X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=NEWS;h=f6acbff8297c3c3756acc8ec24a2db1115399c7d;hb=a2fc961dffe9f9b7994ed880e68c03b2334dc341;hp=729e3ed930e14e4404d261978374069c41576c6c;hpb=b9e04a6e6af3beda74b916eda00b42ac38875563;p=ape.git

diff --git a/NEWS b/NEWS
index 729e3ed..f6acbff 100644
--- a/NEWS
+++ b/NEWS
@@ -1,3 +1,35 @@
+		CHANGES IN APE VERSION 3.0-7
+
+
+NEW FEATURES
+
+    o The new function 'where' searches patterns in DNA sequences.
+
+    o pic() gains an option 'rescaled.tree = FALSE' to return the tree
+      with its branch lengths rescaled for the PIC calculation.
+
+    o clustal(), muscle(), and tcoffee() gain an option
+      'original.ordering = TRUE' to ease the comparisons of
+      alignments.
+
+    o plot.phylo() has a new option, open.angle, used when plotting
+      circular trees.
+
+
+BUG FIXES
+
+    o drop.tip() shuffled node labels on some trees.
+
+    o axisPhylo() now works correctly with circular trees, and gives a
+      sensible error message when type = "r" or "u".
+
+
+OTHER CHANGES
+
+    o .compressTipLabel() is 10 times faster thanks to Joseph Brown.
+
+
+
 		CHANGES IN APE VERSION 3.0-6
 
 
@@ -7,10 +39,9 @@ NEW FEATURES
       index.only = TRUE to return only the vector of indices (the tree
       is unmodified, see ?reorder.phylo for details).
 
-    o The three new functions node.depth.length, node.height, and
+    o The three new functions node.depth.edgelength, node.height, and
       node.height.clado make some internal code available from R. See
-      ?node.depth (which was already available and documented) for
-      details.
+      ?node.depth (which was already documented) for details.
 
 
 BUG FIXES
@@ -18,6 +49,16 @@ BUG FIXES
     o reorder(, "pruningwise") made R crash if the rows of the edge
       matrix are in random order: this is now fixed.
 
+    o drop.tip() sometimes shuffled node labels (thanks to Rebecca
+      Best for the report).
+
+    o drop.tip(phy, "") returned a tree with zero-length tip labels:
+      it now returns the tree unchanged (thanks to Brian Anacker for
+      the report).
+
+    o plot.phylo() made R crash if the tree has zero-length tip
+      labels: it now returns NULL (thanks again to Brian Anacker).
+
 
 OTHER CHANGES
 
@@ -1969,14 +2010,14 @@ BUG FIXES
     o A bug was fixed in phymltest(): the executable couldn't be found
       in some cases.
 
-    o Three bug have been fixed in ace(): computing the likelihood of
+    o Three bugs have been fixed in ace(): computing the likelihood of
       ancestral states of discrete characters failed, custom models
       did not work, and the function failed with a null gradient (a
       warning message is now returned; this latter bug was also
       present in yule.cov() as well and is now fixed).
 
-    o pic() hanged out when missing data were present: a message error
-      is now returned.
+    o pic() hanged out when missing data were present: an error is now
+      returned.
 
     o A small bug was fixed in dist.dna() where the gamma correction
       was not always correctly dispatched.
@@ -2040,7 +2081,7 @@ NEW FEATURES
       DNA sequences by specifying model = "raw".
 
     o dist.phylo() has a new option `full' to possibly compute the
-      distances among all tips and nodes of the tree. The default if
+      distances among all tips and nodes of the tree. The default is
       `full = FALSE'.