{ "_id": "6a1f390cb401979e73428e7c", "Package": "deepgp", "Type": "Package", "Title": "Bayesian Deep Gaussian Processes using MCMC", "Version": "1.2.1", "Date": "2026-02-06", "Authors@R": "person(given = c(\"Annie\", \"S.\"),\nfamily = \"Booth\",\nrole = c(\"aut\", \"cre\"),\nemail = \"annie_booth@vt.edu\")", "Description": "Performs Bayesian posterior inference for deep Gaussian\nprocesses following Sauer, Gramacy, and Higdon (2023,\n). See Sauer (2023,\n) for comprehensive\nmethodological details and\n for a variety of\ncoding examples. Models are trained through MCMC including\nelliptical slice sampling of latent Gaussian layers and\nMetropolis-Hastings sampling of kernel hyperparameters.\nGradient-enhancement and gradient predictions are offered\nfollowing Booth (2025, ).\nVecchia approximation for faster computation is implemented\nfollowing Sauer, Cooper, and Gramacy (2023,\n). Optional monotonic warpings\nare implemented following Barnett et al. (2025,\n). Downstream tasks include\nsequential design through active learning Cohn/integrated mean\nsquared error (ALC/IMSE; Sauer, Gramacy, and Higdon, 2023),\noptimization through expected improvement (EI; Gramacy, Sauer,\nand Wycoff, 2022, ), and contour\nlocation through entropy (Booth, Renganathan, and Gramacy,\n2025, ). Models extend up to\nthree layers deep; a one layer model is equivalent to typical\nGaussian process regression. Incorporates OpenMP and SNOW\nparallelization and utilizes C/C++ under the hood.", "License": "LGPL", "Encoding": "UTF-8", "NeedsCompilation": "yes", "VignetteBuilder": "knitr", "RoxygenNote": "7.3.3", "Packaged": { "Date": "2026-05-10 08:44:15 UTC", "User": "root" }, "Author": "Annie S. Booth [aut, cre]", "Maintainer": "Annie S. Booth ", "Repository": "https://anniesbooth.r-universe.dev", "Date/Publication": "2026-02-09 14:50:02 UTC", "RemoteUrl": "https://github.com/cran/deepgp", "RemoteRef": "HEAD", "RemoteSha": "f05f99030ded706e9a3a19da6cd4c083ad56522b", "MD5sum": "4239e315d8331ffddadb06b5e70c4fb8", "_user": "anniesbooth", "_type": "src", "_file": "deepgp_1.2.1.tar.gz", "_fileid": "7c04ca4bcf7baed041391b6e08ebd9756b51562a521f5b5b872a8ab7dfe16722", "_filesize": 2794678, "_sha256": "7c04ca4bcf7baed041391b6e08ebd9756b51562a521f5b5b872a8ab7dfe16722", "_created": "2026-05-10T08:44:15.000Z", "_published": "2026-06-02T20:11:56.003Z", "_distro": "noble", "_jobs": [ { "job": 79162497497, "time": 172, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "6902421876" }, { "job": 79162497403, "time": 189, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "6902423767" }, { "job": 79162497654, "time": 164, "config": "linux-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "6902420897" }, { "job": 79162497750, "time": 190, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "6902423928" }, { "job": 79162498691, "time": 114, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "6902547991" }, { "job": 79162498295, "time": 293, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "6902543139" }, { "job": 79162497588, "time": 113, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "6902575151" }, { "job": 79162497460, "time": 277, "config": "macos-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "6902522062" }, { "job": 79162497341, "time": 271, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "6902401774" }, { "job": 79162496326, "time": 129, "config": "wasm-release", "r": "4.6.0", "check": "FAIL", "artifact": "" }, { "job": 79162497731, "time": 163, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "6902420664" }, { "job": 79162497955, "time": 159, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "6902420282" }, { "job": 79162497491, "time": 191, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "6902424109" } ], "_buildurl": "https://github.com/r-universe/anniesbooth/actions/runs/25624268291", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/cran/deepgp", "_commit": { "id": "f05f99030ded706e9a3a19da6cd4c083ad56522b", "author": "Annie S. Booth ", "committer": "cran-robot ", "message": "version 1.2.1\n", "time": 1770648602 }, "_maintainer": { "name": "Annie S. Booth", "email": "annie_booth@vt.edu", "login": "anniesbooth", "uuid": 21149883 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.6", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "RcppArmadillo", "role": "LinkingTo" }, { "package": "grDevices", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "doParallel", "role": "Imports" }, { "package": "foreach", "role": "Imports" }, { "package": "parallel", "role": "Imports" }, { "package": "GpGp", "role": "Imports" }, { "package": "fields", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "Rcpp", "role": "Imports" }, { "package": "mvtnorm", "role": "Imports" }, { "package": "FNN", "role": "Imports" }, { "package": "abind", "role": "Imports" }, { "package": "interp", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "cran", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-02", "n": 1 }, { "week": "2026-07", "n": 1 } ], "_tags": [ { "name": "1.2.0", "date": "2026-01-09" }, { "name": "1.2.1", "date": "2026-02-09" } ], "_stars": 1, "_contributors": [ { "user": "anniesbooth", "count": 13, "uuid": 21149883 } ], "_userbio": { "uuid": 21149883, "type": "user", "name": "Annie S. Booth", "description": "Assistant Professor of Statistics,\r\nVirginia Tech" }, "_downloads": { "count": 831, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/deepgp" }, "_searchresults": 30, "_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/deepgp.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_realowner": "anniesbooth", "_cranurl": false, "_releases": [ { "version": "0.1.0", "date": "2020-10-29" }, { "version": "0.2.0", "date": "2020-12-16" }, { "version": "0.2.1", "date": "2021-07-15" }, { "version": "0.3.0", "date": "2021-11-24" }, { "version": "0.3.1", "date": "2021-12-07" }, { "version": "1.0.0", "date": "2022-04-08" }, { "version": "1.0.1", "date": "2022-06-20" }, { "version": "1.1.0", "date": "2022-12-15" }, { "version": "1.1.1", "date": "2023-08-07" }, { "version": "1.1.2", "date": "2024-04-28" }, { "version": "1.1.3", "date": "2024-08-19" }, { "version": "1.2.0", "date": "2026-01-09" }, { "version": "1.2.1", "date": "2026-02-16" } ], "_exports": [ "ALC", "continue", "crps", "fit_one_layer", "fit_three_layer", "fit_two_layer", "IMSE", "post_sample", "rmse", "score", "sq_dist", "to_vec", "trim" ], "_help": [ { "page": "deepgp-package", "title": "Package deepgp", "topics": [ "deepgp-package", "deepgp" ] }, { "page": "ALC", "title": "Active Learning Cohn for Sequential Design", "topics": [ "ALC", "ALC.dgp2", "ALC.dgp3", "ALC.gp" ] }, { "page": "continue", "title": "Continues MCMC sampling", "topics": [ "continue", "continue.dgp2", "continue.dgp2vec", "continue.dgp3", "continue.dgp3vec", "continue.gp", "continue.gpvec" ] }, { "page": "crps", "title": "Calculates CRPS", "topics": [ "crps" ] }, { "page": "fit_one_layer", "title": "MCMC sampling for one layer GP", "topics": [ "fit_one_layer" ] }, { "page": "fit_three_layer", "title": "MCMC sampling for three layer deep GP", "topics": [ "fit_three_layer" ] }, { "page": "fit_two_layer", "title": "MCMC sampling for two layer deep GP", "topics": [ "fit_two_layer" ] }, { "page": "IMSE", "title": "Integrated Mean-Squared (prediction) Error for Sequential Design", "topics": [ "IMSE", "IMSE.dgp2", "IMSE.dgp3", "IMSE.gp" ] }, { "page": "plot", "title": "Plots object from 'deepgp' package", "topics": [ "plot", "plot.dgp2", "plot.dgp2vec", "plot.dgp3", "plot.dgp3vec", "plot.gp", "plot.gpvec" ] }, { "page": "post_sample", "title": "Generates joint posterior samples from a trained GP/DGP", "topics": [ "post_sample", "post_sample.dgp2", "post_sample.dgp2vec", "post_sample.dgp3", "post_sample.dgp3vec", "post_sample.gp", "post_sample.gpvec" ] }, { "page": "predict", "title": "Predict posterior mean and variance/covariance", "topics": [ "predict", "predict.dgp2", "predict.dgp2vec", "predict.dgp3", "predict.dgp3vec", "predict.gp", "predict.gpvec" ] }, { "page": "rmse", "title": "Calculates RMSE", "topics": [ "rmse" ] }, { "page": "score", "title": "Calculates score", "topics": [ "score" ] }, { "page": "sq_dist", "title": "Calculates squared pairwise distances", "topics": [ "sq_dist" ] }, { "page": "to_vec", "title": "Converts non-Vecchia object to its Vecchia version", "topics": [ "to_vec" ] }, { "page": "trim", "title": "Trim/Thin MCMC iterations", "topics": [ "trim", "trim.dgp2", "trim.dgp2vec", "trim.dgp3", "trim.dgp3vec", "trim.gp", "trim.gpvec" ] } ], "_readme": "https://github.com/cran/deepgp/raw/HEAD/README.md", "_rundeps": [ "abind", "BH", "codetools", "doParallel", "dotCall64", "fields", "FNN", "foreach", "GpGp", "iterators", "lattice", "maps", "Matrix", "mvtnorm", "RColorBrewer", "Rcpp", "RcppArmadillo", "spam", "viridisLite" ], "_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": "deepgp.Rmd", "filename": "deepgp.html", "title": "deepgp: an R-package for Bayesian Deep Gaussian Processes", "author": "Annie S. Booth (annie_booth@vt.edu)", "engine": "knitr::rmarkdown", "headings": [ "Overview", "Model Fitting", "One-layer Shallow GP", "Two-layer DGP", "Three-layer DGP", "Evaluation Metrics", "Extensions", "Noisy Modeling", "Vecchia Approximation", "Joint posterior sampling", "Monotonic Warpings", "Separable Lengthscales for One-layer GP", "Gradients", "Active Learning", "Optimization through Expected Improvement", "Contour Location through Entropy", "Minimizing Posterior Variance", "Computational Considerations", "References" ], "created": "2022-12-15 07:40:09", "modified": "2026-02-09 14:50:02", "commits": 6 } ], "_score": 3.4771212547196626, "_indexed": true, "_nocasepkg": "deepgp", "_universes": [ "anniesbooth" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.2.1", "date": "2026-05-10T08:46:51.000Z", "distro": "noble", "arch": "aarch64", "commit": "f05f99030ded706e9a3a19da6cd4c083ad56522b", "fileid": "09ea85cb2acabdfca424d41f2a97cdcbaab0346a768f09ad81a075bc255d4420", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/anniesbooth/actions/runs/25624268291" }, { "r": "4.7.0", "os": "linux", "version": "1.2.1", "date": "2026-05-10T08:47:03.000Z", "distro": "noble", "arch": "x86_64", "commit": "f05f99030ded706e9a3a19da6cd4c083ad56522b", "fileid": "0c2da3349005ed17b1b8cdd581fbe642c7e1aba5de9c365a5c989014a581972d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/anniesbooth/actions/runs/25624268291" }, { "r": "4.6.0", "os": "linux", "version": "1.2.1", "date": "2026-05-10T08:46:46.000Z", "distro": "noble", "arch": "aarch64", "commit": "f05f99030ded706e9a3a19da6cd4c083ad56522b", "fileid": "2970261dc88f7048bfb63ce35690e8428f2ac1b9c131bdfec90b87019a9a75f2", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/anniesbooth/actions/runs/25624268291" }, { "r": "4.6.0", "os": "linux", "version": "1.2.1", "date": "2026-05-10T08:47:05.000Z", "distro": "noble", "arch": "x86_64", "commit": "f05f99030ded706e9a3a19da6cd4c083ad56522b", "fileid": "bda56f241ac626c13da21740c3463d632a3a08c3b87c756d656dfc24e970d12a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/anniesbooth/actions/runs/25624268291" }, { "r": "4.5.3", "os": "mac", "version": "1.2.1", "date": "2026-05-10T09:08:18.000Z", "arch": "aarch64", "commit": "f05f99030ded706e9a3a19da6cd4c083ad56522b", "fileid": "f84804b305f9f307d1c31ac45e76e55c1ef8e8179a0602db36642a02ed5098b6", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/anniesbooth/actions/runs/25624268291" }, { "r": "4.5.3", "os": "mac", "version": "1.2.1", "date": "2026-05-10T09:06:22.000Z", "arch": "x86_64", "commit": "f05f99030ded706e9a3a19da6cd4c083ad56522b", "fileid": "58621f5a72216287d21fe0dd31a1f7e5e8575915eda7c77eb7d223697b81e097", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/anniesbooth/actions/runs/25624268291" }, { "r": "4.6.0", "os": "mac", "version": "1.2.1", "date": "2026-05-10T09:13:07.000Z", "arch": "aarch64", "commit": "f05f99030ded706e9a3a19da6cd4c083ad56522b", "fileid": "4fb434d9399298b90ccbebf23c0477307a8307ba0263a8cc2955dd4f599fc9c4", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/anniesbooth/actions/runs/25624268291" }, { "r": "4.6.0", "os": "mac", "version": "1.2.1", "date": "2026-05-10T09:02:24.000Z", "arch": "x86_64", "commit": "f05f99030ded706e9a3a19da6cd4c083ad56522b", "fileid": "3e79ae8a2e89f46652bb70deff8b3a9cb114d50c25aebbabc95399a18f420c3d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/anniesbooth/actions/runs/25624268291" }, { "r": "4.7.0", "os": "win", "version": "1.2.1", "date": "2026-05-10T08:46:07.000Z", "arch": "x86_64", "commit": "f05f99030ded706e9a3a19da6cd4c083ad56522b", "fileid": "1f70f1e14457134f701bbd3c505d34009b9bddaead7ab247e1e271d621e8e675", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/anniesbooth/actions/runs/25624268291" }, { "r": "4.5.3", "os": "win", "version": "1.2.1", "date": "2026-05-10T08:46:02.000Z", "arch": "x86_64", "commit": "f05f99030ded706e9a3a19da6cd4c083ad56522b", "fileid": "e683bcbb6089f7ea2d61d4d7a02adaabfe2f8463642893d49c50491f74ea7c2e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/anniesbooth/actions/runs/25624268291" }, { "r": "4.6.0", "os": "win", "version": "1.2.1", "date": "2026-05-10T08:46:03.000Z", "arch": "x86_64", "commit": "f05f99030ded706e9a3a19da6cd4c083ad56522b", "fileid": "bbae4b55c07b4cd5499ba99e3c40bd00b2a01fbc540f0c6d8171318b11258a0f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/anniesbooth/actions/runs/25624268291" } ] }