[r-cran-coda] 32/60: Imported Upstream version 0.13-5
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 2fee781576e2e9d195c4d419c66f62da4b4fd15e
Author: Andreas Tille <tille at debian.org>
Date: Fri Dec 16 12:09:59 2016 +0100
Imported Upstream version 0.13-5
---
DESCRIPTION | 10 ++++++----
R/batchSE.R | 9 ++++++++-
R/codamenu.R | 4 ++--
R/mcmclist.R | 21 +++++++++++++++++++++
R/output.R | 2 +-
R/raftery.R | 1 +
R/trellisplots.R | 14 +++++++-------
R/util.R | 2 +-
man/cumuplot.Rd | 2 +-
svn-commit.tmp | 6 ------
10 files changed, 48 insertions(+), 23 deletions(-)
diff --git a/DESCRIPTION b/DESCRIPTION
index f9b8dda..1baeeae 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,11 +1,13 @@
Package: coda
-Version: 0.13-4
-Date: 2009-01-25
+Version: 0.13-5
+Date: 2010-03-19
Title: Output analysis and diagnostics for MCMC
Author: Martyn Plummer, Nicky Best, Kate Cowles, Karen Vines
Maintainer: Martyn Plummer <plummer 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: Sun Jan 25 21:32:17 2009; martyn
+Packaged: 2010-03-19 10:15:39 UTC; martyn
+Repository: CRAN
+Date/Publication: 2010-03-19 12:57:10
diff --git a/R/batchSE.R b/R/batchSE.R
index 01934c2..d6307a8 100644
--- a/R/batchSE.R
+++ b/R/batchSE.R
@@ -44,5 +44,12 @@
## Needed for this function, but generally useful anyway.
as.data.frame.mcmc <- function(x, row.names = NULL, optional=FALSE, ...) {
- as.data.frame.matrix(x,row.names,optional, ...)
+ if (is.matrix(x))
+ as.data.frame.matrix(x,row.names,optional, ...)
+ else {
+ if (is.null(row.names))
+ row.names <- time(x)
+ data.frame("var1"=as.numeric(x), row.names=row.names)
+ }
+
}
diff --git a/R/codamenu.R b/R/codamenu.R
index 01751a8..b31cdab 100644
--- a/R/codamenu.R
+++ b/R/codamenu.R
@@ -112,7 +112,7 @@
if (current.menu == "codamenu.main")
{
cat("A crash has occurred in the main menu\nBailing out\n")
- return();
+ return(invisible());
}
else
{
@@ -839,7 +839,7 @@ function (last.menu)
index.file <- scan(what = character(), sep = "\n", strip.white = TRUE)
}
if (length(index.file) == 0)
- return()
+ return(invisible())
cat("Enter CODA output file names, separated by return key\n")
cat("(leave a blank line when you have finished)\n")
if (is.R()) {
diff --git a/R/mcmclist.R b/R/mcmclist.R
index 774a7de..e0de6b0 100644
--- a/R/mcmclist.R
+++ b/R/mcmclist.R
@@ -205,3 +205,24 @@
return(y)
}
+#FIXME: Check this
+"as.mcmc.list.bugs" <-
+function( x, ... )
+{
+ nchain <- x$n.chains
+
+ start <- x$n.burnin + 1 #FIXME: Is this correct starting value?
+ thin <- x$n.thin
+
+ parameter.names <- x$root.short
+
+ zz <- vector("list", x$n.chains)
+
+ aa <- x$sims.array
+ for( i in 1:nchain) {
+ bb <- aa[,i,]
+
+ zz[[i]] <- mcmc(aa[,i,], start=start, thin=thin)
+ }
+ mcmc.list( zz[-1] )
+}
diff --git a/R/output.R b/R/output.R
index 029c2e0..feb6626 100644
--- a/R/output.R
+++ b/R/output.R
@@ -101,7 +101,7 @@ function (x, col = topo.colors(10), ...)
text(Nvar - ydelta, Nvar, "1", adj = c(1, 1))
text(Nvar - ydelta, 0.5 * Nvar, "-1", adj = c(1, 0))
text(Nvar - ydelta, 0.75 * Nvar, "0", adj = c(1, 0.5))
- return()
+ invisible()
}
"densplot" <-
diff --git a/R/raftery.R b/R/raftery.R
index c8a7bf0..2c88426 100644
--- a/R/raftery.R
+++ b/R/raftery.R
@@ -28,6 +28,7 @@ function (data, q = 0.025, r = 0.005, s = 0.95, converge.eps = 0.001)
while (bic >= 0) {
kthin <- kthin + thin(data)
testres <- as.vector(window.mcmc(dichot, thin = kthin))
+ testres <- factor(testres, levels=c(FALSE,TRUE))
newdim <- length(testres)
testtran <- table(testres[1:(newdim - 2)], testres[2:(newdim -
1)], testres[3:newdim])
diff --git a/R/trellisplots.R b/R/trellisplots.R
index 01c2ee2..0949cb2 100644
--- a/R/trellisplots.R
+++ b/R/trellisplots.R
@@ -174,7 +174,7 @@ densityplot.mcmc <-
### original. But that's true even if the original mcmc object was
### itself already thinned.
- densityplot(form, data = data[subset, ],
+ densityplot(form, data = data[subset, , drop=FALSE],
outer = TRUE,
aspect = aspect,
default.scales = default.scales,
@@ -201,7 +201,7 @@ densityplot.mcmc.list <-
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, ])
+ datalist <- lapply(x, function(x) as.data.frame(x)[subset, ,drop=FALSE])
data <- do.call("rbind", datalist)
form <-
if (outer)
@@ -269,7 +269,7 @@ qqmath.mcmc <-
as.formula(paste("~",
paste(lapply(names(data), as.name),
collapse = "+")))
- qqmath(form, data = data[subset, ],
+ qqmath(form, data = data[subset, ,drop=FALSE],
outer = TRUE,
aspect = aspect,
prepanel = prepanel,
@@ -296,7 +296,7 @@ qqmath.mcmc.list <-
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, ])
+ datalist <- lapply(x, function(x) as.data.frame(x)[subset, , drop=FALSE])
data <- do.call("rbind", datalist)
form <-
if (outer)
@@ -485,7 +485,7 @@ acfplot.mcmc <-
{
as.vector(acf(x, lag.max = lag.max, plot = FALSE)$acf)
}
- data <- as.data.frame(apply(x[subset, ], 2, getAcf, lag.max = lag.max))
+ data <- as.data.frame(apply(as.matrix(x)[subset, ,drop=FALSE], 2, getAcf, lag.max = lag.max))
form <-
eval(parse(text = paste(paste(lapply(names(data), as.name),
collapse = "+"), "~.lag")))
@@ -537,7 +537,7 @@ acfplot.mcmc.list <-
{
datalist <-
lapply(x, function(x)
- as.data.frame(apply(x[subset, ], 2,
+ as.data.frame(apply(as.matrix(x)[subset, ,drop=FALSE], 2,
getAcf, lag.max = lag.max)))
data <- do.call("rbind", datalist)
}
@@ -546,7 +546,7 @@ acfplot.mcmc.list <-
## this is not quite valid, as we are combining multiple
## series, but shouldn't be too bad (FIXME: should we warn?)
- datalist <- lapply(x, function(x) x[subset, ])
+ datalist <- lapply(x, function(x) as.matrix(x)[subset, ,drop=FALSE])
data <-
as.data.frame(apply(do.call("rbind", datalist),
2, getAcf, lag.max = lag.max))
diff --git a/R/util.R b/R/util.R
index f9e09e8..400f5af 100644
--- a/R/util.R
+++ b/R/util.R
@@ -23,7 +23,7 @@ function (string, option)
names(arg) <- option
coda.options(arg)
}
- return()
+ invisible()
}
"coda.options" <-
diff --git a/man/cumuplot.Rd b/man/cumuplot.Rd
index 5a642d0..7603461 100644
--- a/man/cumuplot.Rd
+++ b/man/cumuplot.Rd
@@ -26,6 +26,6 @@
}
\author{
- Arni Magnusson <arnima at u.washington.edu>
+ Arni Magnusson
}
\keyword{hplot}
diff --git a/svn-commit.tmp b/svn-commit.tmp
deleted file mode 100644
index 7358da9..0000000
--- a/svn-commit.tmp
+++ /dev/null
@@ -1,6 +0,0 @@
-Fixing parse errors in documentation
---This line, and those below, will be ignored--
-
-M DESCRIPTION
-M man/heidel.diag.Rd
-M man/gelman.diag.Rd
--
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