[r-cran-coda] 17/60: Imported Upstream version 0.10-7

[Andreas Tille]

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tille pushed a commit to branch master
in repository r-cran-coda.

commit fbe3354117938ae38ce01ac55dca217aa465a018
Author: Andreas Tille <tille at debian.org>
Date:   Fri Dec 16 12:09:56 2016 +0100

    Imported Upstream version 0.10-7
---
 CHANGELOG         | 7 +++++++
 DESCRIPTION       | 6 +++---
 R/codamenu.R      | 2 +-
 R/rejectionRate.R | 5 ++---
 man/bugs2jags.Rd  | 6 ++++++
 5 files changed, 19 insertions(+), 7 deletions(-)

diff --git a/CHANGELOG b/CHANGELOG
index ec4a8c0..a231fbf 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -1,3 +1,10 @@
+0.10-7
+- Documentation clarification for bugs2jags()
+- Made linearity test in codamenu less stringent.
+  Thanks to Bengt Sennblad.
+- Fixed rejectionRate() for single-variable chains.
+  Thanks to Rob Scharpf.
+
 0.10-6
 - Fixed HPDinterval() for univariate chains
   Thanks to David LeBlond
diff --git a/DESCRIPTION b/DESCRIPTION
index 452eb68..630f97b 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: coda
-Version: 0.10-6
-Date: 2006-03-27
+Version: 0.10-7
+Date: 2006-08-29
 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 (>= 2.2.0), lattice
 Description: Output analysis and diagnostics for Markov Chain Monte
   Carlo simulations. 
 License: GPL Version 2 or later.
-Packaged: Wed Jul 26 18:25:25 2006; martyn
+Packaged: Tue Oct 10 19:04:16 2006; martyn
diff --git a/R/codamenu.R b/R/codamenu.R
index 4062250..a49ad5f 100644
--- a/R/codamenu.R
+++ b/R/codamenu.R
@@ -58,7 +58,7 @@
   for (i in 1:nchain(coda.dat)) {
       for (j in 1:nvar(coda.dat)) {
           lm.out <- lm(as.matrix(coda.dat[[i]])[,j] ~ time(coda.dat))
-          if (identical(all.equal(var(residuals(lm.out)), 0), TRUE)) {
+          if (identical(all.equal(sd(residuals(lm.out)), 0), TRUE)) {
               is.linear[j] <- TRUE
           }
       }
diff --git a/R/rejectionRate.R b/R/rejectionRate.R
index 8a3a29f..9831f9f 100644
--- a/R/rejectionRate.R
+++ b/R/rejectionRate.R
@@ -1,7 +1,6 @@
-
 rejectionRate.mcmc <- function (x) {
-  n <- nrow(x)
-  apply(x[1:(n-1),] == x[2:n,],2,mean)
+  x <- as.matrix(x)
+  apply(x[-nrow(x),,drop=FALSE] == x[-1,, drop=FALSE],2,mean)
 }
 
 rejectionRate.mcmc.list <- function (x) {
diff --git a/man/bugs2jags.Rd b/man/bugs2jags.Rd
index 4dffc22..482a573 100644
--- a/man/bugs2jags.Rd
+++ b/man/bugs2jags.Rd
@@ -19,6 +19,12 @@ bugs2jags(infile, outfile)
   automatically reorder the data in arrays, without changing the
   dimension.
 }
+\note{
+  If the input file is saved from WinBUGS, it must be saved in plain text
+  format. The default format for files saved from WinBUGS is a binary
+  compound document format (with extension odc) that cannot be read by
+  bugs2jags.
+}
 \references{
   Spiegelhalter DJ, Thomas A, Best NG and Lunn D (2003).
   \emph{WinBUGS version 1.4 user manual}

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