[r-cran-coda] 48/60: Imported Upstream version 0.18-1
Andreas Tille
tille at debian.org
Fri Dec 16 12:11:27 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 9e48893fac28d4d682d7cdbb4cd4df17cc8af8d0
Author: Andreas Tille <tille at debian.org>
Date: Fri Dec 16 12:10:03 2016 +0100
Imported Upstream version 0.18-1
---
CHANGELOG | 15 +++++++++++
DESCRIPTION | 16 +++++++-----
MD5 | 20 +++++++-------
NAMESPACE | 17 ++++++++----
R/codamenu.R | 16 ------------
R/mcextractor.R | 8 ++++--
R/mcmclist.R | 80 ++++++++++++++++++++++++++++++++++++--------------------
R/util.R | 3 +--
data/line.rda | Bin 9600 -> 9600 bytes
inst/AUTHORS | 15 +++++++++--
man/cumuplot.Rd | 4 +--
11 files changed, 118 insertions(+), 76 deletions(-)
diff --git a/CHANGELOG b/CHANGELOG
index d975c4c..1db2f67 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -1,3 +1,18 @@
+0.18-1 Martyn Plummer <plummer at iarc.fr>
+
+ - Arni Magnusson is fully credited as coauthor
+
+ - Fixed bug in "varnames<-", which failed when the mcmc object was
+ not a matrix. Thanks to Evangelos Evangelou and Pavel Krivitsky.
+
+ - NAMESPACE file now includes imports of functions from base packages.
+
+ - codamenu no longer gives option to save mcmc object on exit.
+
+0.17-2 Martyn Plummer <plummerm at iarc.fr>
+
+ - Avoid redundant copies when subsetting mcmc.list objects
+
0.17-1 Martyn Plummer <plummerm at iarc.fr>
- Moved lattice package from Depends to Imports in DESCRIPTION
diff --git a/DESCRIPTION b/DESCRIPTION
index 22e5648..b382d54 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
Package: coda
-Version: 0.17-1
-Date: 2015-03-02
+Version: 0.18-1
+Date: 2015-10-16
Title: Output Analysis and Diagnostics for MCMC
Authors at R: c(person("Martyn", "Plummer", role=c("aut","cre","trl"),
email="plummerm at iarc.fr"),
@@ -9,7 +9,8 @@ Authors at R: c(person("Martyn", "Plummer", role=c("aut","cre","trl"),
person("Karen", "Vines", role="aut"),
person("Deepayan", "Sarkar", role="aut"),
person("Douglas", "Bates", role="aut"),
- person("Russell", "Almond", role="aut"))
+ person("Russell", "Almond", role="aut"),
+ person("Arni", "Magnusson", role="aut"))
Depends: R (>= 2.14.0)
Imports: lattice
Description: Provides functions for summarizing and plotting the
@@ -17,15 +18,16 @@ Description: Provides functions for summarizing and plotting the
well as diagnostic tests of convergence to the equilibrium
distribution of the Markov chain.
License: GPL (>= 2)
-Packaged: 2015-03-03 17:21:11 UTC; martyn
+NeedsCompilation: no
+Packaged: 2015-10-16 14:52:42 UTC; martyn
Author: Martyn Plummer [aut, cre, trl],
Nicky Best [aut],
Kate Cowles [aut],
Karen Vines [aut],
Deepayan Sarkar [aut],
Douglas Bates [aut],
- Russell Almond [aut]
+ Russell Almond [aut],
+ Arni Magnusson [aut]
Maintainer: Martyn Plummer <plummerm at iarc.fr>
-NeedsCompilation: no
Repository: CRAN
-Date/Publication: 2015-03-03 19:25:43
+Date/Publication: 2015-10-16 20:00:43
diff --git a/MD5 b/MD5
index ab4b1ee..066cbe3 100644
--- a/MD5
+++ b/MD5
@@ -1,28 +1,28 @@
-370fb32c3079904dfc365e55676f04d5 *CHANGELOG
-8bb04518c5614ce417d2ec9ee3fc45de *DESCRIPTION
+5d573790477b5f532496ced708cf98b1 *CHANGELOG
+ee63dce424da3eb1d6694384207193d5 *DESCRIPTION
ff890b50eaa074ed668c6f2fac1b4141 *INDEX
-adcc371105f44cfe439cd60f8ff727d4 *NAMESPACE
+201d6ba76723e5bc6a9a51df4d7f99a3 *NAMESPACE
45f88adec7bcfab586a4deebba1cc02d *R/HPDinterval.R
841853b3b96462cffe376cf9fad6abb9 *R/autocorrdiag.R
02152920c66f540422f88e51c88f0428 *R/batchSE.R
-a22da830a261cd0f28da6052c560d5df *R/codamenu.R
+4e1a55cb0aed5bcaa0f2f9d474e2fdea *R/codamenu.R
df4c85619867ba81878499f5059e875d *R/cumuplot.R
7403a684ac51932afbbb617d1f606a9a *R/gelman.R
a97024cb207bcef6fd4bc7c00283c1ed *R/geweke.R
6fb74d6977e5e3b5190eda35829cdc23 *R/heidel.R
ae77a3ec34f086bd7ec8ea787baeeb1e *R/jags.R
-f3b382582d73aad54d77c4c655513c58 *R/mcextractor.R
+0473eacf2812c4d9641e1c7fd09056b4 *R/mcextractor.R
97fef151be1d2924942ca84de70c87f4 *R/mcmc.R
-36759e063fe91197b2ef29b4b288eaee *R/mcmclist.R
+f60ceb305b2ab088484ab63d938333d1 *R/mcmclist.R
bd120c9296e4467265ee10409799e61f *R/output.R
389758882050a375ac4b5298a42ae35f *R/raftery.R
4caafbeb9941605b240d3ae9f6c8d5ff *R/rejectionRate.R
d41d8cd98f00b204e9800998ecf8427e *R/thin.R
553b1effc0816a68e0ad4dfd7847757f *R/trellisplots.R
-ffc99e7d181a7308c8aef6ea059a8d51 *R/util.R
+1e363c43c22c2a0e9658866463a0542d *R/util.R
4d7d828d6d2b4fee5357d3a4dd108458 *README
-2d8879e17e372a474e9c9c1057129b02 *data/line.rda
-3ad76246334ca13bb7cba54ce71e48bd *inst/AUTHORS
+ff0a8b17ed6881971cbd33c7ddb3fbda *data/line.rda
+52066ed7a20504a282a091060a794d57 *inst/AUTHORS
81c1ae300d47f9a787eb871fbaafeb9f *inst/CITATION
868ded8f4d10a67c7b31854bce6f3d63 *man/Cramer.Rd
7bfe602ce737efac910300e5be5a8552 *man/HPDinterval.Rd
@@ -36,7 +36,7 @@ e704de229cf312aa584094b126529e1a *man/coda.options.Rd
04dd4994917068f5d36fbcff921deb7f *man/codamenu.Rd
d3b21ba8f4c82fd92adfb1d4380d4cc8 *man/crosscorr.Rd
80c2893a13683e442443b36764810498 *man/crosscorr.plot.Rd
-2cc5efe9b602aae1ad07e0f7266142b6 *man/cumuplot.Rd
+18609dc8a896f624c979de557280cbf0 *man/cumuplot.Rd
14365306d891deafd1ca602f59e4520f *man/densplot.Rd
2b5bbbb8d683384c9287a9c8e1f7a01f *man/effectiveSize.Rd
c78c35ac982bcd74befe51f98ba641e4 *man/gelman.diag.Rd
diff --git a/NAMESPACE b/NAMESPACE
index 4230d13..4485dc2 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -123,11 +123,18 @@ S3method(print, raftery.diag)
S3method(print, summary.mcmc)
## Imports
-importFrom(stats, start, end, frequency, time, window, as.ts)
-importFrom(lattice, xyplot, qqmath, densityplot, levelplot, panel.abline,
- panel.xyplot, trellis.par.get, do.breaks, panel.superpose,
- prepanel.qqmathline, splom)
-importFrom(utils, head, tail)
+
+importFrom(grDevices, dev.cur, dev.interactive, dev.off, postscript,
+ topo.colors)
+importFrom(graphics, abline, axis, hist, legend, lines, matplot, par,
+ plot, polygon, text, title)
+importFrom(lattice, xyplot, qqmath, densityplot, levelplot,
+ panel.abline, panel.xyplot, trellis.par.get, do.breaks,
+ panel.superpose, prepanel.qqmathline, splom)
+importFrom(stats, Gamma, IQR, acf, aggregate, ar, as.formula, as.ts,
+ cor, density, end, fft, frequency, glm, lm, lowess, predict, qf,
+ qnorm, quantile, residuals, sd, start, time, ts, var, window)
+importFrom(utils, head, menu, read.table, tail)
## lattice methods
diff --git a/R/codamenu.R b/R/codamenu.R
index cb48d09..e77b13c 100644
--- a/R/codamenu.R
+++ b/R/codamenu.R
@@ -12,7 +12,6 @@
if (is.null(coda.dat)) {
return(invisible())
}
- coda.options(data.saved = FALSE)
}
else if (pick == 2) {
msg <- "\nEnter name of saved object (or type \"exit\" to quit)"
@@ -45,8 +44,6 @@
if (is.matrix(coda.dat[[1]]) && is.null(varnames(coda.dat))) {
varnames(coda.dat) <- varnames(coda.dat, allow.null = FALSE)
}
- on.exit(tidy.up(coda.dat))
-
## Check for variables that are linear functions of the
## iteration number
@@ -874,19 +871,6 @@ function (last.menu)
return(mcmc.list(chains))
}
-"tidy.up" <- function (data)
-{
- cat("\nQuitting codamenu ...\n")
- if (!coda.options("data.saved")) {
- ans <- read.yesno("Do you want to save the mcmc output", default=FALSE)
- if (ans == TRUE) {
- cat("Enter name you want to call this object:\n")
- fname <- scan(what = character(), nmax = 1, strip.white = TRUE)
- assign(fname, data, pos=1)
- }
- }
-}
-
"codamenu.ps" <- function ()
{
if (names(dev.cur()) == "postscript") {
diff --git a/R/mcextractor.R b/R/mcextractor.R
index 47c52c8..4829aa4 100644
--- a/R/mcextractor.R
+++ b/R/mcextractor.R
@@ -38,10 +38,14 @@ function (x, allow.null = TRUE)
function (x, value)
{
if (is.mcmc(x)) {
- dimnames(x)[[2]] <- value
+ if (length(dim(x)) < 2) {
+ dim(x) <- c(length(x), 1)
+ }
+ colnames(x) <- value
}
- else if (is.mcmc.list(x))
+ else if (is.mcmc.list(x)) {
for (i in 1:nchain(x)) varnames(x[[i]]) <- value
+ }
else stop("Not an mcmc or mcmc.list object")
x
}
diff --git a/R/mcmclist.R b/R/mcmclist.R
index 852032c..cfbd265 100644
--- a/R/mcmclist.R
+++ b/R/mcmclist.R
@@ -1,39 +1,61 @@
"[.mcmc.list" <- function (x, i, j, drop = TRUE)
{
- ## In S-PLUS the code is altered so that the user can
- ## pick out particular parameters by calling mcmc.obj[,c("param1", "param2")]
+ ## In S-PLUS the code is altered so that the user can
+ ## pick out particular parameters by calling
+ ## mcmc.obj[,c("param1", "param2")]
- ## Trying to squeeze too much functionality in here
- ## x[p:q] will subset the list
- ## x[p,], x[,q], x[p,q] will be recursively applied to
- ## the elements of the list, even if they are vectors
- if (nargs() < 3 + !missing(drop)) {
- ## Subset the list
- if (is.R()) {
- y <- NextMethod("[")
+ ## Trying to squeeze too much functionality in here
+ ## x[p:q] will subset the list
+ ## x[p,], x[,q], x[p,q] will be recursively applied to
+ ## the elements of the list, even if they are vectors
+
+ if (nargs() < 3 + !missing(drop)) {
+ ## Subset the list
+ if (is.R()) {
+ y <- NextMethod("[")
+ }
+ else {
+ y <- as.matrix(x)[i,j]
+ }
}
else {
- y <- as.matrix(x)[i,j]
+ ## Subset the elements of the list
+ y <- vector("list", length(x))
+ names(y) <- names(x)
+ for (k in 1:length(y)) {
+ y[[k]] <- if (missing(i) && missing(j)) {
+ x[[k]]
+ }
+ else if (is.matrix(x[[k]])) {
+ if (missing(i)) {
+ x[[k]][, j, drop = drop]
+ }
+ else if (missing(j)) {
+ x[[k]][i, , drop = drop]
+ }
+ else {
+ x[[k]][i, j, drop = drop]
+ }
+ }
+ else {
+ ### Coerce x[[k]] to matrix before subsetting
+ z <- as.matrix.mcmc(x[[k]])
+ if (missing(i)) {
+ mcmc(z[, j, drop = TRUE], start(x), end(x), thin(x))
+ }
+ else if (missing(j)) {
+ z[i, , drop = TRUE]
+ }
+ else {
+ z[i, j, drop = TRUE]
+ }
+ }
+ }
}
- }
- else {
- ## Subset the elements of the list
- y <- vector("list", length(x))
- names(y) <- names(x)
- for (k in 1:length(y)) {
- drop1 <- drop | !is.matrix(x[[k]])
- y[[k]] <- if (missing(i) && missing(j))
- x[[k]]
- else if (missing(i))
- mcmc(as.matrix(x[[k]])[, j, drop = drop1], start(x), end(x), thin(x))
- else if (missing(j))
- as.matrix(x[[k]])[i, , drop = drop1]
- else as.matrix(x[[k]])[i, j, drop = drop1]
+ if (is.list(y) && all(sapply(y, is.mcmc, simplify = TRUE))) {
+ y <- mcmc.list(y)
}
- }
- if (is.list(y) && all(sapply(y, is.mcmc, simplify = TRUE)))
- y <- mcmc.list(y)
- return(y)
+ return(y)
}
diff --git a/R/util.R b/R/util.R
index 4644e25..7285315 100644
--- a/R/util.R
+++ b/R/util.R
@@ -244,8 +244,7 @@ function (...)
user.layout = FALSE,
gr.bin = 10,
geweke.nbin = 20,
- gr.max = 50,
- data.saved = TRUE
+ gr.max = 50
)
coda.env <- new.env()
diff --git a/data/line.rda b/data/line.rda
index 815e8b2..960a9f6 100644
Binary files a/data/line.rda and b/data/line.rda differ
diff --git a/inst/AUTHORS b/inst/AUTHORS
index 50ce339..abc4ee6 100644
--- a/inst/AUTHORS
+++ b/inst/AUTHORS
@@ -21,6 +21,19 @@ so that the user is not bound by the menu-driven interface.
All authors, and the MRC Biostatistic Unit, have given permission for
the license terms to be changed to GPL.
+Other authors of CODA
+---------------------
+
+Deepayan Sarkar provided lattice graphics functions (See ?densityplot.mcmc)
+
+Douglas Bates wrote the HPDinterval function.
+
+Russell Almond <almond at acm.org>, <ralmond at ets.org> provided a number
+of cleanups and wrote the functions autocorr.diag, batchSE, and
+rejectionRate.
+
+Arni Magnusson wrote the cumuplot function.
+
Further credits
---------------
@@ -35,5 +48,3 @@ contributed to the Statlib archive by Steven Lewis
Andrew Martin <admartin at wustl.edu> added namespace facilities and
fixed a large number of bugs that this change uncovered (see CHANGELOG)
-Russell Almond <almond at acm.org>, <ralmond at ets.org> provided a number
-of cleanups and additions (see CHANGELOG).
diff --git a/man/cumuplot.Rd b/man/cumuplot.Rd
index 7603461..0a94310 100644
--- a/man/cumuplot.Rd
+++ b/man/cumuplot.Rd
@@ -25,7 +25,5 @@
number of iterations.
}
-\author{
- Arni Magnusson
-}
+\author{Arni Magnusson}
\keyword{hplot}
--
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