Bayesian estimation, particularly using Markov chain Monte

Carlo (MCMC), is an increasingly relevant approach to
statistical estimation. However, few statistical software
packages implement MCMC samplers, and they are non-trivial
 to code by hand. pymc is a python package that implements
the Metropolis-Hastings algorithm as a python class, and is
extremely flexible and applicable to a large suite of problems.
pymc includes methods for summarizing output, plotting,
goodness-of-fit and convergence diagnostics.

WWW:	http://pypi.python.org/pypi/pymc/

PR:		ports/129567
Submitted by:	Wen Heping <wenheping at gmail.com>

4 files changed, 285 insertions, 0 deletions

diff --git a/math/py-pymc/Makefile b/math/py-pymc/Makefile
new file mode 100644
index 000000000000..d6a0571cd8c7
--- /dev/null
+++ b/math/py-pymc/Makefile
@@ -0,0 +1,26 @@
+# New ports collection makefile for:	py-pymc
+# Date created:		2008-12-10
+# Whom:			Wen Heping <wenheping@gmail.com>
+#
+# $FreeBSD$
+#
+
+PORTNAME=	pymc
+PORTVERSION=	2.0r1
+CATEGORIES=	math python
+MASTER_SITES=	CHEESESHOP
+PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
+DISTNAME=	${PORTNAME}-2.0rc1
+
+MAINTAINER=	wenheping@gmail.com
+COMMENT=	Markov Chain Monte Carlo Sampling Toolkit
+
+BUILD_DEPENDS=	${PYNUMPY}
+RUN_DEPENDS=	${BUILD_DEPENDS}
+#LIB_DEPENDS=	lapack.4:${PORTSDIR}/math/lapack
+
+USE_PYTHON=	yes
+USE_PYDISTUTILS=	yes
+PYDISTUTILS_EGGINFO=	${DISTNAME}-${PYTHON_VERSION:S/thon//}.egg-info
+
+.include <bsd.port.mk>
diff --git a/math/py-pymc/distinfo b/math/py-pymc/distinfo
new file mode 100644
index 000000000000..fb3d50705a48
--- /dev/null
+++ b/math/py-pymc/distinfo
@@ -0,0 +1,3 @@
+MD5 (pymc-2.0rc1.tar.gz) = b8e8bc8e72b23a0215d10e13839738d8
+SHA256 (pymc-2.0rc1.tar.gz) = fdb7b27c01509e2293d8905697feee3a157478393683eab3deb46a02f486f70a
+SIZE (pymc-2.0rc1.tar.gz) = 978218
diff --git a/math/py-pymc/pkg-descr b/math/py-pymc/pkg-descr
new file mode 100644
index 000000000000..3ac658827382
--- /dev/null
+++ b/math/py-pymc/pkg-descr
@@ -0,0 +1,11 @@
+Bayesian estimation, particularly using Markov chain Monte
+Carlo (MCMC), is an increasingly relevant approach to
+statistical estimation. However, few statistical software
+packages implement MCMC samplers, and they are non-trivial
+ to code by hand. pymc is a python package that implements
+the Metropolis-Hastings algorithm as a python class, and is
+extremely flexible and applicable to a large suite of problems.
+pymc includes methods for summarizing output, plotting,
+goodness-of-fit and convergence diagnostics.
+
+WWW:	http://pypi.python.org/pypi/pymc/
diff --git a/math/py-pymc/pkg-plist b/math/py-pymc/pkg-plist
new file mode 100644
index 000000000000..c301baf0a474
--- /dev/null
+++ b/math/py-pymc/pkg-plist
@@ -0,0 +1,245 @@
+%%PYTHON_SITELIBDIR%%/pymc/CommonDeterministics.py
+%%PYTHON_SITELIBDIR%%/pymc/CommonDeterministics.pyc
+%%PYTHON_SITELIBDIR%%/pymc/CommonDeterministics.pyo
+%%PYTHON_SITELIBDIR%%/pymc/Container.py
+%%PYTHON_SITELIBDIR%%/pymc/Container.pyc
+%%PYTHON_SITELIBDIR%%/pymc/Container.pyo
+%%PYTHON_SITELIBDIR%%/pymc/Container_values.so
+%%PYTHON_SITELIBDIR%%/pymc/InstantiationDecorators.py
+%%PYTHON_SITELIBDIR%%/pymc/InstantiationDecorators.pyc
+%%PYTHON_SITELIBDIR%%/pymc/InstantiationDecorators.pyo
+%%PYTHON_SITELIBDIR%%/pymc/LazyFunction.so
+%%PYTHON_SITELIBDIR%%/pymc/MCMC.py
+%%PYTHON_SITELIBDIR%%/pymc/MCMC.pyc
+%%PYTHON_SITELIBDIR%%/pymc/MCMC.pyo
+%%PYTHON_SITELIBDIR%%/pymc/Matplot.py
+%%PYTHON_SITELIBDIR%%/pymc/Matplot.pyc
+%%PYTHON_SITELIBDIR%%/pymc/Matplot.pyo
+%%PYTHON_SITELIBDIR%%/pymc/Model.py
+%%PYTHON_SITELIBDIR%%/pymc/Model.pyc
+%%PYTHON_SITELIBDIR%%/pymc/Model.pyo
+%%PYTHON_SITELIBDIR%%/pymc/MultiModelInference/ModelPosterior.py
+%%PYTHON_SITELIBDIR%%/pymc/MultiModelInference/ModelPosterior.pyc
+%%PYTHON_SITELIBDIR%%/pymc/MultiModelInference/ModelPosterior.pyo
+%%PYTHON_SITELIBDIR%%/pymc/MultiModelInference/__init__.py
+%%PYTHON_SITELIBDIR%%/pymc/MultiModelInference/__init__.pyc
+%%PYTHON_SITELIBDIR%%/pymc/MultiModelInference/__init__.pyo
+%%PYTHON_SITELIBDIR%%/pymc/Node.py
+%%PYTHON_SITELIBDIR%%/pymc/Node.pyc
+%%PYTHON_SITELIBDIR%%/pymc/Node.pyo
+%%PYTHON_SITELIBDIR%%/pymc/NormalApproximation.py
+%%PYTHON_SITELIBDIR%%/pymc/NormalApproximation.pyc
+%%PYTHON_SITELIBDIR%%/pymc/NormalApproximation.pyo
+%%PYTHON_SITELIBDIR%%/pymc/PyMCObjects.py
+%%PYTHON_SITELIBDIR%%/pymc/PyMCObjects.pyc
+%%PYTHON_SITELIBDIR%%/pymc/PyMCObjects.pyo
+%%PYTHON_SITELIBDIR%%/pymc/ScipyDistributions.py
+%%PYTHON_SITELIBDIR%%/pymc/ScipyDistributions.pyc
+%%PYTHON_SITELIBDIR%%/pymc/ScipyDistributions.pyo
+%%PYTHON_SITELIBDIR%%/pymc/StepMethods.py
+%%PYTHON_SITELIBDIR%%/pymc/StepMethods.pyc
+%%PYTHON_SITELIBDIR%%/pymc/StepMethods.pyo
+%%PYTHON_SITELIBDIR%%/pymc/__init__.py
+%%PYTHON_SITELIBDIR%%/pymc/__init__.pyc
+%%PYTHON_SITELIBDIR%%/pymc/__init__.pyo
+%%PYTHON_SITELIBDIR%%/pymc/database/__init__.py
+%%PYTHON_SITELIBDIR%%/pymc/database/__init__.pyc
+%%PYTHON_SITELIBDIR%%/pymc/database/__init__.pyo
+%%PYTHON_SITELIBDIR%%/pymc/database/base.py
+%%PYTHON_SITELIBDIR%%/pymc/database/base.pyc
+%%PYTHON_SITELIBDIR%%/pymc/database/base.pyo
+%%PYTHON_SITELIBDIR%%/pymc/database/hdf5.py
+%%PYTHON_SITELIBDIR%%/pymc/database/hdf5.pyc
+%%PYTHON_SITELIBDIR%%/pymc/database/hdf5.pyo
+%%PYTHON_SITELIBDIR%%/pymc/database/mysql.py
+%%PYTHON_SITELIBDIR%%/pymc/database/mysql.pyc
+%%PYTHON_SITELIBDIR%%/pymc/database/mysql.pyo
+%%PYTHON_SITELIBDIR%%/pymc/database/no_trace.py
+%%PYTHON_SITELIBDIR%%/pymc/database/no_trace.pyc
+%%PYTHON_SITELIBDIR%%/pymc/database/no_trace.pyo
+%%PYTHON_SITELIBDIR%%/pymc/database/pickle.py
+%%PYTHON_SITELIBDIR%%/pymc/database/pickle.pyc
+%%PYTHON_SITELIBDIR%%/pymc/database/pickle.pyo
+%%PYTHON_SITELIBDIR%%/pymc/database/ram.py
+%%PYTHON_SITELIBDIR%%/pymc/database/ram.pyc
+%%PYTHON_SITELIBDIR%%/pymc/database/ram.pyo
+%%PYTHON_SITELIBDIR%%/pymc/database/sqlite.py
+%%PYTHON_SITELIBDIR%%/pymc/database/sqlite.pyc
+%%PYTHON_SITELIBDIR%%/pymc/database/sqlite.pyo
+%%PYTHON_SITELIBDIR%%/pymc/database/txt.py
+%%PYTHON_SITELIBDIR%%/pymc/database/txt.pyc
+%%PYTHON_SITELIBDIR%%/pymc/database/txt.pyo
+%%PYTHON_SITELIBDIR%%/pymc/decorators.py
+%%PYTHON_SITELIBDIR%%/pymc/decorators.pyc
+%%PYTHON_SITELIBDIR%%/pymc/decorators.pyo
+%%PYTHON_SITELIBDIR%%/pymc/diagnostics.py
+%%PYTHON_SITELIBDIR%%/pymc/diagnostics.pyc
+%%PYTHON_SITELIBDIR%%/pymc/diagnostics.pyo
+%%PYTHON_SITELIBDIR%%/pymc/distributions.py
+%%PYTHON_SITELIBDIR%%/pymc/distributions.pyc
+%%PYTHON_SITELIBDIR%%/pymc/distributions.pyo
+%%PYTHON_SITELIBDIR%%/pymc/examples/DisasterModel.py
+%%PYTHON_SITELIBDIR%%/pymc/examples/DisasterModel.pyc
+%%PYTHON_SITELIBDIR%%/pymc/examples/DisasterModel.pyo
+%%PYTHON_SITELIBDIR%%/pymc/examples/__init__.py
+%%PYTHON_SITELIBDIR%%/pymc/examples/__init__.pyc
+%%PYTHON_SITELIBDIR%%/pymc/examples/__init__.pyo
+%%PYTHON_SITELIBDIR%%/pymc/examples/custom_step.py
+%%PYTHON_SITELIBDIR%%/pymc/examples/custom_step.pyc
+%%PYTHON_SITELIBDIR%%/pymc/examples/custom_step.pyo
+%%PYTHON_SITELIBDIR%%/pymc/examples/gelman_bioassay.py
+%%PYTHON_SITELIBDIR%%/pymc/examples/gelman_bioassay.pyc
+%%PYTHON_SITELIBDIR%%/pymc/examples/gelman_bioassay.pyo
+%%PYTHON_SITELIBDIR%%/pymc/examples/model_1.py
+%%PYTHON_SITELIBDIR%%/pymc/examples/model_1.pyc
+%%PYTHON_SITELIBDIR%%/pymc/examples/model_1.pyo
+%%PYTHON_SITELIBDIR%%/pymc/examples/model_1_gof.py
+%%PYTHON_SITELIBDIR%%/pymc/examples/model_1_gof.pyc
+%%PYTHON_SITELIBDIR%%/pymc/examples/model_1_gof.pyo
+%%PYTHON_SITELIBDIR%%/pymc/examples/model_1_missing.py
+%%PYTHON_SITELIBDIR%%/pymc/examples/model_1_missing.pyc
+%%PYTHON_SITELIBDIR%%/pymc/examples/model_1_missing.pyo
+%%PYTHON_SITELIBDIR%%/pymc/examples/model_2.py
+%%PYTHON_SITELIBDIR%%/pymc/examples/model_2.pyc
+%%PYTHON_SITELIBDIR%%/pymc/examples/model_2.pyo
+%%PYTHON_SITELIBDIR%%/pymc/examples/model_3.py
+%%PYTHON_SITELIBDIR%%/pymc/examples/model_3.pyc
+%%PYTHON_SITELIBDIR%%/pymc/examples/model_3.pyo
+%%PYTHON_SITELIBDIR%%/pymc/examples/straightlinefit.py
+%%PYTHON_SITELIBDIR%%/pymc/examples/straightlinefit.pyc
+%%PYTHON_SITELIBDIR%%/pymc/examples/straightlinefit.pyo
+%%PYTHON_SITELIBDIR%%/pymc/examples/weibull_fit.py
+%%PYTHON_SITELIBDIR%%/pymc/examples/weibull_fit.pyc
+%%PYTHON_SITELIBDIR%%/pymc/examples/weibull_fit.pyo
+%%PYTHON_SITELIBDIR%%/pymc/flib.so
+%%PYTHON_SITELIBDIR%%/pymc/gp/BasisCovariance.py
+%%PYTHON_SITELIBDIR%%/pymc/gp/BasisCovariance.pyc
+%%PYTHON_SITELIBDIR%%/pymc/gp/BasisCovariance.pyo
+%%PYTHON_SITELIBDIR%%/pymc/gp/Covariance.py
+%%PYTHON_SITELIBDIR%%/pymc/gp/Covariance.pyc
+%%PYTHON_SITELIBDIR%%/pymc/gp/Covariance.pyo
+%%PYTHON_SITELIBDIR%%/pymc/gp/FullRankCovariance.py
+%%PYTHON_SITELIBDIR%%/pymc/gp/FullRankCovariance.pyc
+%%PYTHON_SITELIBDIR%%/pymc/gp/FullRankCovariance.pyo
+%%PYTHON_SITELIBDIR%%/pymc/gp/GPutils.py
+%%PYTHON_SITELIBDIR%%/pymc/gp/GPutils.pyc
+%%PYTHON_SITELIBDIR%%/pymc/gp/GPutils.pyo
+%%PYTHON_SITELIBDIR%%/pymc/gp/Mean.py
+%%PYTHON_SITELIBDIR%%/pymc/gp/Mean.pyc
+%%PYTHON_SITELIBDIR%%/pymc/gp/Mean.pyo
+%%PYTHON_SITELIBDIR%%/pymc/gp/NearlyFullRankCovariance.py
+%%PYTHON_SITELIBDIR%%/pymc/gp/NearlyFullRankCovariance.pyc
+%%PYTHON_SITELIBDIR%%/pymc/gp/NearlyFullRankCovariance.pyo
+%%PYTHON_SITELIBDIR%%/pymc/gp/PyMC_objects.py
+%%PYTHON_SITELIBDIR%%/pymc/gp/PyMC_objects.pyc
+%%PYTHON_SITELIBDIR%%/pymc/gp/PyMC_objects.pyo
+%%PYTHON_SITELIBDIR%%/pymc/gp/Realization.py
+%%PYTHON_SITELIBDIR%%/pymc/gp/Realization.pyc
+%%PYTHON_SITELIBDIR%%/pymc/gp/Realization.pyo
+%%PYTHON_SITELIBDIR%%/pymc/gp/__init__.py
+%%PYTHON_SITELIBDIR%%/pymc/gp/__init__.pyc
+%%PYTHON_SITELIBDIR%%/pymc/gp/__init__.pyo
+%%PYTHON_SITELIBDIR%%/pymc/gp/cov_funs/__init__.py
+%%PYTHON_SITELIBDIR%%/pymc/gp/cov_funs/__init__.pyc
+%%PYTHON_SITELIBDIR%%/pymc/gp/cov_funs/__init__.pyo
+%%PYTHON_SITELIBDIR%%/pymc/gp/cov_funs/bases.py
+%%PYTHON_SITELIBDIR%%/pymc/gp/cov_funs/bases.pyc
+%%PYTHON_SITELIBDIR%%/pymc/gp/cov_funs/bases.pyo
+%%PYTHON_SITELIBDIR%%/pymc/gp/cov_funs/cov_utils.py
+%%PYTHON_SITELIBDIR%%/pymc/gp/cov_funs/cov_utils.pyc
+%%PYTHON_SITELIBDIR%%/pymc/gp/cov_funs/cov_utils.pyo
+%%PYTHON_SITELIBDIR%%/pymc/gp/cov_funs/distances.so
+%%PYTHON_SITELIBDIR%%/pymc/gp/cov_funs/isotropic_cov_funs.so
+%%PYTHON_SITELIBDIR%%/pymc/gp/cov_funs/wrapped_distances.py
+%%PYTHON_SITELIBDIR%%/pymc/gp/cov_funs/wrapped_distances.pyc
+%%PYTHON_SITELIBDIR%%/pymc/gp/cov_funs/wrapped_distances.pyo
+%%PYTHON_SITELIBDIR%%/pymc/gp/gpplots.py
+%%PYTHON_SITELIBDIR%%/pymc/gp/gpplots.pyc
+%%PYTHON_SITELIBDIR%%/pymc/gp/gpplots.pyo
+%%PYTHON_SITELIBDIR%%/pymc/gp/incomplete_chol.so
+%%PYTHON_SITELIBDIR%%/pymc/gp/linalg_utils.so
+%%PYTHON_SITELIBDIR%%/pymc/graph.py
+%%PYTHON_SITELIBDIR%%/pymc/graph.pyc
+%%PYTHON_SITELIBDIR%%/pymc/graph.pyo
+%%PYTHON_SITELIBDIR%%/pymc/tests/__init__.py
+%%PYTHON_SITELIBDIR%%/pymc/tests/__init__.pyc
+%%PYTHON_SITELIBDIR%%/pymc/tests/__init__.pyo
+%%PYTHON_SITELIBDIR%%/pymc/tests/check_dependencies.py
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+%%PYTHON_SITELIBDIR%%/pymc/tests/check_dependencies.pyo
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+%%PYTHON_SITELIBDIR%%/pymc/tests/test_cov.pyo
+%%PYTHON_SITELIBDIR%%/pymc/tests/test_database.py
+%%PYTHON_SITELIBDIR%%/pymc/tests/test_database.pyc
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+%%PYTHON_SITELIBDIR%%/pymc/tests/test_distributions.py
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+%%PYTHON_SITELIBDIR%%/pymc/tests/test_distributions.pyo
+%%PYTHON_SITELIBDIR%%/pymc/tests/test_graph.py
+%%PYTHON_SITELIBDIR%%/pymc/tests/test_graph.pyc
+%%PYTHON_SITELIBDIR%%/pymc/tests/test_graph.pyo
+%%PYTHON_SITELIBDIR%%/pymc/tests/test_instantiation.py
+%%PYTHON_SITELIBDIR%%/pymc/tests/test_instantiation.pyc
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+%%PYTHON_SITELIBDIR%%/pymc/tests/test_interactive.py
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+%%PYTHON_SITELIBDIR%%/pymc/tests/test_mean.py
+%%PYTHON_SITELIBDIR%%/pymc/tests/test_mean.pyc
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+%%PYTHON_SITELIBDIR%%/pymc/tests/test_norm_approx.pyc
+%%PYTHON_SITELIBDIR%%/pymc/tests/test_norm_approx.pyo
+%%PYTHON_SITELIBDIR%%/pymc/tests/test_observation.py
+%%PYTHON_SITELIBDIR%%/pymc/tests/test_observation.pyc
+%%PYTHON_SITELIBDIR%%/pymc/tests/test_observation.pyo
+%%PYTHON_SITELIBDIR%%/pymc/tests/test_realization.py
+%%PYTHON_SITELIBDIR%%/pymc/tests/test_realization.pyc
+%%PYTHON_SITELIBDIR%%/pymc/tests/test_realization.pyo
+%%PYTHON_SITELIBDIR%%/pymc/utils.py
+%%PYTHON_SITELIBDIR%%/pymc/utils.pyc
+%%PYTHON_SITELIBDIR%%/pymc/utils.pyo
+@dirrm %%PYTHON_SITELIBDIR%%/pymc/MultiModelInference
+@dirrm %%PYTHON_SITELIBDIR%%/pymc/database
+@dirrm %%PYTHON_SITELIBDIR%%/pymc/examples
+@dirrm %%PYTHON_SITELIBDIR%%/pymc/gp/cov_funs
+@dirrm %%PYTHON_SITELIBDIR%%/pymc/gp
+@dirrm %%PYTHON_SITELIBDIR%%/pymc/tests
+@dirrm %%PYTHON_SITELIBDIR%%/pymc