Hello, Emmanuel, I overlooked that repo, sorry. OK, so I opened https://github.com/emmanuelparadis/ape/issues/72 and https://github.com/emmanuelparadis/ape/pull/71 Sincerely, V.
Dne úterý 7. března 2023 12:13:49 CET, Emmanuel Paradis napsal(a): > Hi Vojtěch, > The GH repos for ape is: > https://github.com/emmanuelparadis/ape > I had a quick look at your code and these are interesting improvements. > It seems also possible to improve the basic code of dist.topo() (e.g., > using bitsplits) so it is worth opening an issue. > Cheers, > Emmanuel > > ----- Le 6 Mar 23, à 20:43, Vojtěch Zeisek a écrit : > > Hello dear colleagues, > > I use often ape::dist.topo (see here dist.topo.r), which is doing > > the calculations sequentially, which is very slow for large data > > sets. I'm sorry, I haven't found any relevant Git repository or so, > > so I hope Emmanuel won't mind if I discuss it here. > > I discussed various options with ChatGPT and dist.topo.par1.r is the > > simplest solution, basically using mc.lapply instead of 2 for loops. > > Good study material for how to do it in general. Little enhancements > > are in dist.topo.par2.r, which should be slightly better in case some > > pair of comparisons would return NA or so, but from my tests there > > doesn't seem to be any difference. > > And finally there is dist.topo.par3.r which doesn't load parallel > > (and uses plain lapply) for cores==1, while parallel and doParallel > > for multiple cores. It also contains some checks and error handling. > > From my testing it works well. I'm not sure if tryCatch is really > > needed there. In any case, improvements welcomed. :-) > > So, what do You think? Is this usable improvement of ape::dist.topo? > > Sincerely, > > V. -- Vojtěch Zeisek https://trapa.cz/en/ Department of Botany, Faculty of Science Charles University, Prague, Czech Republic https://www.natur.cuni.cz/biology/botany/ https://lab-allience.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 - 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/
