X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=NEWS;h=55d0adc836df886582039bfc36a8f2d039694ada;hb=1ad48c7a70983375138a6500372db588c8a3a134;hp=0bc534026eecdbe12c860c5507e8d876af52e79c;hpb=2e7fdb027f189e7c8eb771dadaf195c43bd41d5f;p=ape.git

diff --git a/NEWS b/NEWS
index 0bc5340..55d0adc 100644
--- a/NEWS
+++ b/NEWS
@@ -1,9 +1,104 @@
+		CHANGES IN APE VERSION 3.0
+
+
+NEW FEATURES
+
+    o plot.phylo() has a new option 'rotate.tree' to rotate unrooted,
+      fan or radial trees around the center of the plot.
+
+
+BUG FIXES
+
+    o mantel.test() could return 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 by default find 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.
+
+
+
+		CHANGES IN APE VERSION 2.8
+
+
+NEW FEATURES
+
+    o Twelve new functions have been written by Andrei-Alin Popescu:
+      additive, ultrametric, is.compatible, arecompatible, mvr, mvrs,
+      njs, bionjs, SDM, treePop, triangMtd, triangMtd*.
+
+    o A new class "bitsplits" has been created by Andrei-Alin Popescu
+      to code splits (aka, bipartition).
+
+    o There is a new generic function as.bitsplits with a method to
+      convert from the class "prop.part" to the class "bitsplits".
+
+    o The new function ltt.coplot plots on the same scales a tree and
+      the derived LTT plot.
+
+    o ltt.plot() has two new options: backward and tol. It can now
+      handle non-ultrametic trees and its internal coding has been
+      improved. The coordinates of the plot can now be computed with
+      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
 
 
 NEW FEATURES
 
-    o There is a new predict() method for compar.gee().
+    o The new function compute.brtime computes and sets branching times.
+
+    o mantel.test() has a new argument 'alternative' which is
+      "two-sided" by default. Previously, this test was one-tailed
+      with no possibility to change.
+
+    o ace() can now do REML estimation with continuous characters,
+      giving better estimates of the variance of the Brownian motion
+      process.
+
+
+BUG FIXES
+
+    o Branch lengths were wrongly updated with bind.tree(, where = <tip>,
+      position = 0). (Thanks to Liam Revell for digging this bug out.)
+
+    o Simulation of OU process with rTraitCont() did not work correctly.
+      This now uses formula from Gillespie (1996) reduced to a BM
+      process when alpha = 0 to avoid division by zero. The option
+      'linear' has been removed.
+
+    o Cross-validation in chronopl() did not work when 'age.max' was
+      used.
+
+    o consensus(, p = 0.5) could return an incorrect tree if some
+      incompatible splits occur in 50% of the trees (especially with
+      small number of trees).
+
+    o c() with "multiPhylo" did not work correctly (thanks to Klaus
+      Schliep for the fix).
+
+    o root() failed in some cases with an outgroup made of several tips.
+      The help page has been clarified a bit.
 
 
 
@@ -17,6 +112,9 @@ NEW FEATURES
       and four conversion methods to the classes "phylo", "networx",
       "network", and "igraph".
 
+    o The new function rTraitMult does multivariate traits simulation
+      with user-defined models.
+
     o plot.phylo() has a new option 'plot = TRUE'. If FALSE, the tree
       is not plotted but the graphical device is set and the
       coordinates are saved as usual.
@@ -30,6 +128,8 @@ NEW FEATURES
     o boot.phylo() now displays a progress bar by default (can be off
       if 'quiet = TRUE').
 
+    o There is a new predict() method for compar.gee().
+
 
 BUG FIXES
 
@@ -44,6 +144,12 @@ BUG FIXES
       presence of identical or nearly identical sequences.
 
 
+OTHER CHANGES
+
+    o The data bird.families, bird.orders, cynipids, and woodmouse are
+      now provided as .rda files.
+
+
 
 		CHANGES IN APE VERSION 2.7-1