reference vegdist(..., 'altGower') for Anderson standardization in decostand

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2267 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
mantel & mantel.partial gained arg na.rm = FALSE

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2268 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
use <-

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2269 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
rephrase

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2270 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
plot.varpart accept 'bg' argument to fill the circles

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2271 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
Merge branches 'r-forge-svn-local' and 'master'
predict methods for radline, radift & radfit.frame

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2285 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
Fix scoping issues in anova(<cca.object>, by=...) cases

This fixes two scoping issues raised by Sven Neulinger:

Date: Sat, 15 Sep 2012 17:12:49 +0200
From: Sven Neulinger <sneulinger@ifam.uni-kiel.de>
To: <jari.oksanen@oulu.fi>

When using the anova.cca() command with argument (1) by="axis" and (2) 
by="terms", respectively, on a partial db-RDA object built with 
capscale(), I get the following error messages:

(1) "Error in eval(expr, envir, enclos) : object 'CondMat' not found";
(2) "Error in model.frame.default(P.formula, data, na.action = na.pass, 
xlev = zlev) : object is not a matrix"

Argument (2) also leads to error message (2) with partial RDA using 
rda() on the same data.



git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2287 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
anova(<prc.object>, by = 'axis') seems to work after r2287

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2288 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
add Sven Neulinger's tests for anova of partial ordination

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2289 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
add fitted.radfit.frame()

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2291 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
predict.radfit gained argument to set the 'total' community size

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2292 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
fitted.rad* return now named vectors or matrices

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2293 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
radfit manual has been out of sync with functions for ages (veiled LN etc)

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2294 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
more consistent UI for radlattice and radfit methods with several new functions to fill the gaps

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2295 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
fix the AIC mess made in r2295 and fix BIC of radlattice since r551 plus add coef.radfit.frame for consistence

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2296 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
upgrade docs to Legendre & Legendre (2012)

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2297 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
restructure and update radfit documentation

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2298 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
fix broken crossref links in Rd files

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2299 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
tweak radfit.Rd

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2300 edb9625f-4e0d-4859-8d74-9fd3b1da38cb