Merge branch 'master' into r-forge-svn-local

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2127 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
Squashed commit of the following:

commit 636a35f0c513b5688b119c16967d97c74eff0ba5
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Wed Apr 11 11:08:46 2012 +0300

    anova(<prc-object>, by = ...) failed due to NAMESPACE issues

    Reported as issue #7 by Eduard Scöcz in github.com

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2128 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
Squashed commit of the following:

commit 511d3642fb58717c78f4f17e5059aa26732f652d
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Sun Apr 15 08:32:20 2012 +0300

    envfit()/factorfit() failed factors had unused levels

    Reported as issue #8 in github.com by Eduard Szöcz and fixed
    in centroids.cca()

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2129 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
Merge branch 'master' into r-forge-svn-local

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2131 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
Squashed commit of the following:

commit 3613e7ddc309f6f186600c0761e1cb8cd5930ef9
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Tue Apr 17 13:15:36 2012 +0300

    adipart assumed constant gamma diversity in all simulations

    The default method ("r2dtable") had constant gamma, but some other
    methods gave variable gamma diversities, and this gave biased
    test results.

    If we are interested in beta, the gamma should *not* vary, and setting
    'relative = TRUE' probably makes sense with variable gamma.

commit 46fc8aca0a2eca71545a84d17ab82aa0583f9bf6
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Tue Apr 17 12:52:39 2012 +0300

    indentation of adipart.R

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2132 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
Merge branch 'master' into r-forge-svn-local

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2133 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
Merge branch 'master' into HEAD

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2135 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
Squashed commit of the following:

commit b5ba108091c8605249f76b6a88a1094a5a44663b
Merge: 11ec6e3 fc59744
Author: jarioksa <jari.oksanen@oulu.fi>
Date:   Sat Apr 21 22:05:48 2012 -0700

    Merge pull request #9 from EDiLD/pyrifos

    added Information about the used transformation.

commit fc59744ead40220dad73caa9d16964a3eaed5f51
Author: edisz <szoe8822@uni-landau.de>
Date:   Sat Apr 21 16:56:53 2012 +0200

    formatting

commit 9863139145f486cb121e5f1ea66ab08a445660df
Author: edisz <szoe8822@uni-landau.de>
Date:   Wed Apr 18 15:01:50 2012 +0200

    added Information about the used transformation.

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2137 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
Squashed commit of the following:

commit 1ac611ee9e29ee427bd1aa411531a50fa32a6768
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Mon Apr 23 10:54:02 2012 +0300

    Squashed commit of the following (clamtest fix):

    commit 30dc4e2690b6ce20adfb43709e18349bab9e63a3
    Merge: b5ba108 947e42d
    Author: Jari Oksanen <jari.oksanen@oulu.fi>
    Date:   Mon Apr 23 10:51:36 2012 +0300

        Merge commit '947e42d' into test

    commit 947e42d71c27895dec8af983201619441af42341
    Author: psolymos <psolymos@gmail.com>
    Date:   Sat Apr 21 23:23:14 2012 -0600

        clamtest: coverage calculation fixed

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2139 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
Merge branch 'master' into r-forge-svn-local

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2142 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
Merge branch 'test' into r-forge-svn-local

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2143 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
multipart ad hiersimu follow adipart (constant gamma fix)

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2144 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
update tests for adipart/hierpat/multipart changes

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2145 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
devel version to vegan_2.1-15

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2146 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
reorder and edit ChangeLog

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2147 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
format references

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2148 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
Merge branches 'r-forge-svn-local' and 'master'