It's hard to evaluate the effect of (5) without knowing what functions we are talking about. I will point out that invisible returns are very confusing to novice R users. -Dave
On Mon, Jan 26, 2026 at 9:31 AM Emmanuel Paradis <[email protected]> wrote: > 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 There are certainly similar outdated statements in the 300 pages of the 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. > > _______________________________________________ > 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]/ > [[alternative HTML version deleted]] _______________________________________________ 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]/
