{ "_id": "6a1d29821d7bb097a0a386a1", "Package": "BSL", "Type": "Package", "Title": "Bayesian Synthetic Likelihood", "Version": "3.2.5", "Date": "2022-11-02", "Authors@R": "c(person(\"Ziwen\",\"An\",role=c(\"aut\"),email=\"ziwen.an@hdr.qut.edu.au\",comment = c(ORCID = \"0000-0002-9947-5182\")),\nperson(\"Leah F.\",\"South\",role=c(\"aut\",\"cre\"),email=\"l1.south@qut.edu.au\",comment = c(ORCID = \"0000-0002-5646-2963\")),\nperson(\"Christopher C.\",\"Drovandi\",role=c(\"aut\"),email=\"c.drovandi@qut.edu.au\",comment = c(ORCID = \"0000-0001-9222-8763\")))", "Description": "Bayesian synthetic likelihood (BSL, Price et al. (2018)\n) is an alternative to\nstandard, non-parametric approximate Bayesian computation\n(ABC). BSL assumes a multivariate normal distribution for the\nsummary statistic likelihood and it is suitable when the\ndistribution of the model summary statistics is sufficiently\nregular. This package provides a Metropolis Hastings Markov\nchain Monte Carlo implementation of four methods (BSL, uBSL,\nsemiBSL and BSLmisspec) and two shrinkage estimators (graphical\nlasso and Warton's estimator). uBSL (Price et al. (2018)\n) uses an unbiased estimator\nto the normal density. A semi-parametric version of BSL\n(semiBSL, An et al. (2018) ) is more robust\nto non-normal summary statistics. BSLmisspec (Frazier et al.\n2019 ) estimates the Gaussian synthetic\nlikelihood whilst acknowledging that there may be\nincompatibility between the model and the observed summary\nstatistic. Shrinkage estimation can help to decrease the number\nof model simulations when the dimension of the summary\nstatistic is high (e.g., BSLasso, An et al. (2019)\n). Extensions to this\npackage are planned. For a journal article describing how to\nuse this package, see An et al. (2022)\n.", "License": "GPL (>= 2)", "LazyLoad": "yes", "LazyData": "true", "RoxygenNote": "7.1.1", "Encoding": "UTF-8", "Collate": "'BSL-package.R' 'RcppExports.R' 's4-MODEL.R' 's4-BSL.R'\n'bsl.R' 'cell.R' 'combinePlotsBSL.R' 'covWarton.R'\n'estimateLoglike.R' 'estimateWhiteningMatrix.R'\n'gaussianRankCorr.R' 'gaussianSynLike.R'\n'gaussianSynLikeGhuryeOlkin.R' 'imports.R' 'kernelCDF.R'\n'logitTransform.R' 'ma2.R' 'mgnk.R' 'myMiniProgressBar.R'\n's4-PENALTY.R' 'selectPenalty.R' 'semiparaKernelEstimate.R'\n'sliceGammaMean.R' 'sliceGammaVariance.R' 'synLikeMisspec.R'\n'toad.R'", "RdMacros": "Rdpack", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-06-01 06:37:02 UTC", "User": "root" }, "Author": "Ziwen An [aut] (), Leah\nF. South [aut, cre] (),\nChristopher C. Drovandi [aut]\n()", "Maintainer": "Leah F. South ", "Repository": "https://cran.r-universe.dev", "Date/Publication": "2022-11-03 08:00:07 UTC", "RemoteUrl": "https://github.com/cran/BSL", "RemoteRef": "HEAD", "RemoteSha": "f23046345c11584e6a2910eb502b7a7abb4bdde7", "MD5sum": "99582746e41fc126cb1d7eec89b9241a", "_user": "cran", "_type": "src", "_file": "BSL_3.2.5.tar.gz", "_fileid": "b201bd98acf783126d034886d5a67fccb5bbdf14ac5cdc7600971408e79724d3", "_filesize": 545256, "_sha256": "b201bd98acf783126d034886d5a67fccb5bbdf14ac5cdc7600971408e79724d3", "_created": "2026-06-01T06:37:02.000Z", "_published": "2026-06-01T06:41:06.597Z", "_distro": "noble", "_jobs": [ { "job": 78799151928, "time": 175, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "7324906902" }, { "job": 78799151945, "time": 194, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7324911772" }, { "job": 78799151937, "time": 178, "config": "linux-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7324908038" }, { "job": 78799151914, "time": 185, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7324909368" }, { "job": 78798682640, "time": 240, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7324863852" }, { "job": 78799151901, "time": 135, "config": "wasm-release", "r": "4.6.0", "check": "FAIL", "artifact": "" } ], "_buildurl": "https://github.com/r-universe/cran/actions/runs/26739112653", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/cran/BSL", "_commit": { "id": "f23046345c11584e6a2910eb502b7a7abb4bdde7", "author": "Leah F. 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South", "email": "l1.south@qut.edu.au", "orcid": "0000-0002-5646-2963" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.3.0", "role": "Depends" }, { "package": "RcppArmadillo", "role": "LinkingTo" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "glasso", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "MASS", "role": "Imports" }, { "package": "mvtnorm", "role": "Imports" }, { "package": "copula", "role": "Imports" }, { "package": "whitening", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "gridExtra", "role": "Imports" }, { "package": "foreach", "role": "Imports" }, { "package": "coda", "role": "Imports" }, { "package": "Rcpp", "role": "Imports" }, { "package": "doRNG", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "Rdpack", "version": ">= 0.7", "role": "Imports" }, { "package": "elliplot", "role": "Suggests" }, { "package": "doParallel", "role": "Suggests" }, { "package": "rbenchmark", "role": "Suggests" }, { "package": "mixtools", "role": "Suggests" } ], "_owner": "cran", "_selfowned": false, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 3, "_userbio": { "uuid": 6899542, "type": "organization", "name": "cran", "description": "Unofficial read-only mirror of all CRAN R packages" }, "_downloads": { "count": 264, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/BSL" }, "_mentions": 13, "_searchresults": 21, "_topics": [ "cpp" ], "_rbuild": "4.6.0", "_assets": [ "extra/BSL.html", "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "manual.pdf" ], "_realowner": "cran", "_cranurl": false, "_releases": [ { "version": "0.1.1", "date": "2018-03-28" }, { "version": "2.0.0", "date": "2019-01-16" }, { "version": "3.0.0", "date": "2019-07-10" }, { "version": "3.2.0", "date": "2020-11-22" }, { "version": "3.2.2", "date": "2021-10-26" }, { "version": "3.2.3", "date": "2022-01-27" }, { "version": "3.2.4", "date": "2022-02-22" }, { "version": "3.2.5", "date": "2022-11-03" } ], "_exports": [ "bsl", "cell_prior", "cell_sim", "cell_sum", "combinePlotsBSL", "cor2cov", "estimateLoglike", "estimateWhiteningMatrix", "gaussianRankCorr", "gaussianSynLike", "gaussianSynLikeGhuryeOlkin", "getGamma", "getLoglike", "getPenalty", "getTheta", "ma2_prior", "ma2_sim", "ma2_sim_vec", "ma2_sum", "mgnk_sim", "mgnk_sum", "newModel", "obsMat2deltax", "plot", "selectPenalty", "semiparaKernelEstimate", "show", "sim_toad", "simulate_cell", "simulation", "summary", "summStat", "synLikeMisspec", "toad_prior", "toad_sim", "toad_sum" ], "_datasets": [ { "name": "cell", "title": "Cell biology example", "object": "cell", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "ma2", "title": "An MA(2) model", "object": "ma2", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "mgnk", "title": "The multivariate G&K example", "object": "mgnk", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "toad", "title": "Toad example", "object": "toad", "class": [ "list" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "BSL-package", "title": "Bayesian synthetic likelihood", "topics": [ "BSL-package", "BSL" ] }, { "page": "bsl", "title": "Performing BSL, uBSL, semiBSL and BSLmisspec", "topics": [ "bsl" ] }, { "page": "BSL-class", "title": "S4 class ``BSL''.", "topics": [ "BSL-class", "BSLclass", "getGamma,BSL-method", "getLoglike,BSL-method", "getTheta,BSL-method", "plot,BSL,ANY-method", "show,BSL-method", "summary,BSL-method" ] }, { "page": "cell", "title": "Cell biology example", "topics": [ "cell", "cell_prior", "cell_sim", "cell_sum" ] }, { "page": "combinePlotsBSL", "title": "Plot the densities of multiple ``bsl'' class objects.", "topics": [ "combinePlotsBSL" ] }, { "page": "cor2cov", "title": "Convert a correlation matrix to a covariance matrix", "topics": [ "cor2cov" ] }, { "page": "estimateLoglike", "title": "Estimate the synthetic likelihood", "topics": [ "estimateLoglike" ] }, { "page": "estimateWhiteningMatrix", "title": "Estimate the Whitening matrix to be used in the ``wBSL'' method of Priddle et al. 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