various bug fixes

[ape.git] / NEWS

diff --git a/NEWS b/NEWS
index 0ca6a14ff076ca1681992b5e4fb3cd9aacfaadb2..de2da102a4fb09c042fc641ee32726b0accbf29d 100644 (file)
--- a/NEWS
+++ b/NEWS
@@ -1,3 +1,57 @@
+               CHANGES IN APE VERSION 3.0-2
+
+
+NEW FEATURES
+
+    o The new function alex (alignment explorator) zooms in a DNA
+      alignment and opens the result in a new window.
+
+
+BUG FIXES
+
+    o compute.brtime() did not completely randomized the order of the
+      branching times.
+
+    o write.nexus() did not work correctly with rooted trees (thanks
+      to Matt Johnson for the fix).
+
+    o mltt.plot(, backward = FALSE) did not set the x-axis correctly.
+
+    o A bug was introduced in prop.clades() with ape 3.0.
+
+    o mantel.test() printed a useless warning message.
+
+    o plot.phylo(, direction = "downward") ignored 'y.lim'.
+
+    o is.monophyletic() did not work correctly if 'tips' was not stored
+      as integers
+
+
+
+               CHANGES IN APE VERSION 3.0-1
+
+
+NEW FEATURES
+
+    o dist.dna() has two new models: "indel" and "indelblock".
+
+    o bind.tree() now accepts 'position' > 0 when the trees have no
+      banch length permitting to create a node in 'x' when grafting
+      'y' (see ?bind.tree for details).
+
+
+BUG FIXES
+
+    o cophyloplot( , rotate = TRUE) made R hanged after a few clicks.
+      Also the tree is no more plotted twice.
+
+    o read.GenBank() has been updated to work with EFetch 2.0.
+
+    o unroot() on trees in "pruningwise" order did not respect this
+      attribute.
+
+
+
                CHANGES IN APE VERSION 3.0
 
 
@@ -15,10 +69,18 @@ NEW FEATURES
     o boot.phylo() and prop.clades() have a new option rooted =
       FALSE. Note that the behaviour of prop.part() is unchanged.
 
+    o edgelabels() has a new option 'date' to place labels on edges of
+      chronograms using the time scale (suggestion by Rob Lanfear).
+
 
 BUG FIXES
 
-    o mantel.test() could return P-values > 1 with the default
+    o In chronopl(), the code setting the initial dates failed in
+      complicated settings (several dates known within intervals).
+      This has been generally improved and should result in faster
+      and more efficient convergence even in simple settings.
+
+    o mantel.test() sometimes returned P-values > 1 with the default
       two-tailed test.
 
     o extract.clade() sometimes shuffled some tip labels (thanks to
@@ -38,6 +100,16 @@ OTHER CHANGES
     o The C code of base.freq() has been improved and is now nearly 8
       times faster.
 
+    o The option 'original.data' of write.nexus() is now deprecated and
+      will be removed in a future release.
+
+    o The code of is.ultrametric() has been improved and is now 3 times
+      faster.
+
+    o The code of vcv.phylo() has been improved and is now 10 or 30
+      times faster for 100 or 1000 tips, respectively. Consequently,
+      fitting models with PGLS will be faster overall.
+
 
 
                CHANGES IN APE VERSION 2.8
@@ -191,8 +263,8 @@ BUG FIXES
 
 OTHER CHANGES
 
-    o identify.phylo() now returns NULL if the user right-(instead of
-      left-)clicks (an error was returned previously).
+    o identify.phylo() now returns NULL if the user right- (instead of
+      left-) clicks (an error was returned previously).
 
     o read.nexus() should be robust to commands inserted in the TREES
       block.