vegandevs/vegan — pull request #46 by jarioksa (2014-09-28 18:13:19+00:00)
Title: Add permustats with support functions, deprecate corresponding densit[plot]

The PR adds new function `permustats` that can extract permutation or simulation results in any **vegan** function returning those. It has the following support functions:
- `summary` that gives the *z* value (a.k.a. standardized effect size, SES) and quantiles of permutations.
- `density` (**stats**) and `densityplot` (**lattice**) for the density of permutations.
- `qqnorm` (**stats**) and `qqmath`(**lattice**) for the Q-Q plots of permutations.

These new functions deprecate old `density` and `densityplot` methods that directly accessed the result objects. In old code, `densityplot` was only available for methods that could return a vector of several statistics (`adonis`, `oecosimu`) but the new **lattice** functions are available for all permutation functions.