consensus tree can often be increased by removing rogue taxa. -URL: +Description: Rogue ('wildcard') taxa are leaves with uncertain phylogenetic + position. + Their position may vary from tree to tree under inference methods that yield a + tree set (e.g. bootstrapping, Bayesian tree searches, maximum parsimony). + The presence of rogue taxa in a tree set can potentially remove all + information from a consensus tree. The information content of a consensus + tree - a function of its resolution and branch support values - can often be + increased by removing rogue taxa. + 'Rogue' provides an explicitly information-theoretic approach to rogue + detection (Smith, forthcoming), and an interface to 'RogueNaRok' + (Aberer et al. 2013) . +URL: https://github.com/ms609/Rogue/, https://github.com/aberer/RogueNaRok/, https://github.com/ms609/RogueNaRok/ @@ -33,7 +36,7 @@ Imports: Rfast, stats, TreeDist (>= 2.1.1), - TreeTools (>= 1.4.5.9007), + TreeTools (>= 1.5.0), utils, Suggests: testthat, @@ -45,9 +48,6 @@ Config/Needs/coverage: covr Config/Needs/memcheck: devtools Config/Needs/metadata: codemetar Config/Needs/website: pkgdown -Remotes: - ms609/TreeDist, - ms609/TreeTools, RdMacros: Rdpack SystemRequirements: C99 ByteCompile: true diff --git a/NEWS.md b/NEWS.md index 4a05345..96f343b 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,26 +1,7 @@ -# RogueNaRok v1.0.0.9005 - -- Upward pass to restore misidentified rogues in `QuickRogue()`. - (Debugged in .9005) - -# RogueNaRok v1.0.0.9003 - -- Allow mean / deviation specification in `TipInstability()`. - -# RogueNaRok v1.0.0.9002 - -- Log-transform instability measure by default: a big improvement at a small - computational cost. - -# RogueNaRok v1.0.0.9001 +# RogueNaRok v2.0.0 - Information theoretic rogue detection (per Smith, forthcoming). -# RogueNaRok v1.0.0.9000 - -- Correct citation information. - # RogueNaRok v1.0.0 - R interface to RogueNaRok. - diff --git a/codemeta.json b/codemeta.json index 3b9e817..bdf5f6d 100644 --- a/codemeta.json +++ b/codemeta.json @@ -5,7 +5,7 @@ ], "@type": "SoftwareSourceCode", "identifier": "Rogue", - "description": "Interface to 'RogueNaRok' (Aberer et al. 2013) \n .\n Rogue taxa are a class of taxa with uncertain position in a\n phylogenetic tree. For inference methods that yield a tree set (bootstrapping,\n Bayesian tree searches), rogue taxa can assume different positions for each\n tree. The presence of rogue taxa in a tree set can potentially remove all\n information from a consensus tree. The sum of branch support \n values in a consensus tree can often be increased by removing rogue taxa.", + "description": "Rogue ('wildcard') taxa are leaves with uncertain phylogenetic\n position.\n Their position may vary from tree to tree under inference methods that yield a\n tree set (e.g. bootstrapping, Bayesian tree searches, maximum parsimony).\n The presence of rogue taxa in a tree set can potentially remove all\n information from a consensus tree. The information content of a consensus\n tree - a function of its resolution and branch support values - can often be\n increased by removing rogue taxa. \n 'Rogue' provides an explicitly information-theoretic approach to rogue\n detection (Smith, forthcoming), and an interface to 'RogueNaRok'\n (Aberer et al. 2013) .", "name": "Rogue: Identify Rogue Taxa in Sets of Phylogenetic Trees", "codeRepository": "https://github.com/ms609/Rogue/", "relatedLink": [ @@ -15,7 +15,7 @@ ], "issueTracker": "https://github.com/ms609/Rogue/issues/", "license": "https://spdx.org/licenses/GPL-3.0", - "version": "1.0.0.9005", + "version": "2.0.0", "programmingLanguage": { "@type": "ComputerLanguage", "name": "R", @@ -180,20 +180,20 @@ "name": "Comprehensive R Archive Network (CRAN)", "url": "https://cran.r-project.org" }, - "sameAs": "https://github.com/ms609/TreeDist" + "sameAs": "https://CRAN.R-project.org/package=TreeDist" }, { "@type": "SoftwareApplication", "identifier": "TreeTools", "name": "TreeTools", - "version": ">= 1.4.5.9007", + "version": ">= 1.5.0", "provider": { "@id": "https://cran.r-project.org", "@type": "Organization", "name": "Comprehensive R Archive Network (CRAN)", "url": "https://cran.r-project.org" }, - "sameAs": "https://github.com/ms609/TreeTools" + "sameAs": "https://CRAN.R-project.org/package=TreeTools" }, { "@type": "SoftwareApplication", @@ -202,7 +202,7 @@ } ], "releaseNotes": "https://github.com/ms609/Rogue/blob/master/NEWS.md", - "fileSize": "2213.275KB", + "fileSize": "2213.035KB", "contIntegration": "https://codecov.io/gh/ms609/Rogue?branch=main", "developmentStatus": "http://www.repostatus.org/#inactive", "citation": [ diff --git a/cran-comments.md b/cran-comments.md index 4acaa0a..5ae075e 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,7 +1,7 @@ ## Test environments * Local PC: - - Windows 10, R 4.1.0-patched + - Windows 10, R 4.1.1 * [GitHub Actions](https://github.com/ms609/Rogue/actions) - Ubuntu 20.04 @@ -16,9 +16,15 @@ ## R CMD check results There were no ERRORs or WARNINGs. -There was one NOTE: +There were two NOTEs: > Possibly mis-spelled words in DESCRIPTION: > RogueNaRok (14:27) -These spellings have been verified. +These spellings are correct. + +> The Description field should not start with the package name, + 'This package' or similar. + +False positive: the word 'Rogue' is used here as an adjective, but happens to +match the name of the package. diff --git a/inst/WORDLIST b/inst/WORDLIST index d5842a3..40cf971 100644 --- a/inst/WORDLIST +++ b/inst/WORDLIST @@ -10,9 +10,12 @@ dropset durham googlemail Krompass +ORCID +Paradis Pattengale's RBIC RogueNaRok +SCIC splitwise Stamatakis sys