Package: basket
Title: Basket Trial Analysis
Version: 0.12.2
Authors@R: c(
  person(given = "Nan", 
         family = "Chen",
         email = "nchen2@mdanderson.org",
         role = c("aut")),
  person(given = "Ryan", 
         family = "Hafen",
         email = "rhafen@gmail.com",
         role = c("ctb")),
  person(given = "Brian", 
         family = "Hobbs",
         email = "bphobbs@gmail.com",
         role = c("aut")),
  person(given = "Alex", 
         family = "Kaizer",
         email = "alex.kaizer@ucdenver.edu",
         role = c("aut")),
  person(given = "Wei", 
         family = "Wei",
         email = "awei.wei@yale.edu",
         role = c("aut")),
  person(given = "Michael J.", 
         family = "Kane",
         email = "michael.kane@yale.edu",
         role = c("aut", "cre"),
         comment = c(ORCID = "http://orcid.org/0000-0003-1899-6662")))
Description: Implementation of multisource exchangeability models for
        Bayesian analyses of prespecified subgroups arising in the
        context of basket trial design and monitoring.  The R 'basket'
        package facilitates implementation of the binary, symmetric
        multi-source exchangeability model (MEM) with posterior
        inference arising from both exact computation and Markov chain
        Monte Carlo sampling. Analysis output includes full posterior
        samples as well as posterior probabilities, highest posterior
        density (HPD) interval boundaries, effective sample sizes
        (ESS), mean and median estimations, posterior exchangeability
        probability matrices, and maximum a posteriori MEMs. In
        addition to providing "basketwise" analyses, the package
        includes similar calculations for "clusterwise" analyses for
        which subgroups are combined into meta-baskets, or clusters,
        using graphical clustering algorithms that treat the posterior
        exchangeability probabilities as edge weights. In addition
        plotting tools are provided to visualize basket and cluster
        densities as well as their exchangeability.  References include
        Hyman, D.M., Puzanov, I., Subbiah, V., Faris, J.E., Chau, I.,
        Blay, J.Y., Wolf, J., Raje, N.S., Diamond, E.L., Hollebecque,
        A. and Gervais, R (2015) <doi:10.1056/NEJMoa1502309>; Hobbs,
        B.P. and Landin, R. (2018) <doi:10.1002/sim.7893>; Hobbs, B.P.,
        Kane, M.J., Hong, D.S. and Landin, R. (2018)
        <doi:10.1093/annonc/mdy457>; and Kaizer, A.M., Koopmeiners,
        J.S. and Hobbs, B.P. (2017) <doi:10.1093/biostatistics/kxx031>.
Depends: R (>= 3.5.0)
License: LGPL-2
Maintainer: Michael J. Kane <michael.kane@yale.edu>
Imports: GenSA, foreach, ggplot2, stats, tibble, tidyr, dplyr, igraph,
        gridExtra, itertools, crayon, cli, RColorBrewer, tidygraph,
        parallel, doParallel, ggraph, partitions, pscl
LazyData: true
Encoding: UTF-8
RoxygenNote: 7.2.3
URL: https://github.com/kaneplusplus/basket
BugReports: https://github.com/kaneplusplus/basket/issues
Suggests: knitr, rmarkdown, testthat (>= 3.0.0),
VignetteBuilder: knitr
Config/testthat/edition: 3
Config/pak/sysreqs: libfontconfig1-dev libfreetype6-dev libglpk-dev
        libgmp3-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: 2026-07-05 08:47:33 UTC; root
Author: Nan Chen [aut],
  Ryan Hafen [ctb],
  Brian Hobbs [aut],
  Alex Kaizer [aut],
  Wei Wei [aut],
  Michael J. Kane [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-1899-6662>)