[Bugs-r-devel] SF.net SVN: bugs-r:[181] trunk/R2OpenBUGS

[<snt...@us...>]

Revision: 181
          http://bugs-r.svn.sourceforge.net/bugs-r/?rev=181&view=rev
Author:   snthomas99
Date:     2011-03-21 19:13:27 +0000 (Mon, 21 Mar 2011)

Log Message:
-----------
added saveExec and restart features for use with OpenBUGS >3.2.1

Modified Paths:
--------------
    trunk/R2OpenBUGS/CreatevalidateOpenBUGS.R
    trunk/R2OpenBUGS/DESCRIPTION
    trunk/R2OpenBUGS/R/bugs.R
    trunk/R2OpenBUGS/R/bugs.script.R
    trunk/R2OpenBUGS/R/print.bugs.R
    trunk/R2OpenBUGS/inst/NEWS
    trunk/R2OpenBUGS/inst/validateInstallOpenBUGS/validOpenBUGSResults.R
    trunk/R2OpenBUGS/man/bugs.Rd
    trunk/R2OpenBUGS/man/bugs.script.Rd

Modified: trunk/R2OpenBUGS/CreatevalidateOpenBUGS.R
===================================================================
--- trunk/R2OpenBUGS/CreatevalidateOpenBUGS.R	2011-03-07 15:09:12 UTC (rev 180)
+++ trunk/R2OpenBUGS/CreatevalidateOpenBUGS.R	2011-03-21 19:13:27 UTC (rev 181)
@@ -25,11 +25,11 @@
                     )
 
 test.modelfile = paste(test.models,"model.txt",sep="")
-test.modelfile<-file.path('C:/Program Files/OpenBUGS/OpenBUGS312/Examples',test.modelfile)
+test.modelfile<-file.path('C:/Program Files/OpenBUGS/OpenBUGS321/Examples',test.modelfile)
 test.datafile = paste(test.models,"data.txt",sep="")
-test.datafile<-file.path('C:/Program Files/OpenBUGS/OpenBUGS312/Examples',test.datafile)
+test.datafile<-file.path('C:/Program Files/OpenBUGS/OpenBUGS321/Examples',test.datafile)
 test.inits = paste(test.models,"inits.txt",sep="")
-test.inits<-file.path('C:/Program Files/OpenBUGS/OpenBUGS312/Examples',test.inits)
+test.inits<-file.path('C:/Program Files/OpenBUGS/OpenBUGS321/Examples',test.inits)
 
 ### Test for posterior means within 1 percent of previously saved values
 

Modified: trunk/R2OpenBUGS/DESCRIPTION
===================================================================
--- trunk/R2OpenBUGS/DESCRIPTION	2011-03-07 15:09:12 UTC (rev 180)
+++ trunk/R2OpenBUGS/DESCRIPTION	2011-03-21 19:13:27 UTC (rev 181)
@@ -1,7 +1,7 @@
 Package: R2OpenBUGS
 Title: Running OpenBUGS from R / S-PLUS
-Date: 2010-09-30
-Version: 3.1-2
+Date: 2011-03-01
+Version: 3.2-1
 Author: originally written as R2WinBUGS by Andrew Gelman <ge...@st...>;
  changes and packaged by Sibylle Sturtz <st...@st...>
  and Uwe Ligges <li...@st...>.
@@ -12,9 +12,8 @@
  it is possible to call a BUGS model, summarize inferences and
  convergence in a table and graph, and save the simulations in arrays for easy access
  in R / S-PLUS. 
-Depends: R (>= 2.9.2), coda (>= 0.11-0)
-SystemRequirements: OpenBUGS >=3.1
-URL: http://www.stat.columbia.edu/~gelman/bugsR/
+Depends: R (>= 2.10.1), coda (>= 0.11-0)
+SystemRequirements: OpenBUGS >=3.2.1
 Maintainer: Uwe Ligges <li...@st...>
 License: GPL-2
 Dialect: R, S-PLUS

Modified: trunk/R2OpenBUGS/R/bugs.R
===================================================================
--- trunk/R2OpenBUGS/R/bugs.R	2011-03-07 15:09:12 UTC (rev 180)
+++ trunk/R2OpenBUGS/R/bugs.R	2011-03-21 19:13:27 UTC (rev 181)
@@ -1,11 +1,12 @@
 "bugs" <-
-function(data, inits, parameters.to.save, n.iter, model.file="model.bug",
+function(data, inits, parameters.to.save, n.iter, model.file="model.txt",
     n.chains=3, n.burnin=floor(n.iter / 2), n.thin=1, 
+    saveExec=FALSE,restart=FALSE,
     debug=FALSE, DIC=TRUE, digits=5, codaPkg=FALSE,
     OpenBUGS.pgm=ifelse(.Platform$OS.type == "windows" | useWINE==TRUE,
       paste("C:/Program Files/OpenBUGS/OpenBUGS",
       version,"/OpenBUGS.exe",sep=""),"OpenBUGS"), 
-    version='312',
+    version='321',
     working.directory=NULL,
     clearWD=FALSE, useWINE=FALSE, WINE=NULL,
     newWINE=TRUE, WINEPATH=NULL, bugs.seed=1, summary.only=FALSE,
@@ -36,6 +37,11 @@
 
   if(! bugs.seed %in% c(1:14))stop("OpenBUGS seed must be integer in 1-14")
 
+  if(!is.function(model.file) && 
+     length(grep("\\.bug", tolower(model.file))))stop("model.file must be renamed with .txt rather than .bug")
+
+  if(is.null(working.directory) && (saveExec || restart))stop("The working directory must be specified when saveExec or restart is TRUE")
+
   if(!is.null(working.directory)) {
     working.directory <- path.expand(working.directory)
     savedWD <- getwd()
@@ -120,7 +126,7 @@
   }
 
   if(DIC) parameters.to.save <- c(parameters.to.save, "deviance")
-  ## Model files with extension ".bug" need to be renamed to ".txt"
+  ## Model files must have extension ".txt"
   if(!length(grep("\\.txt$", tolower(model.file)))) {
     new.model.file <- paste(basename(model.file), ".txt", sep="")
     if(!is.null(working.directory)) new.model.file <- file.path(working.directory, new.model.file)
@@ -129,11 +135,18 @@
   } else {
     new.model.file <- model.file
   }
+
+  ## Create a filename model.file + .bug
+  model.file.bug<-gsub('\\.txt','.bug',basename(new.model.file))
+
+  if(restart && !file.exists(model.file.bug))stop("The .bug restart file was not found in the working directory")
+
   if(useWINE){
         ## Some tweaks for wine (particularly required for Mac OS)
         new.model.file <- gsub("//", "/", new.model.file)
   }
   bugs.script(parameters.to.save, n.chains, n.iter, n.burnin, n.thin,
+              saveExec,restart,model.file.bug,
               new.model.file, debug=debug, is.inits=!is.null(inits),
               DIC=DIC, useWINE=useWINE, newWINE=newWINE,
               WINEPATH=WINEPATH, bugs.seed=bugs.seed, 

Modified: trunk/R2OpenBUGS/R/bugs.script.R
===================================================================
--- trunk/R2OpenBUGS/R/bugs.script.R	2011-03-07 15:09:12 UTC (rev 180)
+++ trunk/R2OpenBUGS/R/bugs.script.R	2011-03-21 19:13:27 UTC (rev 181)
@@ -1,6 +1,7 @@
 "bugs.script" <-
   function(parameters.to.save, n.chains, n.iter, n.burnin,
-           n.thin, model.file, debug=FALSE, is.inits, 
+           n.thin, saveExec, restart, model.file.bug,
+           model.file, debug=FALSE, is.inits, 
            DIC=FALSE, useWINE=FALSE,
            newWINE=TRUE, WINEPATH=NULL, bugs.seed=NULL, summary.only=FALSE,
            save.history=(.Platform$OS.type == "windows" | useWINE==TRUE),
@@ -26,6 +27,9 @@
   coda  <- file.path(working.directory, "/")
   coda <- native2win(coda, useWINE=useWINE, newWINE=newWINE, WINEPATH=WINEPATH)
 
+  model.file.bug<-file.path(working.directory,model.file.bug)
+  model.file.bug<-native2win(model.file.bug, useWINE=useWINE, newWINE=newWINE, WINEPATH=WINEPATH)
+
   logFile <- file.path(working.directory, "log.odc")
   logFile <- native2win(logFile, useWINE=useWINE, newWINE=newWINE, WINEPATH=WINEPATH)
   logFileTxt <- file.path(working.directory, "log.txt")
@@ -51,30 +55,40 @@
 
   cat(
     if(.Platform$OS.type == "windows" | useWINE) "modelDisplay('log')\n",
-    "modelCheck('", model, "')\n",
-    "modelData('", data, "')\n",
-    "modelCompile(", n.chains, ")\n",
-    bugs.seed.cmd,
-    if(is.inits) initlist,
-    "modelGenInits()\n",
-    if(over.relax) 'over.relax("yes")\n',
+    if(restart)c("modelInternalize('", model.file.bug, "')\n"),
+    if(restart && n.burnin>0)c(
+       "samplesClear('*')\n",
+       "summaryClear('*')\n"
+       ),
+    if(!restart)c( 
+      "modelCheck('", model, "')\n",
+      "modelData('", data, "')\n",
+      "modelCompile(", n.chains, ")\n"
+      ),
+    if(!restart)bugs.seed.cmd,
+    if(!restart && is.inits) initlist,
+    if(!restart)"modelGenInits()\n",
+    if(!restart && over.relax) 'over.relax("yes")\n',
+    if((!restart) || (n.burnin>0))c(
     thinUpdate,
     savelist,
-    summarylist,
-    if(DIC) "dicSet()\n",
+    summarylist
+    ),
+    if(((!restart) || (n.burnin>0)) && DIC) "dicSet()\n",
     "modelUpdate(", formatC(n.iter-n.burnin, format='d'), ",", n.thin, 
                   ",",formatC(n.iter-n.burnin, format='d'),")\n", 
     "samplesCoda('*', '", coda, "')\n", 
     "summaryStats('*')\n",
     if(DIC) "dicStats()\n",
     if (save.history) "samplesHistory('*')\n", 
+    if(saveExec)c("modelExternalize('",model.file.bug,"')\n"),
     if(.Platform$OS.type == "windows" | useWINE) c("modelSaveLog('", logFile, "')\n",
     "modelSaveLog('", logFileTxt, "')\n"),
     file=script, sep="", append=FALSE)
 
-  if(!debug) cat("modelQuit('y')\n", file=script, append=TRUE)
+    if(!debug) cat("modelQuit('y')\n", file=script, append=TRUE)
 
-  sims.files <- paste(coda, "CODAchain", 1:n.chains, ".txt", sep="")
+  sims.files <- paste("CODAchain", 1:n.chains, ".txt", sep="")
   for(i in 1:n.chains)
     cat("OpenBUGS did not run correctly.\n", file=sims.files[i], append=FALSE)
 }

Modified: trunk/R2OpenBUGS/R/print.bugs.R
===================================================================
--- trunk/R2OpenBUGS/R/print.bugs.R	2011-03-07 15:09:12 UTC (rev 180)
+++ trunk/R2OpenBUGS/R/print.bugs.R	2011-03-21 19:13:27 UTC (rev 181)
@@ -7,10 +7,10 @@
         cat("Inference for Bugs model at \"", x$model.file, "\", ", sep="")
     if(!is.null(x$program))
         cat("fit using ", x$program, ",", sep="")
-    cat("\n ", x$n.chains, " chains, each with ", x$n.iter,
+    cat("\nCurrent: ", x$n.chains, " chains, each with ", x$n.iter,
         " iterations (first ", x$n.burnin, " discarded)", sep = "")
     if(x$n.thin > 1) cat(", n.thin =", x$n.thin)
-    cat("\n n.sims =", x$n.sims, "iterations saved\n")
+    cat("\nCumulative: n.sims =", x$n.sims, "iterations saved\n")
     print(round(x$summary, digits.summary), ...)
 
     if(x$n.chains > 1) {

Modified: trunk/R2OpenBUGS/inst/NEWS
===================================================================
--- trunk/R2OpenBUGS/inst/NEWS	2011-03-07 15:09:12 UTC (rev 180)
+++ trunk/R2OpenBUGS/inst/NEWS	2011-03-21 19:13:27 UTC (rev 181)
@@ -1,6 +1,15 @@
 Changes to R2OpenBUGS:
 ======================
 
+Update 3.2-1 
+- Added saveExec and restart options to the bugs function that uses
+  the OpenBUGS internalize/externalize feature to allow a user to
+  store the state of the OpenBUGS execution and continue
+  execution after checking results in R.
+
+Update 3.1-2.1 
+- Corrected bug in WINE execution
+
 Update 3.1-2 
 - Set default version of OpenBUGS to 3.1.2
 - Fixed upper/lower case error in read.bugs 

Modified: trunk/R2OpenBUGS/inst/validateInstallOpenBUGS/validOpenBUGSResults.R
===================================================================
--- trunk/R2OpenBUGS/inst/validateInstallOpenBUGS/validOpenBUGSResults.R	2011-03-07 15:09:12 UTC (rev 180)
+++ trunk/R2OpenBUGS/inst/validateInstallOpenBUGS/validOpenBUGSResults.R	2011-03-21 19:13:27 UTC (rev 181)
@@ -20,116 +20,111 @@
 53.13, 55.19025, 60.39, 59.36), .Dim = c(10L, 7L), .Dimnames = list(
     c("alpha", "beta", "rhat[1]", "rhat[2]", "rhat[3]", "rhat[4]", 
     "rhat[5]", "rhat[6]", "rhat[7]", "rhat[8]"), c("mean", "sd", 
-    "2.5%", "25%", "50%", "75%", "97.5%"))), structure(c(106.56037, 
-6.18615, 6.15259, 2.34291, 0.10596, 0.47872, 101.9, 5.977, 5.304, 
-105, 6.117, 5.817, 106.5, 6.187, 6.1185, 108.1, 6.255, 6.452, 
-111.1025, 6.397, 7.177), .Dim = c(3L, 7L), .Dimnames = list(c("mu.beta[1]", 
+    "2.5%", "25%", "50%", "75%", "97.5%"))), structure(c(106.56034, 
+6.18619, 6.15206, 2.34366, 0.10595, 0.47828, 101.9, 5.976, 5.30397, 
+105, 6.117, 5.818, 106.5, 6.187, 6.118, 108.1, 6.254, 6.451, 
+111.2, 6.397, 7.18002), .Dim = c(3L, 7L), .Dimnames = list(c("mu.beta[1]", 
 "mu.beta[2]", "sigma"), c("mean", "sd", "2.5%", "25%", "50%", 
-"75%", "97.5%"))), structure(c(3.2445, 0.02929, 0.02929, 3.20989, 
-0.0081, 0.85113, -0.00963, -0.00963, 0.86281, 2.1011, 2.50802, 
-2.50802, 2.13451, 0.65922, 0.50825, 0.71045, 0.71045, 0.50962, 
-1.14395, -4.77203, -4.77203, 1.101, -0.9073, 0.22139, -1.40502, 
--1.40502, 0.2234, 1.926, -1.638, -1.638, 1.917, -0.66862, 0.49587, 
--0.48102, -0.48102, 0.50065, 2.6875, 0.04017, 0.04017, 2.663, 
-0.01868, 0.7305, -0.00773, -0.00773, 0.74375, 3.89225, 1.715, 
-1.715, 3.82125, 0.68585, 1.07, 0.4545, 0.4545, 1.10125, 8.5671, 
-4.82202, 4.82202, 8.5781, 0.9098, 2.13205, 1.40205, 1.40205, 
-2.18202), .Dim = c(9L, 7L), .Dimnames = list(c("Sigma2[1,1]", 
-"Sigma2[1,2]", "Sigma2[2,1]", "Sigma2[2,2]", "rho", "tau[1,1]", 
-"tau[1,2]", "tau[2,1]", "tau[2,2]"), c("mean", "sd", "2.5%", 
-"25%", "50%", "75%", "97.5%"))), structure(c(1.85767, 2.64973, 
-0.96989, 0.86209, 0.09887, 0.26392, 0.07107, 0.07684, 0.03153, 
-0.0148, 1.323, 2.528, 0.8224, 0.7898, 0.07502, 1.701, 2.604, 
-0.9188, 0.8457, 0.08841, 1.854, 2.642, 0.9689, 0.8646, 0.09723, 
-2.026, 2.691, 1.018, 0.8836, 0.1074, 2.36802, 2.802, 1.122, 0.9144, 
-0.1326), .Dim = c(5L, 7L), .Dimnames = list(c("U3", "alpha", 
-"beta", "gamma", "sigma"), c("mean", "sd", "2.5%", "25%", "50%", 
-"75%", "97.5%"))), structure(c(2399.81116, 2970.23731, 1526.76347, 
-9152.71052, 1072.50035, 22.42927, 0.01173, 1559, 1483, 573.04999, 
-2217, 1515, 1388.49991, 2748, 1526, 2769.24997, 3466, 1539, 10140.49952, 
-5596.37451, 1570), .Dim = c(3L, 7L), .Dimnames = list(c("sigma2.btw", 
-"sigma2.with", "theta"), c("mean", "sd", "2.5%", "25%", "50%", 
-"75%", "97.5%"))), structure(c(0.99767, 1.43476, -0.00865, -0.1804, 
-0.11034, 0.1406, 0.99274, 0.04825, 0.0552, 0.05217, 0.05175, 
-0.03333, 0.05436, 0.05185, 1, 1.327, -0.113, -0.2831, 0.06521, 
-0.04439, 0.8931, 1, 1.4, -0.04039, -0.2121, 0.08657, 0.1057, 
-0.9604, 1, 1.435, -0.00813, -0.1808, 0.1033, 0.1356, 0.9919, 
-1, 1.469, 0.02322, -0.1495, 0.12722, 0.169, 1.023, 1, 1.544, 
-0.0942, -0.07637, 0.1929, 0.2663, 1.099), .Dim = c(7L, 7L), .Dimnames = list(
-    c("equiv", "mu", "phi", "pi", "sigma1", "sigma2", "theta"
-    ), c("mean", "sd", "2.5%", "25%", "50%", "75%", "97.5%"))), 
-    structure(c(0.6029, 0.3971, 536.75923, 548.90934, 3.75937, 
-    0.08421, 0.08421, 0.92221, 1.21365, 0.6111, 0.4326, 0.2359, 
-    535.1, 546.5, 2.917, 0.54737, 0.34, 536.2, 548.2, 3.36175, 
-    0.6039, 0.3961, 536.7, 548.9, 3.654, 0.66, 0.45262, 537.3, 
-    549.7, 4.019, 0.7641, 0.5674, 538.6, 551.2, 5.27107), .Dim = c(5L, 
-    7L), .Dimnames = list(c("P[1]", "P[2]", "lambda[1]", "lambda[2]", 
-    "sigma"), c("mean", "sd", "2.5%", "25%", "50%", "75%", "97.5%"
-    ))), structure(c(2.99564, 0.79689, 1.02513, 0.56926, 0.39621, 
-    0.72729, 1.914, 0.04475, 0.4099, 2.743, 0.6218, 0.625, 2.997, 
-    0.7995, 0.82675, 3.255, 0.9782, 1.16825, 4.08502, 1.541, 
-    2.82), .Dim = c(3L, 7L), .Dimnames = list(c("alpha", "beta", 
-    "sigma"), c("mean", "sd", "2.5%", "25%", "50%", "75%", "97.5%"
-    ))), structure(c(5.26374, 2.19866, -5.88024, 0.25869, 0.27042, 
-    0.2265, 7.82296, 0.1335, 0.16648, 0.14127, 0.11614, 0.137, 
-    0.1076, 1.18539, 4.996, 1.87997, -6.165, 0.1277, 0.1201, 
-    0.1085, 5.90897, 5.187, 2.094, -5.964, 0.1849, 0.1843, 0.1586, 
-    6.984, 5.264, 2.197, -5.879, 0.2318, 0.24, 0.2008, 7.684, 
-    5.342, 2.3, -5.795, 0.2995, 0.3184, 0.26312, 8.521, 5.529, 
-    2.535, -5.603, 0.54651, 0.6038, 0.495, 10.5), .Dim = c(7L, 
-    7L), .Dimnames = list(c("mu[1]", "mu[2]", "mu[3]", "sigma[1]", 
-    "sigma[2]", "sigma[3]", "sigmaC"), c("mean", "sd", "2.5%", 
-    "25%", "50%", "75%", "97.5%"))), structure(c(106.61227, 6.18568, 
-    6.0953, 3.63673, 0.1075, 0.46858, 99.40975, 5.97597, 5.27197, 
-    104.2, 6.114, 5.776, 106.6, 6.187, 6.058, 109.1, 6.258, 6.386, 
-    113.6, 6.394, 7.106), .Dim = c(3L, 7L), .Dimnames = list(
-        c("alpha0", "beta.c", "sigma"), c("mean", "sd", "2.5%", 
-        "25%", "50%", "75%", "97.5%"))), structure(c(0.71462, 
-    1.2978, -0.15277, -39.85965, 0.0106, 0.05567, 0.3192, 0.0106, 
-    0.05567, 0.3192, 0.0106, 0.05567, 0.3192, 3.38943, 0.14307, 
-    0.38863, 0.16594, 12.71407, 0.10241, 0.22928, 0.46618, 0.10241, 
-    0.22928, 0.46618, 0.10241, 0.22928, 0.46618, 0.62795, 0.43279, 
-    0.529, -0.4842, -65.22025, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2.417, 
-    0.62217, 1.049, -0.26012, -48.11, 0, 0, 0, 0, 0, 0, 0, 0, 
-    0, 2.945, 0.7155, 1.294, -0.15245, -39.96, 0, 0, 0, 0, 0, 
-    0, 0, 0, 0, 3.299, 0.8063, 1.545, -0.04546, -31.5775, 0, 
-    0, 1, 0, 0, 1, 0, 0, 1, 3.742, 0.9984, 2.076, 0.1763, -14.38925, 
-    0, 1, 1, 0, 1, 1, 0, 1, 1, 4.84702), .Dim = c(14L, 7L), .Dimnames = list(
-        c("b[1]", "b[2]", "b[3]", "b0", "outlier[3]", "outlier[4]", 
-        "outlier[21]", "outlier[3]", "outlier[4]", "outlier[21]", 
-        "outlier[3]", "outlier[4]", "outlier[21]", "sigma"), 
-        c("mean", "sd", "2.5%", "25%", "50%", "75%", "97.5%"))), 
-    structure(c(0.02054, 0.12633, 0.07461, 0.05794, 0.04233, 
-    0.07062, 0.06659, 0.14758, 0.07197, 0.09058, 0.11631, 0.06903, 
-    0.01981, 0.0272, 0.02389, 0.00813, 0.01381, 0.01821, 0.02022, 
-    0.02414, 0.01787, 0.02864, 0.01984, 0.01339, 0.00053, 0.07787, 
-    0.03467, 0.04313, 0.01952, 0.03927, 0.03268, 0.1034, 0.04114, 
-    0.0432, 0.08016, 0.04533, 0.00614, 0.107, 0.0575, 0.05223, 
-    0.03235, 0.05768, 0.05224, 0.1307, 0.05927, 0.06978, 0.1024, 
-    0.05962, 0.01446, 0.1246, 0.07216, 0.0576, 0.04099, 0.06919, 
-    0.06439, 0.1463, 0.07056, 0.08795, 0.1156, 0.06826, 0.02884, 
-    0.1438, 0.08924, 0.06318, 0.05081, 0.08204, 0.07907, 0.1635, 
-    0.08303, 0.1081, 0.1293, 0.07747, 0.07305, 0.1833, 0.1272, 
-    0.07477, 0.073, 0.1104, 0.1108, 0.1976, 0.1112, 0.1544, 0.1578, 
-    0.09787), .Dim = c(12L, 7L), .Dimnames = list(c("p[1]", "p[2]", 
-    "p[3]", "p[4]", "p[5]", "p[6]", "p[7]", "p[8]", "p[9]", "p[10]", 
-    "p[11]", "p[12]"), c("mean", "sd", "2.5%", "25%", "50%", 
-    "75%", "97.5%"))), structure(c(0.05312, 0.10302, 0.07048, 
-    0.05924, 0.05155, 0.06905, 0.06683, 0.12337, 0.07011, 0.07828, 
-    0.10214, 0.06848, 0.07268, 0.40333, 0.01954, 0.02166, 0.01741, 
-    0.00786, 0.01312, 0.01486, 0.01593, 0.02261, 0.01464, 0.01993, 
-    0.01758, 0.01165, 0.0101, 0.1541, 0.01824, 0.06663, 0.03985, 
-    0.04467, 0.02805, 0.04259, 0.03845, 0.08327, 0.04392, 0.04419, 
-    0.07166, 0.04744, 0.05319, 0.1655, 0.03923, 0.08746, 0.05844, 
-    0.05381, 0.04215, 0.0587, 0.05584, 0.1072, 0.06004, 0.06443, 
-    0.08969, 0.06035, 0.06617, 0.2989, 0.05219, 0.101, 0.06913, 
-    0.05897, 0.05093, 0.0683, 0.06577, 0.1217, 0.06922, 0.07633, 
-    0.1009, 0.06796, 0.07253, 0.3818, 0.0656, 0.1163, 0.08104, 
-    0.06431, 0.06019, 0.07812, 0.07685, 0.1379, 0.07919, 0.08994, 
-    0.1132, 0.07595, 0.07898, 0.48342, 0.09467, 0.1511, 0.1088, 
-    0.07536, 0.07873, 0.101, 0.1011, 0.1716, 0.1015, 0.1226, 
-    0.1401, 0.09301, 0.09334, 0.76511), .Dim = c(14L, 7L), .Dimnames = list(
-        c("p[1]", "p[2]", "p[3]", "p[4]", "p[5]", "p[6]", "p[7]", 
-        "p[8]", "p[9]", "p[10]", "p[11]", "p[12]", "pop.mean", 
-        "sigma"), c("mean", "sd", "2.5%", "25%", "50%", "75%", 
-        "97.5%"))))
+"75%", "97.5%"))), structure(c(3.199, 0.11791, 0.11791, 3.22327, 
+0.03519, 0.84975, -0.03162, -0.03162, 0.84991, 2.0602, 2.46612, 
+2.46612, 2.13682, 0.65527, 0.50303, 0.69675, 0.69675, 0.50508, 
+1.13, -4.57602, -4.57602, 1.11997, -0.9017, 0.22159, -1.38405, 
+-1.38405, 0.2153, 1.93675, -1.571, -1.571, 1.921, -0.65055, 0.4941, 
+-0.49565, -0.49565, 0.4931, 2.663, 0.23045, 0.23045, 2.662, 0.10835, 
+0.7321, -0.04676, -0.04676, 0.73415, 3.804, 1.777, 1.777, 3.848, 
+0.6978, 1.08225, 0.4324, 0.4324, 1.079, 8.43205, 4.69405, 4.69405, 
+8.66835, 0.9054, 2.13005, 1.346, 1.346, 2.16), .Dim = c(9L, 7L
+), .Dimnames = list(c("Sigma2[1,1]", "Sigma2[1,2]", "Sigma2[2,1]", 
+"Sigma2[2,2]", "rho", "tau[1,1]", "tau[1,2]", "tau[2,1]", "tau[2,2]"
+), c("mean", "sd", "2.5%", "25%", "50%", "75%", "97.5%"))), structure(c(1.85767, 
+2.64973, 0.96989, 0.86209, 0.09887, 0.26392, 0.07107, 0.07684, 
+0.03153, 0.0148, 1.323, 2.528, 0.8224, 0.7898, 0.07502, 1.701, 
+2.604, 0.9188, 0.8457, 0.08841, 1.854, 2.642, 0.9689, 0.8646, 
+0.09723, 2.026, 2.691, 1.018, 0.8836, 0.1074, 2.36802, 2.802, 
+1.122, 0.9144, 0.1326), .Dim = c(5L, 7L), .Dimnames = list(c("U3", 
+"alpha", "beta", "gamma", "sigma"), c("mean", "sd", "2.5%", "25%", 
+"50%", "75%", "97.5%"))), structure(c(2399.81116, 2970.23731, 
+1526.76347, 9152.71052, 1072.50035, 22.42927, 0.01173, 1559, 
+1483, 573.04999, 2217, 1515, 1388.49991, 2748, 1526, 2769.24997, 
+3466, 1539, 10140.49952, 5596.37451, 1570), .Dim = c(3L, 7L), .Dimnames = list(
+    c("sigma2.btw", "sigma2.with", "theta"), c("mean", "sd", 
+    "2.5%", "25%", "50%", "75%", "97.5%"))), structure(c(0.99767, 
+1.43476, -0.00865, -0.1804, 0.11034, 0.1406, 0.99274, 0.04825, 
+0.0552, 0.05217, 0.05175, 0.03333, 0.05436, 0.05185, 1, 1.327, 
+-0.113, -0.2831, 0.06521, 0.04439, 0.8931, 1, 1.4, -0.04039, 
+-0.2121, 0.08657, 0.1057, 0.9604, 1, 1.435, -0.00813, -0.1808, 
+0.1033, 0.1356, 0.9919, 1, 1.469, 0.02322, -0.1495, 0.12722, 
+0.169, 1.023, 1, 1.544, 0.0942, -0.07637, 0.1929, 0.2663, 1.099
+), .Dim = c(7L, 7L), .Dimnames = list(c("equiv", "mu", "phi", 
+"pi", "sigma1", "sigma2", "theta"), c("mean", "sd", "2.5%", "25%", 
+"50%", "75%", "97.5%"))), structure(c(0.6029, 0.3971, 536.75923, 
+548.90934, 3.75937, 0.08421, 0.08421, 0.92221, 1.21365, 0.6111, 
+0.4326, 0.2359, 535.1, 546.5, 2.917, 0.54737, 0.34, 536.2, 548.2, 
+3.36175, 0.6039, 0.3961, 536.7, 548.9, 3.654, 0.66, 0.45262, 
+537.3, 549.7, 4.019, 0.7641, 0.5674, 538.6, 551.2, 5.27107), .Dim = c(5L, 
+7L), .Dimnames = list(c("P[1]", "P[2]", "lambda[1]", "lambda[2]", 
+"sigma"), c("mean", "sd", "2.5%", "25%", "50%", "75%", "97.5%"
+))), structure(c(2.99564, 0.79689, 1.02513, 0.56926, 0.39621, 
+0.72729, 1.914, 0.04475, 0.4099, 2.743, 0.6218, 0.625, 2.997, 
+0.7995, 0.82675, 3.255, 0.9782, 1.16825, 4.08502, 1.541, 2.82
+), .Dim = c(3L, 7L), .Dimnames = list(c("alpha", "beta", "sigma"
+), c("mean", "sd", "2.5%", "25%", "50%", "75%", "97.5%"))), structure(c(5.26188, 
+2.19814, -5.8793, 0.25999, 0.26441, 0.22576, 7.8008, 0.13613, 
+0.16157, 0.14278, 0.11727, 0.12765, 0.10712, 1.17804, 4.991, 
+1.883, -6.17302, 0.1279, 0.11789, 0.1088, 5.88897, 5.185, 2.09675, 
+-5.964, 0.1859, 0.18, 0.1573, 6.964, 5.263, 2.195, -5.877, 0.2326, 
+0.2333, 0.1999, 7.6745, 5.34, 2.296, -5.79, 0.30132, 0.3123, 
+0.263, 8.483, 5.527, 2.525, -5.61, 0.55141, 0.59261, 0.492, 10.46
+), .Dim = c(7L, 7L), .Dimnames = list(c("mu[1]", "mu[2]", "mu[3]", 
+"sigma[1]", "sigma[2]", "sigma[3]", "sigmaC"), c("mean", "sd", 
+"2.5%", "25%", "50%", "75%", "97.5%"))), structure(c(106.61227, 
+6.18568, 6.0953, 3.63673, 0.1075, 0.46858, 99.40975, 5.97597, 
+5.27197, 104.2, 6.114, 5.776, 106.6, 6.187, 6.058, 109.1, 6.258, 
+6.386, 113.6, 6.394, 7.106), .Dim = c(3L, 7L), .Dimnames = list(
+    c("alpha0", "beta.c", "sigma"), c("mean", "sd", "2.5%", "25%", 
+    "50%", "75%", "97.5%"))), structure(c(0.71462, 1.2978, -0.15277, 
+-39.85965, 0.0106, 0.05567, 0.3192, 0.0106, 0.05567, 0.3192, 
+0.0106, 0.05567, 0.3192, 3.38943, 0.14307, 0.38863, 0.16594, 
+12.71407, 0.10241, 0.22928, 0.46618, 0.10241, 0.22928, 0.46618, 
+0.10241, 0.22928, 0.46618, 0.62795, 0.43279, 0.529, -0.4842, 
+-65.22025, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2.417, 0.62217, 1.049, 
+-0.26012, -48.11, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2.945, 0.7155, 1.294, 
+-0.15245, -39.96, 0, 0, 0, 0, 0, 0, 0, 0, 0, 3.299, 0.8063, 1.545, 
+-0.04546, -31.5775, 0, 0, 1, 0, 0, 1, 0, 0, 1, 3.742, 0.9984, 
+2.076, 0.1763, -14.38925, 0, 1, 1, 0, 1, 1, 0, 1, 1, 4.84702), .Dim = c(14L, 
+7L), .Dimnames = list(c("b[1]", "b[2]", "b[3]", "b0", "outlier[3]", 
+"outlier[4]", "outlier[21]", "outlier[3]", "outlier[4]", "outlier[21]", 
+"outlier[3]", "outlier[4]", "outlier[21]", "sigma"), c("mean", 
+"sd", "2.5%", "25%", "50%", "75%", "97.5%"))), structure(c(0.02054, 
+0.12633, 0.07461, 0.05794, 0.04233, 0.07062, 0.06659, 0.14758, 
+0.07197, 0.09058, 0.11631, 0.06903, 0.01981, 0.0272, 0.02389, 
+0.00813, 0.01381, 0.01821, 0.02022, 0.02414, 0.01787, 0.02864, 
+0.01984, 0.01339, 0.00053, 0.07787, 0.03467, 0.04313, 0.01952, 
+0.03927, 0.03268, 0.1034, 0.04114, 0.0432, 0.08016, 0.04533, 
+0.00614, 0.107, 0.0575, 0.05223, 0.03235, 0.05768, 0.05224, 0.1307, 
+0.05927, 0.06978, 0.1024, 0.05962, 0.01446, 0.1246, 0.07216, 
+0.0576, 0.04099, 0.06919, 0.06439, 0.1463, 0.07056, 0.08795, 
+0.1156, 0.06826, 0.02884, 0.1438, 0.08924, 0.06318, 0.05081, 
+0.08204, 0.07907, 0.1635, 0.08303, 0.1081, 0.1293, 0.07747, 0.07305, 
+0.1833, 0.1272, 0.07477, 0.073, 0.1104, 0.1108, 0.1976, 0.1112, 
+0.1544, 0.1578, 0.09787), .Dim = c(12L, 7L), .Dimnames = list(
+    c("p[1]", "p[2]", "p[3]", "p[4]", "p[5]", "p[6]", "p[7]", 
+    "p[8]", "p[9]", "p[10]", "p[11]", "p[12]"), c("mean", "sd", 
+    "2.5%", "25%", "50%", "75%", "97.5%"))), structure(c(0.05312, 
+0.10302, 0.07048, 0.05924, 0.05155, 0.06905, 0.06683, 0.12337, 
+0.07011, 0.07828, 0.10214, 0.06848, 0.07268, 0.40333, 0.01954, 
+0.02166, 0.01741, 0.00786, 0.01312, 0.01486, 0.01593, 0.02261, 
+0.01464, 0.01993, 0.01758, 0.01165, 0.0101, 0.1541, 0.01824, 
+0.06663, 0.03985, 0.04467, 0.02805, 0.04259, 0.03845, 0.08327, 
+0.04392, 0.04419, 0.07166, 0.04744, 0.05319, 0.1655, 0.03923, 
+0.08746, 0.05844, 0.05381, 0.04215, 0.0587, 0.05584, 0.1072, 
+0.06004, 0.06443, 0.08969, 0.06035, 0.06617, 0.2989, 0.05219, 
+0.101, 0.06913, 0.05897, 0.05093, 0.0683, 0.06577, 0.1217, 0.06922, 
+0.07633, 0.1009, 0.06796, 0.07253, 0.3818, 0.0656, 0.1163, 0.08104, 
+0.06431, 0.06019, 0.07812, 0.07685, 0.1379, 0.07919, 0.08994, 
+0.1132, 0.07595, 0.07898, 0.48342, 0.09467, 0.1511, 0.1088, 0.07536, 
+0.07873, 0.101, 0.1011, 0.1716, 0.1015, 0.1226, 0.1401, 0.09301, 
+0.09334, 0.76511), .Dim = c(14L, 7L), .Dimnames = list(c("p[1]", 
+"p[2]", "p[3]", "p[4]", "p[5]", "p[6]", "p[7]", "p[8]", "p[9]", 
+"p[10]", "p[11]", "p[12]", "pop.mean", "sigma"), c("mean", "sd", 
+"2.5%", "25%", "50%", "75%", "97.5%"))))

Modified: trunk/R2OpenBUGS/man/bugs.Rd
===================================================================
--- trunk/R2OpenBUGS/man/bugs.Rd	2011-03-07 15:09:12 UTC (rev 180)
+++ trunk/R2OpenBUGS/man/bugs.Rd	2011-03-21 19:13:27 UTC (rev 181)
@@ -7,13 +7,14 @@
   saves the simulations for easy access in \R or S-PLUS.}
 
 \usage{
-bugs(data, inits, parameters.to.save, n.iter, model.file="model.bug",
+bugs(data, inits, parameters.to.save, n.iter, model.file="model.txt",
     n.chains=3, n.burnin=floor(n.iter / 2), n.thin=1, 
+    saveExec=FALSE,restart=FALSE,
     debug=FALSE, DIC=TRUE, digits=5, codaPkg=FALSE,
     OpenBUGS.pgm=ifelse(.Platform$OS.type == "windows" | useWINE==TRUE,
       paste("C:/Program Files/OpenBUGS/OpenBUGS",
       version,"/OpenBUGS.exe",sep=""),"OpenBUGS"), 
-    version='312',
+    version='321',
     working.directory=NULL,
     clearWD=FALSE, useWINE=FALSE, WINE=NULL,
     newWINE=TRUE, WINEPATH=NULL, bugs.seed=1, summary.only=FALSE,
@@ -37,12 +38,12 @@
     e.g. by the function \code{\link{bugs.inits}}.}
   \item{parameters.to.save}{character vector of the names of the
     parameters to save which should be monitored}
-  \item{model.file}{file containing the model written in \pkg{OpenBUGS} code.
-    The extension can be either \file{.bug} or \file{.txt}.
-    If the extension is \file{.bug} and \code{program=="OpenBUGS"},
-    a copy of the file with extension \file{.txt} will be created
-    in the \code{bugs()} call and removed afterwards. Note that
-    similarly named \file{.txt} files will be overwritten.
+  \item{model.file}{File containing the model written in \pkg{OpenBUGS} code.
+    The extension must be \file{.txt}.
+    The old convention allowing model.file to be named \file{.bug} has been eliminated
+    because the new \pkg{OpenBUGS} feature that allows the program image
+    to be saved and later restarted uses the .bug extension for the saved
+    images.  
     Alternatively, \code{model.file} can be an R function that contains a BUGS model that is written to a 
     temporary model file (see \code{\link{tempfile}}) using \code{\link{write.model}}.}
   \item{n.chains}{number of Markov chains (default: 3)}
@@ -57,6 +58,22 @@
     \code{n.iter}.  Setting \code{n.thin}=2, doubles the number of iterations OpenBUGS 
     performs, but does not change \code{n.iter} or \code{n.burnin}.  Thinning implemented
     in this manner is not captured in summaries created by packages such as \pkg{coda}.}
+  \item{saveExec}{If TRUE, a re-startable image of the OpenBUGS execution is
+  saved with \code{basename(model.file)} and extension .bug in the working
+  directory, which must be specified.  The .bug files can be large, so 
+  users should monitor them carefully and remove them when not needed.
+}
+  \item{restart}{If TRUE, execution resumes with the final status from
+  the previous execution stored in the .bug file in the working directory.
+  If \code{n.burnin=0},additional iterations are performed and all iterations since
+  the previous burnin are used (including those from past executions).  If
+ \code{n.burnin>0}, a new burnin is performed, and the previous iterations are 
+  discarded, but execution continues from the status at the end of the previous
+  execution.  When \code{restart=TRUE}, only \code{n.burnin}, \code{n.iter}, 
+  and \code{saveExec} inputs 
+  should be changed from the call creating the .bug file, otherwise 
+  failed or erratic results may be produced.  Note the default has \code{n.burnin>0}.
+}
   \item{debug}{if \code{FALSE} (default), \pkg{OpenBUGS} is closed automatically
     when the script has finished running, otherwise \pkg{OpenBUGS} remains open
     for further investigation.  The debug option is not available for linux execution.}

Modified: trunk/R2OpenBUGS/man/bugs.script.Rd
===================================================================
--- trunk/R2OpenBUGS/man/bugs.script.Rd	2011-03-07 15:09:12 UTC (rev 180)
+++ trunk/R2OpenBUGS/man/bugs.script.Rd	2011-03-21 19:13:27 UTC (rev 181)
@@ -8,7 +8,8 @@
 
 \usage{
 bugs.script(parameters.to.save, n.chains, n.iter, n.burnin,
-           n.thin, model.file, debug=FALSE, is.inits, 
+           n.thin, saveExec, restart, model.file.bug,
+           model.file, debug=FALSE, is.inits, 
            DIC=FALSE, useWINE=FALSE,
            newWINE=TRUE, WINEPATH=NULL, bugs.seed=NULL, summary.only=FALSE,
            save.history=(.Platform$OS.type == "windows" | useWINE==TRUE),
@@ -21,6 +22,26 @@
   \item{n.iter}{number of total iterations (including burn in)}
   \item{n.burnin}{length of burn in}
   \item{n.thin}{thinning parameter}
+  \item{saveExec}{If TRUE, a re-startable image of the OpenBUGS execution is
+  saved with \code{basename(model.file)} and extension .bug in the working
+  directory, which must be specified.  The .bug files can be large, so 
+  users should monitor them carefully and remove them when not needed.
+}
+  \item{restart}{If TRUE, execution resumes with the final status from
+  the previous execution stored in the .bug file in the working directory.
+  If \code{n.burnin=0},additional iterations are performed and all iterations since
+  the previous burnin are used (including those from past executions).  If
+  \code{n.burnin>0}, a new burnin is performed, and the previous iterations are 
+  discarded, but execution continues from the status at the end of the previous
+  execution.  When \code{restart=TRUE}, only \code{n.burnin}, \code{n.iter}, 
+  and \code{saveExec} inputs 
+  should be changed from the call creating the .bug file, otherwise 
+  failed or erratic results may be produced.
+}
+  \item{model.file.bug}{If saveExec or restart is TRUE, then \code{model.file.bug}
+  receives/contains the OpenBUGS program image for restarting the program.  
+  \code{model.file.bug} is the name of the file with its full path
+  }
   \item{model.file}{file containing the model written in \pkg{OpenBUGS} code}
   \item{debug}{if \code{FALSE}, \pkg{OpenBUGS} is closed automatically,
     otherwise \pkg{OpenBUGS} remains open for further investigation. With 


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