v1.2.0 (#55)

.Rbuildignore

@@ -22,4 +22,4 @@ revdep
 ^CODE_OF_CONDUCT\.md$
 ^CONTRIBUTING\.md$
 ^codemeta\.json$
-CRAN-RELEASE
+^CRAN-RELEASE$

.zenodo.json

@@ -2,7 +2,7 @@
     "description": "An R package that calculates distances between phylogenetic topologies, integrating the tqDist algorithm for quartet distances", 
     "license": "gpl-3.0", 
     "title": "Quartet: Comparison of Phylogenetic Trees Using Quartet and Bipartition Measures", 
-    "version": "v1.1.0", 
+    "version": "v1.2.0", 
     "upload_type": "software", 
     "creators": [
         {

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: Quartet
-Version: 1.1.0.9007
+Version: 1.2.0
 Title: Comparison of Phylogenetic Trees Using Quartet and Split Measures
 Description: Calculates the number of four-taxon subtrees consistent with a pair
   of cladograms, calculating the symmetric quartet distance of Bandelt & Dress (1986),
@@ -34,7 +34,7 @@ Imports:
   ape,
   Rdpack,
   Ternary (>= 1.0),
-  TreeTools (>= 1.3.1.9000),
+  TreeTools (>= 1.4.0),
   viridisLite
 Suggests:
   bookdown,
@@ -45,8 +45,6 @@ Suggests:
   testthat,
   usethis,
   vdiffr
-Remotes:
-  ms609/TreeTools
 SystemRequirements: C++11
 RdMacros: Rdpack
 LinkingTo: Rcpp

NEWS.md

@@ -1,42 +1,30 @@
-# Quartet v1.1.0.9007 (development) 
+# Quartet v1.2.0
 
+## New features
+ - `CompareQuartetsMulti()` compares quartet status in one tree with status in
+   multiple others.
+ - `VisualizeQuartets()` depicts contribution of splits to quartet score.
+ - `SimilarityToReference()` allows comparison against specified reference
+   topology.
+
+## Changes
+ - Deprecate `RobinsonFoulds()`: renamed to `RawSymmetricDifference()`.
  - `QuartetState[s]()` now uses sister-of-4 notation, rather than sister-of-1,
    to give values within [0, 3].
- - Small improvements to `PlotQuartet()`.
- - Deprecate `RobinsonFoulds()`: renamed to `RawSymmetricDifference()`.
- - New function `VisualizeQuartets()` shows contribution of splits to quartet
-   score.
-
-# Quartet v1.1.0.9006 (development) 
-
  - `ManyToManyQuartetAgreement()` now returns entries for `N` and `Q`. 
-
-# Quartet v1.1.0.9005 (development) 
-
- - Support for non-identical leaf samples in `QuartetStatus()`.
-
-# Quartet v1.1.0.9004 (development) 
-
- - Remove errant name when comparing unnamed tree pairs.
- - New function `SimilarityToReference()` to compare against reference topology.
-
-# Quartet v1.1.0.9003 (development) 
 
- - C++ implementation of `AllQuartets()` and `QuartetStates()`.
-
-# Quartet v1.1.0.9002 (development) 
-
+## Improvements
+ - Faster C++ implementation of `AllQuartets()` and `QuartetStates()`.
+ -  `QuartetStatus()` now supports non-identical leaf samples.
+ - `SimilarityMetrics()` now handles single tree comparisons.
  - Correctly calculate resolution of unrooted trees with unconventional node
    numbering conventions.
+ - Remove errant name when comparing unnamed tree pairs.
+ - Small improvements to `PlotQuartet()`.
  - Minor efficiency improvements.
-
-# Quartet v1.1.0.9001 (development)
-
- - New function `CompareQuartetsMulti()` compares quartet status in one tree
- with status in multiple others.
- - `SimilarityMetrics()` now handles single tree comparisons.
  - Documentation improvements.
 
+
 # Quartet v1.1.0
 
  - Pass trees directly to C, without writing to temporary intermediate file.

R/Metrics.R

@@ -49,7 +49,7 @@
 #' most relationships but are poorly resolved.
 #' As such, it is essential to contextualize the symmetric difference by
 #' appropriate normalization (Smith 2019).
-#' Mutliple approaches to normalization have been proposed:
+#' Multiple approaches to normalization have been proposed:
 #'
 #' The total number of resolved quartets or partitions present in both trees
 #' (Day 1986):
@@ -72,12 +72,12 @@
 #' quartet's resolution in the reconstructed tree is 'correct', given by
 #' (Asher & Smith forthcoming):
 #' 
-#' * SimilarityToReference (STR): (_s_ + (_r1_ + _r2_ + _u_) / 3) / _Q_
+#' * Similarity to Reference (S2R): (_s_ + (_r1_ + _r2_ + _u_) / 3) / _Q_
 #' 
 #' This may optionally be normalized with reference to the maximum possible
 #' similarity, (_s_ + _d_ + _r2_ + (_r1_ + _u_) / 3) / _Q_, subtracting 
-#' 1/3 (the probability of matching at random) from both the STR score and 
-#' maxmium possible score before dividing; then, a tree scores zero if it
+#' 1/3 (the probability of matching at random) from both the S2R score and 
+#' maximum possible score before dividing; then, a tree scores zero if it
 #' is as different from the true tree as a random or fully unresolved tree,
 #' and one if it is as 'true' as can be known.
 #'

R/Quartet-package.R

@@ -57,7 +57,7 @@
 #'   for comparing phylogenetic trees. Bioinformatics, in production.
 #'   https://dx.doi.org/10.1093/bioinformatics/btaa614/5866976
 #' 
-#' - Smith, M.R. 2021. The importance of methodology when analyzing landscapes of
+#' - Smith, M.R. 2021. The importance of methodology when analysing landscapes of
 #'   phylogenetic trees. Forthcoming.
 #' 
 #' - Steel, M. and Penny, D. 1993. Distributions of tree comparison metrics:

R/VisualizeQuartets.R

@@ -4,14 +4,14 @@
 #' @param setPar Logical specifying whether graphical parameters should be set
 #'  to display trees side by side.
 #' @param style Character string specifying split labels with an unambiguous 
-#' abbrevation of:
+#' abbreviation of:
 #'  - `label`: Label stating proportion of resolved quartets in agreement,
 #'  coloured accordingly;
 #'  - `pie`: Pie chart showing proportion of quartets in agreement, sized
 #'     according to number of quartets influenced by each split;
-#'  - `bar`: Bar showing propotion of quartets in agreement, labelled;
+#'  - `bar`: Bar showing proportion of quartets in agreement, labelled;
 #'  - `size`: Circle coloured according to proportion of quartets in agreement,
-#'  with area corrsponding to number of quartet statements associated with
+#'  with area corresponding to number of quartet statements associated with
 #'  split.
 #' @param precision Integer specifying number of significant figures to display
 #' when reporting matching scores.

R/zzz.R

@@ -11,7 +11,6 @@ release_questions <- function() {
 #
 # codemetar::write_codemeta()
 # check_win_devel(); rhub::check_for_cran()
-# list_my_checks() # list_package_checks
 # revdepcheck::revdep_check()
 # build_vignettes()
 # tools::resaveRdaFiles('data', compress='auto') - is default of bzip2 the optimal?

README.md

@@ -78,13 +78,13 @@ useful to you.
   for comparing phylogenetic trees. Bioinformatics, in production.
   https://dx.doi.org/10.1093/bioinformatics/btaa614/5866976
 
-- Smith, M.R. 2021. The importance of methodology when analyzing landscapes of
+- Smith, M.R. 2021. The importance of methodology when analysing landscapes of
   phylogenetic trees. Forthcoming.
 
 - Steel, M. and Penny, D. 1993. Distributions of tree comparison metrics:
   some new results. Syst. Biol. 42: 126-141.
   https://doi.org/10.1093/sysbio/42.2.126
 
 Please note that the 'Quartet' project is released with a
-[Contributor Code of Conduct](CODE_OF_CONDUCT.md).
+[Contributor Code of Conduct](https://ms609.github.io/Quartet/CODE_OF_CONDUCT.html).
 By contributing to this project, you agree to abide by its terms.

codemeta.json

@@ -10,7 +10,7 @@
   "codeRepository": "https://github.com/ms609/Quartet/",
   "issueTracker": "https://github.com/ms609/Quartet/issues/",
   "license": "https://spdx.org/licenses/GPL-2.0",
-  "version": "1.1.0.9007",
+  "version": "1.2.0",
   "programmingLanguage": {
     "@type": "ComputerLanguage",
     "name": "R",
@@ -198,14 +198,14 @@
       "@type": "SoftwareApplication",
       "identifier": "TreeTools",
       "name": "TreeTools",
-      "version": ">= 1.3.1.9000",
+      "version": ">= 1.4.0",
       "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",
@@ -339,5 +339,5 @@
     "https://ms609.github.io/Quartet",
     "https://ms609.github.io/Quartet/"
   ],
-  "fileSize": "1231.012KB"
+  "fileSize": "1343.465KB"
 }

cran-comments.md

@@ -1,6 +1,6 @@
 ## Test environments
-* local Windows 10 install, R 3.6.1
-* Ubuntu 16.04.6 LTS, R 3.4.2, release and devel, via [Travis CI](https://travis-ci.org/ms609/Quartet)
+* local Windows 10 install, R 4.0.2
+* Ubuntu 16.04.6 LTS, R 3.4.0, release and devel, via [Travis CI](https://travis-ci.org/ms609/Quartet/)
 * Mac OS X 10.13.6, R release, via Travis
 * win-builder, with `check_win_devel()`
 * R-hub, with `check_rhub(platforms = rhub::platforms()[[1]])`
@@ -29,5 +29,5 @@ These URLs are generated from DOIs in citations, and are valid.
 
 ## Downstream dependencies
 
-The modifications do not impact the reverse dependency `CongreveLamsdell2016`
-(which I maintain).  
+The modifications do not impact the reverse dependencies `CongreveLamsdell2016`
+or `TreeDist` (which I maintain).  

inst/WORDLIST

@@ -12,6 +12,7 @@ Meacham
 ORCID
 R's
 Rtools
+S2R
 SJA
 SPR
 SSJA
@@ -21,16 +22,23 @@ SlowQuartet
 Steinhaus
 Stølting
 Syst
+TreeDist
+TreeDistData
+TreeTools
 Zool
 ac
 binom
+btaa
 btu
 codecov
 dQ
 doi
 durham
+dx
 etc
 frac
+io
+github
 memoization
 org
 partitionwise