[Vegan-commits] r2951 - in pkg/vegan: . R man

[noreply at r-forge.r-project.org]

Author: jarioksa
Date: 2015-06-09 11:45:33 +0200 (Tue, 09 Jun 2015)
New Revision: 2951

Modified:
   pkg/vegan/DESCRIPTION
   pkg/vegan/R/centroids.cca.R
   pkg/vegan/R/ordiR2step.R
   pkg/vegan/man/monoMDS.Rd
   pkg/vegan/man/vegan-package.Rd
Log:
Merge branch 'cran-2.3' into r-forge-svn-local

Modified: pkg/vegan/DESCRIPTION
===================================================================
--- pkg/vegan/DESCRIPTION	2015-05-25 06:52:06 UTC (rev 2950)
+++ pkg/vegan/DESCRIPTION	2015-06-09 09:45:33 UTC (rev 2951)
@@ -1,12 +1,12 @@
 Package: vegan
 Title: Community Ecology Package
-Version: 2.3-0
-Date: 2015-05-21
+Version: 2.3-1
+Date: 2015-05-28
 Author: Jari Oksanen, F. Guillaume Blanchet, Roeland Kindt, Pierre Legendre, 
    Peter R. Minchin, R. B. O'Hara, Gavin L. Simpson, Peter Solymos, 
    M. Henry H. Stevens, Helene Wagner  
 Maintainer: Jari Oksanen <jari.oksanen at oulu.fi>
-Depends: permute (>= 0.7-8), lattice, R (>= 2.15.0)
+Depends: permute (>= 0.8-0), lattice, R (>= 2.15.0)
 Suggests: parallel, tcltk
 Imports: MASS, cluster, mgcv
 Description: Ordination methods, diversity analysis and other

Modified: pkg/vegan/R/centroids.cca.R
===================================================================
--- pkg/vegan/R/centroids.cca.R	2015-05-25 06:52:06 UTC (rev 2950)
+++ pkg/vegan/R/centroids.cca.R	2015-06-09 09:45:33 UTC (rev 2951)
@@ -1,7 +1,7 @@
 `centroids.cca` <-
     function(x, mf, wt)
 {
-    facts <- sapply(mf, is.factor)
+    facts <- sapply(mf, is.factor) | sapply(mf, is.character)
     if (!any(facts))
         return(NULL)
     mf <- mf[, facts, drop = FALSE]

Modified: pkg/vegan/R/ordiR2step.R
===================================================================
--- pkg/vegan/R/ordiR2step.R	2015-05-25 06:52:06 UTC (rev 2950)
+++ pkg/vegan/R/ordiR2step.R	2015-06-09 09:45:33 UTC (rev 2951)
@@ -21,6 +21,11 @@
         R2.0 <- 0
     else
         R2.0 <- RsquareAdj(object)$adj.r.squared
+    ## only accepts upper scope
+    if (is.list(scope) && length(scope) <= 2L)
+        scope <- scope$upper
+    if (is.null(scope) || !length(add.scope(object, scope)))
+        stop("needs upper 'scope': no terms can be added")
     ## Get R2 of the scope
     if (inherits(scope, "rda")) 
         scope <- delete.response(formula(scope))

Modified: pkg/vegan/man/monoMDS.Rd
===================================================================
--- pkg/vegan/man/monoMDS.Rd	2015-05-25 06:52:06 UTC (rev 2950)
+++ pkg/vegan/man/monoMDS.Rd	2015-06-09 09:45:33 UTC (rev 2951)
@@ -138,7 +138,7 @@
   components so that the first dimension shows the major variation.
   It is possible to rotate the solution so that the first axis is
   parallel to a given environmental variable using function
-  \code{\link{metaMDSrotate}}.
+  \code{\link{MDSrotate}}.
 
 }
 

Modified: pkg/vegan/man/vegan-package.Rd
===================================================================
--- pkg/vegan/man/vegan-package.Rd	2015-05-25 06:52:06 UTC (rev 2950)
+++ pkg/vegan/man/vegan-package.Rd	2015-06-09 09:45:33 UTC (rev 2951)
@@ -23,11 +23,9 @@
 fields. Package \pkg{BiodiversityR} provides a GUI for a large subset
 of \pkg{vegan} functionality.
 
-The \pkg{vegan} package is developed at R-Forge
-(\url{http://vegan.r-forge.r-project.org}).  The R-Forge provides
-up-to-date information and mailing lists for help queries and bug
-reports. Bug reports can also be emailed to the function authors or to
-the package maintainers.
+The \pkg{vegan} package is developed at GitHub
+(\url{https://github.com/vegandevs/vegan/}).  GitHub provides up-to-date
+information and forums for bug reports.
 
 The \pkg{vegan} documents can be read with \code{\link{vegandocs}}
 function. In addition to \code{\link{vignette}}s of basic usage, you
@@ -49,9 +47,6 @@
 R. Minchin, R. B. O'Hara, Gavin L. Simpson, Peter Solymos, M. Henry
 H. Stevens, Helene Wagner.  Many other people have contributed to
 individual functions: see credits in function help pages.
-
-The maintainers at the R-Forge are Jari Oksanen <jari.oksanen at oulu.fi>
-and Gavin Simpson <gavin.simpson at ucl.ac.uk>.
 }
 \examples{
 ### Example 1: Unconstrained ordination