r-mitml: new package and its dependencies r-jomo and r-pan (#8412)

3 files changed, 120 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/r-jomo/package.py b/var/spack/repos/builtin/packages/r-jomo/package.py
new file mode 100644
index 0000000000..f63a88be6b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-jomo/package.py
@@ -0,0 +1,44 @@
+##############################################################################
+# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/spack/spack
+# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RJomo(RPackage):
+    """Similarly to Schafer's package 'pan', 'jomo' is a package for multilevel
+    joint modelling multiple imputation (Carpenter and Kenward, 2013)
+    <doi:10.1002/9781119942283>. Novel aspects of 'jomo' are the possibility of
+    handling binary and categorical data through latent normal variables, the
+    option to use cluster-specific covariance matrices and to impute compatibly
+    with the substantive model.
+    """
+
+    homepage = "https://cran.r-project.org/package=jomo"
+    url      = "https://cran.r-project.org/src/contrib/jomo_2.6-2.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/jomo"
+
+    version('2.6-2', 'eff4a6c1a971708959d65b3224c98a25')
+
+    depends_on('r-lme4', type=('build', 'run'))
+    depends_on('r-survival', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-mitml/package.py b/var/spack/repos/builtin/packages/r-mitml/package.py
new file mode 100644
index 0000000000..08d506e8ce
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-mitml/package.py
@@ -0,0 +1,41 @@
+##############################################################################
+# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/spack/spack
+# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RMitml(RPackage):
+    """Provides tools for multiple imputation of missing data in multilevel
+    modeling. Includes a user-friendly interface to the packages 'pan' and
+    'jomo', and several functions for visualization, data management and the
+    analysis of multiply imputed data sets."""
+
+    homepage = "https://cran.r-project.org/package=mitml"
+    url      = "https://cran.r-project.org/src/contrib/mitml_0.3-5.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/mitml"
+    version('0.3-5', '6f8659c33696915bf510241287b2a34d')
+
+    depends_on('r-pan', type=('build', 'run'))
+    depends_on('r-jomo', type=('build', 'run'))
+    depends_on('r-haven', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-pan/package.py b/var/spack/repos/builtin/packages/r-pan/package.py
new file mode 100644
index 0000000000..00db43e28d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-pan/package.py
@@ -0,0 +1,35 @@
+##############################################################################
+# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/spack/spack
+# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RPan(RPackage):
+    """Multiple imputation for multivariate panel or clustered data."""
+
+    homepage = "https://cran.r-project.org/package=pan"
+    url      = "https://cran.r-project.org/src/contrib/pan_1.4.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/pan"
+
+    version('1.4', 'cdead963110561fc42dc544a60ac44ed')