v1.2.0 (#35)

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="[email protected]", 
                   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),

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.

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

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).

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"
 }

cran-comments.md

@@ -24,13 +24,14 @@ 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
 'TreeDistData' is not installed.
 
 
 ## 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.

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",

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)

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)