[Vegan-commits] r1796 - in pkg/vegan: . R inst man

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

Author: jarioksa
Date: 2011-09-07 10:55:09 +0200 (Wed, 07 Sep 2011)
New Revision: 1796

Added:
   pkg/vegan/R/vegan-defunct.R
   pkg/vegan/man/vegan-defunct.Rd
Modified:
   pkg/vegan/NAMESPACE
   pkg/vegan/inst/ChangeLog
Log:
functions removed from 'vegan' but renamed in 'permute' are now .Defunct

Modified: pkg/vegan/NAMESPACE
===================================================================
--- pkg/vegan/NAMESPACE	2011-09-07 07:13:12 UTC (rev 1795)
+++ pkg/vegan/NAMESPACE	2011-09-07 08:55:09 UTC (rev 1796)
@@ -34,6 +34,8 @@
 export(anova.cca)
 ## Export as.mcmc for coda
 export(as.mcmc.oecosimu, as.mcmc.permat)
+## DEFUNCT: export names defined in vegan-defunct
+export(permuted.index2, getNumObs)
 
 ## export regular functions with dot names
 

Added: pkg/vegan/R/vegan-defunct.R
===================================================================
--- pkg/vegan/R/vegan-defunct.R	                        (rev 0)
+++ pkg/vegan/R/vegan-defunct.R	2011-09-07 08:55:09 UTC (rev 1796)
@@ -0,0 +1,8 @@
+## "new" permutation code was moved to package 'permute' in R 2.0-0.
+## Here we list as defunct those functions that are not in 'permute'.
+
+`permuted.index2` <- function (n, control = permControl()) 
+    .Defunct("permute::shuffle", package="vegan")
+
+`getNumObs` <- function(object, ...) 
+    .Defunct("nobs", package = "vegan")

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2011-09-07 07:13:12 UTC (rev 1795)
+++ pkg/vegan/inst/ChangeLog	2011-09-07 08:55:09 UTC (rev 1796)
@@ -16,6 +16,9 @@
 	before it turned ten-years-old. After this, wisconsin() is the
 	only unchanged function from the first release.
 
+	* vegan-defunct: put definitions of removed "new" permutation
+	functions to vegan-defunct and have a vegan-defunct.Rd for them. 
+
 Version 1.92-2 (closed September 3, 2011)
 
 	* monoMDS: saves and displays info on the dissimilarities used,

Added: pkg/vegan/man/vegan-defunct.Rd
===================================================================
--- pkg/vegan/man/vegan-defunct.Rd	                        (rev 0)
+++ pkg/vegan/man/vegan-defunct.Rd	2011-09-07 08:55:09 UTC (rev 1796)
@@ -0,0 +1,54 @@
+\name{vegan-defunct}
+%--- The following functions were moved to the 'permute' package and
+%    removed from vegan, but here we document only those that were
+%    renamed and are not documented in 'permute'
+ 
+%\alias{permCheck}
+%\alias{numPerms}
+%\alias{print.permCheck}
+%\alias{print.summary.permCheck}
+%\alias{summary.permCheck}
+\alias{getNumObs}
+%\alias{getNumObs.default}
+%\alias{getNumObs.integer}
+%\alias{getNumObs.numeric}
+%\alias{allPerms}
+%\alias{print.allPerms}
+%\alias{summary.allPerms}
+%\alias{print.summary.allPerms}
+%\alias{permuplot}
+\alias{permuted.index2}
+%\alias{permControl}
+%\alias{print.permControl}
+%\alias{permute}
+
+\alias{vegan-defunct}
+%------ NOTE:  ../R/vegan-deprecated.R   must be synchronized with this!
+\title{Defunct Functions in Package \pkg{vegan}}
+%------ PLEASE: one \alias{.} for EACH ! (+ one \usage{} & \arguments{} for all)
+\description{
+  The functions or variables listed here are no longer part of \pkg{vegan} as
+  they are no longer needed.
+}
+\usage{
+%-- Removed from vegan 2.0-0: now in package permute
+getNumObs(object, \dots)
+\method{getNumObs}{default}(object, \dots)
+\method{getNumObs}{numeric}(object, \dots)
+\method{getNumObs}{integer}(object, \dots)
+
+permuted.index2(n, control = permControl())
+}
+
+\details{ The \dQuote{new} permutation functions were moved to the
+  \pkg{permute} package, and they are documented there.  The
+  \pkg{permute} package replaces \code{permuted.index2} with
+  \code{\link[permute]{shuffle}} and \code{getNumObs} with its specific
+  \code{\link[permute]{nobs-methods}}.
+}
+
+\seealso{
+  \code{\link{Defunct}}, \code{\link{vegan-deprecated}}
+}
+
+\keyword{internal}