[Vegan-commits] r2881 - in pkg/vegan: . R man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Sep 5 13:55:04 CEST 2014
Author: jarioksa
Date: 2014-09-05 13:55:04 +0200 (Fri, 05 Sep 2014)
New Revision: 2881
Removed:
pkg/vegan/R/commsimulator.R
Modified:
pkg/vegan/NAMESPACE
pkg/vegan/R/vegan-defunct.R
pkg/vegan/R/vegan-deprecated.R
pkg/vegan/man/vegan-defunct.Rd
pkg/vegan/man/vegan-deprecated.Rd
Log:
Merge branch 'master' into r-forge-svn-local
Modified: pkg/vegan/NAMESPACE
===================================================================
--- pkg/vegan/NAMESPACE 2014-09-04 06:49:30 UTC (rev 2880)
+++ pkg/vegan/NAMESPACE 2014-09-05 11:55:04 UTC (rev 2881)
@@ -6,7 +6,7 @@
export(CCorA, MOStest, RsquareAdj, SSarrhenius, SSgitay, SSgleason,
SSlomolino, adipart, adonis, anosim, beals, betadisper, betadiver,
bgdispersal, bioenv, bioenvdist, bstick, cIndexKM, calibrate, capscale,
-cascadeKM, cca, commsimulator, contribdiv, clamtest, commsim, decorana,
+cascadeKM, cca, contribdiv, clamtest, commsim, decorana,
decostand, designdist, coverscale, dispweight, dispindmorisita, distconnected,
diversity, downweight, drarefy, eigengrad, eigenvals, envfit,
estaccumR, estimateR, eventstar, factorfit, fisherfit, fitspecaccum,
@@ -38,7 +38,7 @@
## Export as.mcmc for coda
export(as.mcmc.oecosimu, as.mcmc.permat)
## DEFUNCT: export names defined in vegan-defunct
-export(permuted.index2, getNumObs)
+export(metaMDSrotate)
## export regular functions with dot names
@@ -52,7 +52,7 @@
export(panel.ordi, panel.ordiarrows, panel.ordi3d, prepanel.ordi3d)
## Export .Depracated functions (to be removed later)
-export(metaMDSrotate)
+export(commsimulator)
## do NOT export the following internal functions
Deleted: pkg/vegan/R/commsimulator.R
===================================================================
--- pkg/vegan/R/commsimulator.R 2014-09-04 06:49:30 UTC (rev 2880)
+++ pkg/vegan/R/commsimulator.R 2014-09-05 11:55:04 UTC (rev 2881)
@@ -1,14 +0,0 @@
-"commsimulator" <-
-function (x, method, thin = 1)
-{
- method <- match.arg(method,
- c("r0","r1","r2","r00","c0","swap", "tswap",
- "backtrack", "quasiswap"))
- if (method == "r0")
- method <- "r0_old"
- x <- as.matrix(x)
- out <- simulate(nullmodel(x, method), nsim = 1, thin = thin)
- out <- out[,,1]
- attributes(out) <- attributes(x)
- out
-}
Modified: pkg/vegan/R/vegan-defunct.R
===================================================================
--- pkg/vegan/R/vegan-defunct.R 2014-09-04 06:49:30 UTC (rev 2880)
+++ pkg/vegan/R/vegan-defunct.R 2014-09-05 11:55:04 UTC (rev 2881)
@@ -1,8 +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")
+`metaMDSrotate` <-
+ function(object, vec, na.rm = FALSE, ...)
+{
+ .Defunct(new="MDSrotate", "vegan")
+}
Modified: pkg/vegan/R/vegan-deprecated.R
===================================================================
--- pkg/vegan/R/vegan-deprecated.R 2014-09-04 06:49:30 UTC (rev 2880)
+++ pkg/vegan/R/vegan-deprecated.R 2014-09-05 11:55:04 UTC (rev 2881)
@@ -1,6 +1,14 @@
-`metaMDSrotate` <-
- function(object, vec, na.rm = FALSE, ...)
+"commsimulator" <-
+function (x, method, thin = 1)
{
- .Deprecated(new="MDSrotate", "vegan")
- MDSrotate(object = object, vec = vec, na.rm = na.rm, ...)
+ method <- match.arg(method,
+ c("r0","r1","r2","r00","c0","swap", "tswap",
+ "backtrack", "quasiswap"))
+ if (method == "r0")
+ method <- "r0_old"
+ x <- as.matrix(x)
+ out <- simulate(nullmodel(x, method), nsim = 1, thin = thin)
+ out <- out[,,1]
+ attributes(out) <- attributes(x)
+ out
}
Modified: pkg/vegan/man/vegan-defunct.Rd
===================================================================
--- pkg/vegan/man/vegan-defunct.Rd 2014-09-04 06:49:30 UTC (rev 2880)
+++ pkg/vegan/man/vegan-defunct.Rd 2014-09-05 11:55:04 UTC (rev 2881)
@@ -3,24 +3,7 @@
% 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{metaMDSrotate}
\alias{vegan-defunct}
%------ NOTE: ../R/vegan-deprecated.R must be synchronized with this!
@@ -31,20 +14,13 @@
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())
+metaMDSrotate(object, vec, na.rm = FALSE, ...)
}
-\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}}.
+\details{
+ Function \code{metaMDSrotate} is replaced with
+ \code{\link{MDSrotate}} which can handle \code{\link{monoMDS}}
+ results in addition to \code{\link{metaMDS}}.
}
\seealso{
Modified: pkg/vegan/man/vegan-deprecated.Rd
===================================================================
--- pkg/vegan/man/vegan-deprecated.Rd 2014-09-04 06:49:30 UTC (rev 2880)
+++ pkg/vegan/man/vegan-deprecated.Rd 2014-09-05 11:55:04 UTC (rev 2881)
@@ -1,6 +1,5 @@
\encoding{UTF-8}
\name{vegan-deprecated}
-\alias{metaMDSrotate}
\alias{commsimulator}
\alias{vegan-deprecated}
@@ -12,16 +11,10 @@
\pkg{vegan} only, and may be defunct as soon as the next release.
}
\usage{
-metaMDSrotate(object, vec, na.rm = FALSE, ...)
commsimulator(x, method, thin=1)
}
\arguments{
- ## metaMDSrotate
- \item{object}{A result object from \code{metaMDS}.}
- \item{vec}{A continuous site variable (vector).}
- \item{na.rm}{Remove missing values from continuous variable \code{vec}.}
- \item{\dots}{Other parameters passed to functions.}
## commsimulator
\item{x}{Community data for \code{commsimulator}}
\item{method}{Null model method: either a name (character string) of
@@ -39,10 +32,6 @@
%-- Or:
%% explain *why* it's deprecated, and \code{\link{..}} to new
- Function \code{metaMDSrotate} is replaced with
- \code{\link{MDSrotate}} which can handle \code{\link{monoMDS}}
- results in addition to \code{\link{metaMDS}}.
-
Function \code{commsimulator} is replaced with
\code{\link{make.commsim}} which defines the Null models, and
functions \code{\link{nullmodel}} and
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