Character concordance implementation

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: TreeSearch
 Title: Phylogenetic Analysis with Discrete Character Data
-Version: 1.7.0
+Version: 1.8.0
 Authors@R: c(
     person(
       "Martin R.", 'Smith',
@@ -33,10 +33,13 @@ URL: https://ms609.github.io/TreeSearch/ (doc),
   https://github.com/ms609/TreeSearch/ (devel)
 BugReports: https://github.com/ms609/TreeSearch/issues/
 Depends: R (>= 4.0)
-Imports: 
+Imports:
+  abind,
   ape (>= 5.6),
+  base64enc,
   cli (>= 3.0),
   cluster,
+  colorspace,
   fastmap,
   fastmatch (>= 1.1.3),
   fs,

NAMESPACE

@@ -27,6 +27,7 @@ export(Carter1)
 export(CharacterLength)
 export(ClusterStrings)
 export(ClusteringConcordance)
+export(ConcordanceTable)
 export(ConcordantInfo)
 export(ConcordantInformation)
 export(Consistency)
@@ -68,6 +69,9 @@ export(PolEscapa)
 export(PrepareDataIW)
 export(PrepareDataProfile)
 export(PresCont)
+export(QACol)
+export(QALegend)
+export(QCol)
 export(QuartetConcordance)
 export(QuartetResolution)
 export(RandomMorphyTree)
@@ -140,9 +144,11 @@ importFrom(TreeDist,ClusteringInfoDistance)
 importFrom(TreeDist,Entropy)
 importFrom(TreeDist,MutualClusteringInfo)
 importFrom(TreeDist,SharedPhylogeneticInfo)
+importFrom(TreeDist,entropy_int)
 importFrom(TreeTools,AddTipEverywhere)
 importFrom(TreeTools,AddUnconstrained)
 importFrom(TreeTools,CharacterInformation)
+importFrom(TreeTools,CladeSizes)
 importFrom(TreeTools,CladisticInfo)
 importFrom(TreeTools,CompatibleSplits)
 importFrom(TreeTools,Consensus)
@@ -159,6 +165,7 @@ importFrom(TreeTools,Log2Unrooted)
 importFrom(TreeTools,Log2UnrootedMult)
 importFrom(TreeTools,LogDoubleFactorial)
 importFrom(TreeTools,MakeTreeBinary)
+importFrom(TreeTools,MatchStrings)
 importFrom(TreeTools,MatrixToPhyDat)
 importFrom(TreeTools,NRooted)
 importFrom(TreeTools,NSplits)
@@ -189,13 +196,15 @@ importFrom(TreeTools,TipLabels)
 importFrom(TreeTools,TreeIsRooted)
 importFrom(TreeTools,as.Splits)
 importFrom(TreeTools,as.multiPhylo)
+importFrom(abind,abind)
 importFrom(ape,consensus)
 importFrom(ape,keep.tip)
 importFrom(ape,nodelabels)
 importFrom(ape,plot.phylo)
 importFrom(ape,read.nexus)
 importFrom(ape,root)
 importFrom(ape,write.nexus)
+importFrom(base64enc,base64encode)
 importFrom(cli,cli_alert)
 importFrom(cli,cli_alert_danger)
 importFrom(cli,cli_alert_info)
@@ -207,11 +216,17 @@ importFrom(cli,cli_progress_done)
 importFrom(cli,cli_progress_update)
 importFrom(cluster,pam)
 importFrom(cluster,silhouette)
+importFrom(colorspace,hex)
+importFrom(colorspace,max_chroma)
+importFrom(colorspace,polarLUV)
 importFrom(fastmap,fastmap)
 importFrom(fastmatch,"%fin%")
 importFrom(fastmatch,fmatch)
 importFrom(fs,path_sanitize)
 importFrom(future,future)
+importFrom(graphics,abline)
+importFrom(graphics,image)
+importFrom(graphics,mtext)
 importFrom(graphics,par)
 importFrom(promises,future_promise)
 importFrom(protoclust,protoclust)

NEWS.md

@@ -1,5 +1,8 @@
-# TreeSearch 1.7.0.9000 (development)
+# TreeSearch 1.8.0 (2025-01-15)
 
+- Implements the methods of Smith (forthcoming) via `ClusteringConcordance()`,
+  with visualization functions `ConcordanceTable()`, `QACol()` and `QALegend()`.
+- `QuartetConcordance()` gains `return` parameter and fast C++ implementation.
 - Fix regression in `MaximumLength()`.
 
 
@@ -14,6 +17,7 @@
 - Support single-character matrices in `ClusteringConcordance()`
 - Fix `DoNothing(x)` to return `x` (not `NULL`)
 - Remove unused `delete_rawdata()` due to implementation issues.
+- Port `MaximumLength()` to C++ to handle more characters, more efficiently.
 
 
 # TreeSearch 1.6.1 (2025-06-10)