From 2c13e9c0e5a085563b51e904fcb2ee25004f8057 Mon Sep 17 00:00:00 2001 From: Yifan Zhu Date: Wed, 6 Jun 2018 17:44:32 -0500 Subject: r-mitml: new package and its dependencies r-jomo and r-pan (#8412) --- var/spack/repos/builtin/packages/r-jomo/package.py | 44 ++++++++++++++++++++++ .../repos/builtin/packages/r-mitml/package.py | 41 ++++++++++++++++++++ var/spack/repos/builtin/packages/r-pan/package.py | 35 +++++++++++++++++ 3 files changed, 120 insertions(+) create mode 100644 var/spack/repos/builtin/packages/r-jomo/package.py create mode 100644 var/spack/repos/builtin/packages/r-mitml/package.py create mode 100644 var/spack/repos/builtin/packages/r-pan/package.py 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) + . 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') -- cgit v1.2.3-70-g09d2