Package: OncoBayes2 0.8-9

OncoBayes2: Bayesian Logistic Regression for Oncology Dose-Escalation Trials

Bayesian logistic regression model with optional EXchangeability-NonEXchangeability parameter modelling for flexible borrowing from historical or concurrent data-sources. The safety model can guide dose-escalation decisions for adaptive oncology Phase I dose-escalation trials which involve an arbitrary number of drugs. Please refer to Neuenschwander et al. (2008) <doi:10.1002/sim.3230> and Neuenschwander et al. (2016) <doi:10.1080/19466315.2016.1174149> for details on the methodology.

Authors:Novartis Pharma AG [cph], Sebastian Weber [aut, cre], Lukas A. Widmer [aut], Andrew Bean [aut], Trustees of Columbia University [cph]

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OncoBayes2.pdf |OncoBayes2.html✨
OncoBayes2/json (API)
NEWS

# Install 'OncoBayes2' in R:
install.packages('OncoBayes2', repos = c('https://weberse2.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • codata_combo2 - Dataset: historical and concurrent data on a two-way combination
  • dose_info_combo2 - Dataset: trial dose information for a dual-agent combination study
  • drug_info_combo2 - Dataset: drug information for a dual-agent combination study
  • hist_SA - Single-agent example
  • hist_combo2 - Dataset: historical data on two single-agents to inform a combination study
  • hist_combo3 - Dataset: historical and concurrent data on a three-way combination

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

22 exports 0.00 score 66 dependencies 14 scripts 394 downloads

Last updated 1 years agofrom:235d2a8fe8. Checks:OK: 1 NOTE: 8. Indexed: yes.

TargetResultDate
Doc / VignettesOKAug 27 2024
R-4.5-win-x86_64NOTEAug 27 2024
R-4.5-linux-x86_64NOTEAug 27 2024
R-4.4-win-x86_64NOTEAug 27 2024
R-4.4-mac-x86_64NOTEAug 27 2024
R-4.4-mac-aarch64NOTEAug 27 2024
R-4.3-win-x86_64NOTEAug 27 2024
R-4.3-mac-x86_64NOTEAug 27 2024
R-4.3-mac-aarch64NOTEAug 27 2024

Exports:bind_rows_0blrm_exnexblrm_formula_linearblrm_formula_saturatingblrm_trialcritical_quantileexample_modelinv_logitlog_posteriorlogitneff_rationsamplesnuts_paramsplot_toxicity_curveplot_toxicity_intervalsplot_toxicity_intervals_stackedposterior_intervalposterior_linpredposterior_predictpredictive_intervalprior_summaryrhat

Dependencies:abindassertthatbackportsbayesplotBHcallrcheckmateclicolorspacecpp11descdistributionaldplyrfansifarverFormulagenericsggplot2ggridgesgluegridExtragtableinlineisobandlabelinglatticelifecycleloomagrittrMASSMatrixmatrixStatsmgcvmunsellnlmenumDerivpillarpkgbuildpkgconfigplyrposteriorprocessxpspurrrQuickJSRR6RColorBrewerRcppRcppEigenRcppParallelreshape2rlangrstanrstantoolsscalesStanHeadersstringistringrtensorAtibbletidyrtidyselectutf8vctrsviridisLitewithr

Guiding Oncology Dose-Escalation Trials

Andrew Bean, Sebastian Weber, Lukas Widmer

Rendered fromintroduction.Rmdusingknitr::rmarkdownon Aug 27 2024.

Last update: 2022-08-25
Started: 2019-08-29

Readme and manuals

Help Manual

Help pageTopics
Bind rows of multiple data frames with zero fillbind_rows_0
Bayesian Logistic Regression Model for N-compounds with EXNEXblrm_exnex print.blrmfit
Build a BLRM formula with linear interaction term in logit-spaceblrm_formula_linear
Build a BLRM formula with saturating interaction term in logit-spaceblrm_formula_saturating
Dose-Escalation Trials guided by Bayesian Logistic Regression Modelblrm_trial print.blrm_trial
Dataset: historical and concurrent data on a two-way combinationcodata_combo2
Critical quantilecritical_quantile critical_quantile.blrmfit critical_quantile.blrm_trial
Extract Diagnostic Quantities of 'OncoBayes2' Modelsdiagnostic-quantities log_posterior log_posterior.blrmfit neff_ratio neff_ratio.blrmfit nuts_params nuts_params.blrmfit rhat rhat.blrmfit
Dataset: trial dose information for a dual-agent combination studydose_info_combo2
Dataset: drug information for a dual-agent combination studydrug_info_combo2
Runs example modelsexample_model
Two-drug combination exampleexample-combo2
Two-drug combination example using BLRM Trialexample-combo2_trial
Three-drug combination exampleexample-combo3
Single Agent Exampleexample-single-agent
Dataset: historical data on two single-agents to inform a combination studyhist_combo2
Dataset: historical and concurrent data on a three-way combinationhist_combo3
Single-agent examplehist_SA
Logit (log-odds) and inverse-logit function.inv_logit lodds logit
Return the number of posterior samplesnsamples nsamples.blrmfit
OncoBayes2OncoBayes2
Plot a fitted modelplot_blrm plot_toxicity_curve plot_toxicity_curve.blrmfit plot_toxicity_curve.blrm_trial plot_toxicity_intervals plot_toxicity_intervals.blrmfit plot_toxicity_intervals.blrm_trial plot_toxicity_intervals_stacked plot_toxicity_intervals_stacked.blrmfit plot_toxicity_intervals_stacked.blrm_trial
Posterior intervalsposterior_interval posterior_interval.blrmfit
Posterior of linear predictorposterior_linpred posterior_linpred.blrmfit
Posterior of predictiveposterior_predict posterior_predict.blrmfit
Posterior predictive intervalspredictive_interval predictive_interval.blrmfit
Summarise model priorprior_summary prior_summary.blrmfit
Summarise trialsummary.blrm_trial
Summarise model resultssummary.blrmfit
Update data and/or prior of a BLRM trialupdate.blrm_trial
Update data of a BLRM analysisupdate.blrmfit