use 'permutations' matrix in anovacca.byaxis

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2735 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
update anovacca interface and add by = 'margin'

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2738 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
using update is dangerous in functions; use the new setFoo<- functions instead; this means we now depend on permute 0.7-8 or later

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2744 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
update permutest method to the new permute API

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2745 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
document r2744 and r2745

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2746 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
take Random.seed and control from permutationMatrix

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2748 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
use drop.scope

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2749 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
handle null-models without constraints

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2750 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
handle one axis and one constraint cases in anovacca by=

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2751 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
fix comparison for equality of numbers of observation

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2756 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
handle NA in anovacca models (if you can)

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2757 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
handle subsets in anovacca

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2758 edb9625f-4e0d-4859-8d74-9fd3b1da38cb