[r-cran-coda] 21/60: Imported Upstream version 0.12-1
Andreas Tille
tille at debian.org
Fri Dec 16 12:11:23 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository r-cran-coda.
commit d43197f79de7b6bf042928fef7576843d7b479e0
Author: Andreas Tille <tille at debian.org>
Date: Fri Dec 16 12:09:57 2016 +0100
Imported Upstream version 0.12-1
---
CHANGELOG | 6 ++++++
DESCRIPTION | 6 +++---
R/HPDinterval.R | 3 ---
R/batchSE.R | 6 ------
R/codamenu.R | 9 +--------
R/cumuplot.R | 18 ++++++++++++++----
R/gelman.R | 38 ++++++++++++++++++++++++++++++++------
R/geweke.R | 22 +++++++++++++++-------
R/heidel.R | 6 ------
R/mcmclist.R | 5 ++++-
R/output.R | 33 +++++++++++++++++++++------------
R/raftery.R | 3 ---
R/trellisplots.R | 27 +++++++++++++++++++++++++++
R/util.R | 15 ++++++++++-----
man/autocorr.plot.Rd | 3 ++-
man/bugs2jags.Rd | 2 ++
man/codamenu.Rd | 2 +-
man/cumuplot.Rd | 5 +++--
man/gelman.plot.Rd | 5 +++--
man/geweke.plot.Rd | 6 ++++--
man/mcmc.subset.Rd | 4 +++-
man/nchain.Rd | 2 +-
man/trellisplots.Rd | 5 +++++
23 files changed, 157 insertions(+), 74 deletions(-)
diff --git a/CHANGELOG b/CHANGELOG
index 8d5cb6e..2384779 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -1,3 +1,9 @@
+0.12-1
+- Added further changes for S-PLUS from Dawn Woodward.
+
+0.11-3
+- Fixed documentation on subsetting methods for mcmc and mcmc.list objects
+
0.11-2
- The codamenu function has been modified so that it no longer works with
coda.dat and work.dat in the global environment, solving global binding
diff --git a/DESCRIPTION b/DESCRIPTION
index aec2593..e221f9b 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
Package: coda
-Version: 0.11-2
-Date: 2007-06-04
+Version: 0.12-1
+Date: 2007-08-10
Title: Output analysis and diagnostics for MCMC
Author: Martyn Plummer, Nicky Best, Kate Cowles, Karen Vines
Maintainer: Martyn Plummer <plummer at iarc.fr>
@@ -8,4 +8,4 @@ Depends: R (>= 2.5.0), lattice
Description: Output analysis and diagnostics for Markov Chain Monte
Carlo simulations.
License: GPL Version 2 or later.
-Packaged: Mon Jun 4 11:33:42 2007; martyn
+Packaged: Fri Aug 10 08:05:42 2007; martyn
diff --git a/R/HPDinterval.R b/R/HPDinterval.R
index 0f745ab..275f0b5 100644
--- a/R/HPDinterval.R
+++ b/R/HPDinterval.R
@@ -2,9 +2,6 @@ HPDinterval <- function(obj, prob = 0.95, ...) UseMethod("HPDinterval")
HPDinterval.mcmc <- function(obj, prob = 0.95, ...)
{
- if (!is.R()) {
- stop("This function is not yet available in S-PLUS")
- }
obj <- as.matrix(obj)
vals <- apply(obj, 2, sort)
if (!is.matrix(vals)) stop("obj must have nsamp > 1")
diff --git a/R/batchSE.R b/R/batchSE.R
index f0657ab..01934c2 100644
--- a/R/batchSE.R
+++ b/R/batchSE.R
@@ -5,9 +5,6 @@
}
"batchSE.mcmc" <- function(x,batchSize=100) {
- if (!is.R()) {
- stop("This function is not yet available in S-PLUS")
- }
niter <- niter(x)
nbatch <- niter%/%batchSize
## Truncate the odd lot observations
@@ -24,9 +21,6 @@
}
"batchSE.mcmc.list" <- function(x,batchSize=100) {
- if (!is.R()) {
- stop("This function is not yet available in S-PLUS")
- }
nchain <- nchain(x)
niter <- niter(x)
nbatch <- niter%/%batchSize
diff --git a/R/codamenu.R b/R/codamenu.R
index b42cdd3..01751a8 100644
--- a/R/codamenu.R
+++ b/R/codamenu.R
@@ -1,8 +1,5 @@
"codamenu" <- function ()
{
- if (!is.R()) {
- stop("This function is not yet available in S-PLUS")
- }
coda.options(default=TRUE)
file.menu <- c("Read BUGS output files",
"Use an mcmc object",
@@ -831,9 +828,6 @@ function (last.menu)
"read.coda.interactive" <- function ()
{
- if (!is.R()) {
- stop("This function is not yet available in S-PLUS")
- }
repeat {
cat("Enter CODA index file name\n")
cat("(or a blank line to exit)\n")
@@ -842,8 +836,7 @@ function (last.menu)
nlines=1, quiet=TRUE)
}
else {
- index.file <- scan(what = character(), sep = "\n", strip.white = TRUE,
- nlines = 1)
+ index.file <- scan(what = character(), sep = "\n", strip.white = TRUE)
}
if (length(index.file) == 0)
return()
diff --git a/R/cumuplot.R b/R/cumuplot.R
index 446ad10..897bff1 100644
--- a/R/cumuplot.R
+++ b/R/cumuplot.R
@@ -1,16 +1,25 @@
cumuplot <- function(x, probs=c(0.025,0.5,0.975), ylab="", lty=c(2,1),
- lwd=c(1,2), type="l", ask=dev.interactive(),
+ lwd=c(1,2), type="l", ask,
auto.layout=TRUE, col=1, ...)
{
- if (!is.R()) {
- stop("This function is not yet available in S-PLUS")
+ if (missing(ask)) {
+ ask <- if (is.R()) {
+ dev.interactive()
+ }
+ else {
+ interactive()
+ }
}
cquantile <- function(z, probs)
{
## Calculates cumulative quantile of a vector
cquant <- matrix(0, nrow=length(z), length(probs))
for(i in seq(along=z)) # for loop proved faster than apply here
- cquant[i,] <- quantile(z[1:i], probs=probs, names=FALSE)
+ if (is.R()) {
+ cquant[i,] <- quantile(z[1:i], probs=probs, names=FALSE)
+ }else{
+ cquant[i,] <- quantile(z[1:i], probs=probs)
+ }
cquant <- as.data.frame(cquant)
names(cquant) <- paste(formatC(100*probs,format="fg",wid=1,digits=7),
"%", sep="") # just like quantile.default
@@ -31,6 +40,7 @@ cumuplot <- function(x, probs=c(0.025,0.5,0.975), ylab="", lty=c(2,1),
for (i in 1:nchain(x)) {
for (j in 1:nvar(x)) {
Y <- cquantile(as.matrix(x[[i]])[,j], probs=probs)
+ if (!is.R()) Y <- as.matrix(Y)
matplot(Iterations, Y, ylab=ylab, lty=lty, lwd=lwd, type=type,
col=col, ...)
title(paste(varnames(x)[j], ifelse(is.null(chanames(x)),
diff --git a/R/gelman.R b/R/gelman.R
index 85de854..03adba5 100644
--- a/R/gelman.R
+++ b/R/gelman.R
@@ -10,9 +10,6 @@
## Graphical Statistics, 7, 434-455.
{
- if (!is.R()) {
- stop("This function is not yet available in S-PLUS")
- }
x <- as.mcmc.list(x)
if (nchain(x) < 2)
stop("You need at least two chains")
@@ -100,6 +97,13 @@
## improve the normal approximation, variables on [0, Inf) are log
## transformed, and variables on [0,1] are logit-transformed.
{
+ if (!is.R()) {
+ # in S-PLUS this function generates a superfluous warning,
+ # so turn off all warnings during the function.
+ oldWarn <- getOption("warn")
+ options(warn=-1)
+ on.exit(options (warn=oldWarn))
+ }
if (nvar(x) == 1) {
z <- data.frame(lapply(x, unclass))
if (min(z) > 0) {
@@ -147,12 +151,17 @@
"gelman.plot" <-
function (x, bin.width = 10, max.bins = 50, confidence = 0.95,
- transform = FALSE, auto.layout = TRUE, ask = dev.interactive(),
+ transform = FALSE, auto.layout = TRUE, ask,
col = 1:2, lty = 1:2, xlab = "last iteration in chain",
ylab = "shrink factor", type = "l", ...)
{
- if (!is.R()) {
- stop("This function is not yet avialable in S-PLUS")
+ if (missing(ask)) {
+ ask <- if (is.R()) {
+ dev.interactive()
+ }
+ else {
+ interactive()
+ }
}
x <- as.mcmc.list(x)
oldpar <- NULL
@@ -211,6 +220,23 @@
return(list(shrink = shrink, last.iter = last.iter))
}
+if (!is.R()){
+
+qr.solve <- function (a, b, tol = 1e-07) {
+ if (!is.qr(a))
+ a <- qr(a, tol = tol)
+ nc <- ncol(a$qr)
+ if (a$rank != nc)
+ stop("singular matrix 'a' in solve")
+ if (missing(b)) {
+ if (nc != nrow(a$qr))
+ stop("only square matrices can be inverted")
+ b <- diag(1, nc)
+ }
+ return(qr.coef(a, b))
+}
+
+}
diff --git a/R/geweke.R b/R/geweke.R
index 6d26eb2..8bd1a41 100644
--- a/R/geweke.R
+++ b/R/geweke.R
@@ -2,9 +2,6 @@
function (x, frac1 = 0.1, frac2 = 0.5)
##
{
- if (!is.R()) {
- stop("This function is not yet available in S-PLUS")
- }
if (is.mcmc.list(x))
return(lapply(x, geweke.diag, frac1, frac2))
x <- as.mcmc(x)
@@ -24,11 +21,17 @@
"geweke.plot" <-
function (x, frac1 = 0.1, frac2 = 0.5, nbins = 20,
- pvalue = 0.05, auto.layout = TRUE, ask = dev.interactive(), ...)
+ pvalue = 0.05, auto.layout = TRUE, ask, ...)
{
- if (!is.R()) {
- stop("This function is not yet available in S-PLUS")
+ if (missing(ask)) {
+ ask <- if (is.R()) {
+ dev.interactive()
+ }
+ else {
+ interactive()
+ }
}
+
x <- as.mcmc.list(x)
oldpar <- NULL
on.exit(par(oldpar))
@@ -36,8 +39,13 @@
oldpar <- par(mfrow = set.mfrow(Nchains = nchain(x),
Nparms = nvar(x)))
ystart <- seq(from = start(x), to = (start(x) + end(x))/2, length = nbins)
- gcd <- array(dim = c(length(ystart), nvar(x), nchain(x)),
+ if (is.R())
+ gcd <- array(dim = c(length(ystart), nvar(x), nchain(x)),
dimnames = c(ystart, varnames(x), chanames(x)))
+ else
+ gcd <- array(dim = c(length(ystart), nvar(x), nchain(x)),
+ dimnames = list(ystart, varnames(x), chanames(x)))
+
for (n in 1:length(ystart)) {
geweke.out <- geweke.diag(window(x, start = ystart[n]),
frac1 = frac1, frac2 = frac2)
diff --git a/R/heidel.R b/R/heidel.R
index f5777d8..6b97968 100644
--- a/R/heidel.R
+++ b/R/heidel.R
@@ -1,8 +1,5 @@
"heidel.diag" <- function (x, eps = 0.1, pvalue=0.05)
{
- if (!is.R()) {
- stop("This function is not yet available in S-PLUS")
- }
if (is.mcmc.list(x))
return(lapply(x, heidel.diag, eps))
x <- as.mcmc(as.matrix(x))
@@ -175,9 +172,6 @@ effectiveSize <- function(x)
"pcramer" <- function (q, eps=1.0e-5)
{
- if (!is.R()) {
- stop("This function is not yet available in S-PLUS")
- }
## Distribution function of the Cramer-von Mises statistic
##
log.eps <- log(eps)
diff --git a/R/mcmclist.R b/R/mcmclist.R
index bcc6b20..774a7de 100644
--- a/R/mcmclist.R
+++ b/R/mcmclist.R
@@ -56,7 +56,10 @@
if (!all(unlist(lapply(xvarnames, "==", xvarnames[[1]]))))
stop("Different variable names in each chain")
}
- class(x) <- "mcmc.list"
+ if (is.R())
+ class(x) <- "mcmc.list"
+ else
+ oldClass(x) <- "mcmc.list"
return(x)
}
diff --git a/R/output.R b/R/output.R
index d9af9bc..5cbbdeb 100644
--- a/R/output.R
+++ b/R/output.R
@@ -65,9 +65,6 @@ function (x)
"crosscorr.plot" <-
function (x, col = topo.colors(10), ...)
{
- if (!is.R()) {
- stop("This function is not yet available in S-PLUS")
- }
Nvar <- nvar(x)
pcorr <- crosscorr(x)
dens <- ((pcorr + 1) * length(col))%/%2 + (pcorr < 1) + (pcorr <
@@ -81,6 +78,9 @@ function (x, col = topo.colors(10), ...)
oldpar <- c(par(pty = "s", adj = 0.5), oldpar)
plot(0, 0, type = "n", xlim = c(0, Nvar), ylim = c(0, Nvar),
xlab = "", ylab = "", xaxt = "n", yaxt = "n", ...)
+ if (!is.R()){ # In S-PLUS, specify that the y-axis labels should be right-justified
+ par(adj = 1)
+ }
axis(1, at = 1:Nvar - 0.5, labels = abbreviate(varnames(x,
allow.null = FALSE), minlength = 7))
axis(2, at = 1:Nvar - 0.5, labels = abbreviate(varnames(x,
@@ -107,9 +107,6 @@ function (x, col = topo.colors(10), ...)
"densplot" <-
function (x, show.obs = TRUE, bwf, main = "", ylim, ...)
{
- if (!is.R()) {
- stop("This function is not yet available in S-PLUS")
- }
xx <- as.matrix(x)
for (i in 1:nvar(x)) {
y <- xx[, i, drop = TRUE]
@@ -147,9 +144,16 @@ function (x, show.obs = TRUE, bwf, main = "", ylim, ...)
}
if(missing(ylim))
ylim <- c(0, max(dens$y))
- plot(dens, ylab = "", main = main, type = "l",
- xlab = paste("N =", niter(x), " Bandwidth =", formatC(dens$bw)),
- ylim = ylim, ...)
+
+ if (is.R()){
+ plot(dens, ylab = "", main = main, type = "l",
+ xlab = paste("N =", niter(x), " Bandwidth =", formatC(dens$bw)),
+ ylim = ylim, ...)
+ } else { #In S-PLUS the bandwidth is not returned by the "density" function
+ plot(dens, ylab = "", main = main, type = "l",
+ xlab = paste("N =", niter(x), " Bandwidth =", formatC(bw)),
+ ylim = ylim, ...)
+ }
if (show.obs)
lines(y[1:niter(x)], rep(max(dens$y)/100, niter(x)),
type = "h")
@@ -160,6 +164,14 @@ function (x, show.obs = TRUE, bwf, main = "", ylim, ...)
return(invisible(x))
}
+if (!is.R()){
+
+"IQR"<-
+function(x, na.rm = FALSE)
+diff(quantile(as.numeric(x), c(0.25, 0.75), na.rm = na.rm))
+
+}
+
"read.jags" <- function (file = "jags.out", start, end, thin, quiet=FALSE)
{
nc <- nchar(file)
@@ -174,9 +186,6 @@ function (x, show.obs = TRUE, bwf, main = "", ylim, ...)
"read.openbugs" <-
function (stem = "", start, end, thin, quiet = FALSE)
{
- if (!is.R()) {
- stop("This function is not yet available in S-PLUS")
- }
index.file <- paste(stem, "CODAindex.txt", sep = "")
if (!file.exists(index.file))
stop("No index file found")
diff --git a/R/raftery.R b/R/raftery.R
index f42a489..c8a7bf0 100644
--- a/R/raftery.R
+++ b/R/raftery.R
@@ -1,9 +1,6 @@
"raftery.diag" <-
function (data, q = 0.025, r = 0.005, s = 0.95, converge.eps = 0.001)
{
- if (!is.R()) {
- stop("This function is not yet available in S-PLUS")
- }
if (is.mcmc.list(data))
return(lapply(data, raftery.diag, q, r, s, converge.eps))
data <- as.mcmc(data)
diff --git a/R/trellisplots.R b/R/trellisplots.R
index 6c41562..01c2ee2 100644
--- a/R/trellisplots.R
+++ b/R/trellisplots.R
@@ -62,6 +62,9 @@ levelplot.mcmc <-
col.regions = topo.colors(100),
subset = thinned.indices(x, start = start, thin = thin))
{
+ if (!is.R()) {
+ stop("This function is not yet available in S-PLUS")
+ }
cormat <- cor(x[subset, ])
cormat <- cormat[, rev(seq(length = ncol(cormat)))]
levelplot(cormat,
@@ -102,6 +105,9 @@ splom.mcmc <-
{
## cormat <- cor(x[subset, ])
## cormat <- cormat[, rev(seq(length = ncol(cormat)))]
+ if (!is.R()) {
+ stop("This function is not yet available in S-PLUS")
+ }
splom(as.data.frame(x[subset, ]),
as.matrix = as.matrix,
main = main, ...,
@@ -254,6 +260,9 @@ qqmath.mcmc <-
...,
subset = thinned.indices(x, start = start, thin = thin))
{
+ if (!is.R()) {
+ stop("This function is not yet available in S-PLUS")
+ }
if (!missing(outer)) warning("specification of outer ignored")
data <- as.data.frame(x)
form <-
@@ -283,6 +292,9 @@ qqmath.mcmc.list <-
...,
subset = thinned.indices(x[[1]], start = start, thin = thin))
{
+ if (!is.R()) {
+ stop("This function is not yet available in S-PLUS")
+ }
if (groups && outer) warning("'groups=TRUE' ignored when 'outer=TRUE'")
datalist <- lapply(x, function(x) as.data.frame(x)[subset, ])
data <- do.call("rbind", datalist)
@@ -337,6 +349,9 @@ xyplot.mcmc <-
...,
subset = thinned.indices(x, start = start, thin = thin))
{
+ if (!is.R()) {
+ stop("This function is not yet available in S-PLUS")
+ }
if (!missing(outer)) warning("specification of outer ignored")
data <- as.data.frame(x)
form <- eval(parse(text = paste(paste(lapply(names(data), as.name),
@@ -367,6 +382,9 @@ xyplot.mcmc.list <-
...,
subset = thinned.indices(x[[1]], start = start, thin = thin))
{
+ if (!is.R()) {
+ stop("This function is not yet available in S-PLUS")
+ }
if (groups && outer) warning("'groups=TRUE' ignored when 'outer=TRUE'")
datalist <- lapply(x, function(x) as.data.frame(x)[subset, ])
data <- do.call("rbind", datalist)
@@ -423,6 +441,9 @@ xyplot.mcmc.list <-
panel.acfplot <-
function(..., groups = NULL)
{
+ if (!is.R()) {
+ stop("This function is not yet available in S-PLUS")
+ }
reference.line <- trellis.par.get("reference.line")
panel.abline(h = 0,
col = reference.line$col,
@@ -456,6 +477,9 @@ acfplot.mcmc <-
...,
subset = thinned.indices(x, start = start, thin = thin))
{
+ if (!is.R()) {
+ stop("This function is not yet available in S-PLUS")
+ }
if (!missing(outer)) warning("specification of outer ignored")
getAcf <- function(x, lag.max)
{
@@ -501,6 +525,9 @@ acfplot.mcmc.list <-
...,
subset = thinned.indices(x[[1]], start = start, thin = thin))
{
+ if (!is.R()) {
+ stop("This function is not yet available in S-PLUS")
+ }
if (groups && outer) warning("'groups=TRUE' ignored when 'outer=TRUE'")
getAcf <- function(x, lag.max)
{
diff --git a/R/util.R b/R/util.R
index 4c50d01..f9e09e8 100644
--- a/R/util.R
+++ b/R/util.R
@@ -29,13 +29,13 @@ function (string, option)
"coda.options" <-
function (...)
{
- if (!is.R()) {
- stop("This function is not yet available in S-PLUS")
- }
## Set and display coda options
single <- FALSE
copt <- if (exists(".Coda.Options", frame = 1)) {
- get(".Coda.Options", pos=1)
+ if (is.R())
+ get(".Coda.Options", pos=1)
+ else
+ get(".Coda.Options")
}
else {
.Coda.Options.Default
@@ -77,7 +77,10 @@ function (...)
else if (mode(copt[[v]]) == mode(args[[v]]))
copt[v] <- args[v]
}
- assign(".Coda.Options", copt, pos=1)
+ if (is.R())
+ assign(".Coda.Options", copt, pos=1)
+ else
+ assign(".Coda.Options", copt)
invisible(oldvalue)
}
}
@@ -86,6 +89,7 @@ function (...)
{
## Select more than one value from a menu
##
+
if (!missing(title))
cat(title, "\n\n")
mat <- matrix(c(1:length(choices), choices), ncol = 2)
@@ -140,6 +144,7 @@ function (...)
## and answer satisfying the conditions. This entails extensive
## checking of the conditions to make sure they are consistent
## so we don't end up in an infinite loop.
+
have.lower <- !missing(lower)
have.upper <- !missing(upper)
have.ans.in <- !missing(answer.in)
diff --git a/man/autocorr.plot.Rd b/man/autocorr.plot.Rd
index d46df63..a67be13 100644
--- a/man/autocorr.plot.Rd
+++ b/man/autocorr.plot.Rd
@@ -10,7 +10,8 @@
\item{auto.layout}{If \code{TRUE} then, set up own layout for
plots, otherwise use existing one.}
\item{ask}{If \code{TRUE} then prompt user before displaying
- each page of plots.}
+ each page of plots. Default is \code{dev.interactive()} in
+ R and \code{interactive()} in S-PLUS.}
\item{\dots}{graphical parameters}
}
diff --git a/man/bugs2jags.Rd b/man/bugs2jags.Rd
index 482a573..c83ad2a 100644
--- a/man/bugs2jags.Rd
+++ b/man/bugs2jags.Rd
@@ -18,6 +18,8 @@ bugs2jags(infile, outfile)
difference is taken into account by \code{bugs2jags} which will
automatically reorder the data in arrays, without changing the
dimension.
+
+ Not yet available in S-PLUS.
}
\note{
If the input file is saved from WinBUGS, it must be saved in plain text
diff --git a/man/codamenu.Rd b/man/codamenu.Rd
index c16f8f7..361ec6d 100644
--- a/man/codamenu.Rd
+++ b/man/codamenu.Rd
@@ -9,7 +9,7 @@ codamenu()
\description{
\code{codamenu} presents a simple menu-based interface to the functions
in the coda package. It is designed for users who know nothing about
-the R language.}
+the R/S language.}
\author{Kate Cowles, Nicky Best, Karen Vines, Martyn Plummer}
\keyword{utilities}
diff --git a/man/cumuplot.Rd b/man/cumuplot.Rd
index 3630efa..5a642d0 100644
--- a/man/cumuplot.Rd
+++ b/man/cumuplot.Rd
@@ -4,7 +4,7 @@
\usage{
cumuplot(x, probs=c(0.025,0.5,0.975), ylab="",
- lty=c(2,1), lwd=c(1,2), type="l", ask=dev.interactive(),
+ lty=c(2,1), lwd=c(1,2), type="l", ask,
auto.layout=TRUE, col=1, \dots)
}
@@ -15,7 +15,8 @@
\item{auto.layout}{If \code{TRUE}, then set up own layout for
plots, otherwise use existing one.}
\item{ask}{If \code{TRUE} then prompt user before displaying
- each page of plots.}
+ each page of plots. Default is \code{dev.interactive()} in
+ R and \code{interactive()} in S-PLUS.}
\item{\dots}{further graphical parameters}
}
diff --git a/man/gelman.plot.Rd b/man/gelman.plot.Rd
index a58d5ed..262787e 100644
--- a/man/gelman.plot.Rd
+++ b/man/gelman.plot.Rd
@@ -6,7 +6,7 @@
\usage{
gelman.plot(x, bin.width = 10, max.bins = 50,
confidence = 0.95, transform = FALSE, auto.layout = TRUE,
-ask = dev.interactive(), col, lty, xlab, ylab, type, \dots)
+ask, col, lty, xlab, ylab, type, \dots)
}
\arguments{
@@ -18,7 +18,8 @@ ask = dev.interactive(), col, lty, xlab, ylab, type, \dots)
\item{transform}{Automatic variable transformation (see \code{gelman.diag})}
\item{auto.layout}{If \code{TRUE} then, set up own layout for
plots, otherwise use existing one.}
- \item{ask}{Prompt user before displaying each page of plots.}
+ \item{ask}{Prompt user before displaying each page of plots. Default is
+ \code{dev.interactive()} in R and \code{interactive()} in S-PLUS.}
\item{col}{graphical parameter (see \code{par})}
\item{lty}{graphical parameter (see \code{par})}
\item{xlab}{graphical parameter (see \code{par})}
diff --git a/man/geweke.plot.Rd b/man/geweke.plot.Rd
index 733289b..d4daf75 100644
--- a/man/geweke.plot.Rd
+++ b/man/geweke.plot.Rd
@@ -4,7 +4,7 @@
\usage{
geweke.plot(x, frac1 = 0.1, frac2 = 0.5, nbins = 20,
- pvalue = 0.05, auto.layout = TRUE, ask = dev.interactive(), \dots)
+ pvalue = 0.05, auto.layout = TRUE, ask, \dots)
}
\arguments{
@@ -15,7 +15,9 @@ geweke.plot(x, frac1 = 0.1, frac2 = 0.5, nbins = 20,
\item{pvalue}{p-value used to plot confidence limits for the null hypothesis.}
\item{auto.layout}{If \code{TRUE} then, set up own layout for
plots, otherwise use existing one.}
- \item{ask}{Prompt user before displaying each page of plots.}
+ \item{ask}{If \code{TRUE} then prompt user before displaying
+ each page of plots. Default is \code{dev.interactive()} in
+ R and \code{interactive()} in S-PLUS.}
\item{\dots}{Graphical parameters.}
}
diff --git a/man/mcmc.subset.Rd b/man/mcmc.subset.Rd
index 100c55b..26a5df1 100644
--- a/man/mcmc.subset.Rd
+++ b/man/mcmc.subset.Rd
@@ -4,13 +4,15 @@
\title{Extract or replace parts of MCMC objects}
\usage{
-x[i,j]
+\method{[}{mcmc}(x,i,j, drop=missing(i))
+\method{[}{mcmc.list}(x,i,j, drop=TRUE)
}
\arguments{
\item{x}{An \code{mcmc} object}
\item{i}{Row to extract}
\item{j}{Column to extract}
+ \item{drop}{if \code{TRUE}, the redundant dimensions are dropped}
}
\description{
diff --git a/man/nchain.Rd b/man/nchain.Rd
index 1eb4a09..2f77f78 100644
--- a/man/nchain.Rd
+++ b/man/nchain.Rd
@@ -24,7 +24,7 @@ nchain(x)
\describe{
\item{niter(x)}{returns the number of iterations.}
\item{nvar(x)}{returns the number of variables.}
- \item{chain(x)}{returns the number of parallel chains.}
+ \item{nchain(x)}{returns the number of parallel chains.}
}
}
diff --git a/man/trellisplots.Rd b/man/trellisplots.Rd
index 992b54e..4ad1000 100644
--- a/man/trellisplots.Rd
+++ b/man/trellisplots.Rd
@@ -109,6 +109,8 @@ acfplot(x, data, \dots)
plots. The \code{levelplot} method depicts the correlation of the
series. The \code{acfplot} methods plot the auto-correlation in the
series.
+
+ Not yet available in S-PLUS.
}
\arguments{
\item{x}{ an \code{"mcmc"} or \code{"mcmc.list"} object. }
@@ -186,6 +188,8 @@ acfplot(x, data, \dots)
\author{ Deepayan Sarkar \email{Deepayan.Sarkar at R-project.org}}
\examples{
data(line)
+
+\dontrun{
xyplot(line)
xyplot(line[[1]], start = 10)
densityplot(line, start = 10)
@@ -193,4 +197,5 @@ qqmath(line, start = 10)
levelplot(line[[2]])
acfplot(line, outer = TRUE)
}
+}
\keyword{hplot}
--
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