Hi Emmanuel (and list!), These changes are appreciated, and will make dealing with multiPhylo objects much easier. I know I certainly have blocks of code where I need to 'carry' the multiPhylo class tag through every other line; it always been a bit of a chore. However, two questions from the peanut gallery.
1) Does this change result in any change in speed? Have you tested this? (My guess is no practical computational time change, but I was curious.) 2) Will those of us using these particular functions due to a dependency or importing ape functions for our libraries need to alter the way we call those particular functions? Have you tested this with R CHECK? Finally, thank you to you (and the rest of the ape authors) for continuing to maintain and improve ape. Cheers, -Dave On Mon, Oct 3, 2016 at 8:51 AM, Emmanuel Paradis <emmanuel.para...@ird.fr> wrote: > Dear all, > > We are planning to introduce a substantial change in ape: several functions > operating on "phylo" objects will be made generic with methods for "phylo" > and "multiPhylo" objects. The motivation is to make things simpler when > working with lists of trees. For instance, for a list of trees TR, testing > if each tree is rooted can be donc with: > > sapply(TR, is.rooted) > > With the new version, this would be: > > is.rooted(TR) > > which is similar than for a "phylo" object. With functions requiring > additional arguments, e.g., to root all the trees with the same outgroup, > the current code is slightly more complicated: > > TRr <- lapply(TR, root, outgroup = "platypus") > class(TRr) <- class(TR) > > This is because lapply does not propagate the class of its first argument. > The new code will be as simple as with a "phylo" object: > > TRr <- root(TR, "platypus") > > To summarize the future changes: > > 1/ Functions to become generic with methods for "phylo" and "multiPhylo": > > di2multi > drop.tip > is.binary (see below) > is.rooted > is.ultrametric > ladderize > multi2di > Nedge > Nnode > Ntip > reorder > root > unroot > > 2/ is.binary.tree() will be renamed is.binary() since the name is available > (an alias with is.binary.tree will be provided for the next release). > > 3/ Functions already with methods for "phylo" and "multiPhylo" in ape > (nothing to change): > > makeLabel (generic defined in ape) > plot > print > summary > > 4/ The c() methods (currently for "phylo" and "multiPhylo") will be improved > by implementing the 'recursive' option (currently ignored). This will permit > to combine several objects of different classes into a single "multiPhylo" > object (i.e., either a list of trees, or a list of lists depending on the > value of 'recursive'; see ?c). > > 5/ Functions already with methods for "multiPhylo" (nothing to change): > > str > unique > > Comments and suggestions are welcome. These changes will be included in the > next release of ape which will be version 4.0 and is planned this fall. As a > reminder, the changes already implemented are listed in: > > http://ape-package.ird.fr/NEWS > > Best, > > Emmanuel > > _______________________________________________ > R-sig-phylo mailing list - R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ -- David W. Bapst, PhD Adjunct Asst. Professor, Geology and Geol. Eng. South Dakota School of Mines and Technology 501 E. St. Joseph Rapid City, SD 57701 http://webpages.sdsmt.edu/~dbapst/ http://cran.r-project.org/web/packages/paleotree/index.html _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
