[Bugs-r-devel] SF.net SVN: bugs-r: [17] trunk/R2WinBUGS

[<li...@us...>]

Revision: 17
          http://svn.sourceforge.net/bugs-r/?rev=17&view=rev
Author:   ligges
Date:     2007-05-13 09:49:34 -0700 (Sun, 13 May 2007)

Log Message:
-----------
The codetools checks revealed quite a lot of bugs and inconsistencies. Unfortunately we cannot make codetools calm since codetools do not expect S-PLUS.
Again, prepared for release.

Modified Paths:
--------------
    trunk/R2WinBUGS/Changes
    trunk/R2WinBUGS/DESCRIPTION
    trunk/R2WinBUGS/R/attach.all.R
    trunk/R2WinBUGS/R/bugs.R
    trunk/R2WinBUGS/R/bugs.data.R
    trunk/R2WinBUGS/R/bugs.run.R
    trunk/R2WinBUGS/R/bugs.script.R
    trunk/R2WinBUGS/R/bugs.update.settings.R
    trunk/R2WinBUGS/R/openbugs.R
    trunk/R2WinBUGS/R/read.bugs.R
    trunk/R2WinBUGS/R/wineutils.R
    trunk/R2WinBUGS/R/write.model.R
    trunk/R2WinBUGS/man/bugs.run.Rd

Modified: trunk/R2WinBUGS/Changes
===================================================================
--- trunk/R2WinBUGS/Changes	2007-05-13 11:43:49 UTC (rev 16)
+++ trunk/R2WinBUGS/Changes	2007-05-13 16:49:34 UTC (rev 17)
@@ -70,5 +70,7 @@
 - print.bugs / plot.bugs documentation fixes
 - write.model() fix
 
-Update 2.1-2 (12 May 2007):
+Update 2.1-3 (13 May 2007):
 - Ported to S-PLUS by Insightful Corp.
+- some fixes for codetools checks
+

Modified: trunk/R2WinBUGS/DESCRIPTION
===================================================================
--- trunk/R2WinBUGS/DESCRIPTION	2007-05-13 11:43:49 UTC (rev 16)
+++ trunk/R2WinBUGS/DESCRIPTION	2007-05-13 16:49:34 UTC (rev 17)
@@ -1,7 +1,7 @@
 Package: R2WinBUGS
 Title: Running WinBUGS and OpenBUGS from R / S-PLUS
-Date: 2007-05-12
-Version: 2.1-2
+Date: 2007-05-13
+Version: 2.1-3
 Author: originally written by Andrew Gelman <ge...@st...>;
  changes and packaged by Sibylle Sturtz <st...@st...>
  and Uwe Ligges <li...@st...>.

Modified: trunk/R2WinBUGS/R/attach.all.R
===================================================================
--- trunk/R2WinBUGS/R/attach.all.R	2007-05-13 11:43:49 UTC (rev 16)
+++ trunk/R2WinBUGS/R/attach.all.R	2007-05-13 16:49:34 UTC (rev 17)
@@ -29,10 +29,7 @@
     detach("bugs.sims")}
   x$sims.list$n.sims <- x$n.sims   # put n.sims into sims.list for convenience
   r2 <- attach.all(x$sims.list, overwrite = overwrite, name = "bugs.sims")
-  if (is.R())
-    invisible (bugs.sims = r2)
-  else 
-    invisible (r2)
+  invisible (r2)
 }
 
 detach.all <- function(name = "attach.all"){

Modified: trunk/R2WinBUGS/R/bugs.R
===================================================================
--- trunk/R2WinBUGS/R/bugs.R	2007-05-13 11:43:49 UTC (rev 16)
+++ trunk/R2WinBUGS/R/bugs.R	2007-05-13 16:49:34 UTC (rev 17)
@@ -60,7 +60,7 @@
   bugs.script(parameters.to.save, n.chains, n.iter, n.burnin, n.thin,
     new.model.file, debug=debug, is.inits=!is.null(inits),
     bin = bin, DIC = DIC, useWINE = useWINE, newWINE = newWINE, WINEPATH = WINEPATH)
-  bugs.run(n.burnin, bugs.directory, WINE = WINE, useWINE = useWINE)
+  bugs.run(n.burnin, bugs.directory, WINE = WINE, useWINE = useWINE, WINEPATH = WINEPATH)
 
   if(codaPkg)
     return(file.path(getwd(), paste("coda", 1:n.chains, ".txt", sep="")))

Modified: trunk/R2WinBUGS/R/bugs.data.R
===================================================================
--- trunk/R2WinBUGS/R/bugs.data.R	2007-05-13 11:43:49 UTC (rev 16)
+++ trunk/R2WinBUGS/R/bugs.data.R	2007-05-13 16:49:34 UTC (rev 17)
@@ -1,29 +1,28 @@
 "bugs.data" <- 
 function(data, dir = getwd(), digits = 5){
   if(is.numeric(unlist(data)))
-		if(is.R()) {
-			write.datafile(lapply(data, formatC, digits = digits, format = "E"), 
-				file.path(dir, "data.txt"))
-		}
-		else {
-			writeDatafileS4(data, towhere = "data.txt")
-		}
+        if(is.R()) {
+            write.datafile(lapply(data, formatC, digits = digits, format = "E"), 
+                file.path(dir, "data.txt"))
+        }
+        else {
+            writeDatafileS4(data, towhere = "data.txt")
+        }
   else {
-		if(is.R()) {
-			data.list <- lapply(as.list(data), get, pos = parent.frame(2))
-			names(data.list) <- as.list(data)
-			write.datafile(lapply(data.list, formatC, digits = digits, format = "E"), 
-				file.path(dir, "data.txt"))
-		}
-		else {
-			data.list <- lapply(as.list(data), get, where = parent.frame(2))
-			names(data.list) <- unlist(data)
-			writeDatafileS4(data.list, towhere = "data.txt")
-		}
-	}
+        if(is.R()) {
+            data.list <- lapply(as.list(data), get, pos = parent.frame(2))
+            names(data.list) <- as.list(data)
+            write.datafile(lapply(data.list, formatC, digits = digits, format = "E"), 
+                file.path(dir, "data.txt"))
+        }
+        else {
+            data.list <- lapply(as.list(data), get, where = parent.frame(2))
+            names(data.list) <- unlist(data)
+            writeDatafileS4(data.list, towhere = "data.txt")
+        }
+    }
 }
 
-if (!is.R()) {
 
 "writeDatafileS4" <- 
 #
@@ -50,128 +49,128 @@
 # Revision history: 2002-11-19. Fixed to handle missing values properly.
 function(DATA, towhere = "clipboard", fill = TRUE)
 {
-	formatDataS4 = 
-	#
-	# Prepared DATA for input to WinBUGS.
-	function(DATA)
-	{
-		if(!is.list(DATA))
-			stop("DATA must be a named list or data frame.")
-		dlnames <- names(DATA)
-		if(is.data.frame(DATA))
-			DATA <- as.list(DATA)
-		#
-		# Checking for lists in DATA....
-		lind <- sapply(DATA, is.list)
-		# Checking for data frames in DATA....
-		dfind <- sapply(DATA, is.data.frame)
-		# Any lists that are not data frames?...
-		if(any(lind & !dfind)) stop("DATA may not contain lists.")
-		# Checking for unnamed elements of list that are not data frames....
-		if(any(dlnames[!dfind] == "")) stop(
-				"When DATA is a list, all its elements that are not data frames must be named."
-				)
-		# Checking for duplicate names....
-		dupnames <- unique(dlnames[duplicated(dlnames)])
-		if(length(dupnames) > 0)
-			stop(paste(
-				"The following names are used more than once in DATA:",
-				paste(dupnames, collapse = ", ")))
-		if(any(dfind)) {
-			dataold <- DATA
-			DATA <- vector("list", 0)
-			for(i in seq(along = dataold)) {
-				if(dfind[i])
-					DATA <- c(DATA, as.list(dataold[[i]]))
-				else DATA <- c(DATA, dataold[i])
-			}
-			dataold <- NULL
-		}
-		dlnames <- names(DATA)
-		dupnames <- unique(dlnames[duplicated(dlnames)])
-		# Checking for duplicated names again (now that columns of data frames are included)....
-		if(length(dupnames) > 0) stop(paste(
-				"The following names are used more than once in DATA (at least once within a data frame):",
-				paste(dupnames, collapse = ", ")))
-		# Checking for factors....
-		factorind <- sapply(DATA, is.factor)
-		if(any(factorind))
-			stop(paste(
-				"DATA may not include factors. One or more factor variables were detected:",
-				paste(dlnames[factorind], collapse = ", ")))
-		# Checking for character vectors....
-		charind <- sapply(DATA, is.character)
-		if(any(charind))
-			stop(paste(
-				"WinBUGS does not handle character data. One or more character variables were detected:",
-				paste(dlnames[charind], collapse = ", ")))
-		# Checking for complex vectors....
-		complexind <- sapply(DATA, is.complex)
-		if(any(complexind))
-			stop(paste(
-				"WinBUGS does not handle complex data. One or more complex variables were detected:",
-				paste(dlnames[complexind], collapse = ", ")))
-		# Checking for values farther from zero than 1E+38 (which is limit of single precision)....
-		toobigind <- sapply(DATA, function(x)
-		{
-			y <- abs(x[!is.na(x)])
-			any(y[y > 0] > 9.9999999999999998e+37)
-		}
-		)
-		if(any(toobigind))
-			stop(paste(
-				"WinBUGS works in single precision. The following variables contain data outside the range +/-1.0E+38: ",
-				paste(dlnames[toobigind], collapse = ", "),
-				".\n", sep = ""))
-		# Checking for values in range +/-1.0E-38 (which is limit of single precision)....
-		toosmallind <- sapply(DATA, function(x)
-		{
-			y <- abs(x[!is.na(x)])
-			any(y[y > 0] < 9.9999999999999996e-39)
-		}
-		)
-		n <- length(dlnames)
-		data.string <- as.list(rep(NA, n))
-		for(i in 1:n) {
-			if(length(DATA[[i]]) == 1) {
-				ac <- toSingleS4(DATA[[i]])
-				data.string[[i]] <- paste(names(DATA)[i], "=",
-					ac, sep = "")
-				next
-			}
-			if(is.vector(DATA[[i]]) & length(DATA[[i]]) > 1) {
-				ac <- toSingleS4(DATA[[i]])
-				data.string[[i]] <- paste(names(DATA)[i], "=c(",
-					paste(ac, collapse = ", "), ")", sep = 
-					"")
-				next
-			}
-			if(is.array(DATA[[i]])) {
-				ac <- toSingleS4(aperm(DATA[[i]]))
-				data.string[[i]] <- paste(names(DATA)[i], 
-					"= structure(.Data= c(", paste(ac,
-					collapse = ", "), "), \n   .Dim=c(",
-					paste(as.character(dim(DATA[[i]])),
-					collapse = ", "), "))", sep = "")
-			}
-		}
-		data.tofile <- paste("list(", paste(unlist(data.string), 
-			collapse = ", "), ")", sep = "")
-		if(any(toosmallind))
-			warning(paste(
-				"WinBUGS works in single precision. The following variables contained nonzero data",
-				"\ninside the range +/-1.0E-38 that were set to zero: ",
-				paste(dlnames[toosmallind], collapse = ", "),
-				".\n", sep = ""))
-		return(data.tofile)
-	}
-	rslt <- formatDataS4(DATA)
-	cat(rslt, file = towhere, fill = fill)
-	invisible(0)
+    formatDataS4 = 
+    #
+    # Prepared DATA for input to WinBUGS.
+    function(DATA)
+    {
+        if(!is.list(DATA))
+            stop("DATA must be a named list or data frame.")
+        dlnames <- names(DATA)
+        if(is.data.frame(DATA))
+            DATA <- as.list(DATA)
+        #
+        # Checking for lists in DATA....
+        lind <- sapply(DATA, is.list)
+        # Checking for data frames in DATA....
+        dfind <- sapply(DATA, is.data.frame)
+        # Any lists that are not data frames?...
+        if(any(lind & !dfind)) stop("DATA may not contain lists.")
+        # Checking for unnamed elements of list that are not data frames....
+        if(any(dlnames[!dfind] == "")) stop(
+                "When DATA is a list, all its elements that are not data frames must be named."
+                )
+        # Checking for duplicate names....
+        dupnames <- unique(dlnames[duplicated(dlnames)])
+        if(length(dupnames) > 0)
+            stop(paste(
+                "The following names are used more than once in DATA:",
+                paste(dupnames, collapse = ", ")))
+        if(any(dfind)) {
+            dataold <- DATA
+            DATA <- vector("list", 0)
+            for(i in seq(along = dataold)) {
+                if(dfind[i])
+                    DATA <- c(DATA, as.list(dataold[[i]]))
+                else DATA <- c(DATA, dataold[i])
+            }
+            dataold <- NULL
+        }
+        dlnames <- names(DATA)
+        dupnames <- unique(dlnames[duplicated(dlnames)])
+        # Checking for duplicated names again (now that columns of data frames are included)....
+        if(length(dupnames) > 0) stop(paste(
+                "The following names are used more than once in DATA (at least once within a data frame):",
+                paste(dupnames, collapse = ", ")))
+        # Checking for factors....
+        factorind <- sapply(DATA, is.factor)
+        if(any(factorind))
+            stop(paste(
+                "DATA may not include factors. One or more factor variables were detected:",
+                paste(dlnames[factorind], collapse = ", ")))
+        # Checking for character vectors....
+        charind <- sapply(DATA, is.character)
+        if(any(charind))
+            stop(paste(
+                "WinBUGS does not handle character data. One or more character variables were detected:",
+                paste(dlnames[charind], collapse = ", ")))
+        # Checking for complex vectors....
+        complexind <- sapply(DATA, is.complex)
+        if(any(complexind))
+            stop(paste(
+                "WinBUGS does not handle complex data. One or more complex variables were detected:",
+                paste(dlnames[complexind], collapse = ", ")))
+        # Checking for values farther from zero than 1E+38 (which is limit of single precision)....
+        toobigind <- sapply(DATA, function(x)
+        {
+            y <- abs(x[!is.na(x)])
+            any(y[y > 0] > 9.9999999999999998e+37)
+        }
+        )
+        if(any(toobigind))
+            stop(paste(
+                "WinBUGS works in single precision. The following variables contain data outside the range +/-1.0E+38: ",
+                paste(dlnames[toobigind], collapse = ", "),
+                ".\n", sep = ""))
+        # Checking for values in range +/-1.0E-38 (which is limit of single precision)....
+        toosmallind <- sapply(DATA, function(x)
+        {
+            y <- abs(x[!is.na(x)])
+            any(y[y > 0] < 9.9999999999999996e-39)
+        }
+        )
+        n <- length(dlnames)
+        data.string <- as.list(rep(NA, n))
+        for(i in 1:n) {
+            if(length(DATA[[i]]) == 1) {
+                ac <- toSingleS4(DATA[[i]])
+                data.string[[i]] <- paste(names(DATA)[i], "=",
+                    ac, sep = "")
+                next
+            }
+            if(is.vector(DATA[[i]]) & length(DATA[[i]]) > 1) {
+                ac <- toSingleS4(DATA[[i]])
+                data.string[[i]] <- paste(names(DATA)[i], "=c(",
+                    paste(ac, collapse = ", "), ")", sep = 
+                    "")
+                next
+            }
+            if(is.array(DATA[[i]])) {
+                ac <- toSingleS4(aperm(DATA[[i]]))
+                data.string[[i]] <- paste(names(DATA)[i], 
+                    "= structure(.Data= c(", paste(ac,
+                    collapse = ", "), "), \n   .Dim=c(",
+                    paste(as.character(dim(DATA[[i]])),
+                    collapse = ", "), "))", sep = "")
+            }
+        }
+        data.tofile <- paste("list(", paste(unlist(data.string), 
+            collapse = ", "), ")", sep = "")
+        if(any(toosmallind))
+            warning(paste(
+                "WinBUGS works in single precision. The following variables contained nonzero data",
+                "\ninside the range +/-1.0E-38 that were set to zero: ",
+                paste(dlnames[toosmallind], collapse = ", "),
+                ".\n", sep = ""))
+        return(data.tofile)
+    }
+    rslt <- formatDataS4(DATA)
+    cat(rslt, file = towhere, fill = fill)
+    invisible(0)
 }
 
 
-toSingleS4 =
+toSingleS4 <-
 #
 # Takes numeric vector and removes digit of exponent in scientific notation (if any)
 # 
@@ -180,50 +179,48 @@
 # Revision history: 2002-11-19. Fixed to handle missing values properly.
 function(x)
 {
-	xdim <- dim(x)
-	x <- as.character(as.single(x))
+    xdim <- dim(x)
+    x <- as.character(as.single(x))
 
-	# First to look for positives:
-	pplus <- regMatchPos(x, "e\\+0")
-	pplusind <- apply(pplus, 1, function(y)
-	(!any(is.na(y))))
-	if(any(pplusind)) {
-		# Making sure that periods are in mantissa...
-		init <- substring(x[pplusind], 1, pplus[
-			pplusind, 1] - 1)
-		#...preceeding exponent
-		pper <- regMatchPos(init, "\\.")
-		pperind <- apply(pper, 1, function(y)
-		(all(is.na(y))))
-		if(any(pperind))
-			init[pperind] <- paste(init[pperind],
-				".0", sep = "")
-		# Changing the format of the exponent...
-		x[pplusind] <- paste(init, "E+", substring(
-			x[pplusind], pplus[pplusind, 2] + 1),
-			sep = "")
-	}
-	# Then to look for negatives:
-	pminus <- regMatchPos(x, "e\\-0")
-	pminusind <- apply(pminus, 1, function(y)
-	(!any(is.na(y))))
-	if(any(pminusind)) {
-		# Making sure that periods are in mantissa...
-		init <- substring(x[pminusind], 1, pminus[
-			pminusind, 1] - 1)
-		#...preceeding exponent
-		pper <- regMatchPos(init, "\\.")
-		pperind <- apply(pper, 1, function(y)
-		(all(is.na(y))))
-		if(any(pperind))
-			init[pperind] <- paste(init[pperind],
-				".0", sep = "")
-		# Changing the format of the exponent...
-		x[pminusind] <- paste(init, "E-", substring(
-			x[pminusind], pminus[pminusind, 2] +
-			1), sep = "")
-	}
-	x
+    # First to look for positives:
+    pplus <- regMatchPos(x, "e\\+0")
+    pplusind <- apply(pplus, 1, function(y)
+    (!any(is.na(y))))
+    if(any(pplusind)) {
+        # Making sure that periods are in mantissa...
+        init <- substring(x[pplusind], 1, pplus[
+            pplusind, 1] - 1)
+        #...preceeding exponent
+        pper <- regMatchPos(init, "\\.")
+        pperind <- apply(pper, 1, function(y)
+        (all(is.na(y))))
+        if(any(pperind))
+            init[pperind] <- paste(init[pperind],
+                ".0", sep = "")
+        # Changing the format of the exponent...
+        x[pplusind] <- paste(init, "E+", substring(
+            x[pplusind], pplus[pplusind, 2] + 1),
+            sep = "")
+    }
+    # Then to look for negatives:
+    pminus <- regMatchPos(x, "e\\-0")
+    pminusind <- apply(pminus, 1, function(y)
+    (!any(is.na(y))))
+    if(any(pminusind)) {
+        # Making sure that periods are in mantissa...
+        init <- substring(x[pminusind], 1, pminus[
+            pminusind, 1] - 1)
+        #...preceeding exponent
+        pper <- regMatchPos(init, "\\.")
+        pperind <- apply(pper, 1, function(y)
+        (all(is.na(y))))
+        if(any(pperind))
+            init[pperind] <- paste(init[pperind],
+                ".0", sep = "")
+        # Changing the format of the exponent...
+        x[pminusind] <- paste(init, "E-", substring(
+            x[pminusind], pminus[pminusind, 2] +
+            1), sep = "")
+    }
+    x
 }
-
-} # ends if (!is.R())

Modified: trunk/R2WinBUGS/R/bugs.run.R
===================================================================
--- trunk/R2WinBUGS/R/bugs.run.R	2007-05-13 11:43:49 UTC (rev 16)
+++ trunk/R2WinBUGS/R/bugs.run.R	2007-05-13 16:49:34 UTC (rev 17)
@@ -1,6 +1,7 @@
 "bugs.run" <-
     function(n.burnin, bugs.directory, WINE = "", 
-             useWINE = .Platform$OS.type != "windows", newWINE = TRUE){
+             useWINE = .Platform$OS.type != "windows", 
+             newWINE = TRUE, WINEPATH = NULL){
     
 if(useWINE && !is.R())
     stop ("Non-Windows platforms not yet supported in R2WinBUGS for S-PLUS")    
@@ -26,7 +27,7 @@
     stop(paste("WinBUGS executable does not exist in", bugs.directory))
 ## Call Bugs and have it run with script.txt
   bugsCall <- paste("\"", dos.location, "\" /par \"",
-                    native2win(file.path(getwd(), "script.txt"), newWINE = newWINE),
+                    native2win(file.path(getwd(), "script.txt"), newWINE = newWINE, WINEPATH = WINEPATH),
                     "\"", sep = "")
   if (useWINE)
     bugsCall <- paste(WINE, bugsCall)

Modified: trunk/R2WinBUGS/R/bugs.script.R
===================================================================
--- trunk/R2WinBUGS/R/bugs.script.R	2007-05-13 11:43:49 UTC (rev 16)
+++ trunk/R2WinBUGS/R/bugs.script.R	2007-05-13 16:49:34 UTC (rev 17)
@@ -17,7 +17,8 @@
   coda  <- file.path(working.directory, "coda")
   logfile <- file.path(working.directory, "log.odc")
   logfileTxt <- file.path(working.directory, "log.txt")
-  inits <- sapply(paste(working.directory, "/inits", 1:n.chains, ".txt", sep=""), native2win)
+  inits <- sapply(paste(working.directory, "/inits", 1:n.chains, ".txt", sep=""), 
+                  function(x) native2win(x, , WINEPATH = WINEPATH))
   initlist <- paste("inits (", 1:n.chains, ", '", inits, "')\n", sep="")
   savelist <- paste("set (", parameters.to.save, ")\n", sep="")
   redo <- ceiling((n.iter-n.burnin)/(n.thin*bin))
@@ -34,15 +35,15 @@
     ## Therefore, if the samples are read into S-PLUS using the coda package,
     ## the thinning will be correctly labelled in the resulting mcmc object.
     ## In R, the thinning is always labelled as 1, even if thinning was done.
-  	thinUpdateCommand <- paste("update (", n.burnin, ")\n",
-			"thin.samples (", n.thin, ")\n", sep = "")
-		bin = bin * n.thin
+    thinUpdateCommand <- paste("update (", n.burnin, ")\n",
+            "thin.samples (", n.thin, ")\n", sep = "")
+        bin = bin * n.thin
   }
   
   cat(
     "display ('log')\n",
-    "check ('", native2win(model), "')\n",
-    "data ('", native2win(data), "')\n",
+    "check ('", native2win(model, WINEPATH=WINEPATH), "')\n",
+    "data ('", native2win(data, WINEPATH=WINEPATH), "')\n",
     "compile (", n.chains, ")\n",
     if(is.inits) initlist,
     "gen.inits()\n",
@@ -51,12 +52,12 @@
     if(DIC) "dic.set()\n",
     rep(
     c("update (", formatC(ceiling(bin), format = "d"), ")\n",
-    "coda (*, '", native2win(coda), "')\n"),redo),
+    "coda (*, '", native2win(coda, WINEPATH=WINEPATH), "')\n"),redo),
     "stats (*)\n",
     if(DIC) "dic.stats()\n",
-    "history (*, '", native2win(history), "')\n",
-    "save ('", native2win(logfile), "')\n", 
-    "save ('", native2win(logfileTxt), "')\n",
+    "history (*, '", native2win(history, WINEPATH=WINEPATH), "')\n",
+    "save ('", native2win(logfile, WINEPATH=WINEPATH), "')\n", 
+    "save ('", native2win(logfileTxt, WINEPATH=WINEPATH), "')\n",
     file=script, sep="", append=FALSE)
   if (!debug) cat ("quit ()\n", file=script, append=TRUE)
   sims.files <- paste ("coda", 1:n.chains, ".txt", sep="")

Modified: trunk/R2WinBUGS/R/bugs.update.settings.R
===================================================================
--- trunk/R2WinBUGS/R/bugs.update.settings.R	2007-05-13 11:43:49 UTC (rev 16)
+++ trunk/R2WinBUGS/R/bugs.update.settings.R	2007-05-13 16:49:34 UTC (rev 17)
@@ -1,13 +1,13 @@
 "bugs.update.settings" <-
 function (n.burnin, bugs.directory){
-		
+        
   char.burnin <- as.character(n.burnin - 1)
-	if (is.R()){
-  	file.copy(file.path(bugs.directory, "System/Rsrc/Registry.odc"),
+    if (is.R()){
+    file.copy(file.path(bugs.directory, "System/Rsrc/Registry.odc"),
             file.path(bugs.directory, "System/Rsrc/Registry_Rsave.odc"),
            overwrite = TRUE)
   } else {
-  	splus.file.copy(file.path(bugs.directory, "System/Rsrc/Registry.odc"),
+    splus.file.copy(file.path(bugs.directory, "System/Rsrc/Registry.odc"),
             file.path(bugs.directory, "System/Rsrc/Registry_Rsave.odc"),
            overwrite = TRUE)
   }
@@ -15,19 +15,19 @@
                 "character", 400, size = 1, endian = "little")
   locale <- Sys.getlocale("LC_CTYPE")
   Sys.setlocale("LC_CTYPE", "C")
-	if (is.R())  
-		info <- registry[regexpr("Int", registry, fixed = TRUE, useBytes = TRUE) > 0]
-	else  
-		info <- registry[regexpr("Int", registry, fixed = TRUE) > 0]
+    if (is.R())  
+        info <- registry[regexpr("Int", registry, fixed = TRUE, useBytes = TRUE) > 0]
+    else  
+        info <- registry[regexpr("Int", registry, fixed = TRUE) > 0]
   while(regexpr("\r", info) > 0){
     newline <- regexpr("\r", info)
     info <- substring(info, newline + 1)
     line <- substring(info, 1, regexpr("\r", info) - 1)
     if(regexpr("AdaptivePhase", line) > 0){
       if (is.R())
-      	numpos <- regexpr("Int", line, fixed = TRUE, useBytes = TRUE) + 4
+        numpos <- regexpr("Int", line, fixed = TRUE, useBytes = TRUE) + 4
       else
-      	numpos <- regexpr("Int", line, fixed = TRUE) + 4
+        numpos <- regexpr("Int", line, fixed = TRUE) + 4
 
       num <- substring(line, numpos)
       if (as.numeric(num) > n.burnin){
@@ -43,8 +43,6 @@
       file.path(bugs.directory, "System/Rsrc/Registry.odc"), endian = "little")
 }
 
-if (!is.R()){
-
 "splus.file.copy"<-
 function(from, to, overwrite = FALSE)
 {
@@ -57,5 +55,3 @@
                 size = 1)
         invisible(z)
 }
-
-} #ends if (!is.R())

Modified: trunk/R2WinBUGS/R/openbugs.R
===================================================================
--- trunk/R2WinBUGS/R/openbugs.R	2007-05-13 11:43:49 UTC (rev 16)
+++ trunk/R2WinBUGS/R/openbugs.R	2007-05-13 16:49:34 UTC (rev 17)
@@ -33,43 +33,43 @@
     model <- readLines(modelFile)
     try(writeLines(model, modelFile))
   }
-  modelCheck(modelFile)
+  BRugs::modelCheck(modelFile)
   if(!(is.vector(data) && is.character(data) && all(file.exists(data)))) {
-    data <- bugsData(data, digits = digits)
+    data <- BRugs::bugsData(data, digits = digits)
   }
-  modelData(data)
-  modelCompile(numChains)
+  BRugs::modelData(data)
+  BRugs::modelCompile(numChains)
   if(missing(inits) || is.null(inits)) {
-    modelGenInits()
+    BRugs::modelGenInits()
   }
   else {
     if(is.list(inits) || is.function(inits) || (is.character(inits) && 
       !any(file.exists(inits)))){
-      inits <- bugsInits(inits = inits, numChains = numChains, digits = digits)
+      inits <- BRugs::bugsInits(inits = inits, numChains = numChains, digits = digits)
     }
-    modelInits(inits)
-    modelGenInits()
+    BRugs::modelInits(inits)
+    BRugs::modelGenInits()
   }
-  samplesSetThin(nThin)
+  BRugs::samplesSetThin(nThin)
 # set the adaptive phases
   adaptivelines <- scan(system.file("OpenBUGS", "Bugs", "Rsrc", "Registry.txt", package="BRugs"), what="character")
   factories <- sub(".adaptivePhase", "",
                     adaptivelines[grep("adaptivePhase",adaptivelines)])
-  sapply(factories, modelSetAP, max(0, nBurnin-1)) 
+  sapply(factories, BRugs::modelSetAP, max(0, nBurnin-1)) 
   
-  modelUpdate(nBurnin)
+  BRugs::modelUpdate(nBurnin)
   if(!is.null(DIC)) {
-    dicSet()
-    on.exit(dicClear(), add = TRUE)
+    BRugs::dicSet()
+    on.exit(BRugs::dicClear(), add = TRUE)
   }
-  samplesSet(parametersToSave)
-  modelUpdate(nIter)
-  params <- sort.name(samplesMonitors("*"), parametersToSave)
-  samples <- sapply(params, samplesSample)
+  BRugs::samplesSet(parametersToSave)
+  BRugs::modelUpdate(nIter)
+  params <- sort.name(BRugs::samplesMonitors("*"), parametersToSave)
+  samples <- sapply(params, BRugs::samplesSample)
   n.saved.per.chain <- nrow(samples)/numChains
   samples.array <- array(samples, c(n.saved.per.chain, numChains, ncol(samples)))
   dimnames(samples.array)[[3]] <- dimnames(samples)[[2]]
-  if(!is.null(DIC)) DIC <- dicStats()
+  if(!is.null(DIC)) DIC <- BRugs::dicStats()
   bugs.output <- as.bugs.array(samples.array, modelFile, program="OpenBUGS", 
     n.iter=n.iter, n.burnin=n.burnin, n.thin=n.thin, DIC=DIC)
   return(bugs.output)

Modified: trunk/R2WinBUGS/R/read.bugs.R
===================================================================
--- trunk/R2WinBUGS/R/read.bugs.R	2007-05-13 11:43:49 UTC (rev 16)
+++ trunk/R2WinBUGS/R/read.bugs.R	2007-05-13 16:49:34 UTC (rev 17)
@@ -1,7 +1,7 @@
 read.bugs <- function(codafiles, ...){
     if(!require(coda))
         stop("package 'coda' is required to use this function")
-    mcmc.list(lapply(codafiles, read.coda, 
+    coda::mcmc.list(lapply(codafiles, coda::read.coda, 
                      index.file = file.path(dirname(codafiles[1]), "codaIndex.txt"), 
                      ...))
 }

Modified: trunk/R2WinBUGS/R/wineutils.R
===================================================================
--- trunk/R2WinBUGS/R/wineutils.R	2007-05-13 11:43:49 UTC (rev 16)
+++ trunk/R2WinBUGS/R/wineutils.R	2007-05-13 16:49:34 UTC (rev 17)
@@ -52,7 +52,7 @@
 
 } # end if (is.R())
 
-native2win <- function(x, useWINE=.Platform$OS.type != "windows", newWINE=TRUE) { # native -> win
+native2win <- function(x, useWINE=.Platform$OS.type != "windows", newWINE=TRUE, WINEPATH=NULL) { # native -> win
   if(is.R()){
       if (useWINE && !newWINE) return(winedriveRTr(x))
       if (useWINE && newWINE) {

Modified: trunk/R2WinBUGS/R/write.model.R
===================================================================
--- trunk/R2WinBUGS/R/write.model.R	2007-05-13 11:43:49 UTC (rev 16)
+++ trunk/R2WinBUGS/R/write.model.R	2007-05-13 16:49:34 UTC (rev 17)
@@ -21,8 +21,6 @@
   writeLines(model.text, con = con)
 }
 
-if (!is.R()){
-
 replaceScientificNotation <- function(text){
 ## Change the format of any numbers in "text" that are in S-PLUS 
 ## scientific notation to WinBUGS scientific notation
@@ -31,7 +29,7 @@
   ## Find the first instance
   ## Note that the number may or may not have a decimal point.
   sciNoteLoc <- regexpr("[0-9]*\\.{0,1}[0-9]*e\\+0[0-9]{2}", text)
-	
+    
   ## For every instance, replace the number
   while(sciNoteLoc > -1){
     sciNoteEnd <- sciNoteLoc + attr(sciNoteLoc, "match.length")-1
@@ -54,4 +52,3 @@
 
   text
 }
-} ## ends if (!is.R())

Modified: trunk/R2WinBUGS/man/bugs.run.Rd
===================================================================
--- trunk/R2WinBUGS/man/bugs.run.Rd	2007-05-13 11:43:49 UTC (rev 16)
+++ trunk/R2WinBUGS/man/bugs.run.Rd	2007-05-13 16:49:34 UTC (rev 17)
@@ -6,7 +6,8 @@
 calls WinBUGS and runs it with \file{script.txt}. Intended for internal use only}
 \usage{
 bugs.run(n.burnin, bugs.directory, WINE = "", 
-         useWINE = .Platform$OS.type != "windows", newWINE = TRUE)
+         useWINE = .Platform$OS.type != "windows", 
+         newWINE = TRUE, WINEPATH = NULL)
 }
 \arguments{
   \item{n.burnin}{length of burn in}
@@ -16,6 +17,8 @@
     defaults to \code{TRUE} on Windows, and \code{FALSE} otherwise.
     The \code{useWINE = TRUE} option is not available in S-PLUS.}
   \item{newWINE}{set this one to \code{TRUE} for new versions of WINE.} 
+  \item{WINEPATH}{Path the WINE, \code{bugs} tries hard to get the information automatically and 
+    pass it to this function, if not given.}
 }
 \value{
     Does not return anything.


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