X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=ChangeLog;h=c702b68074489aa961044ce2efd6819da03b96c4;hb=d5b85d181648e2761cecc91d75c4c66fa05e4508;hp=abb26160fda15c623d83ff7f149271973307cf58;hpb=f91082164111e17be175283d9fe8335e89424d42;p=ape.git diff --git a/ChangeLog b/ChangeLog index abb2616..c702b68 100644 --- a/ChangeLog +++ b/ChangeLog @@ -1,3 +1,203 @@ + 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 @@ -57,6 +257,9 @@ OTHER CHANGES 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