Version: 2.13.0.9002

Author: ms609

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: TreeDist
 Title: Calculate and Map Distances Between Phylogenetic Trees
-Version: 2.13.0.9001
+Version: 2.13.0.9002
 Authors@R: c(person("Martin R.", "Smith",
                     email = "martin.smith@durham.ac.uk", 
                     role = c("aut", "cre", "cph", "prg"), 

NEWS.md

@@ -1,22 +1,21 @@
-<!-- AI-generated branch summary (2026-03-22) -->
-# Branch: `transfer-consensus` → merge target: `main`
-
-This branch exposes the LAPJV (Jonker–Volgenant) linear assignment solver
-via C++ headers so that downstream packages can link to it (`LinkingTo`),
-and implements a transfer consensus method (`TransferConsensus()`,
-`TransferDist()`).  It also tightens error handling by moving all
-`Rcpp::stop()` / `Rf_error()` calls out of C++ implementation code
-into R-level input validation.
-
-# TreeDist 2.13.0.9001
-
-This branch implements transfer consensus trees (`TransferConsensus()`) and
-a corresponding transfer distance metric (`TransferDist()`), providing a
-consensus method based on the transfer distance rather than the majority-rule
-or strict approaches.  Error handling in C++ code is tightened to validate
-inputs at the R level rather than using `Rcpp::stop()` or `Rf_error()` in
-implementation code.
-<!-- end AI-generated summary -->
+# TreeDist 2.13.0.9002
+
+## New features
+
+- `TransferConsensus()` constructs a consensus tree that minimizes the sum
+  of transfer distances to a set of input trees, using a greedy
+  add-and-prune heuristic.  Unlike majority-rule consensus, which can be
+  highly unresolved when phylogenetic signal is diffuse, the transfer
+  consensus uses the finer-grained transfer distance to produce more
+  resolved trees.
+
+- `TransferDist()` computes the transfer dissimilarity between phylogenetic
+  trees, with scaled and unscaled variants.  Supports all-pairs, cross-pairs,
+  and single-pair computations.
+
+- LAP (Jonker–Volgenant linear assignment) and MCI (Mutual Clustering
+  Information) C++ implementations are now exposed via `inst/include/TreeDist/`
+  headers, allowing downstream packages to use `LinkingTo: TreeDist`.
 
 ## Performance
 

codemeta.json

@@ -8,13 +8,13 @@
   "codeRepository": "https://github.com/ms609/TreeDist/",
   "issueTracker": "https://github.com/ms609/TreeDist/issues/",
   "license": "https://spdx.org/licenses/GPL-3.0",
-  "version": "2.13.0.9001",
+  "version": "2.13.0.9002",
   "programmingLanguage": {
     "@type": "ComputerLanguage",
     "name": "R",
     "url": "https://r-project.org"
   },
-  "runtimePlatform": "R version 4.5.3 (2026-03-11)",
+  "runtimePlatform": "R Under development (unstable) (2025-11-23 r89052 ucrt)",
   "provider": {
     "@id": "https://cran.r-project.org",
     "@type": "Organization",
@@ -505,7 +505,7 @@
     "SystemRequirements": "C++17, pandoc-citeproc"
   },
   "keywords": ["phylogenetics", "tree-distance"],
-  "fileSize": "1926.086KB",
+  "fileSize": "2121.415KB",
   "citation": [
     {
       "@type": "ScholarlyArticle",

src/reduce_tree.h

@@ -41,4 +41,4 @@ extern Rcpp::List reduce_trees(
     const CharacterVector original_label
   );
 
-#endif
+#endif