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 vo...@trapa.cz 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 > > _______________________________________________ > 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/ _______________________________________________ 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/
