X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=NEWS;h=3660ac41656c766a522d731a10cfc489ae01c384;hb=477a8f1b7e5841202ef29d3d8af3c93acd35c043;hp=17f28e25af52fa9bf1440a6c698b0179ac4f1a94;hpb=ef34642fe85694df0a80ef534137b8f6b427b67e;p=ape.git

diff --git a/NEWS b/NEWS
index 17f28e2..3660ac4 100644
--- a/NEWS
+++ b/NEWS
@@ -1,3 +1,151 @@
+		CHANGES IN APE VERSION 3.0-2
+
+
+BUG FIXES
+
+    o birthdeath() now catches errors and warnings much better so that
+      a result is returned in most cases.
+
+
+
+		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. 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
+
+
+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
+
+
+NEW FEATURES
+
+    o The three functions dyule, dbd, and dbdTime calculate the
+      density probability (i.e., the distribution of the number of
+      species) for the Yule, the constant and the time-dependent
+      birth-beath models, respectively. These probabilities can be
+      conditional on no extinction and/or on a log-scale.
+
+    o plot.phylo() has a new option 'rotate.tree' to rotate unrooted,
+      fan, or radial trees around the center of the plot.
+
+    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 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
+      Ludovic Mallet and Mahendra Mariadassou for the fix).
+
+    o clustal() should now find by default the executable under Windows.
+
+
+OTHER CHANGES
+
+    o The code of yule() has been simplified and is now much faster for
+      big trees.
+
+    o The code of mantel.test() has been adjusted to be consistent
+      with common permutation tests.
+
+    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
 
 
@@ -22,6 +170,11 @@ NEW FEATURES
       the new function ltt.plot.coords.
 
 
+BUG FIXES
+
+    o prop.part() crashed if some trees had some multichotomies.
+
+
 
 		CHANGES IN APE VERSION 2.7-3
 
@@ -144,8 +297,8 @@ 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.