[Vegan-commits] r2911 - in pkg/vegan: R vignettes

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

Author: jarioksa
Date: 2014-11-11 15:58:23 +0100 (Tue, 11 Nov 2014)
New Revision: 2911

Modified:
   pkg/vegan/R/plot.envfit.R
   pkg/vegan/vignettes/decision-vegan.Rnw
Log:
Squashed commit of the following:

commit ad5f0dac7e52c2e0c85bd863dd8a47fd88f50975
Author: Jari Oksanen <jari.oksanen at oulu.fi>
Date:   Tue Nov 11 13:46:06 2014 +0200

    Fix labelling envfit plots with a vector of labels

    Fixes bug report #74 at github.com: it was documented that you
    do not need to use a list(vectors=, factors=) to relabel plotted
    items if there is only one type of items (vectors or factors).

commit a2f6b3b49ad94a14b6aa9319830133977a6e502f
Merge: 65e815f a6d876b
Author: Gavin Simpson <ucfagls at gmail.com>
Date:   Mon Nov 10 10:43:22 2014 -0600

    Merge branch 'typo-design-vignette' into cran-2.2

commit a6d876b70b2f91017e84793dea0e2a18560d0ad2
Author: Gavin Simpson <ucfagls at gmail.com>
Date:   Mon Nov 10 09:31:11 2014 -0600

    typo had symbolic forms for species and site scores swapped in table caption?

Modified: pkg/vegan/R/plot.envfit.R
===================================================================
--- pkg/vegan/R/plot.envfit.R	2014-11-10 10:41:55 UTC (rev 2910)
+++ pkg/vegan/R/plot.envfit.R	2014-11-11 14:58:23 UTC (rev 2911)
@@ -21,7 +21,7 @@
                 stop("needs a list with both 'vectors' and 'factors' labels")
             ## need to handle the case where both sets of labels are NULL
             ## such as when used with the default interface and single x
-            ln <- sapply(labs, is.null)
+            ln <- !sapply(labs, is.null)
             if (ln["v"])
                 labs$v <- labels
             if (ln["f"])

Modified: pkg/vegan/vignettes/decision-vegan.Rnw
===================================================================
--- pkg/vegan/vignettes/decision-vegan.Rnw	2014-11-10 10:41:55 UTC (rev 2910)
+++ pkg/vegan/vignettes/decision-vegan.Rnw	2014-11-11 14:58:23 UTC (rev 2911)
@@ -428,8 +428,8 @@
     in the functions \code{prcomp} and \code{princomp}, and the
     one used in the \pkg{vegan} function \code{rda} 
     and the proprietary software \proglang{Canoco}
-    scores in terms of orthonormal species ($u_{ik}$) and site scores
-    ($v_{jk}$), eigenvalues ($\lambda_k$), number of sites  ($n$) and
+    scores in terms of orthonormal species ($v_{ik}$) and site scores
+    ($u_{jk}$), eigenvalues ($\lambda_k$), number of sites  ($n$) and
     species standard deviations ($s_j$). In \code{rda},
     $\mathrm{const} = \sqrt[4]{(n-1) \sum \lambda_k}$.  Corresponding
     negative scaling in \pkg{vegan}