From b06a48a5c4d61eddf2427725b6c61568f7a580e0 Mon Sep 17 00:00:00 2001 From: "Martin R. Smith" Date: Fri, 28 Aug 2020 15:41:52 +0100 Subject: [PATCH] v1.2.0 (#35) --- DESCRIPTION | 4 ++-- NEWS.md | 20 +++++++++----------- R/TreeDist-package.R | 4 ++-- README.md | 2 +- codemeta.json | 7 ++++--- cran-comments.md | 7 ++++--- inst/CITATION | 4 ++-- man/TreeDist-package.Rd | 4 ++-- vignettes/information.Rmd | 2 +- vignettes/using-distances.Rmd | 2 +- 10 files changed, 28 insertions(+), 28 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 344159bad..bcb4f1853 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: TreeDist Type: Package Title: Distances Between Phylogenetic Trees -Version: 1.1.1.9001 +Version: 1.2.0 Authors@R: c(person("Martin R.", 'Smith', email="martin.smith@durham.ac.uk", role=c("aut", "cre", "cph", "prg"), @@ -30,7 +30,7 @@ Description: Implements measures of tree similarity, including Calculates the median of a set of trees under any distance metric. Copyright: Incorporates Jonker-Volgenant Linear Assignment Problem implementation by Roy Jonker, modified by Yong Yang after Yi Cao. -URL: https://ms609.github.io/TreeDist, https://github.com/ms609/TreeDist +URL: https://ms609.github.io/TreeDist/, https://github.com/ms609/TreeDist BugReports: https://github.com/ms609/TreeDist/issues Depends: R (>= 3.4.0), diff --git a/NEWS.md b/NEWS.md index 697acd14d..4f7b2ee0d 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,20 +1,18 @@ -# TreeDist 1.1.1.9001 (development) - -- Improve floating-point arithmetic in `TreeDistance()` functions. - -- Reduce precision of LAPJV so rounding errors do not result in interminable run - times. - -- Fix rounding error in NNI 'Li' upper estimate, and improve NNI performance. - -# TreeDist 1.1.1.9000 +# TreeDist 1.2.0 - `TreeDistance()` and related functions now return a `dist` object when computing all distances between all pairs of trees in a list. +- Improve floating-point arithmetic in `TreeDistance()` functions. + - `TreeDistance()` now returns a distance (as documented), rather than a similarity. +- Fix rounding error in NNI 'Li' upper estimate, and improve NNI performance. + +- Reduce precision of LAPJV so rounding errors do not result in interminable run + times. + # TreeDist 1.1.1 @@ -41,4 +39,4 @@ # TreeDist 1.0.0 - Initial release, building on some draft functions included in - '[TreeSearch](https://ms609.github.io/TreeSearch)' 0.3.2.9005. + '[TreeSearch](https://ms609.github.io/TreeSearch/)' 0.3.2.9005. diff --git a/R/TreeDist-package.R b/R/TreeDist-package.R index 148b9f316..00f294910 100644 --- a/R/TreeDist-package.R +++ b/R/TreeDist-package.R @@ -81,9 +81,9 @@ #' - `dist.topo()`: Path (topological) distance, Robinson-Foulds distance. #' * [phangorn](https://cran.r-project.org/package=phangorn) #' - `treedist()`: Path, Robinson-Foulds and approximate SPR distances. -#' * [Quartet](http://ms609.github.io/Quartet/): Triplet and Quartet distances, +#' * [Quartet](https://ms609.github.io/Quartet/): Triplet and Quartet distances, #' using the tqDist algorithm. -#' * [TBRDist](http://ms609.github.io/TBRDist/): TBR and SPR distances on +#' * [TBRDist](https://ms609.github.io/TBRDist/): TBR and SPR distances on #' unrooted trees, using the 'uspr; C library. #' * [distory](https://cran.r-project.org/package=distory) (unmaintained): #' Geodesic distance diff --git a/README.md b/README.md index aeee4d68f..6e2c27122 100644 --- a/README.md +++ b/README.md @@ -139,7 +139,7 @@ _Bioinformatics_, 22, 117–119. - Smith, M.R. (2020) [Information theoretic Generalized Robinson-Foulds metrics for comparing phylogenetic trees](https://dx.doi.org/10.1093/bioinformatics/btaa614). -_Bioinformatics_, in production. +_Bioinformatics_, online ahead of print. Please note that the 'TreeDist' project is released with a [Contributor Code of Conduct](CODE_OF_CONDUCT.md). diff --git a/codemeta.json b/codemeta.json index f7e7b434b..f740b605d 100644 --- a/codemeta.json +++ b/codemeta.json @@ -10,7 +10,7 @@ "codeRepository": "https://github.com/ms609/TreeDist", "issueTracker": "https://github.com/ms609/TreeDist/issues", "license": "https://spdx.org/licenses/GPL-3.0", - "version": "1.1.1.9001", + "version": "1.2.0", "programmingLanguage": { "@type": "ComputerLanguage", "name": "R", @@ -374,7 +374,8 @@ ], "relatedLink": [ "https://ms609.github.io/TreeDist", - "https://CRAN.R-project.org/package=TreeDist" + "https://CRAN.R-project.org/package=TreeDist", + "https://ms609.github.io/TreeDist/" ], "keywords": ["phylogenetics", "tree-distance", "r", "r-package", "rstats", "phylogenetic-trees", "tree-distances", "trees"], "provider": { @@ -383,5 +384,5 @@ "name": "Comprehensive R Archive Network (CRAN)", "url": "https://cran.r-project.org" }, - "fileSize": "8315.989KB" + "fileSize": "8346.202KB" } diff --git a/cran-comments.md b/cran-comments.md index f36dbabad..a45a8e166 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -24,8 +24,7 @@ There were two NOTEs: [...] > Package suggested but not available for checking: 'TreeDistData' -'TreeDistData' depends on 'TreeDist' v1.1.0, so cannot yet be submitted to CRAN --- but is ready to submit once 'TreeDist' is available. +'TreeDistData' is too large to be submitted on CRAN. All calls to `data(package='TreeDistData')` are wrapped within `if(require('TreeDistData')` to ensure that vignettes fail gracefully when @@ -33,4 +32,6 @@ All calls to `data(package='TreeDistData')` are wrapped within ## Downstream dependencies -There are currently no downstream dependencies for this package. +There is one downstream dependency, 'TBRDist' (which I maintain). + +No changes to worse were identified by a local R CMD CHECK. diff --git a/inst/CITATION b/inst/CITATION index fd3a75022..d7050caf6 100644 --- a/inst/CITATION +++ b/inst/CITATION @@ -4,7 +4,7 @@ citHeader(paste0("When using the package, please acknowledge your use of ", "TreeDist in the article text, and cite the papers ", "describing the metrics that you employ. For example, 'Mutual Phylogenetic ", "Information similarity metrics (Smith 2020a) were calculated using the R package", -" TreeDist v", vers, " (Smith 2020n).")) +" TreeDist v", vers, " (Smith 2020b).")) citEntry(entry = "article", @@ -21,7 +21,7 @@ for comparing phylogenetic trees", " Information theoretic Generalized Robinson-Foulds metrics for comparing phylogenetic trees. ", " Bioinformatics.", - " In production.", + " Online ahead of print.", " doi: 10.1093/bioinformatics/btaa614")) citEntry(entry = "manual", diff --git a/man/TreeDist-package.Rd b/man/TreeDist-package.Rd index c769c6f54..6b6ed2379 100644 --- a/man/TreeDist-package.Rd +++ b/man/TreeDist-package.Rd @@ -101,9 +101,9 @@ Other R packages implementing tree distance functions include: \itemize{ \item \code{treedist()}: Path, Robinson-Foulds and approximate SPR distances. } -\item \href{http://ms609.github.io/Quartet/}{Quartet}: Triplet and Quartet distances, +\item \href{https://ms609.github.io/Quartet/}{Quartet}: Triplet and Quartet distances, using the tqDist algorithm. -\item \href{http://ms609.github.io/TBRDist/}{TBRDist}: TBR and SPR distances on +\item \href{https://ms609.github.io/TBRDist/}{TBRDist}: TBR and SPR distances on unrooted trees, using the 'uspr; C library. \item \href{https://cran.r-project.org/package=distory}{distory} (unmaintained): Geodesic distance diff --git a/vignettes/information.Rmd b/vignettes/information.Rmd index 49b4cc24d..ed9344ccf 100644 --- a/vignettes/information.Rmd +++ b/vignettes/information.Rmd @@ -52,7 +52,7 @@ The information unique to $S_1$ and $S_2$ is $h_{different}(S_1,S_2) = 2h(S_1,S_2) - h(S_1) - h(S_2) \approx 3.91\textrm{ bits}$. These quantities can be calculated using functions in the -'[TreeTools](https://ms609.github.io/TreeTools)' package. +'[TreeTools](https://ms609.github.io/TreeTools/)' package. ```{r} library('TreeTools', quietly = TRUE, warn.conflicts = FALSE) diff --git a/vignettes/using-distances.Rmd b/vignettes/using-distances.Rmd index 12c22707c..a2d3c5571 100644 --- a/vignettes/using-distances.Rmd +++ b/vignettes/using-distances.Rmd @@ -393,7 +393,7 @@ quality, as depicted in the accompanying histogram. You may wish to: -- Explore the [Ternary package](http://ms609.github.io/Ternary/) +- Explore the [Ternary package](https://ms609.github.io/Ternary/) - [Interpret tree distance metrics](https://ms609.github.io/TreeDistData/articles/09-expected-similarity.html)