[Vegan-commits] r1656 - in pkg/permute: . R man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sun Jun 26 13:44:44 CEST 2011
Author: gsimpson
Date: 2011-06-26 13:44:43 +0200 (Sun, 26 Jun 2011)
New Revision: 1656
Added:
pkg/permute/R/nobs-methods.R
pkg/permute/man/nobs.Rd
Removed:
pkg/permute/R/getNumObs.R
pkg/permute/man/getNumObs.Rd
Modified:
pkg/permute/NAMESPACE
pkg/permute/R/allPerms.R
pkg/permute/R/numPerms.R
pkg/permute/R/permCheck.R
pkg/permute/man/numPerms.Rd
pkg/permute/man/shuffle.Rd
Log:
get permute to pass R CMD check, getNumObs() changed to nobs() methods
Modified: pkg/permute/NAMESPACE
===================================================================
--- pkg/permute/NAMESPACE 2011-06-26 10:58:20 UTC (rev 1655)
+++ pkg/permute/NAMESPACE 2011-06-26 11:44:43 UTC (rev 1656)
@@ -1,5 +1,5 @@
## Visible functions:
-export(`allPerms`, `Blocks`, `getNumObs`, `numPerms`, `permCheck`,
+export(`allPerms`, `Blocks`, `numPerms`, `permCheck`,
`permControl`, `permute`, `shuffle`, `Within`)
## Imports
@@ -15,12 +15,8 @@
# summary methods
S3method(`summary`, `allPerms`)
S3method(`summary`, `permCheck`)
-# getNumObs methods
-S3method(`getNumObs`, `default`)
-S3method(`getNumObs`, `numeric`)
-S3method(`getNumObs`, `integer`)
## nobs() methods
S3method(`nobs`, `numeric`)
S3method(`nobs`, `integer`)
S3method(`nobs`, `matrix`)
-S3method(`nobs`, `cca`)
+S3method(`nobs`, `data.frame`)
Modified: pkg/permute/R/allPerms.R
===================================================================
--- pkg/permute/R/allPerms.R 2011-06-26 10:58:20 UTC (rev 1655)
+++ pkg/permute/R/allPerms.R 2011-06-26 11:44:43 UTC (rev 1656)
@@ -18,7 +18,7 @@
if((is.numeric(n) || is.integer(n)) && (length(n) == 1))
v <- seq_len(n)
## number of observations in data
- n <- nobs(v) ## getNumObs
+ n <- nobs(v)
## check permutation scheme and update control
pcheck <- permCheck(v, control = control, make.all = FALSE)
ctrl <- pcheck$control
Deleted: pkg/permute/R/getNumObs.R
===================================================================
--- pkg/permute/R/getNumObs.R 2011-06-26 10:58:20 UTC (rev 1655)
+++ pkg/permute/R/getNumObs.R 2011-06-26 11:44:43 UTC (rev 1656)
@@ -1,33 +0,0 @@
-`getNumObs` <- function(object, ...) UseMethod("getNumObs")
-
-`getNumObs.default` <- function(object, ...)
-{
- NROW(scores(object, display = "sites"))
-}
-
-`getNumObs.numeric` <- function(object, ...)
-{
- length(object)
-}
-
-`getNumObs.integer` <- function(object, ...)
-{
- getNumObs.numeric(object)
-}
-
-## add some nobs() methods - need to be documented
-`nobs.numeric` <- function(object, ...) {
- length(object)
-}
-
-`nobs.integer` <- function(object, ...) {
- nobs.numeric(object, ...)
-}
-
-`nobs.matrix` <- function(object, ...) {
- NROW(object)
-}
-
-`nobs.cca` <- function(object, ...) {
- NROW(scores(object, display = "sites"))
-}
Copied: pkg/permute/R/nobs-methods.R (from rev 1653, pkg/permute/R/getNumObs.R)
===================================================================
--- pkg/permute/R/nobs-methods.R (rev 0)
+++ pkg/permute/R/nobs-methods.R 2011-06-26 11:44:43 UTC (rev 1656)
@@ -0,0 +1,17 @@
+## add some nobs() methods - need to be documented
+`nobs.numeric` <- function(object, ...) {
+ length(object)
+}
+
+`nobs.integer` <- function(object, ...) {
+ nobs.numeric(object, ...)
+}
+
+`nobs.matrix` <- function(object, ...) {
+ NROW(object)
+}
+
+`nobs.data.frame` <- function(object, ...) {
+ NROW(object)
+}
+
Modified: pkg/permute/R/numPerms.R
===================================================================
--- pkg/permute/R/numPerms.R 2011-06-26 10:58:20 UTC (rev 1655)
+++ pkg/permute/R/numPerms.R 2011-06-26 11:44:43 UTC (rev 1656)
@@ -7,7 +7,7 @@
(length(object) == 1))
object <- seq_len(object)
## number of observations in data
- nobs <- getNumObs(object)
+ nobs <- nobs(object)
## within perms object
WITHIN <- control$within
## strata perms object
Modified: pkg/permute/R/permCheck.R
===================================================================
--- pkg/permute/R/permCheck.R 2011-06-26 10:58:20 UTC (rev 1655)
+++ pkg/permute/R/permCheck.R 2011-06-26 11:44:43 UTC (rev 1656)
@@ -7,7 +7,7 @@
(is.integer(object) || is.numeric(object)))
object <- seq_len(object)
## check the number of observations in object
- nobs <- getNumObs(object)
+ nobs <- nobs(object)
## sample permutation type
type <- control$within$type
## if strata, check nobs == length of strata
Deleted: pkg/permute/man/getNumObs.Rd
===================================================================
--- pkg/permute/man/getNumObs.Rd 2011-06-26 10:58:20 UTC (rev 1655)
+++ pkg/permute/man/getNumObs.Rd 2011-06-26 11:44:43 UTC (rev 1656)
@@ -1,54 +0,0 @@
-\name{getNumObs}
-\alias{getNumObs}
-\alias{getNumObs.default}
-\alias{getNumObs.integer}
-\alias{getNumObs.numeric}
-\alias{nobs.numeric}
-\alias{nobs.integer}
-\alias{nobs.matrix}
-\alias{nobs.cca}
-
-\title{Number of observations in a given object}
-\description{
- \code{getNumObs} is a utility function to return the number of
- observations for a range of R and ordination objects.
-}
-\usage{
-getNumObs(object, \dots)
-
-\method{getNumObs}{default}(object, \dots)
-
-\method{getNumObs}{numeric}(object, \dots)
-
-\method{getNumObs}{integer}(object, \dots)
-}
-\arguments{
- \item{object}{any R object handled by \code{\link[vegan]{scores}},
- data frames, matrices, and numeric and integer vectors.}
- \item{\dots}{arguments to other methods.}
-}
-\details{
- Function \code{getNumObs} is a simple generic function to return the
- number of observations in a range of R objects. The default method
- will work for any object for which a \code{\link[vegan]{scores}}
- method exists. This includes matrices and data frames, as well as
- specific methods for numeric or integer vectors.
-}
-\value{
- The (numeric) number of observations in \code{object}.
-}
-\author{Gavin Simpson}
-\examples{
-## vector
-len <- sample(1:10, 1)
-v <- numeric(sample(1:100, len))
-len
-obs <- getNumObs(v)
-isTRUE(all.equal(len, obs))
-
-## integer
-len <- sample(1:10, 1)
-obs <- getNumObs(len)
-isTRUE(all.equal(len, obs))
-
-}
Copied: pkg/permute/man/nobs.Rd (from rev 1653, pkg/permute/man/getNumObs.Rd)
===================================================================
--- pkg/permute/man/nobs.Rd (rev 0)
+++ pkg/permute/man/nobs.Rd 2011-06-26 11:44:43 UTC (rev 1656)
@@ -0,0 +1,50 @@
+\name{nobs-methods}
+\alias{nobs-methods}
+\alias{nobs.numeric}
+\alias{nobs.integer}
+\alias{nobs.matrix}
+\alias{nobs.data.frame}
+
+\title{Number of observations in a given object}
+\description{
+ \code{\link{nobs}} is a generic function to return the number of
+ observations from a model. \code{shuffle} provides a few methods for
+ other types of data object in R.
+}
+\usage{
+
+\method{nobs}{numeric}(object, \dots)
+
+\method{nobs}{integer}(object, \dots)
+
+\method{nobs}{matrix}(object, \dots)
+
+\method{nobs}{data.frame}(object, \dots)
+}
+\arguments{
+ \item{object}{a data frame or matrix, or a numeric or integer vector.}
+ \item{\dots}{arguments to other methods.}
+}
+\details{
+ Function \code{nobs} is a simple generic function to return the
+ number of observations in a range of R model objects. Methods are
+ provided to work with a variety of R objects.
+}
+\value{
+ The (numeric) number of observations in \code{object}.
+}
+\author{Gavin Simpson}
+\examples{
+## vector
+len <- sample(1:10, 1)
+v <- numeric(sample(1:100, len))
+len
+obs <- nobs(v)
+isTRUE(all.equal(len, obs))
+
+## integer
+len <- sample(1:10, 1)
+obs <- nobs(len)
+isTRUE(all.equal(len, obs))
+
+}
Modified: pkg/permute/man/numPerms.Rd
===================================================================
--- pkg/permute/man/numPerms.Rd 2011-06-26 10:58:20 UTC (rev 1655)
+++ pkg/permute/man/numPerms.Rd 2011-06-26 11:44:43 UTC (rev 1656)
@@ -10,7 +10,7 @@
numPerms(object, control = permControl())
}
\arguments{
- \item{object}{any object handled by \code{\link{getNumObs}}.}
+ \item{object}{any object handled by \code{\link{nobs}}.}
\item{control}{a list of control values describing properties of the
permutation design, as returned by a call to
\code{\link{permControl}}.}
@@ -60,19 +60,21 @@
\emph{grid} is not an issue here.
}
\author{Gavin Simpson}
-\seealso{\code{\link{shuffle}} and \code{\link{permControl}}.}
+\seealso{\code{\link{shuffle}} and
+ \code{\link{permControl}}. Additional \code{\link{nobs}} methods are
+ provide, see \code{\link{nobs-methods}}.}
\examples{
## permutation design --- see ?permControl
ctrl <- permControl() ## defaults to freely exchangeable
## vector
v <- 1:10
-(obs <- getNumObs(v))
+(obs <- nobs(v))
numPerms(v, control = ctrl)
## integer
len <- length(v)
-(obs <- getNumObs(len))
+(obs <- nobs(len))
numPerms(len, control = ctrl)
## new design, objects are a time series
Modified: pkg/permute/man/shuffle.Rd
===================================================================
--- pkg/permute/man/shuffle.Rd 2011-06-26 10:58:20 UTC (rev 1655)
+++ pkg/permute/man/shuffle.Rd 2011-06-26 11:44:43 UTC (rev 1656)
@@ -241,7 +241,7 @@
## check the control object
control <- permCheck(x, control)$control
## number of observations
- Nobs <- getNumObs(x)
+ Nobs <- nobs(x)
## group names
lev <- names(table(group))
## vector to hold results, +1 because of observed t
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