crmPack/DESCRIPTION at main · openpharma/crmPack · GitHub

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Package: crmPack
Title: Object-Oriented Implementation of Dose Escalation Designs
Version: 2.1.0.9000
Authors@R: c(
    person("Daniel", "Sabanés Bové", , "daniel.sabanes_bove@rconis.com", role = c("aut", "cre"),
           comment = c(ORCID = "0000-0002-0176-9239")),
    person("Wai", "Yin Yeung", , "winnie.yeung@roche.com", role = "aut"),
    person("Burak Kuersad", "Guenhan", , "burakgunhan@gmail.com", role = "aut"),
    person("Giuseppe", "Palermo", , "giuseppe.palermo@roche.com", role = "aut"),
    person("Thomas", "Jaki", , "jaki.thomas@gmail.com", role = "aut"),
    person("Jiawen", "Zhu", , "zhu.jiawen@gene.com", role = "aut"),
    person("Ziwei", "Liao", , "ziwei.liao.fdu@gmail.com", role = "aut"),
    person("Dimitris", "Kontos", , "dimitris.kontos@bayer.com", role = "aut"),
    person("Marlene", "Schulte-Goebel", , "marlene.schulte-goebel@merckgroup.com", role = "aut"),
    person("Doug", "Kelkhoff", , "doug.kelkhoff@gmail.com", role = "aut",
           comment = c(ORCID = "0009-0003-7845-4061")),
    person("Oliver", "Boix", , "oliver.boix@bayer.com", role = "aut"),
    person("Robert", "Adams", , "robert.adams@bayer.com", role = "aut"),
    person("Clara", "Beck", , "clara.beck@bayer.com", role = "aut"),
    person("John", "Kirkpatrick", , "john@puzzledface.net", role = "aut"),
    person("Wojciech", "Wójciak", , "wojciech.wojciak@gmail.com", role = "aut"),
    person("Guanya", "Peng", , role = "aut"),
    person("Prerana", "Chandratre", , role = "aut"),
    person("F. Hoffmann-La Roche AG", role = c("cph", "fnd")),
    person("Merck Healthcare KGaA", role = c("cph", "fnd")),
    person("Bayer AG", role = c("cph", "fnd")),
    person("RPACT GmbH", role = c("cph", "fnd"))
  )
Description: Implements a wide range of dose escalation
    designs. The focus is on model-based designs, ranging from classical and
    modern continual reassessment methods (CRMs) based on dose-limiting toxicity
    endpoints to dual-endpoint designs taking into account a biomarker/efficacy
    outcome. Bayesian inference is performed via MCMC sampling in JAGS, and it is easy
    to setup a new design with custom JAGS code. However, it is also possible to
    implement 3+3 designs for comparison or models with non-Bayesian estimation.
    The whole package is written in a modular form in the S4 class system, making it
    very flexible for adaptation to new models, escalation or stopping rules.
    Further details are presented in
    Sabanés Bové et al. (2019) <doi:10.18637/jss.v089.i10>.
License: GPL (>= 2)
URL: https://docs.crmpack.org/
BugReports: https://github.com/openpharma/crmPack/issues
Depends:
    ggplot2 (>= 3.0.0),
    graphics,
    R (>= 4.1.0)
Imports:
    checkmate (>= 2.2.0),
    dplyr,
    futile.logger,
    GenSA,
    gridExtra,
    kableExtra,
    knitr,
    lifecycle,
    magrittr,
    methods,
    mvtnorm,
    parallel,
    parallelly,
    Rdpack,
    rjags,
    rlang,
    survival,
    tibble,
    tidyselect (>= 1.2.0),
    tools,
    utils
Suggests:
    bookdown,
    broom,
    covr,
    data.tree,
    decider,
    DiagrammeR,
    ggmcmc,
    quarto (>= 1.4),
    rmarkdown,
    stringr,
    testthat (>= 3.0.0),
    tidyr,
    vdiffr,
    withr
VignetteBuilder:
    knitr,
    quarto
Config/testthat/edition: 3
Encoding: UTF-8
Language: en-US
LazyLoad: yes
Roxygen: list(markdown = TRUE)
RdMacros: Rdpack
Collate:
    'Backfill-validity.R'
    'CrmPackClass-class.R'
    'Rules-validity.R'
    'helpers.R'
    'Rules-class.R'
    'Backfill-class.R'
    'Backfill-methods.R'
    'CrmPackClass-methods.R'
    'Data-validity.R'
    'Data-class.R'
    'helpers_data.R'
    'Data-methods.R'
    'ModelParams-validity.R'
    'ModelParams-class.R'
    'Model-validity.R'
    'helpers_jags.R'
    'Model-class.R'
    'HierarchicalModel-class.R'
    'TwoDrugsCombo-class.R'
    'Design-validity.R'
    'Design-class.R'
    'McmcOptions-validity.R'
    'McmcOptions-class.R'
    'McmcOptions-methods.R'
    'Samples-validity.R'
    'Samples-class.R'
    'logger.R'
    'helpers_covr.R'
    'mcmc.R'
    'Simulations-validity.R'
    'Simulations-class.R'
    'helpers_broom.R'
    'helpers_rules.R'
    'Model-methods.R'
    'checkmate.R'
    'Rules-methods.R'
    'Design-methods.R'
    'HierarchicalDesign-validity.R'
    'HierarchicalDesign-class.R'
    'HierarchicalDesign-methods.R'
    'fromQuantiles.R'
    'Samples-methods.R'
    'Simulations-methods.R'
    'crmPack-package.R'
    'helpers_backfill.R'
    'helpers_design.R'
    'helpers_knitr.R'
    'helpers_knitr_Backfill.R'
    'helpers_knitr_CohortSize.R'
    'helpers_knitr_Design.R'
    'helpers_knitr_GeneralData.R'
    'helpers_knitr_GeneralModel.R'
    'helpers_knitr_Increments.R'
    'helpers_knitr_NextBest.R'
    'helpers_knitr_Opening.R'
    'helpers_knitr_Recruitment.R'
    'helpers_knitr_SafetyWindow.R'
    'helpers_knitr_Stopping.R'
    'helpers_model.R'
    'helpers_samples.R'
    'helpers_simulations.R'
    'utils-pipe.R'
    'utils.R'
Config/roxygen2/version: 8.0.0
Remotes:
    Boehringer-Ingelheim/decider