diff --git a/.github/workflows/memcheck.yml b/.github/workflows/memcheck.yml index 672c411..afbca4b 100644 --- a/.github/workflows/memcheck.yml +++ b/.github/workflows/memcheck.yml @@ -90,9 +90,9 @@ jobs: - name: Install this package run: | cd .. - R CMD build --no-manual --no-resave-data Roguer + R CMD build --no-manual --no-resave-data Rogue R CMD INSTALL Rogue*.tar.gz - cd Roguer + cd Rogue - name: valgrind - memcheck ${{ matrix.config.test }} run: | diff --git a/DESCRIPTION b/DESCRIPTION index 1b852f1..865804a 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -18,10 +18,10 @@ Description: Interface to 'RogueNaRok' (Aberer et al. 2013) information from a consensus tree. The sum of branch support values in a consensus tree can often be increased by removing rogue taxa. URL: - https://github.com/ms609/Roguer/, + https://github.com/ms609/Rogue/, https://github.com/aberer/RogueNaRok/, https://github.com/ms609/RogueNaRok/ -BugReports: https://github.com/ms609/Roguer/issues/ +BugReports: https://github.com/ms609/Rogue/issues/ Depends: R (>= 3.5.0) Imports: ape (>= 5.0), diff --git a/README.md b/README.md index f71369e..e43e3fd 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@ # Rogue - [![Codecov test coverage](https://codecov.io/gh/ms609/Roguer/branch/main/graph/badge.svg)](https://codecov.io/gh/ms609/Roguer?branch=main) + [![Codecov test coverage](https://codecov.io/gh/ms609/Rogue/branch/main/graph/badge.svg)](https://codecov.io/gh/ms609/Rogue?branch=main) [![CRAN Status Badge](http://www.r-pkg.org/badges/version/Rogue)](https://cran.r-project.org/package=Rogue) [![CRAN Downloads](http://cranlogs.r-pkg.org/badges/Rogue)](https://cran.r-project.org/package=Rogue) [![DOI](https://zenodo.org/badge/376830950.svg)](https://zenodo.org/badge/latestdoi/376830950) diff --git a/_pkgdown.yml b/_pkgdown.yml index 930b2c2..364e9bb 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -1,4 +1,4 @@ -url: https://ms609.github.io/Roguer +url: https://ms609.github.io/Rogue authors: Martin R. Smith: diff --git a/codemeta.json b/codemeta.json index c67f33a..3b9e817 100644 --- a/codemeta.json +++ b/codemeta.json @@ -7,21 +7,21 @@ "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.", "name": "Rogue: Identify Rogue Taxa in Sets of Phylogenetic Trees", - "codeRepository": "https://github.com/ms609/Roguer/", + "codeRepository": "https://github.com/ms609/Rogue/", "relatedLink": [ "https://github.com/ms609/RogueNaRok/", "https://github.com/aberer/RogueNaRok/", "https://CRAN.R-project.org/package=Rogue" ], - "issueTracker": "https://github.com/ms609/Roguer/issues/", + "issueTracker": "https://github.com/ms609/Rogue/issues/", "license": "https://spdx.org/licenses/GPL-3.0", - "version": "1.0.0.9000", + "version": "1.0.0.9005", "programmingLanguage": { "@type": "ComputerLanguage", "name": "R", "url": "https://r-project.org" }, - "runtimePlatform": "R version 4.1.0 Patched (2021-06-21 r80544)", + "runtimePlatform": "R version 4.1.1 (2021-08-10)", "author": [ { "@type": "Person", @@ -75,19 +75,6 @@ "url": "https://cran.r-project.org" }, "sameAs": "https://CRAN.R-project.org/package=testthat" - }, - { - "@type": "SoftwareApplication", - "identifier": "TreeTools", - "name": "TreeTools", - "version": ">= 1.4.5", - "provider": { - "@id": "https://cran.r-project.org", - "@type": "Organization", - "name": "Comprehensive R Archive Network (CRAN)", - "url": "https://cran.r-project.org" - }, - "sameAs": "https://CRAN.R-project.org/package=TreeTools" } ], "softwareRequirements": [ @@ -109,11 +96,114 @@ "url": "https://cran.r-project.org" }, "sameAs": "https://CRAN.R-project.org/package=ape" + }, + { + "@type": "SoftwareApplication", + "identifier": "cli", + "name": "cli", + "version": ">= 3.0", + "provider": { + "@id": "https://cran.r-project.org", + "@type": "Organization", + "name": "Comprehensive R Archive Network (CRAN)", + "url": "https://cran.r-project.org" + }, + "sameAs": "https://CRAN.R-project.org/package=cli" + }, + { + "@type": "SoftwareApplication", + "identifier": "fastmatch", + "name": "fastmatch", + "provider": { + "@id": "https://cran.r-project.org", + "@type": "Organization", + "name": "Comprehensive R Archive Network (CRAN)", + "url": "https://cran.r-project.org" + }, + "sameAs": "https://CRAN.R-project.org/package=fastmatch" + }, + { + "@type": "SoftwareApplication", + "identifier": "grDevices", + "name": "grDevices" + }, + { + "@type": "SoftwareApplication", + "identifier": "matrixStats", + "name": "matrixStats", + "provider": { + "@id": "https://cran.r-project.org", + "@type": "Organization", + "name": "Comprehensive R Archive Network (CRAN)", + "url": "https://cran.r-project.org" + }, + "sameAs": "https://CRAN.R-project.org/package=matrixStats" + }, + { + "@type": "SoftwareApplication", + "identifier": "Rdpack", + "name": "Rdpack", + "version": ">= 0.7", + "provider": { + "@id": "https://cran.r-project.org", + "@type": "Organization", + "name": "Comprehensive R Archive Network (CRAN)", + "url": "https://cran.r-project.org" + }, + "sameAs": "https://CRAN.R-project.org/package=Rdpack" + }, + { + "@type": "SoftwareApplication", + "identifier": "Rfast", + "name": "Rfast", + "provider": { + "@id": "https://cran.r-project.org", + "@type": "Organization", + "name": "Comprehensive R Archive Network (CRAN)", + "url": "https://cran.r-project.org" + }, + "sameAs": "https://CRAN.R-project.org/package=Rfast" + }, + { + "@type": "SoftwareApplication", + "identifier": "stats", + "name": "stats" + }, + { + "@type": "SoftwareApplication", + "identifier": "TreeDist", + "name": "TreeDist", + "version": ">= 2.1.1", + "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/TreeDist" + }, + { + "@type": "SoftwareApplication", + "identifier": "TreeTools", + "name": "TreeTools", + "version": ">= 1.4.5.9007", + "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" + }, + { + "@type": "SoftwareApplication", + "identifier": "utils", + "name": "utils" } ], - "releaseNotes": "https://github.com/ms609/Roguer/blob/master/NEWS.md", - "fileSize": "2168.819KB", - "contIntegration": "https://codecov.io/gh/ms609/Roguer?branch=main", + "releaseNotes": "https://github.com/ms609/Rogue/blob/master/NEWS.md", + "fileSize": "2213.275KB", + "contIntegration": "https://codecov.io/gh/ms609/Rogue?branch=main", "developmentStatus": "http://www.repostatus.org/#inactive", "citation": [ { @@ -176,7 +266,7 @@ } } ], - "readme": "https://github.com/ms609/Roguer/blob/main/README.md", + "readme": "https://github.com/ms609/Rogue/blob/main/README.md", "keywords": [ "phylogenetics", "consensus-tree", diff --git a/cran-comments.md b/cran-comments.md index e8bd696..4acaa0a 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -3,7 +3,7 @@ * Local PC: - Windows 10, R 4.1.0-patched -* [GitHub Actions](https://github.com/ms609/Roguer/actions) +* [GitHub Actions](https://github.com/ms609/Rogue/actions) - Ubuntu 20.04 - R 3.6.3 - R release (tests, examples & vignettes run with valgrind) diff --git a/man/Rogue-package.Rd b/man/Rogue-package.Rd index ff0e858..cdf7dd4 100644 --- a/man/Rogue-package.Rd +++ b/man/Rogue-package.Rd @@ -42,10 +42,10 @@ or \insertCite{SmithCons;textual}{Rogue} (SPIC, SCIC), as appropriate. \seealso{ Useful links: \itemize{ - \item \url{https://github.com/ms609/Roguer/} + \item \url{https://github.com/ms609/Rogue/} \item \url{https://github.com/aberer/RogueNaRok/} \item \url{https://github.com/ms609/RogueNaRok/} - \item Report bugs at \url{https://github.com/ms609/Roguer/issues/} + \item Report bugs at \url{https://github.com/ms609/Rogue/issues/} } }