Squashed commit of the following:

commit 82fd87fbbc0176b36aaf90d84f5f7d5b64b9399f
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Sun May 27 09:05:39 2012 +0300

    Revert "Fix calculation of ordimedian"

    This reverts commit 8f956f1ebd9c56174d6c54b1633f4c27133071f3.

commit bc0a08ff5b03206db1b6af1c17422641a66aea98
Merge: 2814a63 eec3be8
Author: jarioksa <jari.oksanen@oulu.fi>
Date:   Sat May 26 22:59:41 2012 -0700

    Merge pull request #11 from bbolker/betadisper

    Betadisper

commit 2814a6332324d7741c828f4d5b0d1f8ca9fec49a
Merge: fc05cf3 b871568
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Sun May 27 08:43:27 2012 +0300

    Merge branch 'r-forge-svn-local'

commit eec3be81187b21aec10ee64ccdb729d779bfb60d
Author: Ben Bolker <bbolker@gmail.com>
Date:   Sat May 26 19:43:41 2012 -0300

    ported changes from main branch (ugh), with slight tweaks

commit 45ba30d6c72f2159d781200f65cdb20149792c7d
Author: Ben Bolker <bbolker@gmail.com>
Date:   Sat May 26 18:08:56 2012 -0300

    save bias adjustment setting as an attribute

commit 25897cf540705449ae49cbb7e1852bbec6ee5527
Merge: 2a95a08 8f956f1
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Tue May 8 16:21:35 2012 +0300

    Merge branch 'ordimedian' into betadisper

commit 2a95a08b1c3d4b81cb1361bbd20c1fcdd870b807
Merge: a10ca2c 3bb2f74
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Tue May 8 16:19:22 2012 +0300

    Merge branch 'master' into betadisper

commit 8f956f1ebd9c56174d6c54b1633f4c27133071f3
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Tue May 8 15:48:14 2012 +0300

    Fix calculation of ordimedian

    Influences also betadisper

commit a10ca2cf02d8ce15fd3f2556bc36380464e284b1
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Thu Apr 19 09:23:19 2012 +0300

    document bias.adjust in betadisper()

commit 2064496d70067ceebefa559de26513da5ed6ea30
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Thu Apr 19 09:19:43 2012 +0300

    canonical way of creating 1x1 diagonal matrices

commit 53c589e7c4d02682155e04deeddb21f57eacfc06
Author: Adrian Stier <adrian.stier@gmail.com>
Date:   Wed Apr 18 10:05:52 2012 +0300

    Bias correction in betadisper with unequal sample sizes

    HI Gavin, Jari, and Marti,

    I'm writing to inquire about the importance of unequal sample sizes in
    deriving and comparing beta diversity estimates across different groups.
    My phd has focused on coral reef fish communities and in response to an
    experiment with unequal sample sizes, a reviewer recently raised the
    issue of unequal sample sizes in biasing beta diversity estimates when
    comparing across groups. I've been working on this project with my
    collaborator Ben Bolker (cc'd here). A numerical simulation he
    constructed suggests that there is indeed bias in estimates of beta
    diversity when sample sizes are unequal and sample sizes are small.

    The solution that Ben converged on was a sqrt(n/(n-1)) correction factor
    that can be applied to estimated distances to centroid for each group
    (i.e. analogous to the correction commonly applied at the for sample
    standard deviations).

     We attach a PDF file showing how we guessed this correction factor
    (which makes sense in hindsight, although I would have difficulty coming
    up with a rigorous derivation).

     We also attach a diff file from the current vegan version on r-forge
    (r2127) which includes an option to correct the bias in this way (as
    well as a one-line fix for an edge case, where there is only one
    non-zero eigenvalue -- we came across this situation in the course of
    running simulations, although it's probably not practically important
    much of the time).  We think this should also work in the presence of NA
    values, although we haven't tested it in that case.)

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2195 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
ChangeLog, doc (\eqn{}) fix plus credit to Adrian Stier and Ben Bolker in doc about bias adjusted betadisper

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2196 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
do not use issue numbers in references

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2197 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
FAQ: some words about local, hybrid and metric scaling and their data size requirements

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2199 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
clumsy fingers and small edits

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2201 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
fix mark-up and update tests

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2204 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
check dimensions of 'newdata' in preict(..., type = 'response'|'working') of a cca() result

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2206 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
tweak warning in predict.cca

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2207 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
one new example on oridplot3d().convert()

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2208 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
Squashed commit of parallel processing in simper:

commit 1d9f4d271633bec61f361292539cc189912217a8
Merge: 68018d8 e6403d4
Author: jarioksa <jari.oksanen@oulu.fi>
Date:   Thu Jun 7 01:13:25 2012 -0700

    Merge pull request #12 from EDiLD/dev-simper

    dev-simper

commit e6403d4a9abf49a7061d142e8906e276c75bf197
Author: edisz <szoe8822@uni-landau.de>
Date:   Sun Jun 3 18:37:24 2012 +0200

    flatten loop...

commit 51ab649b6562635006657f11eda7aa7d09309e91
Author: edisz <szoe8822@uni-landau.de>
Date:   Sun Jun 3 18:02:27 2012 +0200

    updated documentation

commit cce42b35c957f63cf61dacf28502ca35b2387890
Author: edisz <szoe8822@uni-landau.de>
Date:   Sun Jun 3 17:46:13 2012 +0200

    added warning (empty rows)

commit e849723aeceb81ce61e893c1dad2e134dee84163
Author: edisz <szoe8822@uni-landau.de>
Date:   Sun Jun 3 17:42:46 2012 +0200

    parallel processing of permutations

commit ef0809513af9a8aaee1db0a0cc4709ccbd8038f9
Merge: 18d2ec3 6412186
Author: edisz <szoe8822@uni-landau.de>
Date:   Sun Jun 3 03:33:00 2012 +0200

    Merge branch 'dev-simper' of github.com:EDiLD/vegan into dev-simper

commit 18d2ec3247fd4d69c3249003b405cf4e48cd0b98
Author: edisz <szoe8822@uni-landau.de>
Date:   Thu Apr 26 13:14:15 2012 +0200

    work on parallel processing
    updated documentation
    small speed improvement

commit 64121860b390b4ca3c9278c41ba52054571ac4c4
Author: edisz <szoe8822@uni-landau.de>
Date:   Thu Apr 26 13:14:15 2012 +0200

    work on parallel processing
    updated documentation
    small speed improvement

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2213 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
ChangeLog for r2113

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2214 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
plot.envfit gained argument 'bg' to set background colour of labels

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2215 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
vegan release 2.0-4 submitted to CRAN

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2223 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
vegan release 2.0-4 submitted to CRAN

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2223 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
Merge branch 'r-forge-svn-local'
correct length of 'type' if not supplied by user in biplot.rda

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2225 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
the saved call of adipart uses now the generic name instead of full method name

adipart.formula and adipart.default each saved the call as given by
match.call(), and the function was either called adipart.default()
or adipart.formula. Now it is always generic adipart.

For the full force, this also needs the next commit that changes
adipart.formula.
more canonical way of writing adipart.formula (also fixes match.call name)

Function adipart.formula() duplicated the full analysis of adipart.default.
The only difference was the interpretation of the input data. Now
adipart.formula() only interprets the formula and then calls
adipart.default() with the interpreted matrices.

This is also a maintenance issue: now things need be fixed only in
one file, and the methods do not randomly drift apart.

This also means that now the "call" from match.call() is always
set by adipart.default and will be generic adipart() instead of
adipart.formula().
more canonical implementation of hiersimu.formula

hiersimu.formula() only interprets formula and calls hiersimu.default()
without duplicating its code.
more canonical multipart.formula()