changing behaviour of update method

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2163 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
documenting: changing behaviour of update method

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2164 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
change in nullmodel interface calls for version change (to 2.1-16)

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2165 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
update tests for r2164

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2166 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
add warning of possible unequal aspect ratio in ordiplot3d

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2167 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
envift.convert() did not honour choices set in ordiplot3d

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2168 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
Squashed commit of the following:

commit 44e23b3fabc2c7b243432860c46be8fe94fa1885
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Sun May 20 16:30:32 2012 +0300

    bioenv accepts dissimilarities as an alternative to community data

    The change was triggered by a user request by Victor L. Landeiro.
    Now it is possible to use other dissimilarities than those in vegdist.
    In this user request the desire was to use betadiver() dissimilarities.

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2170 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
count only non-zero dissimilarities (= distinct points) for lower limit of sufficient data in monoMDS

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2172 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
ordihull adds labels after drawing all hulls so that they are not shadowed by filled hulls

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2173 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
ordihull centres labels more correctly

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2174 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
put ordihull labels *really* to the centroids

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2175 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
ordihull & ordiellipse default to semitransparent fill colour with draw = 'polygon'

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2176 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
adapt tests to r2176

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2177 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
add select argument to ordipointlabel

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2178 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
only warn about insufficient data in NMDS, but more loudly

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2179 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
length check on select arg only if select is a logical vector

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2180 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
an if() statement was accidentally dropped

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2181 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
FAQ about insufficient data in NMDS

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2182 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
FAQ: update year and html version

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2183 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
Warn about "too good stress" only in metaMDS

Assume that users of monoMDS know what they are doing
and do not warn them. Also no permanent print messages,
but only a run-time warning. 

Reverts commits r2150, 2172, 2179, 2181.


git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2184 edb9625f-4e0d-4859-8d74-9fd3b1da38cb