[r-cran-coda] 38/60: Imported Upstream version 0.14-5
Andreas Tille
tille at debian.org
Fri Dec 16 12:11:25 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 b8cb301dce8948e8341ccf838417390ce894fe20
Author: Andreas Tille <tille at debian.org>
Date: Fri Dec 16 12:10:00 2016 +0100
Imported Upstream version 0.14-5
---
CHANGELOG | 4 +++
DESCRIPTION | 10 +++----
MD5 | 76 ++++++++++++++++++++++++++++++++++++++++++++++++++++++
NAMESPACE | 4 +--
R/codamenu.R | 28 +++++++++++++-------
data/line.rda | Bin 9599 -> 9600 bytes
man/as.ts.mcmc.Rd | 4 +--
7 files changed, 108 insertions(+), 18 deletions(-)
diff --git a/CHANGELOG b/CHANGELOG
index 90ff908..e91faaa 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -1,3 +1,7 @@
+0.14-4
+- Replaced defunct restart() function in codamenu with with try()
+- Changed as.ts.mcmc to be a method for generic function as.ts
+
0.14-3
- Fixed documentation errors in gelman.diag (Thanks to Peng Yu)
- Added CITATION file
diff --git a/DESCRIPTION b/DESCRIPTION
index d1fa158..1048898 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,13 +1,13 @@
Package: coda
-Version: 0.14-4
-Date: 2011-05-20
+Version: 0.14-5
+Date: 2011-11-02
Title: Output analysis and diagnostics for MCMC
Author: Martyn Plummer, Nicky Best, Kate Cowles, Karen Vines
Maintainer: Martyn Plummer <plummerM at iarc.fr>
Depends: R (>= 2.5.0), lattice
Description: Output analysis and diagnostics for Markov Chain Monte
- Carlo simulations.
+ Carlo simulations.
License: GPL (>= 2)
-Packaged: 2011-05-20 11:16:02 UTC; martyn
+Packaged: 2011-11-02 15:23:57 UTC; martyn
Repository: CRAN
-Date/Publication: 2011-05-20 12:41:27
+Date/Publication: 2011-11-03 11:48:07
diff --git a/MD5 b/MD5
new file mode 100644
index 0000000..60c1520
--- /dev/null
+++ b/MD5
@@ -0,0 +1,76 @@
+3ad76246334ca13bb7cba54ce71e48bd *AUTHORS
+c19ee0d76b5aed2df588ce798bbc42a3 *CHANGELOG
+94d55d512a9ba36caa9b7df079bae19f *COPYING
+24a8308dcff89ec69075ffe0cedf0cf8 *DESCRIPTION
+ff890b50eaa074ed668c6f2fac1b4141 *INDEX
+5096b7ad0e6c457ab9fbde263755c84f *NAMESPACE
+45f88adec7bcfab586a4deebba1cc02d *R/HPDinterval.R
+841853b3b96462cffe376cf9fad6abb9 *R/autocorrdiag.R
+02152920c66f540422f88e51c88f0428 *R/batchSE.R
+a22da830a261cd0f28da6052c560d5df *R/codamenu.R
+df4c85619867ba81878499f5059e875d *R/cumuplot.R
+d271b76ea4972b50807e97679515626c *R/gelman.R
+4799c5ceaaa6416d03bc22c31d2196f7 *R/geweke.R
+f63f255e6c07f67631e78d427bd40edc *R/heidel.R
+ae77a3ec34f086bd7ec8ea787baeeb1e *R/jags.R
+f3b382582d73aad54d77c4c655513c58 *R/mcextractor.R
+154e68d755b5c0317257351c3364d4de *R/mcmc.R
+699f3e94ff1f124a5b514e11320136fd *R/mcmclist.R
+29fbc4c9526791d48768136d0c2f059c *R/output.R
+389758882050a375ac4b5298a42ae35f *R/raftery.R
+4caafbeb9941605b240d3ae9f6c8d5ff *R/rejectionRate.R
+d41d8cd98f00b204e9800998ecf8427e *R/thin.R
+b95af999515a96aec97f3d54487eda47 *R/trellisplots.R
+eb953d257fed9708d6848e4976b2b223 *R/util.R
+4d7d828d6d2b4fee5357d3a4dd108458 *README
+a666109f0bb5282078c66640dce7c18f *data/line.rda
+81c1ae300d47f9a787eb871fbaafeb9f *inst/CITATION
+868ded8f4d10a67c7b31854bce6f3d63 *man/Cramer.Rd
+7bfe602ce737efac910300e5be5a8552 *man/HPDinterval.Rd
+f5361dc01c864e905a9c3eb84e060c67 *man/as.ts.mcmc.Rd
+e3af15812b54d807e43283c5a6ca3839 *man/autocorr.Rd
+166b640290894becc49eaa8434e148ee *man/autocorr.diag.Rd
+592996075418b4bc21fc2c8c0016f07b *man/autocorr.plot.Rd
+33d3d5b9225566ddfa188ea1bc2d4e8c *man/batchSE.Rd
+04f62bd5509ba44f8e3d5bd008d37b8d *man/bugs2jags.Rd
+e704de229cf312aa584094b126529e1a *man/coda.options.Rd
+04dd4994917068f5d36fbcff921deb7f *man/codamenu.Rd
+d3b21ba8f4c82fd92adfb1d4380d4cc8 *man/crosscorr.Rd
+80c2893a13683e442443b36764810498 *man/crosscorr.plot.Rd
+2cc5efe9b602aae1ad07e0f7266142b6 *man/cumuplot.Rd
+3551dd04cb13f4b22a221d7de9fa1699 *man/densplot.Rd
+4009d8e9105a4e23590a07623c752627 *man/effectiveSize.Rd
+965a3da0dff536cf54bbf396d098ae25 *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
+e32d079a18aa183c78933b01da34a4b2 *man/mcmc.convert.Rd
+e32462705734dbab825107b00fc3d8b0 *man/mcmc.list.Rd
+8e47ffb91930e7f05171861b666c71b5 *man/mcmc.subset.Rd
+b643882eba3addb4056061302f066dc3 *man/mcmcUpgrade.Rd
+20ab76f06dc525cc257595c45806b9df *man/mcpar.Rd
+abd1a1971d45c3e9879653251c9151bb *man/multi.menu.Rd
+0cdc30ee6925803966d3ab0af99bd66e *man/nchain.Rd
+695aed5c821bd040641f208a77d16e91 *man/plot.mcmc.Rd
+4bcbf725908738ebf08b0fba4076b621 *man/raftery.diag.Rd
+a1ad06e437edaf6302d48a5a727e35db *man/read.and.check.Rd
+16d3c6ae70ad0ed890dc73d182c698c0 *man/read.coda.Rd
+70b940b3dac77266ea945207f7ddfbc2 *man/read.coda.interactive.Rd
+32efc0825ddcecdf1ad52a7acb738905 *man/read.openbugs.Rd
+33c10a06a721c1cc5d0d4439c5d9fb28 *man/rejectionRate.Rd
+ebcd8ee89d1f3af805963f1e1333a2be *man/spectrum0.Rd
+417619066fa9367a3e6a5c6c33a6fa25 *man/spectrum0.ar.Rd
+1e1eca44b09a15921da4416e9e891047 *man/summary.mcmc.Rd
+54f2dfd12079753baa57a248db815ce8 *man/thin.Rd
+21dfd4f22d65bdea5153a83b4dd16840 *man/time.mcmc.Rd
+5790bf954071478cd9a23fd543338b27 *man/traceplot.Rd
+b44246e6c656a238c32b144a97f64482 *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 a90813f..335a0af 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -5,7 +5,6 @@ export(
as.array.mcmc.list,
as.mcmc,
as.mcmc.list,
- as.ts.mcmc,
autocorr,
##RGA
autocorr.diag,
@@ -70,6 +69,7 @@ export(
## register S3 methods
S3method(as.mcmc, default)
S3method(as.mcmc.list, default)
+S3method(as.ts, mcmc)
## as.matrix
S3method(as.matrix, mcmc)
S3method(as.matrix, mcmc.list)
@@ -122,7 +122,7 @@ S3method(print, raftery.diag)
S3method(print, summary.mcmc)
## Imports
-importFrom(stats, start, end, frequency, time, window)
+importFrom(stats, start, end, frequency, time, window, as.ts)
importFrom(lattice, xyplot, qqmath, densityplot, levelplot)
importFrom(utils, head, tail)
diff --git a/R/codamenu.R b/R/codamenu.R
index b31cdab..cb48d09 100644
--- a/R/codamenu.R
+++ b/R/codamenu.R
@@ -663,7 +663,6 @@ function (last.menu)
}
coda.options(bandwidth = bwf)
}, {
- restart()
func.OK <- FALSE
while (!func.OK) {
cat("Enter bandwidth as an expression in terms of x,\n")
@@ -676,14 +675,25 @@ function (last.menu)
bwf <- paste(bwf, ans[i], sep = "")
}
bwf <- paste(bwf, "}", sep = "")
- bwf <- eval(parse(text = bwf))
- ## Carry out simple test to check whether the
- ## function entered makes sense
- ##
- func.OK <- is.numeric(bw <- bwf(1:10)) && (length(bw) == 1)
- if(!func.OK) {
- cat("This is not a suitable function: it must return a single\n")
- cat("numeric value given a numeric vector x.")
+ bwf <- try(eval(parse(text = bwf)), silent=TRUE)
+ if (inherits(bwf, "try-error")) {
+ cat("Invalid expression\n")
+ }
+ else {
+ ## Carry out simple test to check whether the
+ ## function entered makes sense
+ ##
+ bw <- try(bwf(1:10), silent=FALSE)
+ if (inherits(bw, "try-error")) {
+ cat("Error calling function with input 1:10\n")
+ }
+ else {
+ func.OK <- is.numeric(bw) && (length(bw) == 1)
+ if(!func.OK) {
+ cat("This is not a suitable function: it must return a\n")
+ cat("single numeric value given a numeric vector x.\n")
+ }
+ }
}
}
}
diff --git a/data/line.rda b/data/line.rda
index 1ec0287..cda6d1e 100644
Binary files a/data/line.rda and b/data/line.rda differ
diff --git a/man/as.ts.mcmc.Rd b/man/as.ts.mcmc.Rd
index 20fce28..922588e 100644
--- a/man/as.ts.mcmc.Rd
+++ b/man/as.ts.mcmc.Rd
@@ -2,7 +2,7 @@
\alias{as.ts.mcmc}
\title{Coerce mcmc object to time series}
-\usage{as.ts.mcmc(x,\dots)}
+\usage{\method{as.ts}{mcmc}(x,\dots)}
\arguments{
\item{x}{an mcmc object}
@@ -10,7 +10,7 @@
}
\description{
-\code{as.ts.mcmc} will coerce an mcmc object to a time series.}
+the \code{as.ts} method for \code{mcmc} objects coerces an mcmc object to a time series.}
\author{Martyn Plummer}
--
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