{ "_id": "6a229cedcd65a98ecbd57ce7", "Package": "basket", "Title": "Basket Trial Analysis", "Version": "0.12.2", "Authors@R": "c(\nperson(given = \"Nan\",\nfamily = \"Chen\",\nemail = \"nchen2@mdanderson.org\",\nrole = c(\"aut\")),\nperson(given = \"Ryan\",\nfamily = \"Hafen\",\nemail = \"rhafen@gmail.com\",\nrole = c(\"ctb\")),\nperson(given = \"Brian\",\nfamily = \"Hobbs\",\nemail = \"bphobbs@gmail.com\",\nrole = c(\"aut\")),\nperson(given = \"Alex\",\nfamily = \"Kaizer\",\nemail = \"alex.kaizer@ucdenver.edu\",\nrole = c(\"aut\")),\nperson(given = \"Wei\",\nfamily = \"Wei\",\nemail = \"awei.wei@yale.edu\",\nrole = c(\"aut\")),\nperson(given = \"Michael J.\",\nfamily = \"Kane\",\nemail = \"michael.kane@yale.edu\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"http://orcid.org/0000-0003-1899-6662\")))", "Description": "Implementation of multisource exchangeability models for\nBayesian analyses of prespecified subgroups arising in the\ncontext of basket trial design and monitoring. The R 'basket'\npackage facilitates implementation of the binary, symmetric\nmulti-source exchangeability model (MEM) with posterior\ninference arising from both exact computation and Markov chain\nMonte Carlo sampling. Analysis output includes full posterior\nsamples as well as posterior probabilities, highest posterior\ndensity (HPD) interval boundaries, effective sample sizes\n(ESS), mean and median estimations, posterior exchangeability\nprobability matrices, and maximum a posteriori MEMs. In\naddition to providing \"basketwise\" analyses, the package\nincludes similar calculations for \"clusterwise\" analyses for\nwhich subgroups are combined into meta-baskets, or clusters,\nusing graphical clustering algorithms that treat the posterior\nexchangeability probabilities as edge weights. In addition\nplotting tools are provided to visualize basket and cluster\ndensities as well as their exchangeability. References include\nHyman, D.M., Puzanov, I., Subbiah, V., Faris, J.E., Chau, I.,\nBlay, J.Y., Wolf, J., Raje, N.S., Diamond, E.L., Hollebecque,\nA. and Gervais, R (2015) ; Hobbs,\nB.P. and Landin, R. (2018) ; Hobbs, B.P.,\nKane, M.J., Hong, D.S. and Landin, R. (2018)\n; and Kaizer, A.M., Koopmeiners,\nJ.S. and Hobbs, B.P. (2017) .", "License": "LGPL-2", "Maintainer": "Michael J. Kane ", "LazyData": "true", "Encoding": "UTF-8", "RoxygenNote": "7.2.3", "URL": "https://github.com/kaneplusplus/basket", "BugReports": "https://github.com/kaneplusplus/basket/issues", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "Config/pak/sysreqs": "libfontconfig1-dev libfreetype6-dev libglpk-dev\nlibgmp3-dev libicu-dev libxml2-dev", "Repository": "https://kaneplusplus.r-universe.dev", "Date/Publication": "2023-07-17 15:42:01 UTC", "RemoteUrl": "https://github.com/kaneplusplus/basket", "RemoteRef": "HEAD", "RemoteSha": "a665c37a79a193dbc8af33fb40f750b12abefaf4", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-05 09:51:33 UTC", "User": "root" }, "Author": "Nan Chen [aut],\nRyan Hafen [ctb],\nBrian Hobbs [aut],\nAlex Kaizer [aut],\nWei Wei [aut],\nMichael J. Kane [aut, cre] (ORCID:\n)", "MD5sum": "e27304f3668cb329f5514a6158970f3a", "_user": "kaneplusplus", "_type": "src", "_file": "basket_0.12.2.tar.gz", "_fileid": "96591cd3ad9cc8cd942a9540ad95aa8c33eed57cf0c4f74abd6bf88daed8db07", "_filesize": 645122, "_sha256": "96591cd3ad9cc8cd942a9540ad95aa8c33eed57cf0c4f74abd6bf88daed8db07", "_created": "2026-06-05T09:51:33.000Z", "_published": "2026-06-05T09:54:53.401Z", "_distro": "noble", "_jobs": [ { "job": 79704539972, "time": 166, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7433806922" }, { "job": 79704539883, "time": 161, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7433805392" }, { "job": 79704539886, "time": 131, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7433795416" }, { "job": 79704539849, "time": 102, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7433785975" }, { "job": 79703978209, "time": 221, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7433753940" }, { "job": 79704539892, "time": 121, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7433792452" }, { "job": 79704539911, "time": 159, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7433803997" }, { "job": 79704539878, "time": 103, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7433786339" }, { "job": 79704539889, "time": 104, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7433787183" } ], "_buildurl": "https://github.com/r-universe/kaneplusplus/actions/runs/27007877745", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/kaneplusplus/basket", "_commit": { "id": "a665c37a79a193dbc8af33fb40f750b12abefaf4", "author": "Michael J. Kane ", "committer": "Michael J. Kane ", "message": "Small fix.\n", "time": 1689608521 }, "_maintainer": { "name": "Michael J. Kane", "email": "michael.kane@yale.edu", "login": "kaneplusplus", "orcid": "0000-0003-1899-6662", "description": "", "uuid": 175135 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "GenSA", "role": "Imports" }, { "package": "foreach", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "tibble", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "igraph", "role": "Imports" }, { "package": "gridExtra", "role": "Imports" }, { "package": "itertools", "role": "Imports" }, { "package": "crayon", "role": "Imports" }, { "package": "cli", "role": "Imports" }, { "package": "RColorBrewer", "role": "Imports" }, { "package": "tidygraph", "role": "Imports" }, { "package": "parallel", "role": "Imports" }, { "package": "doParallel", "role": "Imports" }, { "package": "ggraph", "role": "Imports" }, 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"extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/kaneplusplus/basket", "_realowner": "kaneplusplus", "_cranurl": true, "_releases": [ { "version": "0.9.2", "date": "2019-05-14" }, { "version": "0.9.10", "date": "2019-10-23" }, { "version": "0.10.1", "date": "2020-03-11" }, { "version": "0.10.2", "date": "2020-04-07" }, { "version": "0.10.11", "date": "2021-10-17" } ], "_exports": [ "basket", "basket_map", "basket_name", "basket_pep", "cluster_baskets", "cluster_map", "cluster_membership", "cluster_pep", "get_seed", "mem_exact", "mem_mcmc", "plot_density", "plot_map", "plot_mem", "plot_pep", "plot_pep_graph", "sample_posterior", "update_p0" ], "_datasets": [ { "name": "vemu", "title": "Summary Data from the Vemurafenib Study", "object": "vemu", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "baskets", "enrolled", "evaluable", "responders", "prior_therapies", "count" ], "rows": 18, "table": true, "tojson": true }, { "name": "vemu_wide", "title": "Summary Data from the Vemurafenib Study", "object": "vemu_wide", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "baskets", "enrolled", "evaluable", "responders", "one_or_fewer_prior_therapy", "two_prior_therapies", "three_or_more_therapies" ], "rows": 6, "table": true, "tojson": true } ], "_help": [ { "page": "basket-package", "title": "Basket Trial Analysis", "topics": [ "basket-package" ] }, { "page": "basket", "title": "Create a Basket Trial Analysis", "topics": [ "basket" ] }, { "page": "basket_map", "title": "Get the Basketwise Maximum A Posteriori Probability Matrix", "topics": [ "basket_map" ] }, { "page": "basket_name", "title": "The Names of the Baskets", "topics": [ "basket_name" ] }, { "page": "basket_pep", "title": "The Basketwise Posterior Exchangeability Probability Matrix", "topics": [ "basket_pep" ] }, { "page": "cluster_baskets", "title": "Get the Cluster Members of MEM Models", "topics": [ "cluster_baskets" ] }, { "page": "cluster_map", "title": "Get the Clusterwise Maximum A Posteriori Probability Matrix", "topics": [ "cluster_map" ] }, { "page": "cluster_membership", "title": "Cluster Baskets Based on the Posterior Exchangeabilities", "topics": [ "cluster_membership" ] }, { "page": "cluster_pep", "title": "Get the Clusterwise Posterior Exchangeability Matrix", "topics": [ "cluster_pep" ] }, { "page": "get_seed", "title": "Get the Current Random Seed", "topics": [ "get_seed" ] }, { "page": "mem_exact", "title": "Fit the Exact MEM Model", "topics": [ "mem_exact" ] }, { "page": "mem_mcmc", "title": "Fit the MEM Model using MCMC", "topics": [ "mem_mcmc" ] }, { "page": "plot_density", "title": "Plot the Response Densities in Basket Trials", "topics": [ "plot_density" ] }, { "page": "plot_map", "title": "Plot the Map Exchangeability of a Basket Trial", "topics": [ "plot_map" ] }, { "page": "plot_mem", "title": "Plot the Prior, MAP, and PEP of a Basket Trial", "topics": [ "plot_mem" ] }, { "page": "plot_pep", "title": "Plot the Posterior Exchangeability of a Basket Trial", "topics": [ "plot_pep" ] }, { "page": "plot_pep_graph", "title": "Plot a Network Graph of the PEP Matrix", "topics": [ "plot_pep_graph" ] }, { "page": "sample_posterior", "title": "Sample Posterior Samples from a Basket Trial", "topics": [ "sample_posterior" ] }, { "page": "update_p0", "title": "Update Full Bayes results with different p0 values", "topics": [ "update_p0" ] }, { "page": "vemu", "title": "Summary Data from the Vemurafenib Study", "topics": [ "vemu", "vemu_wide" ] } ], "_readme": "https://github.com/kaneplusplus/basket/raw/HEAD/README.md", "_rundeps": [ "base64enc", "cachem", "cli", "codetools", "cpp11", "crayon", "doParallel", "dplyr", "farver", "fastmap", "foreach", "generics", "GenSA", "ggforce", "ggplot2", "ggraph", "ggrepel", "glue", "gmp", "graphlayouts", "gridExtra", "gtable", "igraph", "isoband", "iterators", 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