Using OpenBUGS with R - Revision history

Ppomorsk at 03:08, 2 November 2017

2017-11-02T03:08:32Z

Ppomorsk: /* Installation of OpenBUGS */

2017-11-02T03:06:32Z

‎Installation of OpenBUGS

Ppomorsk: instructions for graham

2017-11-02T03:00:52Z

instructions for graham

Ppomorsk at 02:44, 2 November 2017

2017-11-02T02:44:55Z

Ppomorsk: graham

2017-11-02T02:44:43Z

graham

Ppomorsk: {{GrahamUpdate}}

2017-08-31T16:03:28Z

Edward at 15:55, 11 January 2016

2016-01-11T15:55:14Z

Edward at 14:01, 7 January 2016

2016-01-07T14:01:50Z

Bge: /* Using OpenBUGS in R */

2014-12-11T16:55:03Z

‎Using OpenBUGS in R

Bge: /* Using OpenBUGS in R */

2014-12-11T15:52:29Z

‎Using OpenBUGS in R

← Older revision		Revision as of 03:08, 2 November 2017
Line 29:		Line 29:
	install.packages("R2OpenBUGS")		install.packages("R2OpenBUGS")

		+	To make it able to find OpenBUGS at runtime, you need to set the variable that point it to the location where the binary is installed.
		+
		+	export OpenBUGS_PATH=$HOME/bin/OpenBUGS

@@ Line 9: / Line 9: @@
   make
   make install
 ==Installation of R2OpenBUGS==

@@ Line 1: / Line 1: @@
 =Instructions for usage on new Compute Canada clusters (cedar and graham)=
-==Installation==
+==Installation of OpenBUGS==
 First, load the R module.  You can find out which are available by running:

← Older revision		Revision as of 02:44, 2 November 2017
Line 1:		Line 1:
−	~~{{GrahamUpdate}}~~
	=Instructions for usage on new Compute Canada clusters (cedar and graham)=		=Instructions for usage on new Compute Canada clusters (cedar and graham)=

← Older revision		Revision as of 02:44, 2 November 2017
Line 1:		Line 1:
	{{GrahamUpdate}}		{{GrahamUpdate}}
		+	=Instructions for usage on new Compute Canada clusters (cedar and graham)=
		+
		+	==Installation==
		+	First, load the R module. You can find out which are available by running:
		+
		+	module spider r
		+
		+	In this case we choose the latest (as of November, 2017):
		+
		+	module load r/3.4.0
		+
		+	Then start R:
		+
		+	R
		+
		+	and inside it run:
		+
		+	install.packages("R2OpenBUGS")
		+
		+
		+
		+
		+	=Instructions for usage on older SHARCNET clusters (eg. orca)=
		+
	==Obtaining OpenBUGS==		==Obtaining OpenBUGS==

← Older revision		Revision as of 16:03, 31 August 2017
Line 1:		Line 1:
		+	{{GrahamUpdate}}
	==Obtaining OpenBUGS==		==Obtaining OpenBUGS==

← Older revision		Revision as of 15:55, 11 January 2016
Line 1:		Line 1:
−	~~{{Ancient\|27398}}~~
−
	==Obtaining OpenBUGS==		==Obtaining OpenBUGS==

← Older revision		Revision as of 14:01, 7 January 2016
Line 1:		Line 1:
		+	{{Ancient\|27398}}
		+
	==Obtaining OpenBUGS==		==Obtaining OpenBUGS==

@@ Line 60: / Line 60: @@
 ==Using OpenBUGS in R==
-The R2OpenBUGS is an interface to OpenBUGS. In order to user OpenBUGS, you need to tell where OpenBUGS resides. According to the help info, as you would get from R command
+The R2OpenBUGS is an interface to OpenBUGS. In order to use OpenBUGS in R, you need to tell where OpenBUGS resides. According to the help info, as you would get from R command
   >library(R2OpenBUGS)
@@ Line 66: / Line 66: @@
   >help(bugs)
-there are two ways of telling '''bugs()''' where OpenBUGS is. First you may specify the path to OpenBUGS in the call to bugs() in your R code, e.g.
+there are two ways of telling '''bugs()''' where OpenBUGS is. First you may specify the path to OpenBUGS in the call to bugs() in your R code. Assume that OpenBUGS executable is installed in /home/you/bin (you need to change it to where you have put the binary OpenBUGS), the call to bugs() would like something like this
   >schools.sim <- bugs(data, inits, parameters, OpenBUGS.pgm="/home/you/bin/OpenBUGS", model.file="/home/youschools.txt", n.chains = 3, n.iter = 1000, working.directory = NULL)
-Note, this line has the paths to the OpenBUGS and the model file specific to the system you are using. To make your R code portable, you may simply set environment variable at the command line or put the following line in '''.bash_profile''' in your home directory.
+Note, this line has the paths to the OpenBUGS and the model file specific to the system you are using. To make your R code portable, you may simply set environment variable at the command line or put the following line in '''.bash_profile''' in your home directory
   export OpenBUGS_PATH=$HOME/bin/OpenBUGS
@@ Line 78: / Line 78: @@
   >schools.sim <- bugs(data, inits, parameters, model.file="schools.txt", n.chains = 3, n.iter = 1000, working.directory = ".")
-In the example above, it is assumed that OpenBUGS executable is installed in /home/you/bin. You need to change it to where you have put the binary OpenBUGS
+When working.directory is where the input and output are stored. By default, it is set to NULL and the location is unexpected from one system to another.

@@ Line 68: / Line 68: @@
 there are two ways of telling '''bugs()''' where OpenBUGS is. First you may specify the path to OpenBUGS in the call to bugs() in your R code, e.g.
-  >schools.sim <- bugs(data, inits, parameters, OpenBUGS.pgm="/home/you/bin/OpenBUGS", model.file="/home/bge/schools.txt", n.chains = 3, n.iter = 1000, working.directory = NULL)
+  >schools.sim <- bugs(data, inits, parameters, OpenBUGS.pgm="/home/you/bin/OpenBUGS", model.file="/home/youschools.txt", n.chains = 3, n.iter = 1000, working.directory = NULL)
-Or, you may simply set environment variable at the command line or put the following line in '''.bash_profile''' in your home directory.
+Note, this line has the paths to the OpenBUGS and the model file specific to the system you are using. To make your R code portable, you may simply set environment variable at the command line or put the following line in '''.bash_profile''' in your home directory.
   export OpenBUGS_PATH=$HOME/bin/OpenBUGS
-In both cases above, it is assumed that OpenBUGS executable is installed in /home/you/bin.
+and also, set the working directory to the current folder (the last argument) as follows