PairwiseQuartets()

.github/workflows/R-CMD-check.yml

@@ -80,6 +80,13 @@ jobs:
         run: |
           brew install xquartz ghostscript
 
+      - name: Cache R packages
+        uses: actions/cache@v4
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+
       - name: Install dependencies
         if: runner.os != 'Linux'
         run: |
@@ -102,12 +109,16 @@ jobs:
         uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: |
+            waldo@0.5.3
+            testthat@3.2.1
+            vdiffr@1.0.7
+            cpp11@0.5.0
+            httr2@1.0.1
             downlit@0.4.3
             pkgdown@2.0.9
             profvis@0.3.8
             gtable@0.3.5
             evaluate@0.23
-            httr2@1.0.1
             knitr@1.45
             phangorn@2.7.1
             rjson@0.2.20

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: Quartet
-Version: 1.2.7
+Version: 1.3.0
 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
@@ -46,6 +46,7 @@ Suggests:
   Rcpp,
   rmarkdown,
   testthat,
+  TreeDist,
   usethis,
   vdiffr,
 Config/Needs/check:

NAMESPACE

@@ -36,6 +36,7 @@ export(PairSharedQuartetStatus)
 export(PairSharedSplitStatus)
 export(PairsQuartetDistance)
 export(PairsTripletDistance)
+export(PairwiseQuartets)
 export(PlotQuartet)
 export(QuartetAgreement)
 export(QuartetDistance)

NEWS.md

@@ -1,3 +1,7 @@
+# Quartet v1.3.0 (2025-01-16)
+
+- `PairwiseQuartets()` compares quartet statuses between all pairs of trees.
+
 # Quartet v1.2.7 (2024-10-31)
 
 - `VizualizeQuartet()` now returns calculation results.

Quartet.Rproj

@@ -1,4 +1,5 @@
 Version: 1.0
+ProjectId: 69de0ca2-bd58-49e4-8173-98d3d2d703f4
 
 RestoreWorkspace: Yes
 SaveWorkspace: No

R/CompareQuartets.R

@@ -13,7 +13,7 @@
 #' 
 #' @template MRS
 #'
-#' @family quartet counting functions
+#' @family enumeration
 #' @seealso 
 #' States of quartets in given trees: [`QuartetStates()`]
 #' 
@@ -176,7 +176,7 @@ QuartetStates.multiPhylo <- QuartetStates.list
 #' @template MRS
 #'
 #' @family element-by-element comparisons
-#' @family quartet counting functions
+#' @family enumeration
 #' 
 #' @seealso
 #' - [`QuartetStatus()`] generates the same output from a list of trees.
@@ -256,7 +256,7 @@ CompareQuartets <- function (x, cf) {
 #' 
 #' @template MRS
 #' @family element-by-element comparisons
-#' @family quartet counting functions
+#' @family enumeration
 #' 
 #' @examples 
 #' library("TreeTools")

R/Metrics.R

@@ -120,6 +120,7 @@
 #' \insertAllCited{}
 #' 
 #' @template MRS
+#' @family tree comparison
 #' 
 #' @encoding UTF-8
 #' @name SimilarityMetrics

R/PairwiseQuartets.R

@@ -0,0 +1,40 @@
+#' Pairwise quartet distances
+#' 
+#' Computes the quartet distance between each pair of trees in a list.
+#' 
+#' @inheritParams QuartetStatus
+#' @param Measure a function that calculates tree similarity or difference
+#' from quartet statuses. Default is [`QuartetDivergence()`].
+#' @return a matrix specifying the distance between each tree and
+#' each other tree in the `trees`.
+#' 
+#' @template MRS
+#' 
+#' @examples
+#' data("sq_trees")
+#' # Calculate the status of each quartet relative to the first entry in 
+#' # sq_trees
+#' sq_status <- QuartetStatus(sq_trees)
+#' 
+#' # Calculate Estabrook et al's similarity measures:
+#' SimilarityMetrics(sq_status)
+#' 
+#' # Compare trees that include a subset of the taxa 1..10
+#' library("TreeTools", quietly = TRUE, warn.conflict = FALSE)
+#' QuartetStatus(BalancedTree(1:5), BalancedTree(3:8), nTip = 10)
+#' 
+#' # If all taxa studied occur in `trees` or `cf`, set `nTip = TRUE`
+#' QuartetStatus(BalancedTree(1:5), BalancedTree(3:10), nTip = TRUE)
+#'  
+#' @family element-by-element comparisons
+#' @seealso 
+#' - Use splits (groups/clades defined by nodes or edges of the tree) instead
+#'   of quartets as the unit of comparison: [`SplitStatus()`].
+#'  
+#' - Generate distance metrics from quartet statuses: [`SimilarityMetrics()`].
+#' 
+#' @references \insertAllCited{}
+#' @export
+PairwiseQuartets <- function(trees, Measure = QuartetDivergence) {
+  Measure(ManyToManyQuartetAgreement(trees))
+}

R/QuartetDistance.R

@@ -32,6 +32,7 @@ WHICH_OTHER_NODE <- 2:4
 #' PlotQuartet(sq_trees, c(2, 5, 3, 8), overwritePar = FALSE)
 #' par(oPar)
 #' 
+#' @family visualization
 #' @importFrom graphics par plot legend
 #' @importFrom TreeTools NTip RenumberTips
 #' @export

R/ResolvedQuartets.R

@@ -18,7 +18,7 @@
 #'         
 #' @template MRS
 #' 
-#' @family quartet counting functions
+#' @family enumeration
 #' 
 #' @examples
 #' data(sq_trees)

R/TernaryPoints.R

@@ -42,6 +42,7 @@
 #' 
 #' @references \insertAllCited{}
 #' 
+#' @family visualization
 #' @template MRS
 #' 
 #' @export
@@ -98,6 +99,7 @@ SymmetricDifferenceLineEnds <- function (nsd) {
 #' @describeIn SymmetricDifferenceLineEnds Plot the lines onto the active ternary plot.
 #' @param \dots Further parameters to pass to 
 #' \code{\link[Ternary:AddToTernary]{TernaryLines}()}.
+#' @family visualization
 #' @importFrom Ternary TernaryLines
 #' @export
 SymmetricDifferenceLines <- function (nsd, ...) { #nocov start

R/VisualizeQuartets.R

@@ -67,6 +67,7 @@
 #' # restore original graphical parameters
 #' par(origPar)
 #' @template MRS
+#' @family visualization
 #' @importFrom ape plot.phylo
 #' @importFrom PlotTools SpectrumLegend
 #' @importFrom viridisLite viridis

R/tqDist.r

@@ -60,7 +60,8 @@
 #' - Use splits (groups/clades defined by nodes or edges of the tree) instead
 #'   of quartets as the unit of comparison: [`SplitStatus()`].
 #'  
-#' - Generate distance metrics from quartet statuses: [`SimilarityMetrics()`].
+#' - Generate distance metrics from quartet statuses: [`SimilarityMetrics()`],
+#' `[PairwiseQuartets()]`.
 #' 
 #' @references \insertAllCited{}
 #'
@@ -140,6 +141,7 @@ QuartetStatus <- function (trees, cf = trees[[1]], nTip = NULL) {
 #' @importFrom ape write.tree
 #' @template MRS
 #' @useDynLib Quartet, .registration = TRUE
+#' @family TQDist functions
 #' @export
 TQDist <- function (trees) {
   .CheckSize(trees)
@@ -249,8 +251,8 @@ ManyToManyQuartetAgreement <- function (trees, nTip = NULL) {
   }
 }
 
-#' @describeIn QuartetStatus Agreement of each quartet in trees in one list with
-#' each quartet in trees in a second list.
+#' @describeIn QuartetStatus Agreement of each quartet in trees in `trees1` with
+#' each quartet in trees in `trees2`.
 #' @param trees1,trees2 List or `multiPhylo` objects containing
 #'   trees of class `phylo`.
 #' @return `TwoListQuartetAgreement()` returns a three-dimensional array listing,
@@ -367,6 +369,7 @@ TQFile <- function (treeList) {
 #' @references \insertAllCited{}
 #' 
 #' @concept Tree distances
+#' @family TQDist functions
 #' @name Distances
 NULL
 

inst/_pkgdown.yml

@@ -1,3 +1,46 @@
+url: https://ms609.github.io/Quartet
+
+authors:
+  Martin R. Smith:
+    href: https://smithlabdurham.github.io/
+
+development:
+  mode: auto
+
+reference:
+  - title: "Enumeration"
+    desc: >
+      Count quartets within trees
+    contents:
+      - has_concept("enumeration")
+
+  - title: "Comparison"
+    desc: >
+      Compare trees and quartet states
+    contents:
+      - has_concept("element-by-element comparisons")
+      - has_concept("tree comparison")
+
+  - title: "Visualization"
+    desc: >
+      Plot and display quartet statuses and differences
+    contents:
+      - has_concept("visualization")
+
+  - title: "Datasets"
+    desc: >
+      Example datasets for use with Quartet
+    contents:
+      - sq_trees
+      - has_concept("datasets")
+
+  - title: "TQDist wrappers"
+    desc: >
+      Direct access to TQDist functions
+    contents:
+      - has_concept("TQDist functions")
+
+
 template:
   bootstrap: 5
   bslib: