[r-cran-coda] 46/60: Imported Upstream version 0.17-1
Andreas Tille
tille at debian.org
Fri Dec 16 12:11:27 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 500f41fe861d33e67fe0986388100bf087b95217
Author: Andreas Tille <tille at debian.org>
Date: Fri Dec 16 12:10:02 2016 +0100
Imported Upstream version 0.17-1
---
CHANGELOG | 23 ++++++++++++++++++++---
DESCRIPTION | 41 ++++++++++++++++++++++++++---------------
MD5 | 26 +++++++++++---------------
NAMESPACE | 5 ++++-
R/mcmc.R | 4 ++--
R/mcmclist.R | 2 +-
R/trellisplots.R | 2 +-
R/util.R | 15 ++++-----------
data/line.rda | Bin 9601 -> 9600 bytes
AUTHORS => inst/AUTHORS | 0
man/effectiveSize.Rd | 7 ++++---
man/mcmc.Rd | 3 ++-
misc/change.tfoption.Rd | 29 -----------------------------
misc/codamenu2.Rd | 40 ----------------------------------------
misc/read.yesno.Rd | 29 -----------------------------
misc/set.mfrow.Rd | 26 --------------------------
16 files changed, 75 insertions(+), 177 deletions(-)
diff --git a/CHANGELOG b/CHANGELOG
index 2ce6e8f..d975c4c 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -1,7 +1,24 @@
+0.17-1 Martyn Plummer <plummerm at iarc.fr>
+
+ - Moved lattice package from Depends to Imports in DESCRIPTION
+ file. This means that you must load the lattice package to use
+ any of the lattice methods provided for mcmc objects.
+
+ - Russell Almond is fully credited as co-author
+
+ - Moved AUTHORS file into inst/ sub-directory
+
+ - Fixed bug that stopped trellis graphics from working with vector
+ mcmc objects (thinned chains). Thanks to Chris Andrews.
+
+ - Added additional arguments (...) to as.mcmc()
+
+ - coda.options() no longer writes to the global environment
+
0.16-1
- Fixed main title bug in densplot
- Substitute spectrum0.ar for spectrum0 internally
-- densplot parameters fixed when drawing multiple plots
+- densplot parameters fixed when drawing multiple plots
0.15-3
- Correct x axis labelling in xyplot. Thanks to Pavel Krivitsky.
@@ -9,10 +26,10 @@
0.15-2
- Allow default plotting parameters to be overridden in densplot and traceplot.
- Stop overplotting of user-supplied title in densplot.
-- Fix xyplot for univariate chains. Thanks to Pavel Krivitsky.
+- Fix xyplot for univariate chains. Thanks to Pavel Krivitsky.
0.15-1
-- Use Authors at R field in DESCRIPTION
+- Use Authors at R field in DESCRIPTION
- Fixe geweke.diag for long mcmc samples. Thanks to Philip Johnson
0.14-7
diff --git a/DESCRIPTION b/DESCRIPTION
index d3c479a..22e5648 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,20 +1,31 @@
Package: coda
-Version: 0.16-1
-Date: 2012-11-06
-Title: Output analysis and diagnostics for MCMC
+Version: 0.17-1
+Date: 2015-03-02
+Title: Output Analysis and Diagnostics for MCMC
Authors at R: c(person("Martyn", "Plummer", role=c("aut","cre","trl"),
- email="plummerm at iarc.fr"), person("Nicky", "Best", role="aut"),
- person("Kate", "Cowles", role="aut"), person("Karen", "Vines",
- role="aut"), person("Deepayan", "Sarkar", role="aut"),
- person("Russell", "Almond", role="ctb"))
-Depends: R (>= 2.14.0), lattice
-Description: Output analysis and diagnostics for Markov Chain Monte
- Carlo simulations.
+ email="plummerm at iarc.fr"),
+ person("Nicky", "Best", role="aut"),
+ person("Kate", "Cowles", role="aut"),
+ person("Karen", "Vines", role="aut"),
+ person("Deepayan", "Sarkar", role="aut"),
+ person("Douglas", "Bates", role="aut"),
+ person("Russell", "Almond", role="aut"))
+Depends: R (>= 2.14.0)
+Imports: lattice
+Description: Provides functions for summarizing and plotting the
+ output from Markov Chain Monte Carlo (MCMC) simulations, as
+ well as diagnostic tests of convergence to the equilibrium
+ distribution of the Markov chain.
License: GPL (>= 2)
-Packaged: 2012-11-06 13:12:03 UTC; martyn
-Author: Martyn Plummer [aut, cre, trl], Nicky Best [aut], Kate Cowles
- [aut], Karen Vines [aut], Deepayan Sarkar [aut], Russell Almond
- [ctb]
+Packaged: 2015-03-03 17:21:11 UTC; martyn
+Author: Martyn Plummer [aut, cre, trl],
+ Nicky Best [aut],
+ Kate Cowles [aut],
+ Karen Vines [aut],
+ Deepayan Sarkar [aut],
+ Douglas Bates [aut],
+ Russell Almond [aut]
Maintainer: Martyn Plummer <plummerm at iarc.fr>
+NeedsCompilation: no
Repository: CRAN
-Date/Publication: 2012-11-06 13:24:00
+Date/Publication: 2015-03-03 19:25:43
diff --git a/MD5 b/MD5
index 5cfb94d..ab4b1ee 100644
--- a/MD5
+++ b/MD5
@@ -1,8 +1,7 @@
-3ad76246334ca13bb7cba54ce71e48bd *AUTHORS
-ef6d30b24d7eea214c1b28a9569ccd7c *CHANGELOG
-534ec685ff13552a027bf2a9312cae9b *DESCRIPTION
+370fb32c3079904dfc365e55676f04d5 *CHANGELOG
+8bb04518c5614ce417d2ec9ee3fc45de *DESCRIPTION
ff890b50eaa074ed668c6f2fac1b4141 *INDEX
-5096b7ad0e6c457ab9fbde263755c84f *NAMESPACE
+adcc371105f44cfe439cd60f8ff727d4 *NAMESPACE
45f88adec7bcfab586a4deebba1cc02d *R/HPDinterval.R
841853b3b96462cffe376cf9fad6abb9 *R/autocorrdiag.R
02152920c66f540422f88e51c88f0428 *R/batchSE.R
@@ -13,16 +12,17 @@ a97024cb207bcef6fd4bc7c00283c1ed *R/geweke.R
6fb74d6977e5e3b5190eda35829cdc23 *R/heidel.R
ae77a3ec34f086bd7ec8ea787baeeb1e *R/jags.R
f3b382582d73aad54d77c4c655513c58 *R/mcextractor.R
-154e68d755b5c0317257351c3364d4de *R/mcmc.R
-699f3e94ff1f124a5b514e11320136fd *R/mcmclist.R
+97fef151be1d2924942ca84de70c87f4 *R/mcmc.R
+36759e063fe91197b2ef29b4b288eaee *R/mcmclist.R
bd120c9296e4467265ee10409799e61f *R/output.R
389758882050a375ac4b5298a42ae35f *R/raftery.R
4caafbeb9941605b240d3ae9f6c8d5ff *R/rejectionRate.R
d41d8cd98f00b204e9800998ecf8427e *R/thin.R
-8b8caa812439b27b6cc63e9f9fe8edab *R/trellisplots.R
-eb953d257fed9708d6848e4976b2b223 *R/util.R
+553b1effc0816a68e0ad4dfd7847757f *R/trellisplots.R
+ffc99e7d181a7308c8aef6ea059a8d51 *R/util.R
4d7d828d6d2b4fee5357d3a4dd108458 *README
-bd3d2db1b8c3e7b281e1103d8f620e7a *data/line.rda
+2d8879e17e372a474e9c9c1057129b02 *data/line.rda
+3ad76246334ca13bb7cba54ce71e48bd *inst/AUTHORS
81c1ae300d47f9a787eb871fbaafeb9f *inst/CITATION
868ded8f4d10a67c7b31854bce6f3d63 *man/Cramer.Rd
7bfe602ce737efac910300e5be5a8552 *man/HPDinterval.Rd
@@ -38,14 +38,14 @@ d3b21ba8f4c82fd92adfb1d4380d4cc8 *man/crosscorr.Rd
80c2893a13683e442443b36764810498 *man/crosscorr.plot.Rd
2cc5efe9b602aae1ad07e0f7266142b6 *man/cumuplot.Rd
14365306d891deafd1ca602f59e4520f *man/densplot.Rd
-4009d8e9105a4e23590a07623c752627 *man/effectiveSize.Rd
+2b5bbbb8d683384c9287a9c8e1f7a01f *man/effectiveSize.Rd
c78c35ac982bcd74befe51f98ba641e4 *man/gelman.diag.Rd
394ae6df9b067ecb6120067aba37728c *man/gelman.plot.Rd
aa5ee817bb15d58b4fd40089432ba99b *man/geweke.diag.Rd
efd11972209251ece16ec61d8326bdce *man/geweke.plot.Rd
0c3865e05310e0a2ea9af0e4912ed036 *man/heidel.diag.Rd
5fc3363fee1907a6c2ba1567cf40eea2 *man/linepost.Rd
-a4c9188cb776b93605829515d963a501 *man/mcmc.Rd
+0718d4266cbcbf5101b79158dc441920 *man/mcmc.Rd
e32d079a18aa183c78933b01da34a4b2 *man/mcmc.convert.Rd
e32462705734dbab825107b00fc3d8b0 *man/mcmc.list.Rd
8e47ffb91930e7f05171861b666c71b5 *man/mcmc.subset.Rd
@@ -69,7 +69,3 @@ ebcd8ee89d1f3af805963f1e1333a2be *man/spectrum0.Rd
697c427c1b220f52444f66e05a895579 *man/trellisplots.Rd
4b44de8c8b54df57e83be296d9c75ed7 *man/varnames.Rd
18042191cfa6ac3659b1be6a7460bfdb *man/window.mcmc.Rd
-1791a98bb716209178215a857193df65 *misc/change.tfoption.Rd
-6cd3ff4303e827bee23dbcde25ff2166 *misc/codamenu2.Rd
-16193f44e6b133c55468fe1089635bb2 *misc/read.yesno.Rd
-3c47be5304a83158c52b001c60e877cc *misc/set.mfrow.Rd
diff --git a/NAMESPACE b/NAMESPACE
index 335a0af..4230d13 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -98,6 +98,7 @@ S3method(HPDinterval, mcmc)
S3method("[", mcmc.list)
S3method(as.matrix, mcmc.list)
S3method(as.mcmc, mcmc.list)
+S3method(as.array, mcmc.list)
S3method(end, mcmc.list)
S3method(plot, mcmc.list)
S3method(start, mcmc.list)
@@ -123,7 +124,9 @@ S3method(print, summary.mcmc)
## Imports
importFrom(stats, start, end, frequency, time, window, as.ts)
-importFrom(lattice, xyplot, qqmath, densityplot, levelplot)
+importFrom(lattice, xyplot, qqmath, densityplot, levelplot, panel.abline,
+ panel.xyplot, trellis.par.get, do.breaks, panel.superpose,
+ prepanel.qqmathline, splom)
importFrom(utils, head, tail)
## lattice methods
diff --git a/R/mcmc.R b/R/mcmc.R
index c9f3fff..5f5b3db 100644
--- a/R/mcmc.R
+++ b/R/mcmc.R
@@ -18,10 +18,10 @@
return(y)
}
-"as.mcmc" <- function (x)
+"as.mcmc" <- function (x, ...)
UseMethod("as.mcmc")
-"as.mcmc.default" <- function (x)
+"as.mcmc.default" <- function (x, ...)
if (is.mcmc(x)) x else mcmc(x)
"as.ts.mcmc" <- function (x, ...)
diff --git a/R/mcmclist.R b/R/mcmclist.R
index 6e27660..852032c 100644
--- a/R/mcmclist.R
+++ b/R/mcmclist.R
@@ -172,7 +172,7 @@
return(y)
}
-"as.mcmc.mcmc.list" <- function (x)
+"as.mcmc.mcmc.list" <- function (x, ...)
{
if (nchain(x) == 1)
return(x[[1]])
diff --git a/R/trellisplots.R b/R/trellisplots.R
index 6510d45..bb20f2c 100644
--- a/R/trellisplots.R
+++ b/R/trellisplots.R
@@ -15,7 +15,7 @@
-thinned.indices <- function(object, n = nrow(object), start = 1, thin = 1)
+thinned.indices <- function(object, n = NROW(object), start = 1, thin = 1)
{
if (is.mcmc(object) &&
(start * thin != 1) &&
diff --git a/R/util.R b/R/util.R
index 400f5af..4644e25 100644
--- a/R/util.R
+++ b/R/util.R
@@ -31,11 +31,8 @@ function (...)
{
## Set and display coda options
single <- FALSE
- copt <- if (exists(".Coda.Options", frame = 1)) {
- if (is.R())
- get(".Coda.Options", pos=1)
- else
- get(".Coda.Options")
+ copt <- if (exists("options", envir=coda.env, inherits=FALSE)) {
+ get("options", envir=coda.env, inherits=FALSE)
}
else {
.Coda.Options.Default
@@ -77,10 +74,7 @@ function (...)
else if (mode(copt[[v]]) == mode(args[[v]]))
copt[v] <- args[v]
}
- if (is.R())
- assign(".Coda.Options", copt, pos=1)
- else
- assign(".Coda.Options", copt)
+ assign("options", copt, envir=coda.env)
invisible(oldvalue)
}
}
@@ -254,8 +248,7 @@ function (...)
data.saved = TRUE
)
-
-
+coda.env <- new.env()
diff --git a/data/line.rda b/data/line.rda
index bf0a14f..815e8b2 100644
Binary files a/data/line.rda and b/data/line.rda differ
diff --git a/AUTHORS b/inst/AUTHORS
similarity index 100%
rename from AUTHORS
rename to inst/AUTHORS
diff --git a/man/effectiveSize.Rd b/man/effectiveSize.Rd
index 30ef28d..9b53cb4 100644
--- a/man/effectiveSize.Rd
+++ b/man/effectiveSize.Rd
@@ -11,9 +11,10 @@ effectiveSize(x)
\item{x}{An mcmc or mcmc.list object.}
}
\details{
-For a time series \code{x} of length \code{N}, the standard error of
-the mean is \code{var(x)/n} where \code{n} is the effective sample
-size. \code{n = N} only when there is no autocorrelation.
+For a time series \code{x} of length \code{N}, the standard error of the
+mean is the square root of \code{var(x)/n} where \code{n} is the
+effective sample size. \code{n = N} only when there is no
+autocorrelation.
Estimation of the effective sample size requires estimating the
spectral density at frequency zero. This is done by the function
diff --git a/man/mcmc.Rd b/man/mcmc.Rd
index 9e7a982..5d82869 100644
--- a/man/mcmc.Rd
+++ b/man/mcmc.Rd
@@ -8,7 +8,7 @@
\usage{
mcmc(data= NA, start = 1, end = numeric(0), thin = 1)
-as.mcmc(x)
+as.mcmc(x, \dots)
is.mcmc(x)
}
@@ -18,6 +18,7 @@ is.mcmc(x)
\item{end}{the iteration number of the last observation}
\item{thin}{the thinning interval between consecutive observations}
\item{x}{An object that may be coerced to an mcmc object}
+ \item{\dots}{Further arguments to be passed to specific methods}
}
\description{
diff --git a/misc/change.tfoption.Rd b/misc/change.tfoption.Rd
deleted file mode 100644
index 7e91728..0000000
--- a/misc/change.tfoption.Rd
+++ /dev/null
@@ -1,29 +0,0 @@
-\name{change.tfoption}
-\alias{change.tfoption}
-\title{Interactively modify logical codamenu options.}
-
-\usage{
-change.tfoption(string, option)
-}
-
-\arguments{
-\item{string}{Prompt string to print}
-\item{option}{String giving the name of an option to change}
-}
-
-\description{
-Interactively changes logical codamenu options using the
-\code{read.yesno} function.
-}
-
-\note{
-This is a utility function for the codamenu system, and is not
-meant to be called directly by the user.
-}
-
-\seealso{
- \code{\link{coda.options}},
- \code{\link{read.yesno}}.
-}
-
-\keyword{utilities}
diff --git a/misc/codamenu2.Rd b/misc/codamenu2.Rd
deleted file mode 100644
index ee0c64f..0000000
--- a/misc/codamenu2.Rd
+++ /dev/null
@@ -1,40 +0,0 @@
-\name{codamenu2}
-\alias{codamenu.main}
-\alias{codamenu.anal}
-\alias{codamenu.diags}
-\alias{codamenu.diags.autocorr}
-\alias{codamenu.diags.crosscorr}
-\alias{codamenu.diags.heidel}
-\alias{codamenu.diags.raftery}
-\alias{codamenu.diags.gelman}
-\alias{codamenu.diags.geweke}
-\alias{codamenu.options}
-\alias{codamenu.options.data}
-\alias{codamenu.options.diag}
-\alias{codamenu.options.gelman}
-\alias{codamenu.options.geweke.bin}
-\alias{codamenu.options.geweke.win}
-\alias{codamenu.options.heidel}
-\alias{codamenu.options.plot}
-\alias{codamenu.options.plot.kernel}
-\alias{codamenu.options.plot.ps}
-\alias{codamenu.options.raftery}
-\alias{codamenu.options.stats}
-\alias{tidy.up}
-\alias{codamenu.ps}
-\alias{codamenu.output.header}
-
-\title{Submenus for the coda package}
-
-\description{
-These functions are not meant to be called directly by the user, but
-should be accessed via the \code{codamenu} function.
-
-All submenus are called from the \code{codamenu.main} function.
-Each submenu returns a string giving the name of the next submenu to be
-called, or "quit" if the user decides to quit. This system avoids the
-recursive calling of submenus which would accumulate `dead' environments.
-}
-
-\author{Martyn Plummer}
-\keyword{utilities}
diff --git a/misc/read.yesno.Rd b/misc/read.yesno.Rd
deleted file mode 100644
index 1542e79..0000000
--- a/misc/read.yesno.Rd
+++ /dev/null
@@ -1,29 +0,0 @@
-\name{read.yesno}
-\alias{read.yesno}
-\title{Read logical values from the command line}
-
-\usage{
- read.yesno(string, default=TRUE)
-}
-
-\arguments{
- \item{string}{A string to prompt the user with}
- \item{default}{Logical value giving the default answer}
-}
-
-\value{
- A single logical value.
-}
-
-\description{
- This is a utility function for interactively reading a logical
- value from the command line.
-
- The prompt string is printed, along a hint about the default answer.
- Answers "yes", "YES", "no", "NO" or any partial match are accepted.
- If the user enters a blank line, the default value is returned.
-}
-
-\author{Martyn Plummer}
-
-\keyword{utilities}
diff --git a/misc/set.mfrow.Rd b/misc/set.mfrow.Rd
deleted file mode 100644
index 57b2ee0..0000000
--- a/misc/set.mfrow.Rd
+++ /dev/null
@@ -1,26 +0,0 @@
-\name{set.mfrow}
-\alias{set.mfrow}
-\title{Set layout for graphical plots}
-
-\usage{
- set.mfrow (Nchains = 1, Nparms = 1, nplots = 1, sepplot = FALSE)
-}
-
-\arguments{
- \item{Nchains}{Number of chains to plot}
- \item{Nparms}{Number of variables in each chain}
- \item{nplots}{Number of plots to produce}
- \item{sepplot}{Logical value controlling whether separate plots are created for each chain}
-}
-
-\description{
- This utility function is used by plotting functions in the coda package
- to determine the default layout, unless overriden by the \code{user.layout}
- option.
-}
-
-\note{
- This is not meant to be called directly by the user.
-}
-
-\keyword{dplot}
--
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