# Bayesian Logistic Regression for Oncology Dose-Escalation Trials

## Documentation for package ‘OncoBayes2’ version 0.9-3

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

OncoBayes2-package | OncoBayes2
as_draws | Transform 'blrmfit' or 'blrm_trial' to 'draws' objects
as_draws.blrmfit | Transform 'blrmfit' or 'blrm_trial' to 'draws' objects
as_draws.blrm_trial | Transform 'blrmfit' or 'blrm_trial' to 'draws' objects
as_draws_array | Transform 'blrmfit' or 'blrm_trial' to 'draws' objects
as_draws_array.blrmfit | Transform 'blrmfit' or 'blrm_trial' to 'draws' objects
as_draws_array.blrm_trial | Transform 'blrmfit' or 'blrm_trial' to 'draws' objects
as_draws_df | Transform 'blrmfit' or 'blrm_trial' to 'draws' objects
as_draws_df.blrmfit | Transform 'blrmfit' or 'blrm_trial' to 'draws' objects
as_draws_df.blrm_trial | Transform 'blrmfit' or 'blrm_trial' to 'draws' objects
as_draws_list | Transform 'blrmfit' or 'blrm_trial' to 'draws' objects
as_draws_list.blrmfit | Transform 'blrmfit' or 'blrm_trial' to 'draws' objects
as_draws_list.blrm_trial | Transform 'blrmfit' or 'blrm_trial' to 'draws' objects
as_draws_matrix | Transform 'blrmfit' or 'blrm_trial' to 'draws' objects
as_draws_matrix.blrmfit | Transform 'blrmfit' or 'blrm_trial' to 'draws' objects
as_draws_matrix.blrm_trial | Transform 'blrmfit' or 'blrm_trial' to 'draws' objects
as_draws_rvars | Transform 'blrmfit' or 'blrm_trial' to 'draws' objects
as_draws_rvars.blrmfit | Transform 'blrmfit' or 'blrm_trial' to 'draws' objects
as_draws_rvars.blrm_trial | Transform 'blrmfit' or 'blrm_trial' to 'draws' objects
bind_rows_0 | Bind rows of multiple data frames with zero fill
blrm_exnex | Bayesian Logistic Regression Model for N-compounds with EXNEX
blrm_formula_linear | Build a BLRM formula with linear interaction term in logit-space
blrm_formula_saturating | Build a BLRM formula with saturating interaction term in logit-space
blrm_trial | Dose-Escalation Trials guided by Bayesian Logistic Regression Model
codata_combo2 | Dataset: historical and concurrent data on a two-way combination
critical_quantile | Critical quantile
critical_quantile.blrmfit | Critical quantile
critical_quantile.blrm_trial | Critical quantile
diagnostic-quantities | Extract Diagnostic Quantities of 'OncoBayes2' Models
dose_info_combo2 | Dataset: trial dose information for a dual-agent combination study
draws-OncoBayes2 | Transform 'blrmfit' or 'blrm_trial' to 'draws' objects
drug_info_combo2 | Dataset: drug information for a dual-agent combination study
example-combo2 | Two-drug combination example
example-combo2_trial | Two-drug combination example using BLRM Trial
example-combo3 | Three-drug combination example
example-single-agent | Single Agent Example
example_model | Runs example models
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
hist_SA | Single-agent example
inv_logit | Logit (log-odds) and inverse-logit function.
lodds | Logit (log-odds) and inverse-logit function.
logit | Logit (log-odds) and inverse-logit function.
log_posterior | Extract Diagnostic Quantities of 'OncoBayes2' Models
log_posterior.blrmfit | Extract Diagnostic Quantities of 'OncoBayes2' Models
neff_ratio | Extract Diagnostic Quantities of 'OncoBayes2' Models
neff_ratio.blrmfit | Extract Diagnostic Quantities of 'OncoBayes2' Models
nsamples | Return the number of posterior samples
nsamples.blrmfit | Return the number of posterior samples
nuts_params | Extract Diagnostic Quantities of 'OncoBayes2' Models
nuts_params.blrmfit | Extract Diagnostic Quantities of 'OncoBayes2' Models
OncoBayes2 | OncoBayes2
plot_blrm | Plot a fitted model
plot_toxicity_curve | Plot a fitted model
plot_toxicity_curve.blrmfit | Plot a fitted model
plot_toxicity_curve.blrm_trial | Plot a fitted model
plot_toxicity_intervals | Plot a fitted model
plot_toxicity_intervals.blrmfit | Plot a fitted model
plot_toxicity_intervals.blrm_trial | Plot a fitted model
plot_toxicity_intervals_stacked | Plot a fitted model
plot_toxicity_intervals_stacked.blrmfit | Plot a fitted model
plot_toxicity_intervals_stacked.blrm_trial | Plot a fitted model
posterior_interval | Posterior intervals
posterior_interval.blrmfit | Posterior intervals
posterior_linpred | Posterior of linear predictor
posterior_linpred.blrmfit | Posterior of linear predictor
posterior_predict | Posterior of predictive
posterior_predict.blrmfit | Posterior of predictive
predictive_interval | Posterior predictive intervals
predictive_interval.blrmfit | Posterior predictive intervals
print.blrmfit | Bayesian Logistic Regression Model for N-compounds with EXNEX
print.blrm_trial | Dose-Escalation Trials guided by Bayesian Logistic Regression Model
prior_summary | Summarise model prior
prior_summary.blrmfit | Summarise model prior
rhat | Extract Diagnostic Quantities of 'OncoBayes2' Models
rhat.blrmfit | Extract Diagnostic Quantities of 'OncoBayes2' Models
summary.blrmfit | Summarise model results
summary.blrm_trial | Summarise trial
update.blrmfit | Update data of a BLRM analysis
update.blrm_trial | Update data and/or prior of a BLRM trial