X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=ChangeLog;h=13751957239f34beb73b573549fa7c40ef51e7ba;hb=dca7b216e929337836a18374147b13eb793ffd95;hp=8ad799a009ac2d7c8469030d915b855691453cfa;hpb=91cbce9b55b05cef1f7167f646bc30b3e568ebf9;p=ape.git

diff --git a/ChangeLog b/ChangeLog
index 8ad799a..1375195 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,13 +1,94 @@
+		CHANGES IN APE VERSION 2.4
+
+
+NEW FEATURES
+
+    o base.freq() has a new option 'freq' to return the counts; the
+      default is still to return the proportions.
+
+
+BUG FIXES
+
+    o seg.sites() did not handle ambiguous nucleotides correctly: they are
+      now ignored.
+
+
+DEPRECATED & DEFUNCT
+
+    o The functions heterozygosity, nuc.div, theta.h, theta.k and
+      theta.s have been moved from ape to pegas.
+
+
+OTHER CHANGES
+
+    o Deprecated functions are now listed in a help page: see
+      help("ape-defunct"), with the quotes!
+
+
+		CHANGES IN APE VERSION 2.3-3
+
+
+BUG FIXES
+
+    o add.scale.bar() always drew a horizontal bar.
+
+    o zoom() shuffled tips with unrooted trees.
+
+    o write.nexus() failed to write correctly trees with a "TipLabel"
+      attribute.
+
+    o rcoal() failed to compute branch lengths with very large n.
+
+    o A small bug was fixed in compar.cheverud() (thanks to Michael
+      Phelan for the fix).
+
+    o seg.sites() failed when passing a vector.
+
+    o drop.tip() sometimes shuffled tip labels.
+
+    o root() shuffled node labels with 'resolve.root = TRUE'.
+
+
+
+		CHANGES IN APE VERSION 2.3-2
+
+
+BUG FIXES
+
+    o all.equal.phylo() did not compare unrooted trees correctly.
+
+    o dist.topo(... method = "PH85") did not treat unrooted trees
+      correctly (thanks to Tim Wallstrom for the fix).
+
+    o root() sometimes failed to test for the monophyly of the
+      outgroup correctly.
+
+    o extract.clade() sometimes included too many edges.
+
+    o vcv.phylo() did not work correctly when the tree is in
+      "pruningwise" order.
+
+    o nj() did not handle correctly distance matrices with many 0's.
+      The code has also been significantly improved: 7, 70, 160 times
+      faster with n = 100, 500, 1000, respectively.
+
+
+
 		CHANGES IN APE VERSION 2.3-1
 
 
 NEW FEATURES
 
+    o The new function is.monophyletic tests the monophyly of a group.
+
     o There is now a c() method for lists of class "DNAbin".
 
     o yule.cov() now fits the null model, and its help page has been
       corrected with respect to this change.
 
+    o drop.tip() has a new option 'rooted' to force (or not) a tree
+      to be treated as (un)rooted.
+
 
 BUG FIXES
 
@@ -22,6 +103,14 @@ BUG FIXES
 
     o A small bug was fixed in CDAM.global().
 
+    o ace() failed with large data sets. Thanks to Rich FitzJohn for
+      the fix. With other improvements, this function is now about 6
+      times faster.
+
+    o write.tree() failed with objects of class "multiPhylo".
+
+    o drop.tip(, subtree = TRUE) sometimes shuffled tip labels.
+
 
 OTHER CHANGES
 
@@ -33,6 +122,11 @@ OTHER CHANGES
     o rcoal() is now faster.
 
 
+DEPRECATED & DEFUNCT
+
+    o klastorin() has been removed.
+
+
 
 		CHANGES IN APE VERSION 2.3
 
@@ -124,7 +218,7 @@ OTHER CHANGES
 
     o ape has now a namespace.
 
-    o drip.tip() has been improved: it should be much faster and work
+    o drop.tip() has been improved: it should be much faster and work
       better in some cases (e.g., see the example in ?zoom).