Hello, this a perfect idea. :-) I'd love to see one two things: 1) Support for parallelization whenever possible (various distance, work with multi.whatever objects, ...) to speed things up. 2) Removal of all the *.mutliPhylo functions, i.e. IMHO the best would be if every relevant function would support phylo as well as multiPhylo objects. Now it's a bit confusing whenever to use which function... So here are my proposals for the discussion. :-) Sincerely, V.
Dne pondělí 26. ledna 2026 16:31:24, středoevropský standardní čas, Emmanuel Paradis napsal(a): > Dear all, > > We are in the process of reviewing the "old" code in ape (some written in > 2001). Here are a few things that came out recently: > > 1) During a recent discussion, we wondered if the option "..." of > read.tree() is useful; it is passed internally to scan(). A review of the > CRAN packages suggests this option is useless so it could be removed, at > least without breaking those packages. There may be other bits of code that > can be removed safely in other functions. > > 2) Printing of objects could be improved. > > 3) I've (re)introduced a function mafft() in ape. A function with the same > name was formerly in ips which is now orphaned on CRAN. > > 4) A review of the man pages (help) would be useful. For instance, in > ?read.tree one can read: "If there are two root edges (e.g., > "(((A:1,B:1):10):10);"), then the tree is not read and an error message is > issued." [1] which is wrong since all types of Newick tree can be read. > There are certainly similar outdated statements in the 300 pages of the > manual. > > 5) Klaus suggests to have more functions returning their "return value" > invisibly to make easier the use of pipe operators (|> or %>%). > > Any thoughts, ideas, or comments are welcome. > > Best, > > Emmanuel > > [1] In version 5.8-1 currently on CRAN; now fixed on GitHub. -- Vojtěch Zeisek https://trapa.cz/en/ Department of Botany, Faculty of Science Charles University, Prague, Czech Republic https://botany.natur.cuni.cz/ Institute of Botany, Czech Academy of Sciences Průhonice, Czech Republic https://www.ibot.cas.cz/en/ Computing cluster https://sorbus.ibot.cas.cz/en/start
signature.asc
Description: This is a digitally signed message part.
_______________________________________________ R-sig-phylo mailing list - [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/[email protected]/
