[Vegan-commits] r1085 - in pkg/vegan: inst man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Dec 16 17:59:29 CET 2009
Author: psolymos
Date: 2009-12-16 17:59:29 +0100 (Wed, 16 Dec 2009)
New Revision: 1085
Removed:
pkg/vegan/man/plot.permat.Rd
Modified:
pkg/vegan/inst/ChangeLog
pkg/vegan/man/permatfull.Rd
Log:
contents of plot.permat.Rd merged with permatfull.Rd
Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog 2009-12-16 07:20:54 UTC (rev 1084)
+++ pkg/vegan/inst/ChangeLog 2009-12-16 16:59:29 UTC (rev 1085)
@@ -7,8 +7,8 @@
* twostagechao: deleted, because question regarding the
notation in the original article remained unanswered.
- * permat.control: deleted, not needed any longer due to changes
- in oecosimu.
+ * permat* cleanup: permat.control deleted, not needed any longer due to changes
+ in oecosimu, documentation for plot.permat merged with permat* help page.
* goodness.cca: was not using correct weights. Broken in r992 (Sep
6, 2009).
Modified: pkg/vegan/man/permatfull.Rd
===================================================================
--- pkg/vegan/man/permatfull.Rd 2009-12-16 07:20:54 UTC (rev 1084)
+++ pkg/vegan/man/permatfull.Rd 2009-12-16 16:59:29 UTC (rev 1085)
@@ -5,6 +5,10 @@
\alias{summary.permat}
\alias{print.summary.permat}
\alias{print.permat}
+\alias{plot.permat}
+\alias{lines.permat}
+\alias{as.ts.permat}
+\alias{as.mcmc.permat}
\title{Matrix Permutation Algorithms for Presence-Absence and Count Data}
@@ -22,6 +26,11 @@
\method{print}{permat}(x, digits = 3, ...)
\method{summary}{permat}(object, ...)
\method{print}{summary.permat}(x, digits = 2, ...)
+\method{plot}{permat}(x, type = "bray", ylab, xlab, col, lty,
+ lowess = TRUE, plot = TRUE, text = TRUE, ...)
+\method{lines}{permat}(x, type = "bray", ...)
+\method{as.ts}{permat}(x, type = "bray", ...)
+\method{as.mcmc}{permat}(x)
}
\arguments{
\item{m}{A community data matrix with plots (samples) as rows and species (taxa) as columns.}
@@ -35,6 +44,9 @@
\item{thin}{Number of discarded permuted matrices between two evaluations in sequential (\code{"swap", "tswap"}) methods.}
\item{x, object}{Object of class \code{"permat"}}
\item{digits}{Number of digits used for rounding.}
+ \item{ylab, xlab, col, lty}{graphical parameters for the \code{plot} method.}
+ \item{type}{Character, type of plot to be displayed: \code{"bray"} for Bray-Curtis dissimilarities, \code{"chisq"} for Chi-squared values.}
+ \item{lowess, plot, text}{Logical arguments for the \code{plot} method, whether a locally weighted regression curve should be drawn, the plot should be drawn, and statistic values should be printed on the plot.}
\item{\dots}{Other arguments passed to methods.}
}
@@ -82,12 +94,20 @@
because same constraints are forced on submatrices of different dimensions. This
often means, that the number of potential permutations will decrease with their dimensions.
So the more constraints we put, the less randomness can be expected.
+
+The \code{plot} method is useful for graphically testing for trend and independence of permuted matrices. This is especially important when using sequential algorithms (\code{"swap", "tswap", "abuswap"}).
+
+The \code{as.ts} method can be used to extract Bray-Curtis dissimilarities or Chi-squared values as time series. This can further used in testing independence (see Examples). The method \code{as.mcmc} is useful for accessing diagnostic tools available in the 'coda' package.
}
\value{
Functions \code{permatfull} and \code{permatswap} return an object of class \code{"permat"} containing the the function call (\code{call}), the original data matrix used for permutations (\code{orig}) and a list of permuted matrices with length \code{times} (\code{perm}).
The \code{summary} method returns various statistics as a list (including mean Bray-Curtis dissimilarities calculated pairwise among original and permuted matrices, Chi-square statistics, and check results of the constraints; see Examples). Note that when \code{strata} is used in the original call, summary calculation may take longer.
+
+The \code{plot} creates a plot as a side effect.
+
+The \code{as.ts} method returns an object of class 'ts'.
}
\references{
Original references for presence-absence algorithms are given on help
@@ -104,18 +124,18 @@
\seealso{
For other functions to permute matrices: \code{\link{commsimulator}}, \code{\link{r2dtable}}, \code{\link{sample}}, \code{\link[bipartite]{swap.web}}.
-For the use of these permutation algorithms: \code{\link{oecosimu}}, \code{\link{adipart}}.
+For the use of these permutation algorithms: \code{\link{oecosimu}}, \code{\link{adipart}}, \code{\link{hiersimu}}.
-For time-series diagnostics and plotting: \code{\link{as.ts.permat}}, \code{\link{plot.permat}}, \code{\link{lines.permat}}.
+For time-series diagnostics: \code{\link{Box.test}}, \code{\link{lag.plot}}, \code{\link{tsdiag}}, \code{\link{ar}}, \code{\link{arima}}
}
\examples{
## A simple artificial community data matrix.
m <- matrix(c(
- 1,3,2,0,3,1,
- 0,2,1,0,2,1,
- 0,0,1,2,0,3,
- 0,0,0,1,4,3
- ), 4, 6, byrow=TRUE)
+ 1,3,2,0,3,1,
+ 0,2,1,0,2,1,
+ 0,0,1,2,0,3,
+ 0,0,0,1,4,3
+ ), 4, 6, byrow=TRUE)
## Using the quasiswap algorithm to create a
## list of permuted matrices, where
## row/columns sums and matrix fill are preserved:
@@ -134,8 +154,31 @@
## check sums within strata:
x4 <- permatfull(m, strata=c(1,1,2,2))
summary(x4)
+## Not sequential algorithm
+data(BCI)
+a <- permatswap(BCI, "quasiswap")
+## Sequential algorithm
+b <- permatswap(BCI, "abuswap", fixedmar="col",
+ burnin=0, thin=100, times=50)
+opar <- par(mfrow=c(2,2))
+plot(a, main="Not sequential")
+plot(b, main="Sequential")
+plot(a, "chisq")
+plot(b, "chisq")
+par(opar)
+## Extract Bray-Curtis dissimilarities
+## as time series
+bc <- as.ts(b)
+## Lag plot
+lag.plot(bc)
+## First order autoregressive model
+mar <- arima(bc, c(1,0,0))
+mar
+## Ljung-Box test of residuals
+Box.test(mar$residuals)
+## Graphical diagnostics
+tsdiag(mar)
}
\keyword{multivariate}
\keyword{datagen}
-
Deleted: pkg/vegan/man/plot.permat.Rd
===================================================================
--- pkg/vegan/man/plot.permat.Rd 2009-12-16 07:20:54 UTC (rev 1084)
+++ pkg/vegan/man/plot.permat.Rd 2009-12-16 16:59:29 UTC (rev 1085)
@@ -1,74 +0,0 @@
-\encoding{UTF-8}
-\name{diagnose.permat}
-\alias{plot.permat}
-\alias{lines.permat}
-\alias{as.ts.permat}
-\alias{as.mcmc.permat}
-
-\title{Plotting Methods for Matrix Permutation Algorithms}
-
-\description{ Plotting and time series extraction methods for 'permat' objects, that are useful in evaluating the performance of different null model settings, especially that of the sequential algorithms.}
-
-\usage{
-\method{plot}{permat}(x, type = "bray", ylab, xlab, col, lty,
- lowess = TRUE, plot = TRUE, text = TRUE, ...)
-\method{lines}{permat}(x, type = "bray", ...)
-\method{as.ts}{permat}(x, type = "bray", ...)
-\method{as.mcmc}{permat}(x)
-}
-\arguments{
- \item{x}{Object of class \code{"permat"} created by the functions \code{\link{permatfull}} and \code{\link{permatswap}}.}
- \item{ylab, xlab, col, lty}{graphical parameters for the \code{plot} method.}
- \item{type}{Character, type of plot to be displayed: \code{"bray"} for Bray-Curtis dissimilarities, \code{"chisq"} for Chi-squared values.}
- \item{lowess, plot, text}{Logical arguments for the \code{plot} method, whether a lowess curve should be drawn, the plot should be drawn, and statistic values should be printed on the plot.}
- \item{\dots}{Other arguments passed to methods.}
-}
-
-\details{
-
-The \code{plot} method is useful for graphically testing for trend and independence of permuted matrices. This is especially important when using sequential algorithms (\code{"swap", "tswap", "abuswap"}).
-
-
-The \code{as.ts} method can be used to extract Bray-Curtis dissimilarities or Chi-squared values as time series. This can further used in testing independence (see Examples). The method \code{as.mcmc} is useful for accessing diagnostic tools available in the 'coda' package.
-}
-
-\value{
-The \code{plot} creates a plot as a side effect.
-
-The \code{as.ts} method returns an object of class 'ts'.
-}
-\author{\enc{P\'eter S\'olymos}{Peter Solymos}, \email{solymos at ualberta.ca}}
-
-\seealso{
-For functions to create 'permat' objects: \code{\link{permatfull}}, \code{\link{permatswap}}
-
-For time-series diagnostics: \code{\link{Box.test}}, \code{\link{lag.plot}}, \code{\link{tsdiag}}, \code{\link{ar}}, \code{\link{arima}}
-}
-\examples{
-data(BCI)
-## Not sequential algorithm
-a <- permatswap(BCI, "quasiswap")
-## Sequential algorithm
-b <- permatswap(BCI, "abuswap", fixedmar="col",
-burnin=0, thin=100, times=50)
-opar <- par(mfrow=c(2,2))
-plot(a, main="Not sequential")
-plot(b, main="Sequential")
-plot(a, "chisq")
-plot(b, "chisq")
-par(opar)
-## Extract Bray-Curtis dissimilarities
-## as time series
-bc <- as.ts(b)
-## Lag plot
-lag.plot(bc)
-## First order autoregressive model
-mar <- arima(bc, c(1,0,0))
-mar
-## Ljung-Box test of residuals
-Box.test(mar$residuals)
-## Graphical diagnostics
-tsdiag(mar)
-}
-
-\keyword{multivariate}
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