X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=ChangeLog;h=a4985e5dfcc71b19f3d191007abe15da6ec9bbab;hb=6603d33385e67db10a1d48f3ab7ec1910ce295ca;hp=0e8021260d28bed95db39a36b15ab75bd782feb2;hpb=06c3113db74a7cfa54c15a6f18163cd9b2c1f6db;p=ape.git

diff --git a/ChangeLog b/ChangeLog
index 0e80212..a4985e5 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,184 @@
+		CHANGES IN APE VERSION 2.6-3
+
+
+NEW FEATURES
+
+    o rTraitCont() and rTraitDisc() gains a '...' argument used with
+      user-defined models (suggestion by Gene Hunt).
+
+
+BUG FIXES
+
+    o as.hclust.phylo() now returns an error with unrooted trees.
+
+    o as.hclust.phylo() failed with trees with node labels (thanks to
+      Jinlong Zhang for pointing this bug out).
+
+    o read.dna(, "fasta") failed if sequences were not all of the same
+      length.
+
+
+OTHER CHANGES
+
+    o In drop.fossil() the default tol = 0 has been raised to 1e-8.
+
+
+
+		CHANGES IN APE VERSION 2.6-2
+
+
+NEW FEATURES
+
+    o Two new functions, pic.ortho and varCompPhylip, implements the
+      orthonormal contrasts of Felsenstein (2008, Am Nat, 171:713). The
+      second function requires Phylip to be installed on the computer.
+
+    o bd.ext() has a new option conditional = TRUE to use probabilities
+      conditioned on no extinction for the taxonomic data.
+
+
+BUG FIXES
+
+    o write.tree() failed to output correctly tree names.
+
+    o dist.nodes() returned duplicated column(s) with unrooted and/or
+      multichotomous trees.
+
+    o mcmc.popsize() terminated unexpectedly if the progress bar was
+      turned off.
+
+    o prop.part(x) made R frozen if 'x' is of class "multiPhylo".
+
+    o Compilation under Mandriva failed (thanks to Jos Käfer for the fix).
+
+    o drop.tip() shuffled tip labels with subtree = TRUE or trim.internal
+      = FALSE.
+
+    o Objects returned by as.hclust.phylo() failed when analysed with
+      cutree() or rect.hclust().
+
+    o write.tree() did not output correctly node labels (thanks to Naim
+      Matasci and Jeremy Beaulieu for the fix).
+
+    o ace(type = "discrete") has been improved thanks to Naim Marasci and
+      Jeremy Beaulieu.
+
+
+
+		CHANGES IN APE VERSION 2.6-1
+
+
+NEW FEATURES
+
+    o The new function speciesTree calculates the species tree from a set
+      of gene trees. Several methods are available including maximum tree
+      and shallowest divergence tree.
+
+
+BUG FIXES
+
+    o A bug introduced in write.tree() with ape 2.6 has been fixed.
+
+    o as.list.DNAbin() did not work correctly with vectors.
+
+    o as.hclust.phylo() failed with trees with node labels (thanks to
+      Filipe Vieira for the fix).
+
+
+
+		CHANGES IN APE VERSION 2.6
+
+
+NEW FEATURES
+
+    o The new functions rlineage and rbdtree simulate phylogenies under
+      any user-defined time-dependent speciation-extinction model. They
+      use continuous time algorithms.
+
+    o The new function drop.fossil removes the extinct species from a
+      phylogeny.
+
+    o The new function bd.time fits a user-defined time-dependent
+      birth-death model. It is a generalization of yule.time() taking
+      extinction into account.
+
+    o The new function MPR does most parsimonious reconstruction of
+      discrete characters.
+
+    o The new function Ftab computes the contingency table of base
+      frequencies from a pair of sequences.
+
+    o There is now an 'as.list' method for the class "DNAbin".
+
+    o dist.dna() can compute the number of transitions or transversions
+      with the option model = "Ts" or model = "Tv", respectively.
+
+    o [node|tip|edge]labels() gain three options with default values to
+      control the aspect of thermometers: horiz = TRUE, width = NULL,
+      and height = NULL.
+
+    o compar.gee() has been improved with the new option 'corStruct' as an
+      alternative to 'phy' to specify the correlation structure, and
+      calculation of the QIC (Pan 2001, Biometrics). The display of the
+      results has also been improved.
+
+    o read.GenBank() has a new option 'gene.names' to return the name of
+      the gene (FALSE by default).
+
+
+BUG FIXES
+
+    o extract.clade() sometimes shuffled the tip labels.
+
+    o plot.phylo(type = "unrooted") did not force asp = 1 (thanks to Klaus
+      Schliep for the fix)
+
+    o dist.dna(model = "logdet") used to divide distances by 4. The
+      documentation has been clarified on the formulae used.
+
+
+OTHER CHANGES
+
+    o rTraitCont(model = "OU") has an option 'linear = TRUE' to possibly
+      change the parameterisation (see ?rTraitCont for details).
+
+    o pic() now returns a vector with the node labels of the tree (if
+      available) as names.
+
+    o write.tree() and read.tree() have been substantially improved thanks
+      to contributions by Klaus Schliep.
+
+
+
+		CHANGES IN APE VERSION 2.5-3
+
+
+NEW FEATURES
+
+    o The new function mixedFontLabel helps to make labels with bits of
+      text to be plotted in different fonts.
+
+    o There are now replacement operators for [, [[, and $ for the class
+      "multiPhylo" (i.e., TREES[11:20] <- rmtree(10, 100)). They possibly
+      check that the tip labels are the same in all trees.
+
+    o Objects of class "multiPhylo" can be built with c(): there are
+      methods for the classes "phylo" and "multiPhylo".
+
+    o The internal functions .compressTipLabel and .uncompressTipLabel are
+      now documented.
+
+
+BUG FIXES
+
+    o bind.tree(x, y, where, position = 0) did not work correctly if 'y'
+      was a single-edge tree and 'where' was a tip.
+
+    o rTraitCont() did not use the square-root of branch lengths when
+      simulating a Brownian motion model.
+
+
+
 		CHANGES IN APE VERSION 2.5-2
 
 
@@ -5,6 +186,11 @@ NEW FEATURES
 
     o There is now a print method for results from ace().
 
+    o There is a labels() method for objects of class "DNAbin".
+
+    o read.dna() has a new option 'as.matrix' to possibly force sequences
+      in a FASTA file to be stored in a matrix (see ?read.dna for details).
+
 
 BUG FIXES
 
@@ -20,14 +206,22 @@ DEPRECATED & DEFUNCT
 
     o evolve.phylo() and plot.ancestral() have been removed.
 
+    o chronogram(), ratogram(), and NPRS.criterion() have been removed.
+
 
 OTHER CHANGES
 
     o nj() has been improved and is now about 30% faster.
 
+    o The default option 'drop' of [.DNAbin has been changed to FALSE to
+      avoid dropping rownames when selecting a single sequence.
+
+    o print.DNAbin() has been changed to summary.DNAbin() which has been
+      removed.
+
 
 
- 		CHANGES IN APE VERSION 2.5-1
+		CHANGES IN APE VERSION 2.5-1
 
 
 NEW FEATURES
@@ -74,7 +268,7 @@ OTHER CHANGES
 
 
 
-	CHANGES IN APE VERSION 2.5
+		CHANGES IN APE VERSION 2.5
 
 
 NEW FEATURES