{ "_id": "6a26644c794753ddbc3e62c8", "Package": "geommc", "Title": "Geometric Markov Chain Sampling", "Type": "Package", "Version": "1.3.2", "Authors@R": "person(\"Vivekananda\", \"Roy\", , \"vroy@iastate.edu\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-2964-9503\"))", "Maintainer": "Vivekananda Roy ", "Date": "2026-5-9", "Description": "Simulates from discrete and continuous target\ndistributions using geometric Metropolis-Hastings (MH)\nalgorithms. Users specify the target distribution by an R\nfunction that evaluates the log un-normalized pdf or pmf. The\npackage also contains a function implementing a specific\ngeometric MH algorithm for performing high-dimensional Bayesian\nvariable selection.", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "URL": "https://github.com/vroys/geommc", "License": "GPL (>= 3)", "VignetteBuilder": "knitr", "Config/roxygen2/version": "8.0.0", "Config/pak/sysreqs": "make", "Repository": "https://vroys.r-universe.dev", "Date/Publication": "2026-05-09 14:01:22 UTC", "RemoteUrl": "https://github.com/vroys/geommc", "RemoteRef": "HEAD", "RemoteSha": "dd0de3e5b8256ff37f10a516db08c8336b8a5191", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-06-08 06:36:44 UTC", "User": "root" }, "Author": "Vivekananda Roy [aut, cre] (ORCID:\n)", "MD5sum": "c88d55db8def63989a08df6fa3f867c9", "_user": "vroys", "_type": "src", "_file": "geommc_1.3.2.tar.gz", "_fileid": "8d5be51b6d9d6b3d384b49502c7ed00ac8313d526933b5041a60d86106aadda0", "_filesize": 3856083, "_sha256": "8d5be51b6d9d6b3d384b49502c7ed00ac8313d526933b5041a60d86106aadda0", "_created": "2026-06-08T06:36:44.000Z", "_published": "2026-06-08T06:42:20.203Z", "_distro": "noble", "_jobs": [ { "job": 80036016433, "time": 172, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "7473183200" }, { "job": 80036016435, "time": 185, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7473186156" }, { "job": 80036016432, "time": 167, "config": "linux-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7473181950" }, { "job": 80036016417, "time": 151, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7473177113" }, { "job": 80036016403, "time": 237, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7473191258" }, { "job": 80036016416, "time": 81, "config": "macos-oldrel-x86_64", "r": "", "check": "FAIL", "artifact": "" }, { "job": 80036016394, "time": 68, "config": "macos-release-arm64", "r": "", "check": "FAIL", "artifact": "" }, { "job": 80036016413, "time": 99, "config": "macos-release-x86_64", "r": "", "check": "FAIL", "artifact": "" }, { "job": 80035438719, "time": 271, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7473135648" }, { "job": 80036016371, "time": 131, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7473171164" }, { "job": 80036016385, "time": 212, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7473193126" }, { "job": 80036016400, "time": 147, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7473176005" }, { "job": 80036016366, "time": 43, "config": "windows-release", "r": "", "check": "FAIL", "artifact": "" } ], "_buildurl": "https://github.com/r-universe/vroys/actions/runs/27120221546", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/vroys/geommc", "_commit": { "id": "dd0de3e5b8256ff37f10a516db08c8336b8a5191", "author": "Vivekananda Roy ", "committer": "Vivekananda Roy ", "message": "allowing some list arguments\n", "time": 1778335282 }, "_maintainer": { "name": "Vivekananda Roy", "email": "vroy@iastate.edu", "login": "vroys", "description": "I'm a professor of statistics at Iowa State University.", "uuid": 5176503, "orcid": "0000-0002-2964-9503" }, "_registered": true, "_dependencies": [ { "package": "Rcpp", "role": "LinkingTo" }, { "package": "RcppArmadillo", "role": "LinkingTo" }, { "package": "Rcpp", "role": "Imports" }, { "package": "cubature", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "numDeriv", "role": "Imports" }, { "package": "progress", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "sass", "role": "Suggests" }, { "package": "bslib", "role": "Suggests" } ], "_owner": "vroys", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-49", "n": 2 }, { "week": "2025-50", "n": 2 }, { "week": "2026-02", "n": 2 }, { "week": "2026-06", "n": 2 }, { "week": "2026-19", "n": 1 } ], "_tags": [], "_stars": 1, "_contributors": [ { "user": "vroys", "count": 24, "uuid": 5176503 } ], "_userbio": { "uuid": 5176503, "type": "user", "name": "Vivekananda Roy", "description": "I'm a professor of statistics at Iowa State University." }, "_downloads": { "count": 488, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/geommc" }, "_devurl": "https://github.com/vroys/geommc", "_searchresults": 3, "_topics": [ "openblas", "cpp", "openmp" ], "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/geommc.html", "manual.pdf" ], "_homeurl": "https://github.com/vroys/geommc", "_realowner": "vroys", "_cranurl": true, "_releases": [ { "version": "0.0.0", "date": "2024-06-17" }, { "version": "0.0.1", "date": "2024-06-27" }, { "version": "0.1.1", "date": "2024-10-18" }, { "version": "1.3.1", "date": "2026-02-27" }, { "version": "1.3.2", "date": "2026-05-09" } ], "_exports": [ "geomc", "geomc.vs", "logp.vs" ], "_help": [ { "page": "geomc", "title": "Markov chain Monte Carlo for discrete and continuous distributions using geometric MH algorithms.", "topics": [ "geomc" ] }, { "page": "geomc.vs", "title": "Markov chain Monte Carlo for Bayesian variable selection using a geometric MH algorithm.", "topics": [ "geomc.vs" ] }, { "page": "logp.vs", "title": "The log-unnormalized posterior probability of a model for Bayesian variable selection.", "topics": [ "logp.vs" ] } ], "_rundeps": [ "cli", "crayon", "cubature", "glue", "hms", "lattice", "lifecycle", "Matrix", "numDeriv", "pkgconfig", "prettyunits", "progress", "R6", "Rcpp", "RcppArmadillo", "rlang", "vctrs" ], "_sysdeps": [ { "shlib": "liblapack", "package": "libopenblas0-pthread", "source": "openblas", "version": "0.3.26+ds-1ubuntu0.1", "name": "openblas", "homepage": "https://www.openblas.net/", "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)" }, { "shlib": "libblas", "package": "libopenblas0-pthread", "source": "openblas", "version": "0.3.26+ds-1ubuntu0.1", "name": "openblas", "homepage": "https://www.openblas.net/", "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)" }, { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "14.2.0-4ubuntu2~24.04.1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" }, { "shlib": "libgomp", "package": "libgomp1", "source": "gcc", "version": "14.2.0-4ubuntu2~24.04.1", "name": "openmp", "homepage": "http://gcc.gnu.org/", "description": "GCC OpenMP (GOMP) support library" } ], "_vignettes": [ { "source": "geomc-vs.Rmd", "filename": "geomc-vs.html", "title": "Bayesian variable selection with geomc.vs", "author": "Vivekananda Roy", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "The Variable Selection Problem", "Why Bayesian Variable Selection?", "Basic Usage", "Example 1:", "Small Sparse Model", "Data Generation", "Run geomc.vs for Variable Selection", "Examining the Results", "Marginal Inclusion Probabilities (MIP)", "Visualizing Marginal Inclusion Probabilities", "The Median Probability Model", "Posterior Mean of Coefficients", "Model Space Exploration", "Example 2:", "Another Example to Illustrate Different Data Structures and Tuning Parameters", "Generate Sparse Data", "Visualize Sparse Matrix Structure", "Memory Comparison", "Generate Response Variable", "Variable Selection using geomc.vs with Symmetric Random Walk Base", "Understanding the Output", "MCMC Samples", "Log Posterior Values", "Results Analysis", "Marginal Inclusion Probabilities", "Visualizing MIPs", "Visualizing WMIPs", "Model Selection Performance", "Weighted Average Model", "Coefficient Estimates", "Key Takeaways", "Variable Selection using geomc.vs with an Asymmetric Random Walk Base", "Additional Parameters", "Key Parameters", "Summary", "Appendix: The Model", "Prior Specification", "Posterior Computation", "References" ], "created": "2026-02-05 02:28:28", "modified": "2026-02-05 02:28:28", "commits": 1 }, { "source": "geomc.Rmd", "filename": "geomc.pdf", "title": "Geometric MCMC sampling with geomc", "author": "Vivekananda Roy", "engine": "knitr::rmarkdown", "headings": [ "What is Geometric approach to MCMC?", "Basic Usage", "Example 1: Sampling from a Multivariate Normal", "Examining the Results", "Visualizing the Results", "Example 2: Bayesian Inference for Normal Data", "Model Setup", "Trace plots", "Posterior Summaries", "Visualizing the Posterior", "Understanding the Output", "Example 3: Univariate Mixture of Normals", "Univariate Mixture of Normals: Run geomc with Default Settings", "Univariate Mixture of Normals: Run geomc with Custom Random Walk Base Density", "Univariate Mixture of Normals: Run geomc with Informed Approximate Targets", "Univariate Mixture of Normals: Run geomc with Informed Approximate Targets along with a Custom Random Walk Base Density", "Univariate Mixture of Normals: Run geomc with other choices of eps", "Univariate Mixture of Normals: Run geomc with another (non-Gaussian) Informed Approximate Target", "Univariate Mixture of Normals: Importance Sampling to estimate inner products for non-Gaussian densities", "Example 4: Bivariate Mixture of Normals", "Bivariate Mixture of Normals: Run geomc with Informed Approximate Targets along with a Custom Random Walk Base Density", "Visualizing Bivariate Mixture Results", "Bivariate Mixture of Normals: Run geomc with a diffuse $g$", "Bivariate Mixture of Normals: Comparison with Random Walk Metropolis", "Example 2 Continued: Bayesian Inference for Normal Data with MALA Base Density", "Example 5: Discrete Distribution (Binomial)", "Discrete Distribution (Binomial): Run geomc with Random Walk Base (and user defined bhat.coef function)", "Comparing with True Distribution", "Discrete Distribution (Binomial): Run geomc with Reflecting Random Walk Base (and user defined bhat.coef function)", "Discrete Distribution (Binomial): Run geomc with Uniform Base (an example with ind set as TRUE)", "Summary of Non-Default Settings", "When to Use Custom Specifications", "References" ], "created": "2026-02-05 02:28:28", "modified": "2026-05-09 14:01:22", "commits": 2 } ], "_score": 4, "_indexed": true, "_nocasepkg": "geommc", "_universes": [ "vroys" ], "_binaries": [ { "r": "4.5.3", "os": "mac", "version": "1.3.2", "date": "2026-05-09T15:16:41.000Z", "arch": "x86_64", "commit": "dd0de3e5b8256ff37f10a516db08c8336b8a5191", "fileid": "0fb5eb47223fd63acf90636d99ebb7f3cc904e75c0556d520314156bae8bafbb", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/vroys/actions/runs/25604349903" }, { "r": "4.6.0", "os": "mac", "version": "1.3.2", "date": "2026-05-09T15:15:05.000Z", "arch": "aarch64", "commit": "dd0de3e5b8256ff37f10a516db08c8336b8a5191", "fileid": "8e4c9c0d857b7097ab710843025cb9a6fce3f8ea77518035bf8a57b94c6b59a3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/vroys/actions/runs/25604349903" }, { "r": "4.6.0", "os": "mac", "version": "1.3.2", "date": "2026-05-09T15:15:51.000Z", "arch": "x86_64", "commit": "dd0de3e5b8256ff37f10a516db08c8336b8a5191", "fileid": "940bffe50804034779d776ec4781862c6c758053dd2ef173dee3f553c4fdd2a0", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/vroys/actions/runs/25604349903" }, { "r": "4.6.0", "os": "win", "version": "1.3.2", "date": "2026-05-09T15:14:42.000Z", "arch": "x86_64", "commit": "dd0de3e5b8256ff37f10a516db08c8336b8a5191", "fileid": "676ec1d3ecb0ef19c412cee924be806725bad0a549e38227dbb7cd1c2eb197ad", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/vroys/actions/runs/25604349903" }, { "r": "4.7.0", "os": "linux", "version": "1.3.2", "date": "2026-06-08T06:40:12.000Z", "distro": "noble", "arch": "aarch64", "commit": "dd0de3e5b8256ff37f10a516db08c8336b8a5191", "fileid": "286231855d781ada6457744bc3a571848cbfccff3d15f7d1308b15b022835e57", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/vroys/actions/runs/27120221546" }, { "r": "4.7.0", "os": "linux", "version": "1.3.2", "date": "2026-06-08T06:40:22.000Z", "distro": "noble", "arch": "x86_64", "commit": "dd0de3e5b8256ff37f10a516db08c8336b8a5191", "fileid": "8de546f1e9bebb2c54370e2f36563308317185a477cbf80bccd9a72d241a6cb2", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/vroys/actions/runs/27120221546" }, { "r": "4.6.0", "os": "linux", "version": "1.3.2", "date": "2026-06-08T06:40:06.000Z", "distro": "noble", "arch": "aarch64", "commit": "dd0de3e5b8256ff37f10a516db08c8336b8a5191", "fileid": "d41cbb233a2212a8114e109975741a8e9e773f7fc9829570727c6ae75a904bfb", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/vroys/actions/runs/27120221546" }, { "r": "4.6.0", "os": "linux", "version": "1.3.2", "date": "2026-06-08T06:39:49.000Z", "distro": "noble", "arch": "x86_64", "commit": "dd0de3e5b8256ff37f10a516db08c8336b8a5191", "fileid": "154506c4f5f479276b4d2829bfa18551f3ae49691380ddb0b1e68773efcd36f2", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/vroys/actions/runs/27120221546" }, { "r": "4.5.3", "os": "mac", "version": "1.3.2", "date": "2026-06-08T06:40:55.000Z", "arch": "aarch64", "commit": "dd0de3e5b8256ff37f10a516db08c8336b8a5191", "fileid": "e218e697b4b0372359c14847aaddf397f9a36552cadd1707ef82fd1fd1abf549", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/vroys/actions/runs/27120221546" }, { "r": "4.6.0", "os": "wasm", "version": "1.3.2", "date": "2026-06-08T06:39:56.000Z", "arch": "emscripten", "commit": "dd0de3e5b8256ff37f10a516db08c8336b8a5191", "fileid": "b9320dffdfd7b07d7c46a75b5604ffac612cd832331804e7bca51452b3d7342f", "status": "success", "buildurl": "https://github.com/r-universe/vroys/actions/runs/27120221546" }, { "r": "4.7.0", "os": "win", "version": "1.3.2", "date": "2026-06-08T06:39:25.000Z", "arch": "x86_64", "commit": "dd0de3e5b8256ff37f10a516db08c8336b8a5191", "fileid": "f7d9c1d7b557bd3416246ed71506bc4c9b6fbae54ba7b13ea2030bc6fee303e3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/vroys/actions/runs/27120221546" }, { "r": "4.5.3", "os": "win", "version": "1.3.2", "date": "2026-06-08T06:39:13.000Z", "arch": "x86_64", "commit": "dd0de3e5b8256ff37f10a516db08c8336b8a5191", "fileid": "eab076b36d3d0f9f41c9868d03a6ed46bf36b3fe5c19fe277bd916484545a8e6", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/vroys/actions/runs/27120221546" } ] }