From 716978e00c3989760adf3e9b3c15ab30c5750705 Mon Sep 17 00:00:00 2001 From: Glenn Johnson Date: Mon, 10 Feb 2020 03:40:47 -0600 Subject: New package: r-copula (#14874) This PR adds the r-copula package and dependencies. - new package: r-adgoftest - new package: r-gsl - new package: r-pspline - new package: r-stabledist --- .../repos/builtin/packages/r-adgoftest/package.py | 17 ++++++++++ .../repos/builtin/packages/r-copula/package.py | 39 ++++++++++++++++++++++ var/spack/repos/builtin/packages/r-gsl/package.py | 21 ++++++++++++ .../repos/builtin/packages/r-pspline/package.py | 18 ++++++++++ .../repos/builtin/packages/r-stabledist/package.py | 20 +++++++++++ 5 files changed, 115 insertions(+) create mode 100644 var/spack/repos/builtin/packages/r-adgoftest/package.py create mode 100644 var/spack/repos/builtin/packages/r-copula/package.py create mode 100644 var/spack/repos/builtin/packages/r-gsl/package.py create mode 100644 var/spack/repos/builtin/packages/r-pspline/package.py create mode 100644 var/spack/repos/builtin/packages/r-stabledist/package.py diff --git a/var/spack/repos/builtin/packages/r-adgoftest/package.py b/var/spack/repos/builtin/packages/r-adgoftest/package.py new file mode 100644 index 0000000000..1117c5c986 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-adgoftest/package.py @@ -0,0 +1,17 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RAdgoftest(RPackage): + """Anderson-Darling GoF test with p-value calculation based on Marsaglia's + 2004 paper 'Evaluating the Anderson-Darling Distribution'""" + + homepage = "https://cloud.r-project.org/package=ADGofTest" + url = "https://cloud.r-project.org/src/contrib/ADGofTest_0.3.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/ADGofTest" + + version('0.3', sha256='9cd9313954f6ecd82480d373f6c5371ca84ab33e3f5c39d972d35cfcf1096846') diff --git a/var/spack/repos/builtin/packages/r-copula/package.py b/var/spack/repos/builtin/packages/r-copula/package.py new file mode 100644 index 0000000000..0090a65a79 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-copula/package.py @@ -0,0 +1,39 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RCopula(RPackage): + """Classes (S4) of commonly used elliptical, Archimedean, extreme-value and + other copula families, as well as their rotations, mixtures and + asymmetrizations. Nested Archimedean copulas, related tools and special + functions. Methods for density, distribution, random number generation, + bivariate dependence measures, Rosenblatt transform, Kendall distribution + function, perspective and contour plots. Fitting of copula models with + potentially partly fixed parameters, including standard errors. Serial + independence tests, copula specification tests (independence, + exchangeability, radial symmetry, extreme-value dependence, + goodness-of-fit) and model selection based on cross-validation. Empirical + copula, smoothed versions, and non-parametric estimators of the Pickands + dependence function.""" + + homepage = "http://copula.r-forge.r-project.org/" + url = "https://cloud.r-project.org/src/contrib/copula_0.999-20.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/copula" + + version('0.999-20', sha256='7d3d47bce2dacb05b94a772f84dbf3d83c99ac2ac11e5f1b4b03d50d9d5c0fb0') + + depends_on('r@3.2.0:', type=('build', 'run')) + depends_on('r-matrix', type=('build', 'run')) + depends_on('r-lattice', type=('build', 'run')) + depends_on('r-colorspace', type=('build', 'run')) + depends_on('r-gsl', type=('build', 'run')) + depends_on('r-adgoftest', type=('build', 'run')) + depends_on('r-stabledist@0.6-4:', type=('build', 'run')) + depends_on('r-mvtnorm', type=('build', 'run')) + depends_on('r-pcapp', type=('build', 'run')) + depends_on('r-pspline', type=('build', 'run')) + depends_on('r-numderiv', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-gsl/package.py b/var/spack/repos/builtin/packages/r-gsl/package.py new file mode 100644 index 0000000000..8aa7f77859 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-gsl/package.py @@ -0,0 +1,21 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RGsl(RPackage): + """An R wrapper for some of the functionality of the Gnu Scientific + Library.""" + + homepage = "https://github.com/RobinHankin/gsl.git" + url = "https://cloud.r-project.org/src/contrib/gsl_2.1-6.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/gsl" + + version('2.1-6', sha256='f5d463239693f146617018987687db31b163653708cbae0b730b9b7bed81995c') + + depends_on('r@3.1.0:', type=('build', 'run')) + + depends_on('gsl@2.1:') diff --git a/var/spack/repos/builtin/packages/r-pspline/package.py b/var/spack/repos/builtin/packages/r-pspline/package.py new file mode 100644 index 0000000000..7a33098c15 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-pspline/package.py @@ -0,0 +1,18 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RPspline(RPackage): + """Smoothing splines with penalties on order m derivatives.""" + + homepage = "https://cloud.r-project.org/package=pspline" + url = "https://cloud.r-project.org/src/contrib/pspline_1.0-18.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/pspline" + + version('1.0-18', sha256='f71cf293bd5462e510ac5ad16c4a96eda18891a0bfa6447dd881c65845e19ac7') + + depends_on('r@2.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-stabledist/package.py b/var/spack/repos/builtin/packages/r-stabledist/package.py new file mode 100644 index 0000000000..c187d4771e --- /dev/null +++ b/var/spack/repos/builtin/packages/r-stabledist/package.py @@ -0,0 +1,20 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RStabledist(RPackage): + """Density, Probability and Quantile functions, and random number + generation for (skew) stable distributions, using the parametrizations of + Nolan.""" + + homepage = "http://www.rmetrics.org/" + url = "https://cloud.r-project.org/src/contrib/stabledist_0.7-1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/stabledist" + + version('0.7-1', sha256='06c5704d3a3c179fa389675c537c39a006867bc6e4f23dd7e406476ed2c88a69') + + depends_on('r@3.1.0:', type=('build', 'run')) -- cgit v1.2.3-70-g09d2