final warp for ape 3.0-2

[ape.git] / NEWS

diff --git a/NEWS b/NEWS
index 87f4ffa73ae62dc802aa1b1b0006335d9048c378..18485974832ad5157a9c413d79334e09afdce807 100644 (file)
--- a/NEWS
+++ b/NEWS
@@ -17,6 +17,39 @@ BUG FIXES
 
     o mltt.plot(, backward = FALSE) did not set the x-axis correctly.
 
+    o A bug was introduced in prop.clades() with ape 3.0. The help page
+      has been clarified relative to the use of the option 'rooted'.
+
+    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.
+
+    o prop.part() could make R crash if the first tree had many
+      multichotomies.
+
+    o njs(), bionjs(), and mvrs() now return an error if 'fs < 1'.
+
+    o SDM() did not work correctly. The code has also been generally
+      improved.
+
+
+OTHER CHANGES
+
+    o The DESCRIPTION file has been updated.
+
+    o The option 'original.data' of write.nexus() has been removed.
+
+    o The files bionjs.c, mvr.c, mvrs.c, njs.c, triangMtd.c, and
+      triangMtds.c have been improved which should fix some bugs in
+      the corresponding functions.
+
+    o dist.gene() now coerces input data frame as matrix resulting in
+      much faster calculations (thanks to a suggestion by Markus
+      Schlegel).
+
 
 
                CHANGES IN APE VERSION 3.0-1