[r-cran-coda] 09/60: Imported Upstream version 0.10-3
Andreas Tille
tille at debian.org
Fri Dec 16 12:11:22 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 7005e7d0cd99121f686c2ea00fc06affef9a53f4
Author: Andreas Tille <tille at debian.org>
Date: Fri Dec 16 12:09:54 2016 +0100
Imported Upstream version 0.10-3
---
CHANGELOG | 4 ++++
DESCRIPTION | 6 +++---
INDEX | 6 +++---
R/trellisplots.R | 32 +++++++++++++++++++++-----------
man/trellisplots.Rd | 21 +++++++++++----------
5 files changed, 42 insertions(+), 27 deletions(-)
diff --git a/CHANGELOG b/CHANGELOG
index ac6facb..363ef96 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -1,3 +1,7 @@
+
+0.12-3
+- added 'data' in lattice generics for compatibility
+
0.10-2
- Import generics from lattice
- In plotting functions, "ask" now defaults to dev.interactive(),
diff --git a/DESCRIPTION b/DESCRIPTION
index 5569570..b048134 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
Package: coda
-Version: 0.10-2
-Date: 2005-11-10
+Version: 0.10-3
+Date: 2005-12-16
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: Thu Nov 10 18:19:02 2005; martyn
+Packaged: Fri Dec 16 13:47:28 2005; deepayan
diff --git a/INDEX b/INDEX
index 0c61bd9..76a9a44 100644
--- a/INDEX
+++ b/INDEX
@@ -1,3 +1,5 @@
+HPDinterval Highest Posterior Density intervals
+[.mcmc Extract or replace parts of MCMC objects
as.matrix.mcmc Conversions of MCMC objects
as.ts.mcmc Coerce mcmc object to time series
autocorr Autocorrelation function for Markov chains
@@ -5,8 +7,8 @@ autocorr.diag Autocorrelation function for Markov chains
autocorr.plot Plot autocorrelations for Markov Chains
batchSE Batch Standard Error
bugs2jags Convert WinBUGS data file to JAGS data file
-codamenu Main menu driver for the coda package
coda.options Options settings for the codamenu driver
+codamenu Main menu driver for the coda package
crosscorr Cross correlations for MCMC output
crosscorr.plot Plot image of correlation matrix
cumuplot Cumulative quantile plot
@@ -19,10 +21,8 @@ gelman.plot Gelman-Rubin-Brooks plot
geweke.diag Geweke's convergence diagnostic
geweke.plot Geweke-Brooks plot
heidel.diag Heidelberger and Welch's convergence diagnostic
-HPDinterval Highest Posterior Density intervals
line Simple linear regression example
mcmc Markov Chain Monte Carlo Objects
-[.mcmc Extract or replace parts of MCMC objects
mcmc.list Replicated Markov Chain Monte Carlo Objects
mcmcUpgrade Upgrade mcmc objects in obsolete format
mcpar Mcpar attribute of MCMC objects
diff --git a/R/trellisplots.R b/R/trellisplots.R
index c17a822..554864e 100644
--- a/R/trellisplots.R
+++ b/R/trellisplots.R
@@ -52,7 +52,8 @@ thinned.indices <- function(object, n = nrow(object), start = 1, thin = 1)
levelplot.mcmc <-
- function(x, main = attr(x, "title"),
+ function(x, data = NULL,
+ main = attr(x, "title"),
start = 1, thin = 1,
...,
xlab = "", ylab = "",
@@ -87,7 +88,8 @@ levelplot.mcmc <-
splom.mcmc <-
- function(x, main = attr(x, "title"),
+ function(x, data = NULL,
+ main = attr(x, "title"),
start = 1, thin = 1,
as.matrix = TRUE,
xlab = "", ylab = "",
@@ -125,7 +127,8 @@ splom.mcmc <-
densityplot.mcmc <-
- function(x, outer, aspect = "xy",
+ function(x, data = NULL,
+ outer, aspect = "xy",
default.scales = list(relation = "free"),
start = 1, thin = 1,
main = attr(x, "title"),
@@ -174,7 +177,8 @@ densityplot.mcmc <-
densityplot.mcmc.list <-
- function(x, outer = FALSE, groups = !outer,
+ function(x, data = NULL,
+ outer = FALSE, groups = !outer,
aspect = "xy",
default.scales = list(relation = "free"),
start = 1, thin = 1,
@@ -234,7 +238,8 @@ densityplot.mcmc.list <-
qqmath.mcmc <-
- function(x, outer, aspect = "xy",
+ function(x, data = NULL,
+ outer, aspect = "xy",
default.scales = list(y = list(relation = "free")),
prepanel = prepanel.qqmathline,
start = 1, thin = 1,
@@ -261,7 +266,8 @@ qqmath.mcmc <-
qqmath.mcmc.list <-
- function(x, outer = FALSE, groups = !outer,
+ function(x, data = NULL,
+ outer = FALSE, groups = !outer,
aspect = "xy",
default.scales = list(y = list(relation = "free")),
prepanel = prepanel.qqmathline,
@@ -313,7 +319,8 @@ qqmath.mcmc.list <-
xyplot.mcmc <-
- function(x, outer, layout = c(1, ncol(x)),
+ function(x, data = NULL,
+ outer, layout = c(1, ncol(x)),
default.scales = list(y = list(relation = "free")),
type = 'l',
start = 1, thin = 1,
@@ -342,7 +349,8 @@ xyplot.mcmc <-
xyplot.mcmc.list <-
- function(x, outer = FALSE, groups = !outer,
+ function(x, data = NULL,
+ outer = FALSE, groups = !outer,
aspect = "xy", layout = c(1, ncol(x[[1]])),
default.scales = list(y = list(relation = "free")),
type = 'l',
@@ -421,13 +429,14 @@ panel.acfplot <-
-acfplot <- function(x, ...)
+acfplot <- function(x, data, ...)
UseMethod("acfplot")
acfplot.mcmc <-
- function(x, outer,
+ function(x, data = NULL,
+ outer,
prepanel = function(x, y, ...) list(ylim= c(-1, 1) * max(abs(y[-1]))),
panel = panel.acfplot,
type = "h",
@@ -466,7 +475,8 @@ acfplot.mcmc <-
acfplot.mcmc.list <-
- function(x, outer = FALSE, groups = !outer,
+ function(x, data = NULL,
+ outer = FALSE, groups = !outer,
prepanel = function(x, y, ..., groups = NULL, subscripts) {
if (is.null(groups)) list(ylim= c(-1, 1) * max(abs(y[-1])))
else list(ylim = c(-1, 1) * max(sapply(split(y, groups[subscripts]),
diff --git a/man/trellisplots.Rd b/man/trellisplots.Rd
index 9b86395..368be93 100644
--- a/man/trellisplots.Rd
+++ b/man/trellisplots.Rd
@@ -12,7 +12,7 @@
\alias{acfplot.mcmc}
\alias{acfplot.mcmc.list}
\usage{
-\method{densityplot}{mcmc}(x,
+\method{densityplot}{mcmc}(x, data,
outer, aspect = "xy",
default.scales = list(relation = "free"),
start = 1, thin = 1,
@@ -21,7 +21,7 @@
plot.points = "rug",
\dots,
subset)
-\method{densityplot}{mcmc.list}(x,
+\method{densityplot}{mcmc.list}(x, data,
outer = FALSE, groups = !outer,
aspect = "xy",
default.scales = list(relation = "free"),
@@ -31,14 +31,14 @@
plot.points = "rug",
\dots,
subset)
-\method{levelplot}{mcmc}(x, main = attr(x, "title"),
+\method{levelplot}{mcmc}(x, data, main = attr(x, "title"),
start = 1, thin = 1,
\dots,
xlab = "", ylab = "",
cuts = 10, at,
col.regions = topo.colors(100),
subset)
-\method{qqmath}{mcmc}(x,
+\method{qqmath}{mcmc}(x, data,
outer, aspect = "xy",
default.scales = list(y = list(relation = "free")),
prepanel = prepanel.qqmathline,
@@ -47,7 +47,7 @@
ylab = "",
\dots,
subset)
-\method{qqmath}{mcmc.list}(x,
+\method{qqmath}{mcmc.list}(x, data,
outer = FALSE, groups = !outer,
aspect = "xy",
default.scales = list(y = list(relation = "free")),
@@ -57,7 +57,7 @@
ylab = "",
\dots,
subset)
-\method{xyplot}{mcmc}(x,
+\method{xyplot}{mcmc}(x, data,
outer, layout = c(1, ncol(x)),
default.scales = list(y = list(relation = "free")),
type = 'l',
@@ -67,7 +67,7 @@
main = attr(x, "title"),
\dots,
subset)
-\method{xyplot}{mcmc.list}(x, outer = FALSE, groups = !outer,
+\method{xyplot}{mcmc.list}(x, data, outer = FALSE, groups = !outer,
aspect = "xy", layout = c(1, ncol(x[[1]])),
default.scales = list(y = list(relation = "free")),
type = 'l',
@@ -76,8 +76,8 @@
ylab = "",
\dots,
subset)
-acfplot(x, \dots)
-\method{acfplot}{mcmc}(x, outer,
+acfplot(x, data, \dots)
+\method{acfplot}{mcmc}(x, data, outer,
prepanel, panel,
type = 'h',
aspect = "xy",
@@ -88,7 +88,7 @@ acfplot(x, \dots)
main = attr(x, "title"),
...,
subset)
-\method{acfplot}{mcmc.list}(x, outer = FALSE, groups = !outer,
+\method{acfplot}{mcmc.list}(x, data, outer = FALSE, groups = !outer,
prepanel, panel,
type = if (groups) 'b' else 'h',
aspect = "xy",
@@ -112,6 +112,7 @@ acfplot(x, \dots)
}
\arguments{
\item{x}{ an \code{"mcmc"} or \code{"mcmc.list"} object. }
+ \item{data}{ ignored, present for consistency with generic. }
\item{outer}{ for the \code{"mcmc.list"} methods, a logical flag to
control whether multiple runs of a series are displayed in the same
panel (they are if \code{FALSE}, not if \code{TRUE}). If specified
--
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