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[Bugs-r-devel] SF.net SVN: bugs-r:[254] trunk/BRugs
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From: <li...@us...> - 2012-07-23 17:47:56
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Revision: 254
http://bugs-r.svn.sourceforge.net/bugs-r/?rev=254&view=rev
Author: ligges
Date: 2012-07-23 17:47:46 +0000 (Mon, 23 Jul 2012)
Log Message:
-----------
make BRugs OpenBUGS 3.2.2 compatible (and drop back compatibility) and some more fixes for R >= 2.15.1; bump version number
Modified Paths:
--------------
trunk/BRugs/DESCRIPTION
trunk/BRugs/NEWS
trunk/BRugs/R/info.modules.R
trunk/BRugs/R/info.node.R
trunk/BRugs/R/info.updaters.R
trunk/BRugs/R/model.setWD.R
trunk/BRugs/tests/BRugs.Rout.save
trunk/BRugs/tests/examples.Rout.save
trunk/BRugs/tests/functions.Rout.save
Modified: trunk/BRugs/DESCRIPTION
===================================================================
--- trunk/BRugs/DESCRIPTION 2012-07-12 02:22:12 UTC (rev 253)
+++ trunk/BRugs/DESCRIPTION 2012-07-23 17:47:46 UTC (rev 254)
@@ -1,12 +1,12 @@
Package: BRugs
Title: R interface to the OpenBUGS MCMC software
-Version: 0.7-5
-Date: 2012-01-06
+Version: 0.8-0
+Date: 2012-07-23
Author: OpenBUGS was developed by Andrew Thomas, Dave Lunn, David Spiegelhalter and Nicky Best. R interface developed by Uwe Ligges, Sibylle Sturtz, Andrew Gelman, Gregor Gorjanc and Chris Jackson. Linux port and most recent developments by Chris Jackson.
Description: Fully-interactive R interface to the OpenBUGS software for Bayesian analysis using MCMC sampling. Runs natively and stably in 32-bit R under Windows. Versions running on Linux and on 64-bit R under Windows are in "beta" status and less efficient.
Maintainer: Uwe Ligges <li...@st...>
Depends: R (>= 2.11.0), coda
Imports: utils, coda
-SystemRequirements: OpenBUGS (>= 3.2.1), hence Windows or Linux
+SystemRequirements: OpenBUGS (>= 3.2.2), hence Windows or Linux
License: GPL-2
URL: http://www.openbugs.info/
Modified: trunk/BRugs/NEWS
===================================================================
--- trunk/BRugs/NEWS 2012-07-12 02:22:12 UTC (rev 253)
+++ trunk/BRugs/NEWS 2012-07-23 17:47:46 UTC (rev 254)
@@ -1,5 +1,20 @@
Changes to BRugs:
=====================
+
+Version 0.8.0 (23 July 2012)
+-------------
+BRugs now works with an existing installation of OpenBUGS (>?)= 3.2.2.
+
+modelSetWD is exported from the NAMESPACE
+
+bugfixed to find examples on various Linux installations
+
+
+Version 0.7.4, 0.7.5
+--------------------
+bugfix releases
+
+
Version 0.7.3 (02 January 2012)
-------------
BRugs now supports 64-bit R on Windows, using the same helper program
Modified: trunk/BRugs/R/info.modules.R
===================================================================
--- trunk/BRugs/R/info.modules.R 2012-07-12 02:22:12 UTC (rev 253)
+++ trunk/BRugs/R/info.modules.R 2012-07-23 17:47:46 UTC (rev 254)
@@ -5,7 +5,7 @@
command <- "BugsEmbed.Modules"
.CmdInterpreter(command)
buffer <- file.path(tempdir(), "buffer.txt")
- result <- read.fwf(buffer, c(50, 12, 12, 12, 12, 10), skip = 1, as.is=TRUE)
+ result <- read.table(buffer, skip = 1, as.is=TRUE, sep="\t")[,-1]
for(i in c(1,4,5,6))
result[,i] <- gsub(" ", "", result[,i])
names(result) <- c("Module", "Clients", "Version", "Maintainer", "Compiled", "Loaded")
Modified: trunk/BRugs/R/info.node.R
===================================================================
--- trunk/BRugs/R/info.node.R 2012-07-12 02:22:12 UTC (rev 253)
+++ trunk/BRugs/R/info.node.R 2012-07-23 17:47:46 UTC (rev 254)
@@ -1,42 +1,42 @@
-"infoNodeValues" <-
-function(nodeLabel)
-# Get current value of node
-{
- nodeLabel <- as.character(nodeLabel)
- out <- .OpenBUGS(c("BugsRobjects.SetVariable", "BugsRobjects.GetSize"),
- c("CharArray","Integer"),
- list(nodeLabel, NA))
- nodeSize <- out[[2]]
- if(nodeSize == -1)
- stop(nodeLabel, " is not a node in BUGS model")
- numChains <- getNumChains()
- out <- .OpenBUGS(c("BugsRobjects.SetVariable", "BugsRobjects.GetValues"),
- c("CharArray","RealArray"),
- list(nodeLabel, double(nodeSize*numChains)))
- values <- matrix(out[[2]], nrow=nodeSize, ncol=numChains)
- values
-}
-
-infoNodeMethods <- function(nodeLabel)
-{
- nodeName <- sQuote(nodeLabel)
- command <- paste("BugsEmbed.SetNode(",nodeName,"); BugsEmbed.Methods");
- .CmdInterpreter(command)
- buffer <- file.path(tempdir(), "buffer.txt")
- result <- read.fwf(buffer, c(25, 25, 25, 25), skip = 1, as.is=TRUE, col.names=c("Node","Type", "Size", "Depth"))
- for (i in 1:2)
- result[,i] <- gsub(" ", "", result[,i])
- result
-}
-
-infoNodeTypes <- function(nodeLabel)
-{
- nodeName <- sQuote(nodeLabel)
- command <- paste("BugsEmbed.SetNode(",nodeName,"); BugsEmbed.Types");
- .CmdInterpreter(command)
- buffer <- file.path(tempdir(), "buffer.txt")
- result <- read.fwf(buffer, c(25, 25), skip = 1, as.is=TRUE, col.names=c("Node","Type"))
- for (i in 1:2)
- result[,i] <- gsub(" ", "", result[,i])
- result
-}
+"infoNodeValues" <-
+function(nodeLabel)
+# Get current value of node
+{
+ nodeLabel <- as.character(nodeLabel)
+ out <- .OpenBUGS(c("BugsRobjects.SetVariable", "BugsRobjects.GetSize"),
+ c("CharArray","Integer"),
+ list(nodeLabel, NA))
+ nodeSize <- out[[2]]
+ if(nodeSize == -1)
+ stop(nodeLabel, " is not a node in BUGS model")
+ numChains <- getNumChains()
+ out <- .OpenBUGS(c("BugsRobjects.SetVariable", "BugsRobjects.GetValues"),
+ c("CharArray","RealArray"),
+ list(nodeLabel, double(nodeSize*numChains)))
+ values <- matrix(out[[2]], nrow=nodeSize, ncol=numChains)
+ values
+}
+
+infoNodeMethods <- function(nodeLabel)
+{
+ nodeName <- sQuote(nodeLabel)
+ command <- paste("BugsEmbed.SetNode(",nodeName,"); BugsEmbed.Methods");
+ .CmdInterpreter(command)
+ buffer <- file.path(tempdir(), "buffer.txt")
+ result <- read.table(buffer, sep="\t", skip = 1, as.is=TRUE, col.names=c("empty", "Node", "Type", "Size", "Depth"))[,-1]
+ for (i in 1:2)
+ result[,i] <- gsub(" ", "", result[,i])
+ result
+}
+
+infoNodeTypes <- function(nodeLabel)
+{
+ nodeName <- sQuote(nodeLabel)
+ command <- paste("BugsEmbed.SetNode(",nodeName,"); BugsEmbed.Types");
+ .CmdInterpreter(command)
+ buffer <- file.path(tempdir(), "buffer.txt")
+ result <- read.table(buffer, sep="\t", skip = 1, as.is=TRUE, col.names=c("empty", "Node", "Type"))[,-1]
+ for (i in 1:2)
+ result[,i] <- gsub(" ", "", result[,i])
+ result
+}
Modified: trunk/BRugs/R/info.updaters.R
===================================================================
--- trunk/BRugs/R/info.updaters.R 2012-07-12 02:22:12 UTC (rev 253)
+++ trunk/BRugs/R/info.updaters.R 2012-07-23 17:47:46 UTC (rev 254)
@@ -8,8 +8,8 @@
if (readLines(buffer)[1]=="BugsCmds:NotCompiled")
stop("Model not compiled")
buffer <- file.path(tempdir(), "Updater types.txt")
- result <- read.fwf(buffer, c(25, 50, 10, 10), skip = 1, as.is=TRUE,
- row.names=1, col.names=c("Node","Type", "Size","Depth"))
+ result <- read.table(buffer, sep="\t", skip=1, as.is=TRUE,
+ row.names=2, col.names=c("empty", "Node", "Type", "Size", "Depth"))[,-1]
## strip leading and trailing spaces
for (i in 1:2) {
result[,i] <- gsub("^ +", "\\1", result[,i])
@@ -30,8 +30,8 @@
if (readLines(buffer)[1]=="BugsCmds:NotCompiled")
stop("Model not compiled")
buffer <- file.path(tempdir(), "Updater types.txt")
- result <- read.fwf(buffer, c(25, 50, 10, 10), skip = 1, as.is=TRUE,
- row.names=1, col.names=c("Node","Type", "Size","Depth"))
+ result <- read.table(buffer, sep="\t", skip=1, as.is=TRUE,
+ row.names=2, col.names=c("empty", "Node", "Type", "Size", "Depth"))[,-1]
## strip leading and trailing spaces
for (i in 1:2) {
result[,i] <- gsub("^ +", "\\1", result[,i])
Modified: trunk/BRugs/R/model.setWD.R
===================================================================
--- trunk/BRugs/R/model.setWD.R 2012-07-12 02:22:12 UTC (rev 253)
+++ trunk/BRugs/R/model.setWD.R 2012-07-23 17:47:46 UTC (rev 254)
@@ -1,3 +1,3 @@
## Simple alias to mimic the OpenBUGS script command
-"modelSetWD" <- setwd
+"modelSetWD" <- function(dir) setwd(dir)
Modified: trunk/BRugs/tests/BRugs.Rout.save
===================================================================
--- trunk/BRugs/tests/BRugs.Rout.save 2012-07-12 02:22:12 UTC (rev 253)
+++ trunk/BRugs/tests/BRugs.Rout.save 2012-07-23 17:47:46 UTC (rev 254)
@@ -80,7 +80,7 @@
+ }
Loading required package: coda
Loading required package: lattice
-Welcome to BRugs connected to OpenBUGS version 3.2.1
+Welcome to BRugs connected to OpenBUGS version 3.2.2
model is syntactically correct
data loaded
model compiled
Modified: trunk/BRugs/tests/examples.Rout.save
===================================================================
--- trunk/BRugs/tests/examples.Rout.save 2012-07-12 02:22:12 UTC (rev 253)
+++ trunk/BRugs/tests/examples.Rout.save 2012-07-23 17:47:46 UTC (rev 254)
@@ -68,7 +68,7 @@
+ }
Loading required package: coda
Loading required package: lattice
-Welcome to BRugs connected to OpenBUGS version 3.2.1
+Welcome to BRugs connected to OpenBUGS version 3.2.2
model is syntactically correct
data loaded
model compiled
@@ -89,7 +89,7 @@
model is initialized
model is already initialized
5000 updates took 0 s
-can not calculate deviance for this model
+can not calculate DIC for this model
monitor set for variable 'bronchitis'
monitor set for variable 'either'
monitor set for variable 'lung.cancer'
@@ -128,7 +128,7 @@
model is initialized
model is already initialized
5000 updates took 0 s
-can not calculate deviance for this model
+can not calculate DIC for this model
monitor set for variable 'Sigma2'
monitor set for variable 'rho'
monitor set for variable 'tau'
@@ -187,7 +187,7 @@
initial values loaded but chain contain uninitialized variables
initial values generated, model initialized
5000 updates took 0 s
-can not calculate deviance for this model
+can not calculate DIC for this model
monitor set for variable 'P'
monitor set for variable 'lambda'
monitor set for variable 'sigma'
Modified: trunk/BRugs/tests/functions.Rout.save
===================================================================
--- trunk/BRugs/tests/functions.Rout.save 2012-07-12 02:22:12 UTC (rev 253)
+++ trunk/BRugs/tests/functions.Rout.save 2012-07-23 17:47:46 UTC (rev 254)
@@ -151,7 +151,7 @@
+ }
Loading required package: coda
Loading required package: lattice
-Welcome to BRugs connected to OpenBUGS version 3.2.1
+Welcome to BRugs connected to OpenBUGS version 3.2.2
model is syntactically correct
data loaded
model compiled
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