[Vegan-commits] r2673 - in pkg/permute: . man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Nov 8 04:01:46 CET 2013
Author: gsimpson
Date: 2013-11-08 04:01:42 +0100 (Fri, 08 Nov 2013)
New Revision: 2673
Modified:
pkg/permute/NAMESPACE
pkg/permute/man/check.Rd
Log:
don't export and un-document permuplot
Modified: pkg/permute/NAMESPACE
===================================================================
--- pkg/permute/NAMESPACE 2013-11-07 22:56:34 UTC (rev 2672)
+++ pkg/permute/NAMESPACE 2013-11-08 03:01:42 UTC (rev 2673)
@@ -5,7 +5,7 @@
`getBlocks`, `getWithin`, `getStrata`, `getType`, `getMirror`,
`getConstant`, `getPlots`, `getRow`, `getCol`, `getDim`,
`getNperm`,`getMaxperm`, `getMinperm`, `getComplete`, `shuffleSet`,
- `permuplot`,`how`)
+ `how`)
### Imports: nobs() only exists in R 2.13.0 for import. We define the
### same nobs() generic in permute for export in older R.
Modified: pkg/permute/man/check.Rd
===================================================================
--- pkg/permute/man/check.Rd 2013-11-07 22:56:34 UTC (rev 2672)
+++ pkg/permute/man/check.Rd 2013-11-08 03:01:42 UTC (rev 2673)
@@ -3,7 +3,6 @@
\alias{print.check}
\alias{print.summary.check}
\alias{summary.check}
-\alias{permuplot}
\title{Utility functions for permutation schemes}
\description{
@@ -15,44 +14,24 @@
check(object, control = how(), make.all = TRUE, observed = FALSE)
\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"}.}
+ \item{object}{an R object. See Details for a complete description,
+ especially for \code{\link{numPerms}}. For
+ \code{\link{summary.check}} an object of class \code{"check"}.}
\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{permCheck} generate all
+ 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{observed}{logical; if making all possible permutations, should
the set include the observed permutation too?}
- \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.}
+ \item{\dots}{arguments to other methods.}
}
\details{
- \code{check} and \code{permuplot} are utility functions for working
- with the new permutation schemes available in \code{\link{shuffle}}.
+ \code{check} is a 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
@@ -62,7 +41,7 @@
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 main problem is requesting more permutations than is 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
@@ -72,23 +51,6 @@
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
@@ -168,15 +130,14 @@
(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
+## turn on mirroring
ctrl <- update(ctrl, within = update(getWithin(ctrl), 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(tmp)
summary(tmp2)
## different numbers of observations per level of strata
@@ -190,11 +151,6 @@
ctrl <- how(within = Within(type = "series"), plots = Plots(strata = fac))
numPerms(7, control = ctrl)
allPerms(7, control = ctrl)
-
-%% FIXME - need all these updating to new API in how...
-%% moved permuplot examples out of package until I can fix it
-%% properly
-
}
\keyword{ utilities }
\keyword{ design }
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