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 There are certainly similar outdated statements in the 300 pages of the manual. 5) Klaus suggests to have more functions returning their "return value" invisibly to make easier the use of pipe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]/
