R devel - Sep 2014 - vegan moved to GitHub and vegan 2.2-0 is coming (are you ready?)

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

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
> ______________________________________________
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