https://github.com/cran/ape
Tip revision: 9f7a2cb574406c664e4d56b58a979e1a0f536e37 authored by Emmanuel Paradis on 06 June 2003, 00:00:00 UTC
version 1.1-1
version 1.1-1
Tip revision: 9f7a2cb
Changes
CHANGES IN APE VERSION 1.1-1
BUG FIXES
o A bug in read.tree() introduced in APE 1.1 was fixed.
o A bug in compar.gee() resulted in an error when trying to fit
a model with `family = "binomial"'. This is now fixed.
CHANGES IN APE VERSION 1.1
NEW FEATURES
o The Klastorin (1982) method as suggested by Misawa and Tajima
(2000, Mol. Biol. Evol. 17:1879-1884) for classifying genes
on the basis of phylogenetic trees has been implemented (see
the function klastorin()).
o Functions have been added to convert APE's "phylo" objects in
"hclust" cluster objects and vice versa (see the help page of
as.phylo for details).
o Three new functions, ratogram(), chronogram() and NPRS.criterion(),
are introduced for the estimation of absolute evolutionary rates
(ratogram) and dated clock-like trees (chronogram) from
phylogenetic trees using the non-parametric rate smoothing approach
by MJ Sanderson (1997, Mol. Biol. Evol. 14:1218-1231).
o A summary method is now provided printing a summary information on a
phylogenetic tree with, for instance, `summary(tree)'.
o The behaviour of read.tree() was changed so that all spaces and
tabulations in tree files are now ignored. Consequently, spaces in tip
labels are no more allowed. Another side effect is that read.nexus()
now does not replace the underscores (_) in tip labels with spaces
(this behaviour was undocumented).
o The function plot.phylo() has a new option (`underscore') which
specifies whether the underscores in tip labels should be written on
the plot as such or replaced with spaces (the default).
o The function birthdeath() now computes 95 % confidence intervals of
the estimated parameters using profile likelihood.
o Three new data sets are included: a gene tree estimated from 36
landplant rbcL sequences, a gene tree estimated from 32 opsin
sequences, and a gene tree for 50 BRCA1 mammalian sequences.
BUG FIXES
o A bug was fixed in dist.gene() where nothing was returned.
o A bug in plot.mst() was fixed.
o A bug in vcv.phylo() resulted in false correlations when the
option `cor = TRUE' was used (now fixed).
CHANGES IN APE VERSION 1.0
NEW FEATURES
o Two new functions, read.dna() and write.dna(), read/write in a file
DNA sequences in interleaved or in sequential format.
o Two new functions, read.nexus() and write.nexus(), read/write trees
in a NEXUS file.
o The new function bind.tree() allows to bind two trees together,
possibly handling root edges to give internal branches.
o The new function drop.tip() removes the tips in a phylogenetic tree,
and trims (or not) the corresponding internal branches.
o The new function is.ultrametric() tests if a tree is ultrametric.
o The function plot.phylo() has more functionalities such as drawing the
branches with different colours and/or different widths, showing the
node labels, controling the position and font of the labels, rotating
the labels, and controling the space around the plot.
o The function read.tree() can now read trees with no branch length,
such as "(a,b),c);". Consequently, the element `edge.length' in
objects of class "phylo" is now optional.
o The function write.tree() has a new default behaviour: if the default
for the option `file' is used (i.e. file = ""), then a variable of
mode character containing the tree in Newick format is returned which
can thus be assigned (e.g., tree <- write.tree(phy)).
o The function read.tree() has a new argument `text' which allows
to read the tree in a variable of mode character.
o A new data set is included: the phylogenetic relationships among
the orders of birds from Sibley and Ahlquist (1990).
CHANGES IN APE VERSION 0.2-1
BUG FIXES
o Several bugs were fixed in the help pages.
CHANGES IN APE VERSION 0.2
NEW FEATURES
o The function write.tree() writes phylogenetic trees (objects of class
"phylo") in an ASCII file using the Newick parenthetic format.
o The function birthdeath() fits a birth-death model to branching times
by maximum likelihood, and estimates the corresponding speciation and
extinction rates.
o The function scale.bar() adds a scale bar to a plot of a phylogenetic
tree.
o The function is.binary.tree() tests whether a phylogeny is binary.
o Two generic functions, coalescent.intervals() and collapsed.intervals(),
as well as some methods are introduced.
o Several functions, including some generics and methods, for computing
skyline plot estimates (classic and generalized) of effective
population size through time are introduced and replace the function
skyline.plot() in version 0.1.
o Two data sets are now included: the phylogenetic relationships among
the families of birds from Sibley and Ahlquist (1990), and an
estimated clock-like phylogeny of HIV sequences sampled in the
Democratic Republic of Congo.
DEPRECATED & DEFUNCT
o The function skyline.plot() in ape 0.1 has been deprecated and
replaced by more elaborate functions (see above).
BUG FIXES
o Two important bugs were fixed in plot.phylo(): phylogenies with
multichotomies not at the root or not with only terminal branches,
and phylogenies with a single node (i.e. only terminal branches)
did not plot. These trees should be plotted correctly now.
o Several bugs were fixed in diversi.time() in the computation of
AICs and LRTs.
o Various errors were corrected in the help pages.