[Vegan-commits] r1065 - in pkg/vegan: R inst man

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

Author: jarioksa
Date: 2009-11-04 18:46:57 +0100 (Wed, 04 Nov 2009)
New Revision: 1065

Modified:
   pkg/vegan/R/alias.cca.R
   pkg/vegan/inst/ChangeLog
   pkg/vegan/man/goodness.cca.Rd
Log:
alias.cca gained argument names.only = FALSE

Modified: pkg/vegan/R/alias.cca.R
===================================================================
--- pkg/vegan/R/alias.cca.R	2009-10-30 08:21:24 UTC (rev 1064)
+++ pkg/vegan/R/alias.cca.R	2009-11-04 17:46:57 UTC (rev 1065)
@@ -1,6 +1,8 @@
-"alias.cca" <-
-function (object, ...) 
+`alias.cca` <-
+    function (object, names.only = FALSE, ...) 
 {
+    if (names.only)
+        return(object$CCA$alias)
     CompPatt <- function(x, ...) {
         x[abs(x) < 1e-06] <- 0
         class(x) <- "mtable"

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2009-10-30 08:21:24 UTC (rev 1064)
+++ pkg/vegan/inst/ChangeLog	2009-11-04 17:46:57 UTC (rev 1065)
@@ -4,6 +4,10 @@
 
 Version 1.16-32 (opened October 24, 2009)
 
+	* alias.cca: gained argument 'names.only' (defaults FALSE) to only
+	return the names of the aliased variables insted of their defining
+	equations. 
+
 	* rarefy: failed with one site and many sample sizes like
 	rarefy(rpois(10, 2), sample=2:3).
 

Modified: pkg/vegan/man/goodness.cca.Rd
===================================================================
--- pkg/vegan/man/goodness.cca.Rd	2009-10-30 08:21:24 UTC (rev 1064)
+++ pkg/vegan/man/goodness.cca.Rd	2009-11-04 17:46:57 UTC (rev 1065)
@@ -27,7 +27,7 @@
 spenvcor(object)
 intersetcor(object)
 vif.cca(object)
-\method{alias}{cca}(object, ...)
+\method{alias}{cca}(object, names.only = FALSE, ...)
 }
 
 \arguments{
@@ -44,6 +44,8 @@
   \item{summarize}{Show only the accumulated total. }
   \item{proportional}{Give the inertia components as proportional for
     the corresponding total.}
+  \item{names.only}{Return only names of aliased variable(s) instead of
+    defining equations.}
   \item{\dots}{Other parameters to the functions.}
 }
 \details{
@@ -88,7 +90,8 @@
   from the estimation, and no biplot scores or centroids are calculated
   for these aliased constraints. A note will be printed with default
   output if there are aliased constraints. Function \code{alias} will
-  give the linear coefficients defining the aliased constraints. 
+  give the linear coefficients defining the aliased constraints, or 
+  only their names with argument \code{names.only = TRUE}.
 }
 
 \value{