v2.0.0 (#16)

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 = "[email protected]", 
                     role = c("aut", "cre", "cph"), 
@@ -9,15 +9,18 @@ Authors@R: c(person("Martin R.", 'Smith',
                     email = "[email protected]")
             )
 License: GPL (>= 3)
-Description: Interface to 'RogueNaRok' (Aberer et al. 2013) 
-  <doi:10.1093/sysbio/sys078>.
-  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) <doi:10.1093/sysbio/sys078>.
+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

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.
-

codemeta.json

@@ -5,7 +5,7 @@
   ],
   "@type": "SoftwareSourceCode",
   "identifier": "Rogue",
-  "description": "Interface to 'RogueNaRok' (Aberer et al. 2013) \n  <doi:10.1093/sysbio/sys078>.\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) <doi:10.1093/sysbio/sys078>.",
   "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": [

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.

inst/WORDLIST

@@ -10,9 +10,12 @@ dropset
 durham
 googlemail
 Krompass
+ORCID
+Paradis
 Pattengale's
 RBIC
 RogueNaRok
+SCIC
 splitwise
 Stamatakis
 sys