Squashed commit of the following:

commit 857c8e06410d0cbe1cec8fe92f08fc7714bb3323
Merge: e6e7d99 98731c7
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Tue Oct 14 11:37:41 2014 +0300

    Merge pull request #56 from jarioksa/permustats-fixes

    Permustats fixes

commit 98731c71d47d9c17fa713f43c1c54865a1a682ee
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Tue Oct 14 11:30:44 2014 +0300

    summary of permustats failed with a vector of permutations

    Function assumed that permutations are in a column matrix (one
    column for each statistic). Now vectors of a single statistic are
    coerced to a column matrix. The summary failed with the following
    results: anosim, mantel (+ mantel.partial), mrpp and permutest.cca.

commit edfb8a7f98449f3539ced28e995ea67b51ffa1af
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Tue Oct 14 11:05:52 2014 +0300

    export permutest.protest

commit e6e7d99abcf8a663d5e6156369f96589cd8e0cb6
Merge: 6b29357 6a45940
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Tue Oct 14 10:48:38 2014 +0300

    Merge pull request #54 from gavinsimpson/improve-betadisper-ptest

    Improve permutest.betadisper returned object

commit 6a45940e7482dba683a0a838a48ae7e0462c5507
Author: Gavin Simpson <ucfagls@gmail.com>
Date:   Mon Oct 13 20:37:38 2014 -0600

    update author info

commit 74cd7296e5891de05f4caa82c6a2d1dba591f423
Author: Gavin Simpson <ucfagls@gmail.com>
Date:   Mon Oct 13 19:22:26 2014 -0600

    Updated reference material

commit 1a90a2339e66754441353cef67ae32a1ab773493
Author: Gavin Simpson <ucfagls@gmail.com>
Date:   Mon Oct 13 16:39:43 2014 -0600

    Need to replicate alternative if methods only supply a single alternative for multiple statistics, as per permustats.adonis and first example in ?permustats

commit 9647f58ea2c5f4c91cf5a48171137940e16c486c
Author: Gavin Simpson <ucfagls@gmail.com>
Date:   Mon Oct 13 16:15:56 2014 -0600

    update the test material for examples

commit aaef90cf317fab5f7c2898abbfc1607df70f9e91
Author: Gavin Simpson <ucfagls@gmail.com>
Date:   Mon Oct 13 15:37:55 2014 -0600

    Modification to the help to reflect removal of 'probs' and addition of 'interval'; other tweaks and minor changes

commit 8bac53666101084dd216b17147670dc6ddb7d908
Author: Gavin Simpson <ucfagls@gmail.com>
Date:   Mon Oct 13 15:34:53 2014 -0600

    include an indication of the type of test statistic in the names of the statistic component of the returned object

commit 560696a5692738059c26999401d0debe636ef3e2
Author: Gavin Simpson <ucfagls@gmail.com>
Date:   Mon Oct 13 14:50:04 2014 -0600

    don't transpose permutations; treat printed elements as test statistics 'tst.ind' in printCoefmat

commit 5c598511130d071272d84802ff6bb6a794486e74
Author: Gavin Simpson <ucfagls@gmail.com>
Date:   Mon Oct 13 11:03:34 2014 -0600

    Update the reference materials for testing examples

commit 1f7b4ce38daed82facab430dc658901a9b6063cf
Author: Gavin Simpson <ucfagls@gmail.com>
Date:   Mon Oct 13 10:44:20 2014 -0600

    really fix the printed interval statement; didn't set the separator

commit c95defa9e1eb79213f7f09d8c6cf18457e23de25
Author: Gavin Simpson <ucfagls@gmail.com>
Date:   Mon Oct 13 10:38:29 2014 -0600

    update the Rd fiile for permustats to remove argument probs and add argument interval

commit f5b0ed8d66fecd1363ade3c51265d3b1563f7564
Author: Gavin Simpson <ucfagls@gmail.com>
Date:   Mon Oct 13 10:36:11 2014 -0600

    update the example for permustats to illustrate use of interval

commit c75da6cd115b0f4155ff567e6c35b26c3b9b9b8f
Author: Gavin Simpson <ucfagls@gmail.com>
Date:   Mon Oct 13 10:35:00 2014 -0600

    tweak interval statement in print method

commit 41f31de7c9a014af5b2547e24cb39bfae2bf282d
Author: Gavin Simpson <ucfagls@gmail.com>
Date:   Mon Oct 13 10:34:08 2014 -0600

    implement Jari's suggestion of a single table with lower and upper defined for user-specified interval; for less and greater, upper and lower will be blank, respectively, under this scenario.

commit d11462a1bbb61eea5f70ae2b0172014cdc885a84
Author: Gavin Simpson <ucfagls@gmail.com>
Date:   Sun Oct 12 21:03:15 2014 -0600

     * Add some tests of user-supplied 'probs'
     * rbind together tests with same alternative

commit 8adf8fddd7d048c7523fe35d51dfb747a0105671
Author: Gavin Simpson <ucfagls@gmail.com>
Date:   Sun Oct 12 21:01:55 2014 -0600

    add an example of specifying probs

commit 06ed3ccd2b354235b94345db3045c887cf1f9c9c
Author: Gavin Simpson <ucfagls@gmail.com>
Date:   Sun Oct 12 20:59:56 2014 -0600

    set dimnames rather than colnames

commit ce59956d7de3c892e6f7766fd39f9a790934156d
Author: Gavin Simpson <ucfagls@gmail.com>
Date:   Sun Oct 12 17:28:42 2014 -0600

    document that probs can be a list if a vector of alternatives is present.

commit 7a2d3c77dc3a09005240a4a4c9fc7ce229bca532
Author: Gavin Simpson <ucfagls@gmail.com>
Date:   Sun Oct 12 16:33:54 2014 -0600

    Additional improvements following discussions with Jari:

     * summary.permustats now handles multiple types of alternative hypotheses
     * print.summary.permustats prints different types of alternatives in separate tables
     * permustats.permutest.betadisper now correctly specifies the multiple alternative hypoetheses if pairwise tests were performed in permutest.betadisper

commit 9efe4b8de20c65b1e8f7ff16ff634e047088819e
Author: Gavin Simpson <ucfagls@gmail.com>
Date:   Sat Oct 11 12:30:28 2014 -0600

    update reference materials

commit 1d423b3a9e009a0e0045ab5f495df7ed6bf501ab
Author: Gavin Simpson <ucfagls@gmail.com>
Date:   Sat Oct 11 12:12:59 2014 -0600

    update example to use the new permustats method & draw some plots

commit fb7b12eff0588de8676fa29e451c81db6714fc0f
Author: Gavin Simpson <ucfagls@gmail.com>
Date:   Sat Oct 11 12:12:17 2014 -0600

    add a permustats method for class 'permutest.betadisper'

commit 42b18892d752d74eff0cc40b43b22135979cb38a
Author: Gavin Simpson <ucfagls@gmail.com>
Date:   Sat Oct 11 11:19:33 2014 -0600

    return vector of observed statistic(s) and matrix of permuted values of the statistic(s) under the null hypothesis

git-svn-id: svn://svn.r-forge.r-project.org/svnroot/vegan@2900 edb9625f-4e0d-4859-8d74-9fd3b1da38cb