X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=NEWS;h=807a2e4fe3fc37650dc74b45bb914126c94cb59a;hb=refs%2Fheads%2Fmaster;hp=1f2cd220f396a79f3bc7b53b25555fa3bf2a683c;hpb=a0436318d70829a2d16134be7ca1d6d454613a20;p=ape.git diff --git a/NEWS b/NEWS index 1f2cd22..807a2e4 100644 --- a/NEWS +++ b/NEWS @@ -1,9 +1,57 @@ + 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 - The new function chronos .......... + 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. @@ -36,9 +84,8 @@ OTHER CHANGES o base.freq() is now faster with lists. - as.matrix.DNAbin() ............ should be faster.... now accepts vectors, - - read.dna() has a new for FASTA files............. faster C code. + o as.matrix.DNAbin() should be faster and more efficient with + lists; it now accepts vectors. @@ -480,7 +527,7 @@ NEW FEATURES 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.