X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=Changes;h=854ae1949d3b84ed1ca5e8ade91a4cf660ef94a2;hb=19e6ab24fb4e4b32cb867aef0b5bf57707344641;hp=ae08426ccfaa98d289c9fc3642a76748eb501eb1;hpb=1d0651b1374592d87400614a03b34b4e0cc63aae;p=ape.git diff --git a/Changes b/Changes index ae08426..854ae19 100644 --- a/Changes +++ b/Changes @@ -1,11 +1,191 @@ + CHANGES IN APE VERSION 2.2-2 + + +NEW FEATURES + + o dist.gene() has been substantially improved and gains an option + 'pairwise.deletion'. + + +BUG FIXES + + o prop.part() failed with a single tree with the default option + 'check.labels = TRUE'. + + o summary.DNAbin() failed to display correctly the summary of + sequence lengths with lists of sequences of 10,000 bases or more + (because summary.default uses 4 significant digits by default). + + o read.nexus() failed to read a file with a single tree with line + breaks in the Newick string. + + o del.gaps() returned a list of empty sequences when there were no + gaps. + + +OTHER CHANGES + + o The data sets bird.orders and bird.families are now stored as + Newick strings; i.e., the command data(bird.orders) calls + read.tree(). + + + + CHANGES IN APE VERSION 2.2-1 + + +NEW FEATURES + + o The new function makeLabel() helps to modify labels of trees, + lists of trees, or DNA sequences, with several utilities to + truncate and/or make them unique, substituting some + characters, and so on. + + o The new function del.gaps() removes insertion gaps ("-") in a + set of DNA sequences. + + o read.dna() can now read Clustal files (*.aln). + + +BUG FIXES + + o root() failed with 'resolve.root = TRUE' when the root was + already the specified root. + + o Several bugs were fixed in mlphylo(). + + o collapsed.singles() did not propagate the 'Nnode' and + 'node.labels' elements (thanks to Elizabeth Purdom for the fix). + + o read.nexus() failed to remove correctly the comments within + trees. + + o read.nexus() failed to read a file with a single tree and no + translation of tip labels. + + o read.nexus() failed to place correctly tip labels when reading + a single tree with no edge lengths. + + o A bug was fixed in sh.test(). + + +OTHER CHANGES + + o unique.multiPhylo() is faster thanks to a suggestion by Vladimir + Minin. + + o The option 'check.labels' of consensus() and prop.part() is now + TRUE by default. + + o write.dna() now does not truncate names to 10 characters with + the Phylip formats. + + + + CHANGES IN APE VERSION 2.2 + + +NEW FEATURES + + o Four new functions have been written by Damien de Vienne for the + graphical exploration of large trees (cophyloplot, subtrees, + subtreeplot), and to return the graphical coordinates of tree + (without plotting). + + o The new functions corPagel and corBlomberg implement the Pagel's + "lambda" and Blomberg et al.'s "ACDC" correlation structures. + + o chronopl() has been improved and gains several options: see its + help page for details. + + o boot.phylo() has now an option 'trees' to possibly return the + bootstraped trees (the default is FALSE). + + o prop.part() has been improved and should now be faster in all + situations. + + +BUG FIXES + + o read.dna() failed if "?" occurred in the first 10 sites of the + first sequence. + + o The x/y aspect of the plot is now respected when plotting a + circular tree (type = "r" or "f"). + + o Drawing the tip labels sometimes failed when plotting circular + trees. + + o zoom() failed when tip labels were used instead of their numbers + (thanks to Yan Wong for the fix). + + o drop.tip() failed with some trees (fixed by Yan Wong). + + o seg.sites() failed with a list. + + o consensus() failed in some cases. The function has been improved + as well and is faster. + + + + CHANGES IN APE VERSION 2.1-3 + + +BUG FIXES + + o A bug in read.nexus() made the Windows R-GUI crash. + + o An error was fixed in the computation of ancestral character + states by generalized least squares in ace(). + + o di2multi() did not modify node labels correctly. + + o multi2di() failed if the tree had its attribute "order" set to + "cladewise". + + + CHANGES IN APE VERSION 2.1-2 NEW FEATURES + o There three new methods for the "multiPhylo" class: str, $, + and [[. + o root() gains the options 'node' and 'resolve.root' (FALSE by default) as well as its code being improved. + o mltt.plot() has now an option 'log' used in the same way + than in plot.default(). + + +BUG FIXES + + o mltt.plot() failed to display the legend with an unnamed + list of trees. + + o nodelabels() with pies now correcly uses the argument + 'cex' to draw symbols of different sizes (which has + worked already for thermometers). + + o read.nexus() generally failed to read very big files. + + +OTHER CHANGES + + o The argument 'family' of compar.gee() can now be a function + as well as a character string. + + o read.tree() and read.nexus() now return an unnamed list if + 'tree.names = NULL'. + + o read.nexus() now returns a modified object of class "multiPhylo" + when there is a TRANSLATE block in the NEXUS file: the individual + trees have no 'tip.label' vector, but the list has a 'TipLabel' + attribute. The new methods '$' and '[[' set these elements + correctly when extracting trees. + CHANGES IN APE VERSION 2.1-1 @@ -78,9 +258,9 @@ BUG FIXES OTHER CHANGES - o The code of mlphylo() has almost entirely rewritten, and should - much stabler now. The options have been also greatly simplified - (see ?mlphylo and ?DNAmodel for details). + o The code of mlphylo() has been almost entirely rewritten, and + should be much stabler. The options have been also greatly + simplified (see ?mlphylo and ?DNAmodel for details). o The internal function nTips has been renamed klastorin_nTips.