Dear R-Devels, My apologies for using a wrong list. Please ignore my messages. I would undo this if I only could, but what's done can't be undone (not the the first time in my life when I've learnt this).
Cheers, Jari Oksanen On 13/09/2014, at 08:13 AM, Jari Oksanen wrote: > Dear vegan team, > > Vegan development happens now completely in github. R-Forge repository is no > more in sync with github. I tried to commit all github changes to R-Forge, > but a week ago I got a conflict in file and I haven't had time to resolve > that conflict. You can follow vegan development and vegan discussion also > without signing to github. The system seems to be completely open and does > not require any user credentials (and this is good to remember when we > discuss about things). The developer front page is > > https://github.com/vegandevs > > We have prepared for the vegan 2.2-0 release. This would be a major release > that would close the gap between current development version and CRAN. I > haven't set any firm date for the release, but I think R 3.2.0 will be out in > October, and we should try to be concurrent with that -- in particular as the > 2.0-10 in CRAN will give warnings in R check for that version. > > We have now solved a couple of major issues. > > - on technical side: the next R release will spit out tens of warnings for > namespace issues (visibility of functions). These were solved in > https://github.com/vegandevs/vegan/pull/28 > > - all vegan functions doing permutation are now based on Gav's permute > package. This means that they can use any constrained permutation scheme of > the permute package. This also concerns functions that earlier only had > simple permutation. Of course, you do not need to use fancy permutation > schemes, but the default is still simple permutation and this can be > expressed by giving just the number of permutations on the command line. The > functions using the new permutation scheme are adonis, anosim, anova.cca for > CCA/RDA/dbRDA and hence also for ordistep etc., CCorA, envfit, mantel & > mantel.partial, mrpp, mso, permutest.betadisper, permutest.cca, protest and > simper. The change for functions is now complete, but same clean up and > updating of documentation is still to be done. This is discussed in > https://github.com/vegandevs/vegan/issues/31 > > - vegan 2.2-0 will also use parallel processing in several functions. This > was already done in several functions in vegan development. The discussion on > extending parallel processing to other functions was just opened in > https://github.com/vegandevs/vegan/issues/36 . Currently the following > functions can use parallel processing: adonis, anosim, anova.cca, mantel, > mantel.partial, mrpp and simper can use it permutations, bioenv can asses > several competing models in parallel, metaMDS can launch several random > starts in parallel and oecosimu can use parallel processing in evaluating the > statistics for null communities. If you compare this to the previous list of > permutation functions, you see that the following permutation methods do not > use parallel procesing: CCorA, envfit, mso, permutest.betadisper and protest. > The question is if these also should be parallelized or can we leave them > like they are, at least for the next release. > > - A more controversial issue is that Gav suggested moving rgl-based functions > away from vegan to a separate package > (https://github.com/vegandevs/vegan/issues/29 ). The main reason was that rgl > can cause problems in several platforms and even prevent installing vegan. > Indeed, when I tested these functions, they crashed in this Mac laptop. We > have now a separate vegan3d package for these functions > https://github.com/vegandevs/vegan3d . In addition to ordirgl + friends, > rgl.isomap and rgl.renyiaccum it also has oriplot3d package. This package has > now the same functionality as these functions had in vegan, and our purpose > is to release that concurrently with vegan 2.2-0. I recently suggested to > remove these functions from vegan, but we haven't made that change yet so > that you can express your opinion on the move. See > https://github.com/vegandevs/vegan/pull/37 > > There are some simpler and smaller things, but you can see those if you > follow github. > > I have now mainly worked with my private fork of vegan and "pushed to vegan > upstream" changes when they have looked more or less finished. At this stage, > I have made a "pull request", and normally waited for possible comments. To > get a second opinion, I have usually waited that Gav has a look at the > functions and let him merge them to vegan. Sometimes there has been a long > discussion before merge and we have edited the functions before the merge > (e.g., https://github.com/vegandevs/vegan/pull/34 ). If changes are small and > isolated bug fixes, I have pushed them directly to the vegan upstream, > though. I have found this pretty good way of working in github. > > Cheers, Jari Oksanen > ______________________________________________ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
