vegandevs/vegan — pull request #30 by jarioksa (2014-09-04 13:44:30+00:00)
Title: Deprecated defunct

This PR will deprecate, make defunct or remove defunct functions:

* `commismulator` is deprecated. It is still functional (but issues a warning), although it is replaced with the new `nullmodel` & `commsim`.
* `metaMDSrotate` is made defunct. It was replaced with `MDSrotate` in **vegan** 2.0-0 and been deprecated since then.
* `getNumObs` is removed completely. It was first moved to **permute** and deprecated then in **vegan** (2.0-0), and probably gone from **permute** , too.
* `permuted.index2` was gone with the **permute** package, too. Now it is removed completely.

The PR will change `NAMESPACE` and this may cause conflicts with other open branches which change `NAMESPACE` (jarioksa/vegan:parallel, guiblanchet/vegan:master). However, the changes are not physically close to each other so that these may pass.