+ CHANGES IN APE VERSION 3.0-8
+
+
+NEW FEATURES
+
+ o The new function ewLasso tests whether an incomplete set of
+ distances uniquely determines the edge weights of a given
+ unrooted topology using the 'Lasso' method by Dress et
+ al. (2012, J. Math. Biol. 65:77).
+
+ o ace() gains a new option 'use.expm' to use expm() from the
+ package of the same name in place of matexpo().
+
+
+BUG FIXES
+
+ o read.dna(, "fasta") may add '\r' in labels: this is fixed.
+
+ o prop.clades() returned wrong numbers when the tip labels of
+ 'phy' are not in the same order than the list of trees (thanks
+ to Rupert Collins for the report).
+
+ o CADM.post() displayed "1" on the diagonal of the matrix of
+ Mantel p-values. It now displays "NA" on the diagonal,
+ indicating that no test of significance is computed between a
+ distance matrix and itself.
+
+ o rtree(n, rooted = FALSE) returned trees with an 'edge' matrix
+ stored as doubles instead of integers for n > 4.
+
+
+OTHER CHANGES
+
+ o The files CDAM.global.R and CDAM.post.R have been renamed
+ CADM.global.R and CADM.post.R.
+
+ o ace() has a new default for its option 'method': this is "REML"
+ for continuous characters and "ML" for discrete ones.
+
+ o ape does not import gee anymore so the latter doesn't need to
+ be installed.
+
+
+
+ CHANGES IN APE VERSION 3.0-7
+
+
+NEW FEATURES
+
+ o The new function chronos estimates chronograms by penalised
+ likelihood and maximum likelihood with a completely reworked
+ code and interface. There is a new function makeChronosCalib to
+ set the calibration points easily. chronos() will eventually
+ replace chronopl().
+
+ 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.
+
+ o as.matrix.DNAbin() should be faster and more efficient with
+ lists; it now accepts vectors.
+
+
+
CHANGES IN APE VERSION 3.0-6
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.length, node.height, and
+ 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 available and documented) for
- details.
+ ?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 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
+ o write.nexus() now writes tree names in the NEXUS file if given a
list of trees with names.
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.
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'.
projects / ape.git / blobdiff