[Vegan-commits] r1463 - pkg/vegan/man

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

Author: jarioksa
Date: 2011-01-18 18:22:35 +0100 (Tue, 18 Jan 2011)
New Revision: 1463

Modified:
   pkg/vegan/man/anova.cca.Rd
   pkg/vegan/man/cca.object.Rd
Log:
small comments on anova.cca in help fles

Modified: pkg/vegan/man/anova.cca.Rd
===================================================================
--- pkg/vegan/man/anova.cca.Rd	2011-01-18 17:07:39 UTC (rev 1462)
+++ pkg/vegan/man/anova.cca.Rd	2011-01-18 17:22:35 UTC (rev 1463)
@@ -137,6 +137,10 @@
   \code{\link{anova}} table and uses \code{\link{print.anova}} for printing.
 }
 \note{
+  Some cases of \code{anova} need access to the original data on
+  constraints (at least \code{by = "term"} and \code{by = "margin"}),
+  and they may fail if data are unavailable.
+ 
   The default permutation \code{model} changed from \code{"direct"} to
   \code{"reduced"} in \pkg{vegan} version 1.14-11 (release version
   1.15-0), and you must explicitly set \code{model = "direct"} for

Modified: pkg/vegan/man/cca.object.Rd
===================================================================
--- pkg/vegan/man/cca.object.Rd	2011-01-18 17:07:39 UTC (rev 1462)
+++ pkg/vegan/man/cca.object.Rd	2011-01-18 17:22:35 UTC (rev 1463)
@@ -134,9 +134,11 @@
     \item{\code{subset}}{subset evaluated as a logical vector
       (\code{TRUE} for included cases).}
     \item{\code{na.action}}{The object returned by
-    \code{\link{na.action}} which is a named vector of indices of
-    removed items. The class of the vector is either \code{"omit"} or
-    \code{"exclude"} as set by \code{\link{na.action}}.}
+      \code{\link{na.action}} which is a named vector of indices of
+      removed items. The class of the vector is either \code{"omit"} or
+      \code{"exclude"} as set by \code{\link{na.action}}. The \code{na.action}
+      is applied after \code{subset} so that the indices refer to the subset
+      data.}
   \item{\code{residuals.zombie}}{A zombie vector of the length of
     number of rows in the residual ordination. Some standard \R
     functions find the number of valid observations from this vector,