correct (= up-to-date) Examples in tests/

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2488 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
big changes to ordisurf in one nice commit that can be reverted easily. See Changelog for details.

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2490 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
build formulae for different options and fit via a single gam call, not via separate hard-coded gam calls; also allows nicer printing of the actual formula used

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2491 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
adds fx argument to fit fixed degree freedom regression splines

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2492 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
some of the bases don't work in 2-D 's()' smooths; 'fx = TRUE' and 'select = TRUE' are not compatible; updated all examples to reflect new defaults and options; updated the help page significantly with new notes, warnings etc.

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2493 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
update tests/Examples for ordisurf changes

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2494 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
Merge branch 'r-forge-svn-local'
Fix twisted tests in oecosimu.

Change direction of one-sided tests to their opposite, and explain
the sidedness in comprehensible terms in printout. 
Fixes issue #14 in GitHub (opened by jumanbar)


git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2495 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
Merge branch 'r-forge-svn-local': fixes issue #14
use crossprod()

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2496 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
Avoid visible ~ in pdf documents (such as Figure~1)

The invisible space marker "~" was visible due to a
texi2dvi bug. This was most visible in legends like "Figure~1",
where "~" was added by LaTeX. Most (or all) self-made
instances of "~" were already removed or replaced with "\;".
It seems that (unnecessary) \usepackage[english]{babel} fixes
this issue.


git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2497 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
raupcrick adapted to r2495: change test directions in onesided oecosimu

(this was spotted by tests/oecosimu-tests)


git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2498 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
Merge branch 'r-forge-svn-local'
implement Mahalanobis, Manhattan and Gower metrics for bioenv

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2499 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
rankindex gained Mahalanobis and Manhattan metrics for gradients

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2500 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
add Mahalanobis to vegdist

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2501 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
Merge branch 'r-forge-svn-local'
use 'symmetric' eigen analysis in veganMahatrans

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2502 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
Merge branch 'r-forge-svn-local'
bioenv passes ... to cor() like documented

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2503 edb9625f-4e0d-4859-8d74-9fd3b1da38cb