[Vegan-commits] r1445 - in pkg/vegan: . R inst man

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

Author: jarioksa
Date: 2011-01-09 16:15:04 +0100 (Sun, 09 Jan 2011)
New Revision: 1445

Modified:
   pkg/vegan/DESCRIPTION
   pkg/vegan/R/capscale.R
   pkg/vegan/inst/ChangeLog
   pkg/vegan/man/cca.object.Rd
Log:
return 'ac' when 'add = TRUE'

Modified: pkg/vegan/DESCRIPTION
===================================================================
--- pkg/vegan/DESCRIPTION	2011-01-09 14:19:12 UTC (rev 1444)
+++ pkg/vegan/DESCRIPTION	2011-01-09 15:15:04 UTC (rev 1445)
@@ -1,7 +1,7 @@
 Package: vegan
 Title: Community Ecology Package
-Version: 1.18-20
-Date: January 3, 2011
+Version: 1.18-21
+Date: January 9, 2011
 Author: Jari Oksanen, F. Guillaume Blanchet, Roeland Kindt, Pierre Legendre, 
    R. B. O'Hara, Gavin L. Simpson, Peter Solymos, M. Henry H. Stevens, 
    Helene Wagner  

Modified: pkg/vegan/R/capscale.R
===================================================================
--- pkg/vegan/R/capscale.R	2011-01-09 14:19:12 UTC (rev 1444)
+++ pkg/vegan/R/capscale.R	2011-01-09 15:15:04 UTC (rev 1445)
@@ -131,6 +131,8 @@
     sol$call$formula <- formula(d$terms, width.cutoff = 500)
     sol$call$formula[[2]] <- formula[[2]]
     sol$method <- "capscale"
+    if (add)
+        sol$ac <- X$ac
     sol$inertia <- inertia
     if (metaMDSdist)
         sol$metaMDSdist <- commname

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2011-01-09 14:19:12 UTC (rev 1444)
+++ pkg/vegan/inst/ChangeLog	2011-01-09 15:15:04 UTC (rev 1445)
@@ -2,8 +2,12 @@
 
 VEGAN DEVEL VERSIONS at http://r-forge.r-project.org/
 
-Version 1.18-20 (opened January 3, 2011)
+Version 1.18-21 (opened January 9, 2011)
 
+	* capscale: return additive constant ('ac') when 'add = TRUE'. 
+
+Version 1.18-20 (closed January 9, 2011)
+
 	* capscale: the total inertia was defined as the sum of absolute
 	values of inertia so that negative eigenvalues of imaginary
 	dimensions increase inertia (changes in 1.18-17 and release

Modified: pkg/vegan/man/cca.object.Rd
===================================================================
--- pkg/vegan/man/cca.object.Rd	2011-01-09 14:19:12 UTC (rev 1444)
+++ pkg/vegan/man/cca.object.Rd	2011-01-09 15:15:04 UTC (rev 1445)
@@ -151,6 +151,15 @@
     ordination with identical conditions as above.}
   }
 }
+
+\section{capscale}{
+  Function \code{capscale} may add some items depending on its arguments:
+  \describe{
+    \item{\code{metaMDSdist}}{The data set name if 
+       \code{metaMDSdist = TRUE}.} 
+    \item{\code{ac}}{Additive constant used if \code{add = TRUE}.}
+  }
+}
   
 \seealso{The description here provides a hacker's interface.  For more
   user friendly access to the \code{cca} object see