[r-cran-coda] 42/60: Imported Upstream version 0.14-7

Fri Dec 16 12:11:26 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 95a1d42ac18e3c585628b71af0b183fed63f1a0f
Author: Andreas Tille <tille at debian.org>
Date:   Fri Dec 16 12:10:01 2016 +0100

    Imported Upstream version 0.14-7
---
 CHANGELOG          |  11 +++++++++--
 DESCRIPTION        |  10 +++++-----
 MD5                |  10 +++++-----
 R/gelman.R         |   4 ++--
 data/line.rda      | Bin 9600 -> 9601 bytes
 man/gelman.diag.Rd |   6 +++++-
 6 files changed, 26 insertions(+), 15 deletions(-)

diff --git a/CHANGELOG b/CHANGELOG
index 2567dd9..d7d2091 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -1,10 +1,17 @@
-0.14-5
+0.14-7
+- In gelman.diag, the multivariate potential scale reduction factor
+  is now optional and can be turned off with the argument multivariate=FALSE.
+
+0.14-6
 - Removed deprecated top-level file COPYING
 
-0.14-4
+0.14-5
 - Replaced defunct restart() function in codamenu with with try()
 - Changed as.ts.mcmc to be a method for generic function as.ts
 
+0.14-4
+- Arguments of gelman.plot are now consistent with gelman.diag.
+
 0.14-3
 - Fixed documentation errors in gelman.diag (Thanks to Peng Yu)
 - Added CITATION file
diff --git a/DESCRIPTION b/DESCRIPTION
index 6919e39..0edeaa0 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,13 +1,13 @@
 Package: coda
-Version: 0.14-6
-Date: 2011-11-04
+Version: 0.14-7
+Date: 2012-04-02
 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: 2011-11-04 16:12:18 UTC; martyn
+Packaged: 2012-04-02 09:19:00 UTC; martyn
 Repository: CRAN
-Date/Publication: 2011-11-04 20:14:10
+Date/Publication: 2012-04-02 17:47:24
diff --git a/MD5 b/MD5
index ca502de..c428ea6 100644
--- a/MD5
+++ b/MD5
@@ -1,6 +1,6 @@
 3ad76246334ca13bb7cba54ce71e48bd *AUTHORS
-da8f601a40023d7c64ce633381e41d8b *CHANGELOG
-4e48209abab326ebf7a8d4b21c495432 *DESCRIPTION
+b4191ed8eaf048c11836f626b9c2a96e *CHANGELOG
+923c73a9b3ff49dab50f1184608efa0c *DESCRIPTION
 ff890b50eaa074ed668c6f2fac1b4141 *INDEX
 5096b7ad0e6c457ab9fbde263755c84f *NAMESPACE
 45f88adec7bcfab586a4deebba1cc02d *R/HPDinterval.R
@@ -8,7 +8,7 @@ ff890b50eaa074ed668c6f2fac1b4141 *INDEX
 02152920c66f540422f88e51c88f0428 *R/batchSE.R
 a22da830a261cd0f28da6052c560d5df *R/codamenu.R
 df4c85619867ba81878499f5059e875d *R/cumuplot.R
-d271b76ea4972b50807e97679515626c *R/gelman.R
+7403a684ac51932afbbb617d1f606a9a *R/gelman.R
 4799c5ceaaa6416d03bc22c31d2196f7 *R/geweke.R
 f63f255e6c07f67631e78d427bd40edc *R/heidel.R
 ae77a3ec34f086bd7ec8ea787baeeb1e *R/jags.R
@@ -22,7 +22,7 @@ d41d8cd98f00b204e9800998ecf8427e *R/thin.R
 b95af999515a96aec97f3d54487eda47 *R/trellisplots.R
 eb953d257fed9708d6848e4976b2b223 *R/util.R
 4d7d828d6d2b4fee5357d3a4dd108458 *README
-a666109f0bb5282078c66640dce7c18f *data/line.rda
+11dbe265fe46b9d1471466dbdc692fcc *data/line.rda
 81c1ae300d47f9a787eb871fbaafeb9f *inst/CITATION
 868ded8f4d10a67c7b31854bce6f3d63 *man/Cramer.Rd
 7bfe602ce737efac910300e5be5a8552 *man/HPDinterval.Rd
@@ -39,7 +39,7 @@ d3b21ba8f4c82fd92adfb1d4380d4cc8 *man/crosscorr.Rd
 2cc5efe9b602aae1ad07e0f7266142b6 *man/cumuplot.Rd
 3551dd04cb13f4b22a221d7de9fa1699 *man/densplot.Rd
 4009d8e9105a4e23590a07623c752627 *man/effectiveSize.Rd
-965a3da0dff536cf54bbf396d098ae25 *man/gelman.diag.Rd
+c78c35ac982bcd74befe51f98ba641e4 *man/gelman.diag.Rd
 394ae6df9b067ecb6120067aba37728c *man/gelman.plot.Rd
 aa5ee817bb15d58b4fd40089432ba99b *man/geweke.diag.Rd
 efd11972209251ece16ec61d8326bdce *man/geweke.plot.Rd
diff --git a/R/gelman.R b/R/gelman.R
index 203938b..b6bc0bf 100644
--- a/R/gelman.R
+++ b/R/gelman.R
@@ -1,5 +1,5 @@
 "gelman.diag" <- function (x, confidence = 0.95, transform = FALSE,
-                           autoburnin=TRUE) 
+                           autoburnin=TRUE, multivariate=TRUE) 
   ## Gelman and Rubin's diagnostic
   ## Gelman, A. and Rubin, D (1992). Inference from iterative simulation
   ## using multiple sequences.  Statistical Science, 7, 457-551.
@@ -37,7 +37,7 @@
                  ncol=Nchain)
   B <- Niter * var(t(xbar))
 
-  if(Nvar > 1) {
+  if(Nvar > 1 && multivariate) {
       ## We want the maximal eigenvalue of the square matrix X that
       ## solves WX = B. It is numerically easier to work with a
       ## symmetric matrix that has the same eigenvalues as X.
diff --git a/data/line.rda b/data/line.rda
index cda6d1e..a98ca81 100644
Binary files a/data/line.rda and b/data/line.rda differ
diff --git a/man/gelman.diag.Rd b/man/gelman.diag.Rd
index b8e4e1a..60e58e4 100644
--- a/man/gelman.diag.Rd
+++ b/man/gelman.diag.Rd
@@ -5,7 +5,8 @@
 %\alias{print.gelman.diag}
 \title{Gelman and Rubin's convergence diagnostic}
 
-\usage{gelman.diag(x, confidence = 0.95, transform=FALSE, autoburnin=TRUE)}
+\usage{gelman.diag(x, confidence = 0.95, transform=FALSE, autoburnin=TRUE,
+                   multivariate=TRUE)}
 
 \arguments{
 \item{x}{An \code{mcmc.list} object with more than one chain,
@@ -21,6 +22,9 @@ appropriate, will be applied.}
   of the series should be used in the computation.  If set to TRUE
   (default) and \code{start(x)} is less than \code{end(x)/2} then start
   of series will be adjusted so that only second half of series is used.}
+\item{multivariate}{a logical flag indicating whether the multivariate
+potential scale reduction factor should be calculated for multivariate
+chains}
 }
 
 \description{

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-science/packages/r-cran-coda.git

