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

5 files changed, 115 insertions, 0 deletions

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'))