X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=ChangeLog;h=c702b68074489aa961044ce2efd6819da03b96c4;hb=e64b298d9074561ebd0b07859e959fcc0dc980b2;hp=8df6cc8b7aa06925ce5d54d8928a1742363128c8;hpb=269a1dbc3927260e5fc96f535f752fc09596e96e;p=ape.git

diff --git a/ChangeLog b/ChangeLog
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+++ b/ChangeLog
@@ -1,3 +1,267 @@
+		CHANGES IN APE VERSION 2.7-2
+
+
+NEW FEATURES
+
+    o plot.phylo() has a new option 'draw = TRUE'. If FALSE, the tree
+      is not plotted but the graphical device is set and the
+      coordinates are saved as normal.
+
+
+
+		CHANGES IN APE VERSION 2.7-1
+
+
+NEW FEATURES
+
+    o The new function trex does tree exploration with multiple
+      graphical devices.
+
+    o The new function kronoviz plots several rooted (dated) trees on
+      the scale scale.
+
+    o identify.phylo() has a new option 'quiet' (FALSE by default).
+
+
+BUG FIXES
+
+    o A bug was introduced in read.nexus() in ape 2.7.
+
+    o image.DNAbin() did not colour correctly the bases if there were
+      some '-' and no 'N'.
+
+    o .compressTipLabel() failed with a list with a single tree.
+
+    o identify.phylo() returned a wrong answer when the x- and y-scales
+      are very different.
+
+    o write.nexus() failed with lists of trees with compressed labels.
+
+
+OTHER CHANGES
+
+    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.
+
+
+
+		CHANGES IN APE VERSION 2.7
+
+
+NEW FEATURES
+
+    o There is a new image() method for "DNAbin" objects: it plots DNA
+      alignments in a flexible and efficient way.
+
+    o Two new functions as.network.phylo and as.igraph.phylo convert
+      trees of class "phylo" into these respective network classes
+      defined in the packages of the same names.
+
+    o The three new functions clustal, muscle, and tcoffee perform
+      nucleotide sequence alignment by calling the external programs
+      of the same names.
+
+    o Four new functions, diversity.contrast.test, mcconwaysims.test,
+      richness.yule.test, and slowinskiguyer.test, implement various
+      tests of diversification shifts using sister-clade comparisons.
+
+    o base.freq() gains an option 'all' to count all the possible bases
+      including the ambiguous ones (defaults to FALSE).
+
+    o read.nexus() now writes tree names in the NEXUS file if given a
+      list of trees with names.
+
+
+BUG FIXES
+
+    o prop.part() failed in some situations with unrooted trees.
+
+    o read.nexus() shuffled node labels when a TRANSLATE block was
+      present.
+
+    o varCompPhylip() did not work if 'exec' was specified.
+
+    o bind.tree() shuffled node labels when position > 0 and 'where'
+      was not the root.
+
+
+OTHER CHANGES
+
+    o BaseProportion in src/dist_dna.c has been modified.
+
+    o A number of functions in src/tree_build.c have been modified.
+
+    o The matching representation has now only two columns as the third
+      column was redundant.
+
+
+
+		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.
+
+    o plot.phylo() did not recycle values of 'font', 'cex' and
+      'tip.color' correctly when type = "fan" or "radial".
+
+    o plot.phylo() ignored 'label.offset' when type = "radial", "fan", or
+      "unrooted" with lab4ut = "axial" (the placement of tip labels still
+      needs to be improved with lab4ut = "horizontal").
+
+
+OTHER CHANGES
+
+    o In drop.fossil() the default tol = 0 has been raised to 1e-8.
+
+    o The help command ?phylo now points to the man page of read.tree()
+      where this class is described. Similarly, ?matching points to the
+      man page of as.matching().
+
+
+
+		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