[Vegan-commits] r1105 - branches/1.17/inst branches/1.17/man pkg/vegan/inst pkg/vegan/man

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

Author: jarioksa
Date: 2010-01-06 16:54:21 +0100 (Wed, 06 Jan 2010)
New Revision: 1105

Modified:
   branches/1.17/inst/ChangeLog
   branches/1.17/man/cca.object.Rd
   pkg/vegan/inst/ChangeLog
   pkg/vegan/man/cca.object.Rd
Log:
documented na.action in cca.object.Rd

Modified: branches/1.17/inst/ChangeLog
===================================================================
--- branches/1.17/inst/ChangeLog	2010-01-05 12:21:36 UTC (rev 1104)
+++ branches/1.17/inst/ChangeLog	2010-01-06 15:54:21 UTC (rev 1105)
@@ -8,6 +8,8 @@
 
 	* removed treedist().
 
+	* Documented na.action in cca.object (copied from 1.18-0). 
+
 VEGAN DEVEL VERSIONS at http://r-forge.r-project.org/
 
 Version 1.16-34 (closed January 2, 2010) -- (codename: Lucia)
@@ -15,8 +17,9 @@
 	* twostagechao: deleted, because question regarding the
 	notation in the original article remained unanswered.
 
-	* permat* cleanup: permat.control deleted, not needed any longer  due to changes
-	in oecosimu, documentation for plot.permat merged with permat* help page.
+	* permat* cleanup: permat.control deleted, not needed any longer
+	due to changes in oecosimu, documentation for plot.permat merged
+	with permat* help page.
 
 	* goodness.cca: was not using correct weights. Broken in r992 (Sep
 	6, 2009).

Modified: branches/1.17/man/cca.object.Rd
===================================================================
--- branches/1.17/man/cca.object.Rd	2010-01-05 12:21:36 UTC (rev 1104)
+++ branches/1.17/man/cca.object.Rd	2010-01-06 15:54:21 UTC (rev 1105)
@@ -125,6 +125,32 @@
       \code{\link{scale}}.} }
   }
 }
+
+\section{NA Action}{
+  If the constraints had missing values, and \code{\link{na.action}}
+  was set to  \code{\link{na.exclude}} or \code{\link{na.omit}}, the
+  result will have some extra items:
+  \describe{
+    \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}}.}
+  \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,
+    and it is provided for their use although this is useless in
+    \pkg{vegan}.}
+  \item{\code{rowsum.excluded}}{Row sums of removed observations. Only
+    in \code{\link{cca}}.}
+  \item{\code{CCA$wa.excluded}}{The WA scores for sites (found from
+    community data) in constrained ordinaiton if
+    \code{\link{na.action}}  was \code{\link{na.exclude}} and the
+    scores could be calculated. The scores cannot be found for 
+    \code{\link{capscale}} and in partial ordination.}
+  \item{\code{CA$u.excluded}}{Row scores for sites in unconstrained
+    ordination with identical conditions as above.}
+  }
+}
   
 \seealso{The description here provides a hacker's interface.  For more
   user friendly access to the \code{cca} object see

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2010-01-05 12:21:36 UTC (rev 1104)
+++ pkg/vegan/inst/ChangeLog	2010-01-06 15:54:21 UTC (rev 1105)
@@ -4,6 +4,8 @@
 
 Version 1.18-0 (opened January 2, 2010)
 
+	* Documented na.action in cca.object.
+
 	* Opened concurrently with copying 1.16-34 (at rev 1087) to
 	branches/1.17 for a new release.
 

Modified: pkg/vegan/man/cca.object.Rd
===================================================================
--- pkg/vegan/man/cca.object.Rd	2010-01-05 12:21:36 UTC (rev 1104)
+++ pkg/vegan/man/cca.object.Rd	2010-01-06 15:54:21 UTC (rev 1105)
@@ -125,6 +125,32 @@
       \code{\link{scale}}.} }
   }
 }
+
+\section{NA Action}{
+  If the constraints had missing values, and \code{\link{na.action}}
+  was set to  \code{\link{na.exclude}} or \code{\link{na.omit}}, the
+  result will have some extra items:
+  \describe{
+    \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}}.}
+  \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,
+    and it is provided for their use although this is useless in
+    \pkg{vegan}.}
+  \item{\code{rowsum.excluded}}{Row sums of removed observations. Only
+    in \code{\link{cca}}.}
+  \item{\code{CCA$wa.excluded}}{The WA scores for sites (found from
+    community data) in constrained ordinaiton if
+    \code{\link{na.action}}  was \code{\link{na.exclude}} and the
+    scores could be calculated. The scores cannot be found for 
+    \code{\link{capscale}} and in partial ordination.}
+  \item{\code{CA$u.excluded}}{Row scores for sites in unconstrained
+    ordination with identical conditions as above.}
+  }
+}
   
 \seealso{The description here provides a hacker's interface.  For more
   user friendly access to the \code{cca} object see