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trialr: Clinical Trial Designs in 'rstan'

A collection of clinical trial designs and methods, implemented in 'rstan' and R, including: the Continual Reassessment Method by O'Quigley et al. (1990) <doi:10.2307/2531628>; EffTox by Thall & Cook (2004) <doi:10.1111/j.0006-341X.2004.00218.x>; the two-parameter logistic method of Neuenschwander, Branson & Sponer (2008) <doi:10.1002/sim.3230>; and the Augmented Binary method by Wason & Seaman (2013) <doi:10.1002/sim.5867>; and more. We provide functions to aid model-fitting and analysis. The 'rstan' implementations may also serve as a cookbook to anyone looking to extend or embellish these models. We hope that this package encourages the use of Bayesian methods in clinical trials. There is a preponderance of early phase trial designs because this is where Bayesian methods are used most. If there is a method you would like implemented, please get in touch.

Version: 0.1.6
Depends: R (≥ 3.5.0), methods, Rcpp (≥ 1.0.1)
Imports: rstan (≥ 2.18.2), rstantools (≥ 1.5.1), rlang (≥ 0.4.5), dplyr, purrr, magrittr, stringr, ggplot2, gtools, coda, tidybayes (≥ 2.0.3), tibble (≥ 3.0.0), binom, MASS
LinkingTo: StanHeaders (≥ 2.18.1), rstan (≥ 2.18.2), BH (≥ 1.69.0-1), Rcpp (≥ 1.0.1), RcppEigen (≥ 0.3.3.5.0), RcppParallel (≥ 5.0.2)
Suggests: testthat, knitr, rmarkdown, tidyr, ggridges, DiagrammeR
Published: 2023-03-12
DOI: 10.32614/CRAN.package.trialr
Author: Kristian Brock ORCID iD [aut, cre], Trustees of Columbia University [cph]
Maintainer: Kristian Brock <kristian.brock at gmail.com>
BugReports: https://github.com/brockk/trialr/issues
License: GPL (≥ 3)
URL: https://github.com/brockk/trialr
NeedsCompilation: yes
SystemRequirements: GNU make
Materials: README NEWS
CRAN checks: trialr results

Documentation:

Reference manual: trialr.pdf
Vignettes: CRM: Continual Reassessment Method
Visualisation with CRM
Dose pathways with CRM
CRM Case Study 1 - Levy et al (2006)
Time-to-Event Continual Reassessment Method
NeuenschwanderBransonGsponer
EffTox
Hierarchical Bayesian Model for Binary Responses
BEBOP: Bayesian Evaluation of Bivariate Binary Outcomes and Predictive Information

Downloads:

Package source: trialr_0.1.6.tar.gz
Windows binaries: r-devel: trialr_0.1.6.zip, r-release: trialr_0.1.6.zip, r-oldrel: trialr_0.1.6.zip
macOS binaries: r-release (arm64): trialr_0.1.6.tgz, r-oldrel (arm64): trialr_0.1.6.tgz, r-release (x86_64): trialr_0.1.6.tgz, r-oldrel (x86_64): trialr_0.1.6.tgz
Old sources: trialr archive

Reverse dependencies:

Reverse imports: brms.mmrm, escalation, historicalborrowlong

Linking:

Please use the canonical form https://CRAN.R-project.org/package=trialr to link to this page.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.