Add jags, Just Another Gibbs Sampler. A program for Bayesian analysis of

graphical models via Gibbs sampling, not wholy unlike classic BUGS.

PR:		ports/66648
Submitted by:	Eric van Gyzen <vangyzen@stat.duke.edu>

5 files changed, 440 insertions, 0 deletions

diff --git a/math/jags/Makefile b/math/jags/Makefile
new file mode 100644
index 000000000000..7d51506eae31
--- /dev/null
+++ b/math/jags/Makefile
@@ -0,0 +1,48 @@
+# Ports collection Makefile for:	jags
+# Date created:				21 April 2004
+# Whom:					Eric van Gyzen <vangyzen@stat.duke.edu>
+#
+# $FreeBSD$
+#
+
+PORTNAME=	jags
+PORTVERSION=	0.50
+CATEGORIES=	math
+MASTER_SITES=	http://www-fis.iarc.fr/~martyn/software/jags/
+DISTNAME=	${PORTNAME:U}-${PORTVERSION}
+.if !defined(NOPORTDOCS)
+DISTFILES=	${DISTNAME}${EXTRACT_SUFX} bugs-examples.tar.gz manual.pdf
+EXTRACT_ONLY=	${DISTNAME}${EXTRACT_SUFX}
+.endif
+
+MAINTAINER=	vangyzen@stat.duke.edu
+COMMENT=	Just Another Gibbs Sampler
+
+LIB_DEPENDS=	Rmath.0:${PORTSDIR}/math/libRmath
+
+.if defined(WITH_ATLAS)
+LIB_DEPENDS+=	f77blas.1:${PORTSDIR}/math/atlas
+CONFIGURE_ARGS=	--with-lapack=-lalapack --with-blas=-lf77blas
+.else
+LIB_DEPENDS+=	lapack.3:${PORTSDIR}/math/lapack
+CONFIGURE_ARGS=	--with-lapack=-llapack --with-blas=-lblas
+.endif
+
+USE_BISON=	yes
+
+DIST_SUBDIR=	${PORTNAME}
+
+GNU_CONFIGURE=	yes
+CONFIGURE_ENV=	CPPFLAGS=-I${PREFIX}/include LDFLAGS=-L${PREFIX}/lib
+
+post-install:
+.if !defined(NOPORTDOCS)
+	${MKDIR} ${DOCSDIR}
+	${INSTALL_DATA} ${DISTDIR}/${DIST_SUBDIR}/manual.pdf ${DOCSDIR}
+	${MKDIR} ${EXAMPLESDIR}
+	( cd ${EXAMPLESDIR}; \
+	  ${PAX} -rzf ${DISTDIR}/${DIST_SUBDIR}/bugs-examples.tar.gz \
+	    -s ':^bugs-examples/*::' )
+.endif
+
+.include <bsd.port.mk>
diff --git a/math/jags/distinfo b/math/jags/distinfo
new file mode 100644
index 000000000000..0c0bfa5d7136
--- /dev/null
+++ b/math/jags/distinfo
@@ -0,0 +1,6 @@
+MD5 (jags/JAGS-0.50.tar.gz) = 13a068aa43b84f812e476129fbdb03db
+MD5 (jags/bugs-examples.tar.gz) = c5baddf2f29bab79f8a6c7d0b3873727
+MD5 (jags/manual.pdf) = 8cc1b0371872472ea9bd496bfdbd49f4
+SIZE (jags/JAGS-0.50.tar.gz) = 481609
+SIZE (jags/bugs-examples.tar.gz) = 72373
+SIZE (jags/manual.pdf) = 130157
diff --git a/math/jags/files/patch-src-terminal-parser.yy b/math/jags/files/patch-src-terminal-parser.yy
new file mode 100644
index 000000000000..f448825ef643
--- /dev/null
+++ b/math/jags/files/patch-src-terminal-parser.yy
@@ -0,0 +1,10 @@
+--- src/terminal/parser.yy.orig	Tue Mar 30 09:43:35 2004
++++ src/terminal/parser.yy	Thu May 27 16:59:09 2004
+@@ -3,6 +3,7 @@
+ #include <iostream>
+ #include <fstream>
+ #include <map>
++#include <time.h>
+ #define MATHLIB_STANDALONE
+ #include <Rmath.h>
+ #include <JAGSVersion.h>
diff --git a/math/jags/pkg-descr b/math/jags/pkg-descr
new file mode 100644
index 000000000000..0bb03bb175f5
--- /dev/null
+++ b/math/jags/pkg-descr
@@ -0,0 +1,14 @@
+JAGS is Just Another Gibbs Sampler -- a program for Bayesian analysis of
+graphical models via Gibbs Sampling, not wholly unlike classic BUGS.
+
+The functionality of JAGS is based on the BUGS program created by the
+MRC Biostatistics Unit (http://www.mrc-bsu.cam.ac.uk/). There is a short
+manual that describes the differences between JAGS and BUGS.
+
+The manual is installed as /usr/local/share/doc/jags/manual.pdf.
+
+Some of the BUGS examples have been modified to run with JAGS, and have
+been turned into a test suite.  They are installed under
+/usr/local/share/examples/jags/.
+
+WWW: http://www-fis.iarc.fr/~martyn/software/jags/
diff --git a/math/jags/pkg-plist b/math/jags/pkg-plist
new file mode 100644
index 000000000000..437b72eb2965
--- /dev/null
+++ b/math/jags/pkg-plist
@@ -0,0 +1,362 @@
+bin/jags
+include/JAGS/Console.h
+include/JAGS/JAGSVersion.h
+include/JAGS/distributions/DistDiscrete.h
+include/JAGS/distributions/DistFinite.h
+include/JAGS/distributions/DistReal.h
+include/JAGS/distributions/DistTab.h
+include/JAGS/distributions/Distribution.h
+include/JAGS/functions/FuncTab.h
+include/JAGS/functions/Function.h
+include/JAGS/functions/InverseLinkFunc.h
+include/JAGS/functions/ScalarArgScalarFunc.h
+include/JAGS/functions/ScalarFunc.h
+include/JAGS/graph/AggNode.h
+include/JAGS/graph/ConstantNode.h
+include/JAGS/graph/DeterministicNode.h
+include/JAGS/graph/Graph.h
+include/JAGS/graph/GraphMarks.h
+include/JAGS/graph/LogicalNode.h
+include/JAGS/graph/MixtureNode.h
+include/JAGS/graph/Node.h
+include/JAGS/graph/NodeError.h
+include/JAGS/graph/OffsetNode.h
+include/JAGS/graph/StochasticNode.h
+include/JAGS/graph/SubSetIndex.h
+include/JAGS/graph/SubSetNode.h
+include/JAGS/matrix/lapack.h
+include/JAGS/matrix/matexp.h
+include/JAGS/matrix/matrix.h
+include/JAGS/model/Compiler.h
+include/JAGS/model/Counter.h
+include/JAGS/model/CounterTab.h
+include/JAGS/model/LogicalFactory.h
+include/JAGS/model/Model.h
+include/JAGS/model/NodeArray.h
+include/JAGS/model/ParseTree.h
+include/JAGS/model/SymTab.h
+include/JAGS/model/TraceMonitor.h
+include/JAGS/model/parser.h
+include/JAGS/model/parser_extra.h
+include/JAGS/sampler/ConjugateBeta.h
+include/JAGS/sampler/ConjugateDirichlet.h
+include/JAGS/sampler/ConjugateFactory.h
+include/JAGS/sampler/ConjugateGamma.h
+include/JAGS/sampler/ConjugateMNormal.h
+include/JAGS/sampler/ConjugateNormal.h
+include/JAGS/sampler/ConjugateSampler.h
+include/JAGS/sampler/ConjugateWishart.h
+include/JAGS/sampler/FiniteFactory.h
+include/JAGS/sampler/FiniteSampler.h
+include/JAGS/sampler/GibbsFactory.h
+include/JAGS/sampler/GibbsSampler.h
+include/JAGS/sampler/Sampler.h
+include/JAGS/sampler/SamplerFactory.h
+include/JAGS/sampler/SliceFactory.h
+include/JAGS/sampler/SliceSampler.h
+include/JAGS/sarray/Index.h
+include/JAGS/sarray/LeftRangeIterator.h
+include/JAGS/sarray/Range.h
+include/JAGS/sarray/RightRangeIterator.h
+include/JAGS/sarray/SArray.h
+lib/libjags.a
+lib/libjags.la
+%%PORTDOCS%%%%DOCSDIR%%/manual.pdf
+%%PORTDOCS%%%%EXAMPLESDIR%%/R/bench.R
+%%PORTDOCS%%%%EXAMPLESDIR%%/R/check.R
+%%PORTDOCS%%%%EXAMPLESDIR%%/ReadMe
+%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/Makefile
+%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/blocker/ReadMe
+%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/blocker/bench-test1.R
+%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/blocker/bench-test2.R
+%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/blocker/bench-test3.R
+%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/blocker/blocker-data.R
+%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/blocker/blocker-init.R
+%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/blocker/blocker.bug
+%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/blocker/blockert-init.R
+%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/blocker/blockert.bug
+%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/blocker/blockht-data.R
+%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/blocker/blockht.bug
+%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/blocker/notest2.cmd
+%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/blocker/notest3.cmd
+%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/blocker/test1.cmd
+%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/bones/bench-test1.R
+%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/bones/bones-data.R
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+%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/jaw/jaw-data.R
+%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/jaw/jaw-inits.R
+%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/jaw/jaw-linear.bug
+%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/jaw/jaw-quadratic.bug
+%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/jaw/test1.cmd
+%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/jaw/test2.cmd
+%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/jaw/test3.cmd
+%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/orange/ReadMe
+%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/orange/mvotree-data.R
+%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/orange/mvotree-inits.R
+%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/orange/mvotree.bug
+%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/orange/orange-data.R
+%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/orange/orange-inits.R
+%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/orange/otree.bug
+%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/orange/otree.dat
+%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/orange/otree.in
+%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/orange/test1.cmd
+%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/pigs/pigs-data.R
+%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/pigs/pigs-inits.R
+%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/pigs/pigs.bug
+%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/pigs/test1.cmd
+%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/schools/schools-data.R
+%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/schools/schools-inits.R
+%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/schools/schools.bug
+%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/schools/schools.dat
+%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/schools/test.bug
+%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/schools/test1.cmd
+%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/stagnant/ReadMe
+%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/stagnant/notest1.cmd
+%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/stagnant/notest2.cmd
+%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/stagnant/stagnant-data.R
+%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/stagnant/stagnant-inits1.R
+%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/stagnant/stagnant-inits2.R
+%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/stagnant/stagnant-inits3.R
+%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/stagnant/stagnant-inits4.R
+%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/stagnant/stagnant.bug
+%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/stagnant/stagnant2.bug
+%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/stagnant/test3.cmd
+%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/stagnant/test4.cmd
+@dirrm include/JAGS/sarray
+@dirrm include/JAGS/sampler
+@dirrm include/JAGS/model
+@dirrm include/JAGS/matrix
+@dirrm include/JAGS/graph
+@dirrm include/JAGS/functions
+@dirrm include/JAGS/distributions
+@dirrm include/JAGS
+%%PORTDOCS%%@dirrm %%DOCSDIR%%
+%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol2/stagnant
+%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol2/schools
+%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol2/pigs
+%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol2/orange
+%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol2/jaw
+%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol2/ice
+%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol2/hearts
+%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol2/eyes
+%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol2/dugongs
+%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol2/cervix
+%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol2/birats
+%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol2/biops
+%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol2/beetles
+%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol2/asia
+%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol2/alli
+%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol2/air
+%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol2
+%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol1/seeds
+%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol1/salm
+%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol1/rats
+%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol1/pump
+%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol1/oxford/old
+%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol1/oxford
+%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol1/mice
+%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol1/lsat
+%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol1/litters
+%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol1/line
+%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol1/leuk
+%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol1/kidney
+%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol1/equiv
+%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol1/epil
+%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol1/dyes
+%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol1/bones
+%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol1/blocker
+%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol1
+%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/R
+%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%