v1.4.0

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: TreeSearch
 Title: Phylogenetic Analysis with Discrete Character Data
-Version: 1.3.2.9002
+Version: 1.4.0
 Authors@R: c(
     person(
       "Martin R.", 'Smith',

NEWS.md

@@ -1,29 +1,37 @@
-# TreeSearch 1.3.2.9002 (development)
+# TreeSearch 1.4.0 (2023-08-18)
 
+## New features
 - `TaxonInfluence()` calculates influence of individual taxa on 
   phylogenetic inference
+
+## Search improvements
 - Default to use equal weighting during ratchet iterations
 - Support null constraints in `AdditionTree()`
+
+## App improvements
 - Exclude taxa from search in app
 - Allow search to continue when loading a new file with different taxon names
   into the app
+
+## Housekeeping
 - Update calls to `DescendantEdges()` for compatibility with 'TreeTools' 1.10.0
 
+
 # TreeSearch 1.3.2 (2023-04-27)
 
 - Use `PlotTools::SpectrumLegend()` for continuous scales in app
 - Restore auto-termination of `.t` files
 
 
-# TreeSearch 1.3.1
+# TreeSearch 1.3.1 (2023-03-29)
 
 - `PlotCharacter()` now returns invisibly
 - Fix missing character in Wills 2012 dataset
 - Search by character text in GUI
 - Call C functions using symbols
 
 
-# TreeSearch 1.3.0
+# TreeSearch 1.3.0 (2023-02-20)
 
 ## New features
 - New function `LengthAdded()` tests which characters contribute to taxon
@@ -38,7 +46,7 @@
 - Use K-means++ clustering
 
 
-# TreeSearch 1.2.0
+# TreeSearch 1.2.0 (2022-07-35)
 
 - 'shiny' GUI improvements:
   - Export log of tree search commands
@@ -50,15 +58,15 @@
   each of a list of trees
 
 
-# TreeSearch 1.1.2
+# TreeSearch 1.1.2 (2022-05-11)
 
 - Check tree order & rootedness before scoring ([#133](https://github.com/ms609/TreeSearch/issues/133))
 - Improve error handling
 - Replace `throw` with `stop` in C++
 - Remove test of elapsed times, for CRAN compliance
 
 
-# TreeSearch 1.1.1
+# TreeSearch 1.1.1 (2022-03-22)
 
 - GUI allows selection of subset of trees, for easier analysis of Bayesian
   tree sets
@@ -67,21 +75,21 @@
 - Update tests for TreeSearch 1.7
 
 
-# TreeSearch 1.1.0
+# TreeSearch 1.1.0 (2022-01-17)
 
 - Improvements to 'shiny' GUI
 - Better integration of rogue taxon exploration
 - New vignette describing profile parsimony
 - `MinimumLength()` fully supports ambiguous applicability
 
 
-# TreeSearch 1.0.1
+# TreeSearch 1.0.1 (2021-09-27)
 
 - Memory management with invalid input
 - Corrections to metadata
 
 
-# TreeSearch 1.0.0
+# TreeSearch 1.0.0 (2021-09-21)
 
 ## New functions
  - `EasyTrees()` 'shiny' graphical user interface for tree search
@@ -115,23 +123,23 @@
  - Remove redundant internal function `LogisticPoints()`
 
 
-# TreeSearch 0.4.3
+# TreeSearch 0.4.3 (2020-07-09)
 
  - Update tests for compatibility with 'TreeTools' v1.1.0
  - Improve memory and pointer handling
 
 
-# TreeSearch 0.4.2
+# TreeSearch 0.4.2 (2020-07-07)
 
  - Update tests for compatibility with 'TreeTools' v1.1.0
 
 
-# TreeSearch 0.4.1
+# TreeSearch 0.4.1 (2020-06-09)
 
  - Compatibility with 'TreeTools' v1.0.0
 
 
-# TreeSearch 0.4.0
+# TreeSearch 0.4.0 (2020-02-06)
 
 ## New features
  - `PhyDatToMatrix()`, complementing `MatrixToPhyDat()`
@@ -149,12 +157,12 @@
  - Use `message` in place of `cat`, to allow use of `suppressMessages()`
 
 
-# TreeSearch 0.3.2
+# TreeSearch 0.3.2 (2019-06-03)
 
  - Improve text, content and build speed of vignettes
 
 
-# TreeSearch 0.3.1
+# TreeSearch 0.3.1 
 
 ## New features
  - `NyeTreeSimilarity()` function implements the tree similarity metric of
@@ -167,7 +175,7 @@
    to avoid crashes on unsupported input
 
 
-# TreeSearch 0.3.0
+# TreeSearch 0.3.0 (2019-03-21)
 
 ## New features
  - Implement an information theoretic tree distance measure (Smith, 2020)
@@ -180,39 +188,39 @@
  - Correct some mistakes in the documentation
 
 
-# TreeSearch 0.2.2
+# TreeSearch 0.2.2 (2019-01-02)
 
  - Correct vignette titles
 
 
-# TreeSearch 0.2.1
+# TreeSearch 0.2.1 (2018-12-07)
 
 ## New features
- - `CollapseNodes` and `CollapseEdges` allow the creation of polytomies
- - `Tree2Splits` lists the bipartition splits implied by a tree topology
+ - `CollapseNodes()` and `CollapseEdges()` allow the creation of polytomies
+ - `Tree2Splits()` lists the bipartition splits implied by a tree topology
 
 ## Enhancements
- - `SplitFrequency` now supports larger trees
- - Can specify tip labels directly to `ReadTntTree`, to avoid reliance on
+ - `SplitFrequency()` now supports larger trees
+ - Can specify tip labels directly to `ReadTntTree()`, to avoid reliance on
    generative file
 
 ## Bug fixes
  - Export missing functions
 
 
-# TreeSearch 0.2.0
+# TreeSearch 0.2.0 (2018-09-10)
 
 ## New features
- - `RootTree` function allows rooting of tree on incompletely specified
+ - `RootTree()` allows rooting of tree on incompletely specified
     or single-taxon outgroup
- - `AllTBR` returns all trees one TBR rearrangement away
- - `TBRMoves` reports all possible TBR rearrangements
- - `Jackknife` conducts Jackknife resampling
- - `SplitFrequency` reports frequency of clades in a forest
- - `SupportColour` allows visual marking of support values
- - `ApeTime` reports the creation date of an ape-exported tree
- - `SortTree` flips nodes into a consistent left-right order
- - `AsBinary` supports 0
+ - `AllTBR()` returns all trees one TBR rearrangement away
+ - `TBRMoves()` reports all possible TBR rearrangements
+ - `Jackknife()` conducts Jackknife resampling
+ - `SplitFrequency()` reports frequency of clades in a forest
+ - `SupportColour()` allows visual marking of support values
+ - `ApeTime()` reports the creation date of an ape-exported tree
+ - `SortTree()` flips nodes into a consistent left-right order
+ - `AsBinary()` supports 0
 
 ## Enhancements
  - `[IW]RatchetConsensus()` renamed to `[IW]MultiRatchet()`, giving a better
@@ -227,27 +235,28 @@
    a different number of times
 
 
-# TreeSearch 0.1.2
+# TreeSearch 0.1.2 (2018-03-20)
 
 - Update MorphyLib library to fix C warnings
 - Remove non-ASCII characters from data
 - Disable slow-building and problematic vignette
 - Use local copy of citation style when building vignettes
 
 
-# TreeSearch 0.1.0
+# TreeSearch 0.1.0 (2018-03-14)
 
 ## New features
 - Helper functions to read Nexus and TNT data and trees
 - Brewer palette in local data to allow easier colouring
 
 ## Enhancements
-- Allow additional parameters to be passed to `consensus` via `ConsensusWithout`
+- Allow additional parameters to be passed to `consensus()` via
+ `ConsensusWithout()`
 
 ## Bug fixes
 - C11 compliance
-- `IWRatchetConsensus` now relays concavity value to subsequent functions
-- `ReadCharacters` returns labels for all characters and states if
+- `IWRatchetConsensus()` now relays concavity value to subsequent functions
+- `ReadCharacters()` returns labels for all characters and states if
   `character_num = NULL`