X-Git-Url: https://git.donarmstrong.com/?p=ape.git;a=blobdiff_plain;f=NEWS;h=57d1924cccdeffb9e41b43d9a2934a04ebe6aa68;hp=0fb711979f9b827a89a072ca869d5606a6b1e201;hb=be6a044200152fd83d0b72f348012a0adc2593c5;hpb=c14b15358e1f21302d929a980484e9f08c748c20

diff --git a/NEWS b/NEWS
index 0fb7119..57d1924 100644
--- a/NEWS
+++ b/NEWS
@@ -1,3 +1,327 @@
+		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.
+
+    o The new function read.FASTA reads FASTA files much faster and
+      more efficiently. It is called internally by read.dna(, "fasta")
+      or can be called directly.
+
+
+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.
+
+    o base.freq() is now faster with lists.
+
+
+
+		CHANGES IN APE VERSION 3.0-6
+
+
+NEW FEATURES
+
+    o reorder.phylo() has a new order, "postorder", and a new option
+      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.edgelength, node.height, and
+      node.height.clado make some internal code available from R. See
+      ?node.depth (which was already documented) for details.
+
+
+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
+
+    o dist.nodes() is now 6 to 10 times faster.
+
+    o reorder(, "cladewise") is now faster. The change is not very
+      visible for small trees (n < 1000) but this can be more than
+      1000 faster for big trees (n >= 1e4).
+
+    o The attribute "order" of the objects of class "phylo" is now
+      strongly recommended, though not mandatory. Most functions in
+      ape should return a tree with this attribute correctly set.
+
+    o dbd() is now vectorized on both arguments 'x' (number of species
+      in clade) and 't' (clade age) to make likelihood calculations
+      easier and faster.
+
+
+
+		CHANGES IN APE VERSION 3.0-5
+
+
+BUG FIXES
+
+    o ace() should better catch errors when SEs cannot be computed.
+
+
+OTHER CHANGES
+
+    o write.dna(format = "fasta") now conforms more closely to the
+      FASTA standard thanks to François Michonneau.
+
+    o print.DNAbin() does not print base compositions if there are more
+      than one million nucleotides.
+
+
+
+		CHANGES IN APE VERSION 3.0-4
+
+
+BUG FIXES
+
+    o read.dna() failed to read Phylip files if the first line used
+      tabulations instead of white spaces.
+
+    o read.dna() failed to read Phylip or Clustal files with less than
+      10 nucleotides. (See other changes in this function below.)
+
+OTHER CHANGES
+
+    o read.dna() now requires at least one space (or tab) between the
+      taxa names and the sequences (whatever the length of taxa
+      names). write.dna() now follows the same rule.
+
+    o The option 'seq.names' of read.dna has been removed.
+
+    o The files ape-defunct.R and ape-defunct.Rd, which have not been
+      modified for almost two years, have been removed.
+
+    o The C code of bionj() has been reworked: it is more stable (by
+      avoiding passing character strings), slightly faster (by about
+      20%), and numerically more accurate.
+
+    o The C code of fastme.*() has been slightly modified and should
+      be more stable by avoiding passing character strings (the
+      results are identical to the previous versions).
+
+    o The file src/newick.c has been removed.
+
+
+
+		CHANGES IN APE VERSION 3.0-3
+
+
+BUG FIXES
+
+    o birthdeath() now catches errors and warnings much better so that
+      a result is returned in most cases.
+
+
+OTHER CHANGES
+
+    o Because of problems with character string manipulation in C, the
+      examples in ?bionj and in ?fastme have been disallowed. In the
+      meantime, these functions might be unstable. This will be solved
+      for the next release.
+
+
+
+		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
+
+
+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
 
 
@@ -31,7 +355,11 @@ BUG FIXES
       incompatible splits occur in 50% of the trees (especially with
       small number of trees).
 
-    o c() with "multiPhylo" did not work correctly.
+    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.
 
 
 
@@ -115,8 +443,8 @@ 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.
@@ -1688,14 +2016,14 @@ 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.
@@ -1759,7 +2087,7 @@ 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'.