[Vegan-commits] r2513 - in pkg/permute: inst man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Jun 12 17:50:07 CEST 2013
Author: gsimpson
Date: 2013-06-12 17:50:07 +0200 (Wed, 12 Jun 2013)
New Revision: 2513
Added:
pkg/permute/inst/TODO.md
pkg/permute/man/check.Rd
pkg/permute/man/permControl-deprecated.Rd
pkg/permute/man/permute-deprecated.Rd
Removed:
pkg/permute/inst/TODO
pkg/permute/man/permCheck.Rd
pkg/permute/man/permControl-dprecated.Rd
Modified:
pkg/permute/inst/ChangeLog
Log:
complete the deprecation of permControl, permCheck
Modified: pkg/permute/inst/ChangeLog
===================================================================
--- pkg/permute/inst/ChangeLog 2013-06-12 05:22:29 UTC (rev 2512)
+++ pkg/permute/inst/ChangeLog 2013-06-12 15:50:07 UTC (rev 2513)
@@ -4,7 +4,10 @@
Version 0.7-4
- *
+ * Deprecated functions: Completed the deprecation of `permCheck()`
+ and `permControl()`. These functions will be made defunct following
+ the release of version 0.8-0, with a view to complete removal from
+ version 0.9-0 onwards.
Version 0.7-3
Deleted: pkg/permute/inst/TODO
===================================================================
--- pkg/permute/inst/TODO 2013-06-12 05:22:29 UTC (rev 2512)
+++ pkg/permute/inst/TODO 2013-06-12 15:50:07 UTC (rev 2513)
@@ -1,25 +0,0 @@
-# TODO List
-
-A TODO list for **permute** - or things I know are broken or needed.
-
- * `summary.allPerms` - is not printing the permutation scheme
-
- * `print.permControl` - this needs to be updated to new API, and I don't
- like the `*** Foo ***` headings I used before.
-
- * Need a way to update the permutation scheme, e.g. when a control
- object already exists and want to tweak it. Example is in `?allPerms`
- where I turn mirroring on via
-
- ctrl$within$mirror <- TRUE
-
- But how? Best idea currently is an `update.permControl` method. The
- generic is in namespace `stats`.
-
- * `permControl` - deprecate this in favour of `how` as in "how to
- permute"?
-
- * `permuplot` - this may be fundamentally bust - it only worked in the
- original API and never got updated. Now the API is 2 versions further
- on! It is also more complex than the original - not sure it'll be
- easy without a lot of work to visualise all possible schemes.
\ No newline at end of file
Copied: pkg/permute/inst/TODO.md (from rev 2507, pkg/permute/inst/TODO)
===================================================================
--- pkg/permute/inst/TODO.md (rev 0)
+++ pkg/permute/inst/TODO.md 2013-06-12 15:50:07 UTC (rev 2513)
@@ -0,0 +1,29 @@
+# TODO List
+
+A TODO list for **permute** - or things I know are broken or needed.
+
+ * `summary.allPerms` - is not printing the permutation scheme
+
+ * `print.permControl` - this needs to be updated to new API, and I don't
+ like the `*** Foo ***` headings I used before. *Done in 0.7-3*
+
+ * Need a way to update the permutation scheme, e.g. when a control
+ object already exists and want to tweak it. Example is in `?allPerms`
+ where I turn mirroring on via
+
+ ctrl$within$mirror <- TRUE
+
+ But how? Best idea currently is an `update.permControl` method. The
+ generic is in namespace `stats`. Or a `modify()` function, perhaps
+ coupled with specific replacement functions for certain components.
+
+ * `permControl` - deprecate this in favour of `how` as in "how to
+ permute"? *DONE Completed in 0.7-4*
+
+ * `permuplot` - this may be fundamentally bust - it only worked in the
+ original API and never got updated. Now the API is 2 versions further
+ on! It is also more complex than the original - not sure it'll be
+ easy without a lot of work to visualise all possible schemes.
+
+ * `check` insists on returning all permutations *without* the observed
+ on.
\ No newline at end of file
Copied: pkg/permute/man/check.Rd (from rev 2511, pkg/permute/man/permCheck.Rd)
===================================================================
--- pkg/permute/man/check.Rd (rev 0)
+++ pkg/permute/man/check.Rd 2013-06-12 15:50:07 UTC (rev 2513)
@@ -0,0 +1,267 @@
+\name{check}
+\alias{check}
+\alias{permCheck} % for the deprecated function
+\alias{permCheck-deprecated} % for the deprecated function
+\alias{print.check}
+\alias{print.summary.check}
+\alias{summary.check}
+\alias{permuplot}
+
+\title{Utility functions for permutation schemes}
+\description{
+ \code{check} provides checking of permutation schemes for
+ validity. \code{permuplot} produces a graphical representation of the
+ selected permutation design.
+}
+\usage{
+check(object, control = how(), make.all = TRUE)
+
+\method{summary}{check}(object, \dots)
+
+permuplot(n, control = how(), col = par("col"),
+ hcol = "red", shade = "lightgrey", xlim = NULL, ylim = NULL,
+ inset = 0.1, main = NULL, sub = NULL, ann = par("ann"),
+ cex = par("cex"), \dots)
+}
+
+\arguments{
+ \item{object}{an R object. See Details for a
+ complete description, especially for \code{numPerms}. For
+ \code{\link{summary.check}} an object of class
+ \code{"check"}. For \code{\link{summary.allPerms}} an object of
+ class \code{"allPerms"}.}
+ \item{control}{a list of control values describing properties of the
+ permutation design, as returned by a call to
+ \code{\link{how}}.}
+ \item{make.all}{logical; should \code{check} generate all
+ possible permutations? Useful if want to check permutation design
+ but not produce the matrix of all permutations.}
+ \item{n}{the number of observations or an 'object' from which the
+ number of observations can be determined via \code{getNumObs}.}
+ \item{col, xlim, ylim, main, sub, ann, cex}{Graphical parameters.}
+ \item{hcol}{Colour to use for highlighting observations and the border
+ colour of the polygons drawn when \code{type = "strata"}.}
+ \item{shade}{The polygon shading colour (passed to argument \code{col}
+ of function \code{\link{polygon}}) when \code{type = "strata"}.}
+ \item{inset}{Proportion of range of x and y coordinates to add to the
+ plot x and y limits. Used to create a bit of extra space around the
+ margin of each plot.}
+ \item{\dots}{arguments to other methods. For \code{permuplot}
+ graphical parameters can be passed to plotting functions, though
+ note that not all parameters will be accepted gracefully at the
+ moment.}
+}
+\details{
+ \code{check} and \code{permuplot} are utility functions for working
+ with the new permutation schemes available in \code{\link{shuffle}}.
+
+ \code{check} is used to check the current permutation schemes
+ against the object to which it will be applied. It calculates the
+ maximum number of possible permutations for the number of observations
+ in \code{object} and the permutation scheme described by
+ \code{control}. The returned object contains component \code{control},
+ an object of class \code{"how"} suitably modified if
+ \code{check} identifies a problem.
+
+ The main problem is requesting more permutations than possible with
+ the number of observations and the permutation design. In such cases,
+ \code{nperm} is reduced to equal the number of possible permutations,
+ and complete enumeration of all permutations is turned on
+ (\code{control$complete} is set to \code{TRUE}).
+
+ Alternatively, if the number of possible permutations is low, and less
+ than \code{control$minperm}, it is better to enumerate all possible
+ permutations, and as such complete enumeration of all permutations is
+ turned on (\code{control$complete} is set to \code{TRUE}).
+
+ \code{permuplot} is a graphical utility function, which produces a
+ graphical representation of a permutation design. It takes the number
+ of observations and an object returned by \code{\link{how}} as
+ arguments and produces a plot on the currently active device. If
+ strata are present in the design, the plotting region is split into
+ sufficient plotting regions (one for each stratum), and the design in
+ each stratum plotted.
+
+ Free permutation designs are represented by plotting the observation
+ number at random x and y coordinates. Series designs (time series or
+ line transects) are represented by plotting the observation numbers
+ comprising the series in a circle and the start of the permuted series
+ is highlighted using colour \code{hcol}. Grid designs are drawn on a
+ regular grid and the top left observation in the original grid is
+ highlighted using colour \code{hcol}. Note the ordering used is R's
+ standard ordering for matrices - columns are filled first.
+}
+\value{
+ For \code{check} a list containing the maximum number of
+ permutations possible and an object of class
+ \code{"\link{how}"}.
+
+ For \code{permuplot}, a plot on the currently active device.
+}
+\author{Gavin L. Simpson}
+\seealso{\code{\link{shuffle}} and \code{\link{how}}.}
+
+\examples{
+
+## use example data from ?pyrifos in package vegan
+require(vegan)
+example(pyrifos)
+
+## Demonstrate the maximum number of permutations for the pyrifos data
+## under a series of permutation schemes
+
+## no restrictions - lots of perms
+CONTROL <- how(within = Within(type = "free"))
+(check1 <- check(pyrifos, CONTROL))
+##summary(check1)
+
+## no strata but data are series with no mirroring, so 132 permutations
+CONTROL <- how(within = Within(type = "series", mirror = FALSE))
+check(pyrifos, CONTROL)
+
+## no strata but data are series with mirroring, so 264 permutations
+CONTROL <- how(within = Within(type = "series", mirror = TRUE))
+check(pyrifos, control = CONTROL)
+
+## unrestricted within strata
+check(pyrifos, control = how(plots = Plots(strata = ditch),
+ within = Within(type = "free")))
+
+## time series within strata, no mirroring
+check(pyrifos,
+ control = how(plots = Plots(strata = ditch),
+ within = Within(type = "series", mirror = FALSE)))
+
+## time series within strata, with mirroring
+check(pyrifos,
+ control = how(plots = Plots(strata = ditch),
+ within = Within(type = "series", mirror = TRUE)))
+
+\dontrun{ % FIXME these fail in allStrata needing 235.5 Gb RAM!!
+## time series within strata, no mirroring, same permutation
+## within strata
+check(pyrifos,
+ control = how(plots = Plots(strata = ditch),
+ within = Within(type = "series", constant = TRUE)))
+
+## time series within strata, with mirroring, same permutation
+## within strata
+check(pyrifos,
+ control = how(plots = Plots(strata = ditch),
+ within = Within(type = "series", mirror = TRUE,
+ constant = TRUE)))
+
+## permute strata
+check(pyrifos, how(plots = Plots(strata = ditch, type = "free"),
+ within = Within(type = "none")))
+}
+
+## this should also also for arbitrary vectors
+vec1 <- check(1:100)
+vec2 <- check(1:100, how())
+all.equal(vec1, vec2)
+vec3 <- check(1:100, how(within = Within(type = "series")))
+all.equal(100, vec3$n)
+vec4 <- check(1:100, how(within = Within(type= "series", mirror = TRUE)))
+all.equal(vec4$n, 200)
+
+## enumerate all possible permutations
+fac <- gl(2,6)
+ctrl <- how(plots = Plots(strata = fac),
+ within = Within(type = "grid", mirror = FALSE,
+ constant = TRUE, nrow = 3, ncol = 2))
+check(1:12, ctrl)
+
+numPerms(1:12, control = ctrl)
+(tmp <- allPerms(12, control = ctrl, observed = TRUE))
+(tmp2 <- allPerms(12, control = ctrl))
+
+## turn on mirroring %%FIXME needs a proper method to do this
+ctrl$within$mirror <- TRUE
+numPerms(1:12, control = ctrl)
+(tmp3 <- allPerms(12, control = ctrl, observed = TRUE))
+(tmp4 <- allPerms(12, control = ctrl))
+## prints out details of the permutation scheme as
+## well as the matrix of permutations
+summary(tmp) %% FIXME these don't print the scheme
+summary(tmp2)
+
+## different numbers of observations per level of strata
+fac <- factor(rep(1:3, times = c(3,2,2)))
+## free permutations in levels of strata
+numPerms(7, how(within = Within(type = "free"),
+ plots = Plots(strata = fac, type = "none")))
+%% FIXME - need all these updating to new API in how...
+%% Fixed one, above, but there may still be problems with some of
+%% the code below:
+\dontrun{
+allPerms(7, how(type = "free", strata = fac))
+## series permutations in levels of strata
+numPerms(7, how(type = "series", strata = fac))
+allPerms(7, how(type = "series", strata = fac))
+
+## allPerms can work with a vector
+vec <- c(3,4,5)
+allPerms(vec)
+
+## Tests for permuplot
+n <- 25
+## standard permutation designs
+permuplot(n, how(type = "free"))
+permuplot(n, how(type = "series"))
+permuplot(n, how(type = "grid", nrow = 5, ncol = 5))
+
+## restricted perms with mirroring
+permuplot(n, how(type = "series", mirror = TRUE))
+permuplot(n, how(type = "grid", nrow = 5, ncol = 5,
+ mirror = TRUE))
+
+## perms within strata
+fac <- gl(6, 20)
+control <- how(type = "free", strata = fac)
+permuplot(120, control = control, cex = 0.8)
+control <- how(type = "series", strata = fac)
+permuplot(120, control = control, cex = 0.8)
+fac <- gl(6, 25)
+control <- how(type = "grid", strata = fac,
+ nrow = 5, ncol = 5)
+permuplot(150, control = control, cex = 0.8)
+
+## perms within strata with mirroring
+fac <- gl(6, 20)
+control <- how(type = "series", strata = fac,
+ mirror = TRUE)
+permuplot(120, control = control, cex = 0.8)
+fac <- gl(6, 25)
+control <- how(type = "grid", strata = fac,
+ nrow = 5, ncol = 5, mirror = TRUE)
+permuplot(150, control = control, cex = 0.8)
+
+## same perms within strata
+fac <- gl(6, 20)
+control <- how(type = "free", strata = fac,
+ constant = TRUE)
+permuplot(120, control = control, cex = 0.8)
+control <- how(type = "series", strata = fac,
+ constant = TRUE)
+permuplot(120, control = control, cex = 0.8)
+fac <- gl(6, 25)
+control <- how(type = "grid", strata = fac,
+ nrow = 5, ncol = 5, constant = TRUE)
+permuplot(150, control = control, cex = 0.8)
+
+## same perms within strata with mirroring
+fac <- gl(6, 20)
+control <- how(type = "series", strata = fac,
+ mirror = TRUE, constant = TRUE)
+permuplot(120, control = control, cex = 0.8)
+fac <- gl(6, 25)
+control <- how(type = "grid", strata = fac,
+ nrow = 5, ncol = 5, mirror = TRUE,
+ constant = TRUE)
+permuplot(150, control = control, cex = 0.8)
+}
+}
+\keyword{ utilities }
+\keyword{ design }
+\keyword{ methods }
Deleted: pkg/permute/man/permCheck.Rd
===================================================================
--- pkg/permute/man/permCheck.Rd 2013-06-12 05:22:29 UTC (rev 2512)
+++ pkg/permute/man/permCheck.Rd 2013-06-12 15:50:07 UTC (rev 2513)
@@ -1,274 +0,0 @@
-\name{check}
-\alias{check}
-\alias{permCheck} % for the deprecated function
-\alias{print.check}
-\alias{print.summary.check}
-\alias{summary.check}
-\alias{permuplot}
-
-\title{Utility functions for permutation schemes}
-\description{
- \code{check} provides checking of permutation schemes for
- validity. \code{permuplot} produces a graphical representation of the
- selected permutation design.
-}
-\usage{
-check(object, control = how(), make.all = TRUE)
-
-\method{summary}{check}(object, \dots)
-
-permuplot(n, control = how(), col = par("col"),
- hcol = "red", shade = "lightgrey", xlim = NULL, ylim = NULL,
- inset = 0.1, main = NULL, sub = NULL, ann = par("ann"),
- cex = par("cex"), \dots)
-}
-
-\arguments{
- \item{object}{an R object. See Details for a
- complete description, especially for \code{numPerms}. For
- \code{\link{summary.check}} an object of class
- \code{"check"}. For \code{\link{summary.allPerms}} an object of
- class \code{"allPerms"}.}
- \item{control}{a list of control values describing properties of the
- permutation design, as returned by a call to
- \code{\link{how}}.}
- \item{make.all}{logical; should \code{check} generate all
- possible permutations? Useful if want to check permutation design
- but not produce the matrix of all permutations.}
- \item{n}{the number of observations or an 'object' from which the
- number of observations can be determined via \code{getNumObs}.}
- \item{col, xlim, ylim, main, sub, ann, cex}{Graphical parameters.}
- \item{hcol}{Colour to use for highlighting observations and the border
- colour of the polygons drawn when \code{type = "strata"}.}
- \item{shade}{The polygon shading colour (passed to argument \code{col}
- of function \code{\link{polygon}}) when \code{type = "strata"}.}
- \item{inset}{Proportion of range of x and y coordinates to add to the
- plot x and y limits. Used to create a bit of extra space around the
- margin of each plot.}
- \item{\dots}{arguments to other methods. For \code{permuplot}
- graphical parameters can be passed to plotting functions, though
- note that not all parameters will be accepted gracefully at the
- moment.}
-}
-\details{
- \code{check} and \code{permuplot} are utility functions for working
- with the new permutation schemes available in \code{\link{shuffle}}.
-
- \code{check} is used to check the current permutation schemes
- against the object to which it will be applied. It calculates the
- maximum number of possible permutations for the number of observations
- in \code{object} and the permutation scheme described by
- \code{control}. The returned object contains component \code{control},
- an object of class \code{"how"} suitably modified if
- \code{check} identifies a problem.
-
- The main problem is requesting more permutations than possible with
- the number of observations and the permutation design. In such cases,
- \code{nperm} is reduced to equal the number of possible permutations,
- and complete enumeration of all permutations is turned on
- (\code{control$complete} is set to \code{TRUE}).
-
- Alternatively, if the number of possible permutations is low, and less
- than \code{control$minperm}, it is better to enumerate all possible
- permutations, and as such complete enumeration of all permutations is
- turned on (\code{control$complete} is set to \code{TRUE}).
-
- % 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.
-
- \code{permuplot} is a graphical utility function, which produces a
- graphical representation of a permutation design. It takes the number
- of observations and an object returned by \code{\link{how}} as
- arguments and produces a plot on the currently active device. If
- strata are present in the design, the plotting region is split into
- sufficient plotting regions (one for each stratum), and the design in
- each stratum plotted.
-
- Free permutation designs are represented by plotting the observation
- number at random x and y coordinates. Series designs (time series or
- line transects) are represented by plotting the observation numbers
- comprising the series in a circle and the start of the permuted series
- is highlighted using colour \code{hcol}. Grid designs are drawn on a
- regular grid and the top left observation in the original grid is
- highlighted using colour \code{hcol}. Note the ordering used is R's
- standard ordering for matrices - columns are filled first.
-}
-\value{
- For \code{check} a list containing the maximum number of
- permutations possible and an object of class
- \code{"\link{how}"}.
-
- For \code{permuplot}, a plot on the currently active device.
-}
-%\references{
-%}
-\author{Gavin Simpson}
-\seealso{\code{\link{shuffle}} and \code{\link{how}}.}
-
-\examples{
-
-## use example data from ?pyrifos in package vegan
-require(vegan)
-example(pyrifos)
-
-## Demonstrate the maximum number of permutations for the pyrifos data
-## under a series of permutation schemes
-
-## no restrictions - lots of perms
-CONTROL <- how(within = Within(type = "free"))
-(check1 <- check(pyrifos, CONTROL))
-##summary(check1)
-
-## no strata but data are series with no mirroring, so 132 permutations
-CONTROL <- how(within = Within(type = "series", mirror = FALSE))
-check(pyrifos, CONTROL)
-
-## no strata but data are series with mirroring, so 264 permutations
-CONTROL <- how(within = Within(type = "series", mirror = TRUE))
-check(pyrifos, control = CONTROL)
-
-## unrestricted within strata
-check(pyrifos, control = how(plots = Plots(strata = ditch),
- within = Within(type = "free")))
-
-## time series within strata, no mirroring
-check(pyrifos,
- control = how(plots = Plots(strata = ditch),
- within = Within(type = "series", mirror = FALSE)))
-
-## time series within strata, with mirroring
-check(pyrifos,
- control = how(plots = Plots(strata = ditch),
- within = Within(type = "series", mirror = TRUE)))
-
-\dontrun{ % FIXME these fail in allStrata needing 235.5 Gb RAM!!
-## time series within strata, no mirroring, same permutation
-## within strata
-check(pyrifos,
- control = how(plots = Plots(strata = ditch),
- within = Within(type = "series", constant = TRUE)))
-
-## time series within strata, with mirroring, same permutation
-## within strata
-check(pyrifos,
- control = how(plots = Plots(strata = ditch),
- within = Within(type = "series", mirror = TRUE,
- constant = TRUE)))
-
-## permute strata
-check(pyrifos, how(plots = Plots(strata = ditch, type = "free"),
- within = Within(type = "none")))
-}
-
-## this should also also for arbitrary vectors
-vec1 <- check(1:100)
-vec2 <- check(1:100, how())
-all.equal(vec1, vec2)
-vec3 <- check(1:100, how(within = Within(type = "series")))
-all.equal(100, vec3$n)
-vec4 <- check(1:100, how(within = Within(type= "series", mirror = TRUE)))
-all.equal(vec4$n, 200)
-
-## enumerate all possible permutations
-fac <- gl(2,6)
-ctrl <- how(plots = Plots(strata = fac),
- within = Within(type = "grid", mirror = FALSE,
- constant = TRUE, nrow = 3, ncol = 2))
-check(1:12, ctrl)
-
-numPerms(1:12, control = ctrl)
-(tmp <- allPerms(12, control = ctrl, observed = TRUE))
-(tmp2 <- allPerms(12, control = ctrl))
-
-## turn on mirroring %%FIXME needs a proper method to do this
-ctrl$within$mirror <- TRUE
-numPerms(1:12, control = ctrl)
-(tmp3 <- allPerms(12, control = ctrl, observed = TRUE))
-(tmp4 <- allPerms(12, control = ctrl))
-## prints out details of the permutation scheme as
-## well as the matrix of permutations
-summary(tmp) %% FIXME these don't print the scheme
-summary(tmp2)
-
-## different numbers of observations per level of strata
-fac <- factor(rep(1:3, times = c(3,2,2)))
-## free permutations in levels of strata
-numPerms(7, how(within = Within(type = "free"),
- plots = Plots(strata = fac, type = "none")))
-%% FIXME - need all these updating to new API in how...
-%% Fixed one, above, but there may still be problems with some of
-%% the code below:
-\dontrun{
-allPerms(7, how(type = "free", strata = fac))
-## series permutations in levels of strata
-numPerms(7, how(type = "series", strata = fac))
-allPerms(7, how(type = "series", strata = fac))
-
-## allPerms can work with a vector
-vec <- c(3,4,5)
-allPerms(vec)
-
-## Tests for permuplot
-n <- 25
-## standard permutation designs
-permuplot(n, how(type = "free"))
-permuplot(n, how(type = "series"))
-permuplot(n, how(type = "grid", nrow = 5, ncol = 5))
-
-## restricted perms with mirroring
-permuplot(n, how(type = "series", mirror = TRUE))
-permuplot(n, how(type = "grid", nrow = 5, ncol = 5,
- mirror = TRUE))
-
-## perms within strata
-fac <- gl(6, 20)
-control <- how(type = "free", strata = fac)
-permuplot(120, control = control, cex = 0.8)
-control <- how(type = "series", strata = fac)
-permuplot(120, control = control, cex = 0.8)
-fac <- gl(6, 25)
-control <- how(type = "grid", strata = fac,
- nrow = 5, ncol = 5)
-permuplot(150, control = control, cex = 0.8)
-
-## perms within strata with mirroring
-fac <- gl(6, 20)
-control <- how(type = "series", strata = fac,
- mirror = TRUE)
-permuplot(120, control = control, cex = 0.8)
-fac <- gl(6, 25)
-control <- how(type = "grid", strata = fac,
- nrow = 5, ncol = 5, mirror = TRUE)
-permuplot(150, control = control, cex = 0.8)
-
-## same perms within strata
-fac <- gl(6, 20)
-control <- how(type = "free", strata = fac,
- constant = TRUE)
-permuplot(120, control = control, cex = 0.8)
-control <- how(type = "series", strata = fac,
- constant = TRUE)
-permuplot(120, control = control, cex = 0.8)
-fac <- gl(6, 25)
-control <- how(type = "grid", strata = fac,
- nrow = 5, ncol = 5, constant = TRUE)
-permuplot(150, control = control, cex = 0.8)
-
-## same perms within strata with mirroring
-fac <- gl(6, 20)
-control <- how(type = "series", strata = fac,
- mirror = TRUE, constant = TRUE)
-permuplot(120, control = control, cex = 0.8)
-fac <- gl(6, 25)
-control <- how(type = "grid", strata = fac,
- nrow = 5, ncol = 5, mirror = TRUE,
- constant = TRUE)
-permuplot(150, control = control, cex = 0.8)
-}
-}
-\keyword{ utilities }
-\keyword{ design }
-\keyword{ methods }
Copied: pkg/permute/man/permControl-deprecated.Rd (from rev 2511, pkg/permute/man/permControl-dprecated.Rd)
===================================================================
--- pkg/permute/man/permControl-deprecated.Rd (rev 0)
+++ pkg/permute/man/permControl-deprecated.Rd 2013-06-12 15:50:07 UTC (rev 2513)
@@ -0,0 +1,82 @@
+\name{permControl-deprecated}
+\alias{permControl}
+\alias{print.permControl}
+\alias{print.permControl-deprecated}
+
+\title{How to define a permutation design?}
+
+\description{
+ Utility functions to describe unrestricted and restricted permutation
+ designs for time series, line transects, spatial grids and blocking
+ factors.
+}
+
+\usage{
+permControl(within = Within(), plots = Plots(), blocks = NULL,
+ nperm = 199, complete = FALSE, maxperm = 9999,
+ minperm = 99, all.perms = NULL, observed = FALSE)
+}
+
+\arguments{
+ \item{within, plots, blocks}{Permutation designs for samples within the
+ levels of \code{plots} (\code{within}), permutation of \code{plots}
+ themselves, or for the definition of blocking structures which
+ further restrict permutations (\code{blocks}). \code{within} and
+ \code{plots} each require a named list as produced by \code{Within}
+ and \code{Plots} respectively. \code{blocks} takes a factor, the
+ levels of which define the blocking structure.}
+ \item{nperm}{the number of permutations.}
+ \item{complete}{logical; should complete enumeration of all
+ permutations be performed?}
+ \item{maxperm}{the maximum number of permutations to
+ perform. Currently unused.}
+ \item{minperm}{the lower limit to the number of possible permutations
+ at which complete enumeration is performed. See argument
+ \code{complete} and Details, below.}
+ \item{all.perms}{an object of class \code{allPerms}, the result of a
+ call to \code{\link{allPerms}}.}
+ \item{observed}{logical; should the observed permutation be returned
+ as part of the set of all permutations?}
+}
+\details{
+ Argument \code{mirror} determines whether grid or series permutations
+ can be mirrored. Consider the sequence 1,2,3,4. The relationship
+ between consecutive observations is preserved if we reverse the
+ sequence to 4,3,2,1. If there is no inherent direction in your
+ experimental design, mirrored permutations can be considered
+ part of the Null model, and as such increase the number of possible
+ permutations. The default is to not use mirroring so you must
+ explicitly turn this on using \code{mirror = TRUE} in
+ \code{permControl}.
+
+ To permute plots rather than the observations within plots (the
+ levels of \code{strata}), use \code{Within(type = "none")} and
+ \code{Plots(type = foo)}, where \code{foo} is how you want the plots
+ to be permuted. However, note that the number of observations within
+ each plot \strong{must} be equal!
+
+ For some experiments, such as BACI designs, one might wish to use the
+ same permutation within each plot. This is controlled by
+ argument \code{constant}. If \code{constant = TRUE} then the same
+ permutation will be generated for each level of \code{strata}. The
+ default is \code{constant = FALSE}.
+}
+\value{
+ For \code{permControl} a list with components for each
+ of the possible arguments.
+}
+\references{
+ \code{shuffle()} is modelled after the permutation schemes of Canoco
+ 3.1 (ter Braak, 1990); see also Besag & Clifford (1989).
+
+ Besag, J. and Clifford, P. (1989) Generalized Monte Carlo significance
+ tests. \emph{Biometrika} \strong{76}; 633--642.
+
+ ter Braak, C. J. F. (1990). \emph{Update notes: CANOCO version
+ 3.1}. Wageningen: Agricultural Mathematics Group. (UR).
+}
+\author{Gavin L. Simpson}
+\seealso{\code{\link{shuffle}} for permuting from a design,
+ \code{\link{check}}, a utility function for checking permutation
+ schemedesign described by \code{\link{how}}.}
+\keyword{ utils }
\ No newline at end of file
Deleted: pkg/permute/man/permControl-dprecated.Rd
===================================================================
--- pkg/permute/man/permControl-dprecated.Rd 2013-06-12 05:22:29 UTC (rev 2512)
+++ pkg/permute/man/permControl-dprecated.Rd 2013-06-12 15:50:07 UTC (rev 2513)
@@ -1,81 +0,0 @@
-\name{permControl-deprecated}
-\alias{permControl}
-\alias{print.permControl}
-
-\title{How to define a permutation design?}
-
-\description{
- Utility functions to describe unrestricted and restricted permutation
- designs for time series, line transects, spatial grids and blocking
- factors.
-}
-
-\usage{
-permControl(within = Within(), plots = Plots(), blocks = NULL,
- nperm = 199, complete = FALSE, maxperm = 9999,
- minperm = 99, all.perms = NULL, observed = FALSE)
-}
-
-\arguments{
- \item{within, plots, blocks}{Permutation designs for samples within the
- levels of \code{plots} (\code{within}), permutation of \code{plots}
- themselves, or for the definition of blocking structures which
- further restrict permutations (\code{blocks}). \code{within} and
- \code{plots} each require a named list as produced by \code{Within}
- and \code{Plots} respectively. \code{blocks} takes a factor, the
- levels of which define the blocking structure.}
- \item{nperm}{the number of permutations.}
- \item{complete}{logical; should complete enumeration of all
- permutations be performed?}
- \item{maxperm}{the maximum number of permutations to
- perform. Currently unused.}
- \item{minperm}{the lower limit to the number of possible permutations
- at which complete enumeration is performed. See argument
- \code{complete} and Details, below.}
- \item{all.perms}{an object of class \code{allPerms}, the result of a
- call to \code{\link{allPerms}}.}
- \item{observed}{logical; should the observed permutation be returned
- as part of the set of all permutations?}
-}
-\details{
- Argument \code{mirror} determines whether grid or series permutations
- can be mirrored. Consider the sequence 1,2,3,4. The relationship
- between consecutive observations is preserved if we reverse the
- sequence to 4,3,2,1. If there is no inherent direction in your
- experimental design, mirrored permutations can be considered
- part of the Null model, and as such increase the number of possible
- permutations. The default is to not use mirroring so you must
- explicitly turn this on using \code{mirror = TRUE} in
- \code{permControl}.
-
- To permute plots rather than the observations within plots (the
- levels of \code{strata}), use \code{Within(type = "none")} and
- \code{Plots(type = foo)}, where \code{foo} is how you want the plots
- to be permuted. However, note that the number of observations within
- each plot \strong{must} be equal!
-
- For some experiments, such as BACI designs, one might wish to use the
- same permutation within each plot. This is controlled by
- argument \code{constant}. If \code{constant = TRUE} then the same
- permutation will be generated for each level of \code{strata}. The
- default is \code{constant = FALSE}.
-}
-\value{
- For \code{permControl} a list with components for each
- of the possible arguments.
-}
-\references{
- \code{shuffle()} is modelled after the permutation schemes of Canoco
- 3.1 (ter Braak, 1990); see also Besag & Clifford (1989).
-
- Besag, J. and Clifford, P. (1989) Generalized Monte Carlo significance
- tests. \emph{Biometrika} \strong{76}; 633--642.
-
- ter Braak, C. J. F. (1990). \emph{Update notes: CANOCO version
- 3.1}. Wageningen: Agricultural Mathematics Group. (UR).
-}
-\author{Gavin Simpson}
-\seealso{\code{\link{shuffle}} for permuting from a design,
- \code{\link{check}}, a utility function for checking permutation
- schemedesign described by \code{\link{how}}.}
-\keyword{ utils }
\ No newline at end of file
Added: pkg/permute/man/permute-deprecated.Rd
===================================================================
--- pkg/permute/man/permute-deprecated.Rd (rev 0)
+++ pkg/permute/man/permute-deprecated.Rd 2013-06-12 15:50:07 UTC (rev 2513)
@@ -0,0 +1,25 @@
+\name{permute-deprecated}
+
+\title{Deprecated functions in package permute}
+
+\description{
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/vegan -r 2513
More information about the Vegan-commits
mailing list