r-twosamplemr: add new package and dependencies (#35683)

var/spack/repos/builtin/packages/r-arrangements/package.py

@@ -0,0 +1,27 @@
+# Copyright 2013-2023 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.package import *
+
+
+class RArrangements(RPackage):
+    """Fast Generators and Iterators for Permutations, Combinations, Integer
+    Partitions and Compositions.
+
+    Fast generators and iterators for permutations, combinations, integer
+    partitions and compositions. The arrangements are in lexicographical order
+    and generated iteratively in a memory efficient manner. It has been
+    demonstrated that 'arrangements' outperforms most existing packages of
+    similar kind. Benchmarks could be found at
+    <https://randy3k.github.io/arrangements/articles/benchmark.html>."""
+
+    cran = "arrangements"
+
+    version("1.1.9", sha256="e9b5dcb185ec9b28201b196384b04a8d5a15f4ddb9e0b0b2a0c718635ff7345b")
+
+    depends_on("r@3.4.0:", type=("build", "run"))
+    depends_on("r-gmp", type=("build", "run"))
+    depends_on("r-r6", type=("build", "run"))
+    depends_on("gmp@4.2.3:")

var/spack/repos/builtin/packages/r-googleauthr/package.py

@@ -0,0 +1,28 @@
+# Copyright 2013-2023 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.package import *
+
+
+class RGoogleauthr(RPackage):
+    """Authenticate and Create Google APIs.
+
+    Create R functions that interact with OAuth2 Google APIs
+    <https://developers.google.com/apis-explorer/> easily, with auto-refresh
+    and Shiny compatibility."""
+
+    cran = "googleAuthR"
+
+    version("2.0.0", sha256="ba504baf3bde2e1b3e988bee7602df5765cc6ca542cf0ab76a782c4e60966feb")
+
+    depends_on("r@3.3.0:", type=("build", "run"))
+    depends_on("r-assertthat", type=("build", "run"))
+    depends_on("r-cli", type=("build", "run"))
+    depends_on("r-digest", type=("build", "run"))
+    depends_on("r-gargle@1.2.0:", type=("build", "run"))
+    depends_on("r-httr@1.4.0:", type=("build", "run"))
+    depends_on("r-jsonlite@1.6:", type=("build", "run"))
+    depends_on("r-memoise@1.1.0:", type=("build", "run"))
+    depends_on("r-rlang", type=("build", "run"))

var/spack/repos/builtin/packages/r-ieugwasr/package.py

@@ -0,0 +1,26 @@
+# Copyright 2013-2023 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.package import *
+
+
+class RIeugwasr(RPackage):
+    """R Interface to the OpenGWAS Database API.
+
+    R interface to the OpenGWAS database API. Includes a wrapper
+    to make generic calls to the API, plus convenience functions for
+    specific queries."""
+
+    homepage = "https://github.com/MRCIEU/ieugwasr"
+    url = "https://github.com/MRCIEU/ieugwasr/archive/refs/tags/0.1.5.tar.gz"
+
+    version("0.1.5", sha256="8d900d5a780f23836c80191f9635fbf48a0ca94f828452948c0f445e3217f422")
+
+    depends_on("r@3.6.0:", type=("build", "run"))
+    depends_on("r-magrittr", type=("build", "run"))
+    depends_on("r-googleauthr", type=("build", "run"))
+    depends_on("r-dplyr", type=("build", "run"))
+    depends_on("r-httr", type=("build", "run"))
+    depends_on("r-jsonlite", type=("build", "run"))

var/spack/repos/builtin/packages/r-iterpc/package.py

@@ -0,0 +1,29 @@
+# Copyright 2013-2023 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.package import *
+
+
+class RIterpc(RPackage):
+    """Efficient Iterator for Permutations and Combinations.
+
+    Iterator for generating permutations and combinations. They can be either
+    drawn with or without replacement, or with distinct/ non-distinct items
+    (multiset). The generated sequences are in lexicographical order
+    (dictionary order). The algorithms to generate permutations and
+    combinations are memory efficient. These iterative algorithms enable users
+    to process all sequences without putting all results in the memory at the
+    same time. The algorithms are written in C/C++ for faster performance.
+    Note: 'iterpc' is no longer being maintained. Users are recommended to
+    switch to 'arrangements'."""
+
+    cran = "iterpc"
+
+    version("0.4.2", sha256="38bd464042a27536f676e889263eb2c257a431b59083f58cb54473f42ba2071b")
+
+    depends_on("r@3.0.0:", type=("build", "run"))
+    depends_on("r-iterators", type=("build", "run"))
+    depends_on("r-gmp@0.5-12:", type=("build", "run"))
+    depends_on("r-arrangements@1.0.0:", type=("build", "run"))

var/spack/repos/builtin/packages/r-mendelianrandomization/package.py

@@ -0,0 +1,32 @@
+# Copyright 2013-2023 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.package import *
+
+
+class RMendelianrandomization(RPackage):
+    """Mendelian Randomization Package.
+
+    Encodes several methods for performing Mendelian randomization analyses
+    with summarized data. Summarized data on genetic associations with the
+    exposure and with the outcome can be obtained from large consortia. These
+    data can be used for obtaining causal estimates using instrumental variable
+    methods."""
+
+    cran = "MendelianRandomization"
+
+    version("0.7.0", sha256="cad7cc1b6964fc7d299864378694c5fd947caa83796a1958e581299796b854c7")
+
+    depends_on("r@3.0.1:", type=("build", "run"))
+    depends_on("r-knitr", type=("build", "run"))
+    depends_on("r-rmarkdown", type=("build", "run"))
+    depends_on("r-plotly@3.6.0:", type=("build", "run"))
+    depends_on("r-ggplot2@1.0.1:", type=("build", "run"))
+    depends_on("r-robustbase@0.92-6:", type=("build", "run"))
+    depends_on("r-matrix@1.2:", type=("build", "run"))
+    depends_on("r-iterpc@0.3:", type=("build", "run"))
+    depends_on("r-quantreg@5.01:", type=("build", "run"))
+    depends_on("r-rjson", type=("build", "run"))
+    depends_on("r-glmnet", type=("build", "run"))

var/spack/repos/builtin/packages/r-meta/package.py

@@ -0,0 +1,33 @@
+# Copyright 2013-2023 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.package import *
+
+
+class RMeta(RPackage):
+    """General Package for Meta-Analysis.
+
+    User-friendly general package providing standard methods for meta-analysis
+    and supporting Schwarzer, Carpenter, and Rücker
+    <doi:10.1007/978-3-319-21416-0>, "Meta-Analysis with R" (2015): - common
+    effect and random effects meta-analysis; - several plots (forest, funnel,
+    Galbraith / radial, L'Abbe, Baujat, bubble); - three-level meta-analysis
+    model; - generalised linear mixed model; - Hartung-Knapp method for random
+    effects model; - Kenward-Roger method for random effects model; -
+    prediction interval; - statistical tests for funnel plot asymmetry; -
+    trim-and-fill method to evaluate bias in meta-analysis; - meta-regression;
+    - cumulative meta-analysis and leave-one-out meta-analysis; - import data
+    from 'RevMan 5'; - produce forest plot summarising several (subgroup)
+    meta-analyses."""
+
+    cran = "meta"
+
+    version("6.2-0", sha256="8ec8fb412996bbe17d3ca073f15c191a77bad486b08f39d7b8c2d07360ad5781")
+
+    depends_on("r@4.0.0:", type=("build", "run"))
+    depends_on("r-metafor@3.0-0:", type=("build", "run"))
+    depends_on("r-lme4", type=("build", "run"))
+    depends_on("r-compquadform", type=("build", "run"))
+    depends_on("r-xml2", type=("build", "run"))

var/spack/repos/builtin/packages/r-metadat/package.py

@@ -0,0 +1,21 @@
+# Copyright 2013-2023 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.package import *
+
+
+class RMetadat(RPackage):
+    """Meta-Analysis Datasets.
+
+    A collection of meta-analysis datasets for teaching purposes,
+    illustrating/testing meta-analytic methods, and validating published
+    analyses."""
+
+    cran = "metadat"
+
+    version("1.2-0", sha256="f0cce5e30c3d256eaf5a41e4f52ffc7108e195016a4b99409e0ab4c2ef58f5b8")
+
+    depends_on("r@4.0.0:", type=("build", "run"))
+    depends_on("r-mathjaxr", type=("build", "run"))

var/spack/repos/builtin/packages/r-metafor/package.py

@@ -0,0 +1,39 @@
+# Copyright 2013-2023 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.package import *
+
+
+class RMetafor(RPackage):
+    """Meta-Analysis Package for R.
+
+    A comprehensive collection of functions for conducting meta-analyses in R.
+    The package includes functions to calculate various effect sizes or outcome
+    measures, fit equal-, fixed-, random-, and mixed-effects models to such
+    data, carry out moderator and meta-regression analyses, and create various
+    types of meta-analytical plots (e.g., forest, funnel, radial, L'Abbe,
+    Baujat, bubble, and GOSH plots). For meta-analyses of binomial and
+    person-time data, the package also provides functions that implement
+    specialized methods, including the Mantel-Haenszel method, Peto's method,
+    and a variety of suitable generalized linear (mixed-effects) models (i.e.,
+    mixed-effects logistic and Poisson regression models). Finally, the package
+    provides functionality for fitting meta-analytic multivariate/multilevel
+    models that account for non-independent sampling errors and/or true effects
+    (e.g., due to the inclusion of multiple treatment studies, multiple
+    endpoints, or other forms of clustering). Network meta-analyses and
+    meta-analyses accounting for known correlation structures (e.g., due to
+    phylogenetic relatedness) can also be conducted. An introduction to the
+    package can be found in Viechtbauer (2010) <doi:10.18637/jss.v036.i03>."""
+
+    cran = "metafor"
+
+    version("3.8-1", sha256="d694577f954144d8a5eeab6521fe1c87e68ddf9ecfd7ccc915d01533371b0514")
+
+    depends_on("r@4.0.0:", type=("build", "run"))
+    depends_on("r-matrix", type=("build", "run"))
+    depends_on("r-metadat", type=("build", "run"))
+    depends_on("r-nlme", type=("build", "run"))
+    depends_on("r-mathjaxr", type=("build", "run"))
+    depends_on("r-pbapply", type=("build", "run"))

var/spack/repos/builtin/packages/r-mr-raps/package.py

@@ -0,0 +1,24 @@
+# Copyright 2013-2023 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.package import *
+
+
+class RMrRaps(RPackage):
+    """Two Sample Mendelian Randomization using Robust Adjusted Profile Score.
+
+    Mendelian randomization is a method of identifying and estimating a
+    confounded causal effect using genetic instrumental variables. This
+    packages implements methods for two-sample Mendelian randomization with
+    summary statistics by using Robust Adjusted Profile Score (RAPS).
+    References: Qingyuan Zhao, Jingshu Wang, Jack Bowden, Dylan S. Small.
+    Statistical inference in two-sample summary-data Mendelian randomization
+    using robust adjusted profile score. <arXiv:1801.09652>."""
+
+    cran = "mr.raps"
+
+    version("0.2", sha256="c899f6143dac99e1232ff0a8d9f5fe099d4f69960782e6843db5b0d7f4f63b19")
+
+    depends_on("r-nortest", type=("build", "run"))

var/spack/repos/builtin/packages/r-mrinstruments/package.py

@@ -0,0 +1,19 @@
+# Copyright 2013-2023 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.package import *
+
+
+class RMrinstruments(RPackage):
+    """Data sources for genetic instruments to be used in MR.
+
+    Datasets of eQTLs, GWAS catalogs, etc."""
+
+    homepage = "https://github.com/MRCIEU/MRInstruments"
+    url = "https://github.com/MRCIEU/MRInstruments/archive/refs/tags/0.3.3.tar.gz"
+
+    version("0.3.3", sha256="4ddbaf6335133e8f7baef469d6bc1f89212462b9f4062c9e4ddda37b12eb3486")
+
+    depends_on("r@2.10:", type=("build", "run"))

var/spack/repos/builtin/packages/r-mrmix/package.py

@@ -0,0 +1,18 @@
+# Copyright 2013-2023 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.package import *
+
+
+class RMrmix(RPackage):
+    """Mendelian Randomization Analysis Using Mixture Models (MRMix).
+
+    This package gives robust estimation of causal effects by conducting
+    Mendelian randomization analysis using a mixture model approach."""
+
+    homepage = "https://github.com/gqi/MRMix"
+    git = "https://github.com/gqi/MRMix"
+
+    version("0.1.0", commit="56afdb2bc96760842405396f5d3f02e60e305039")

var/spack/repos/builtin/packages/r-mrpresso/package.py

@@ -0,0 +1,21 @@
+# Copyright 2013-2023 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.package import *
+
+
+class RMrpresso(RPackage):
+    """Performs the Mendelian Randomization Pleiotropy RESidual Sum and Outlier
+    (MR-PRESSO) test.
+
+    MR-PRESSO (Mendelian Randomization Pleiotropy RESidual Sum and Outlier) is
+    a framework that allows for the evaluation of pleiotropy in
+    multi-instrument Mendelian Randomization utilizing genome-wide summary
+    association statistics."""
+
+    homepage = "https://github.com/rondolab/MR-PRESSO"
+    git = "https://github.com/rondolab/MR-PRESSO"
+
+    version("1.0", commit="cece763b47e59763a7916974de43c7cb93843e41")

var/spack/repos/builtin/packages/r-radialmr/package.py

@@ -0,0 +1,23 @@
+# Copyright 2013-2023 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.package import *
+
+
+class RRadialmr(RPackage):
+    """RadialMR.
+
+    A package for implementing radial inverse variance weighted and MR-Egger
+    methods."""
+
+    homepage = "https://github.com/WSpiller/RadialMR"
+    git = "https://github.com/WSpiller/RadialMR"
+
+    version("1.0", commit="d63d3fc8270836ab441b9e14a5ba3eeb2795d7cb")
+
+    depends_on("r@3.5.0:", type=("build", "run"))
+    depends_on("r-ggplot2", type=("build", "run"))
+    depends_on("r-magrittr", type=("build", "run"))
+    depends_on("r-plotly", type=("build", "run"))

var/spack/repos/builtin/packages/r-twosamplemr/package.py

@@ -0,0 +1,51 @@
+# Copyright 2013-2023 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.package import *
+
+
+class RTwosamplemr(RPackage):
+    """Two Sample MR functions and interface to MR Base database.
+
+    A package for performing Mendelian randomization using GWAS summary data.
+    It uses the IEU GWAS database to obtain data automatically, and a wide
+    range of methods to run the analysis. You can use the MR-Base web app to
+    try out a limited range of the functionality in this package, but for any
+    serious work we strongly recommend using this R package."""
+
+    homepage = "https://mrcieu.github.io/TwoSampleMR/"
+    url = "https://github.com/MRCIEU/TwoSampleMR/archive/refs/tags/v0.5.6.tar.gz"
+
+    version("0.5.6", sha256="c63eb008ab7ed08a6f30ccbf0c299beb31b2f5835e5e2aa1b59c5e4fe284a30c")
+
+    depends_on("r@3.6.0:", type=("build", "run"))
+    depends_on("r-ieugwasr@0.1.5:", type=("build", "run"))
+    depends_on("r-ggplot2", type=("build", "run"))
+    depends_on("r-gridextra", type=("build", "run"))
+    depends_on("r-cowplot", type=("build", "run"))
+    depends_on("r-plyr", type=("build", "run"))
+    depends_on("r-reshape2", type=("build", "run"))
+    depends_on("r-stringr", type=("build", "run"))
+    depends_on("r-knitr", type=("build", "run"))
+    depends_on("r-markdown", type=("build", "run"))
+    depends_on("r-gtable", type=("build", "run"))
+    depends_on("r-rmarkdown", type=("build", "run"))
+    depends_on("r-mendelianrandomization", type=("build", "run"))
+    depends_on("r-dplyr", type=("build", "run"))
+    depends_on("r-mr-raps", type=("build", "run"))
+    depends_on("r-psych", type=("build", "run"))
+    depends_on("r-magrittr", type=("build", "run"))
+    depends_on("r-car", type=("build", "run"))
+    depends_on("r-randomforest", type=("build", "run"))
+    depends_on("r-meta", type=("build", "run"))
+    depends_on("r-data-table", type=("build", "run"))
+    depends_on("r-mrpresso", type=("build", "run"))
+    depends_on("r-mrinstruments", type=("build", "run"))
+    depends_on("r-radialmr", type=("build", "run"))
+    depends_on("r-mrmix", type=("build", "run"))
+    depends_on("r-glmnet", type=("build", "run"))
+    depends_on("r-lattice", type=("build", "run"))
+    depends_on("r-pbapply", type=("build", "run"))
+    depends_on("r-mass", type=("build", "run"))