# Clinical Trial Designs in 'RStan'

## Documentation for package ‘trialr’ version 0.0.1

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

## Help Pages

trialr-package | Clinical Trial Designs in 'RStan'
BebopInPeps2 | Stan model for BEBOP implementation in PePS2 clinical trial
EffTox | Stan model for EffTox dose-finding design
efftox_analysis | Processed results of an EffTox dose-update analysis
efftox_analysis_to_df | EffTox analysis to data.frame
efftox_contour_plot | Plot EffTox utility contours
efftox_dtps | Calculate dose-transition pathways for an EffTox study
efftox_get_tox | Get the probability of toxicity for probability-of-efficacy and utility pairs
efftox_parameters_demo | Get parameters to run the EffTox demo
efftox_params | Parameters to be passed to EffTox model in Stan
efftox_parse_outcomes | Parse a string of EffTox outcomes to binary vector notation.
efftox_process | Process RStan samples from an EffTox model
efftox_simulate | Run EffTox simulations
efftox_solve_p | Calculate the p-index for EffTox utility contours
efftox_superiority | Get dose-superiority matrix in EffTox
efftox_utility | Get the utility of efficacy & toxicity probability pairs
efftox_utility_density_plot | Plot densities of EffTox dose utilities
model_BebopInPeps2 | Stan model for BEBOP implementation in PePS2 clinical trial
model_EffTox | Stan model for EffTox dose-finding design
model_ThallHierachicalBinary | Stan model for Thall et al.'s hierarchical Bayesian model for binary data
model_ThallHierarchicalBinary | Stan model for Thall et al.'s hierarchical Bayesian model for binary data
peps2_get_data | Get data to run the PePS2 trial example
peps2_params | Parameters to be passed to 'BebopInPeps2' model in Stan
peps2_process | Process RStan samples from a BEBOP model fit to PePS2 data
peps2_run_sims | Run simulations of BEBOP in PePS2
ranBin2 | Sample pairs of correlated binary events
Rcpp_model_BebopInPeps2 | Compiled Stan model for BEBOP implementation in PePS2 clinical trial
Rcpp_model_BebopInPeps2-class | Compiled Stan model for BEBOP implementation in PePS2 clinical trial
Rcpp_model_EffTox | Compiled Stan model for EffTox dose-finding design
Rcpp_model_EffTox-class | Compiled Stan model for EffTox dose-finding design
Rcpp_model_ThallHierachicalBinary | Compiled Stan model for Thall et al.'s hierarchical Bayesian model for binary data
Rcpp_model_ThallHierachicalBinary-class | Compiled Stan model for Thall et al.'s hierarchical Bayesian model for binary data
Rcpp_model_ThallHierarchicalBinary | Compiled Stan model for Thall et al.'s hierarchical Bayesian model for binary data
Rcpp_model_ThallHierarchicalBinary-class | Compiled Stan model for Thall et al.'s hierarchical Bayesian model for binary data
stanmodels | Stan models used by trialr
stan_files | Stan file locations
ThallHierachicalBinary | Stan model for Thall et al.'s hierarchical Bayesian model for binary data
ThallHierarchicalBinary | Stan model for Thall et al.'s hierarchical Bayesian model for binary data
thallhierarchicalbinary_parameters_demo | Get parameters to run the demo of Thall Hierarchical Binary model
thallhierarchicalbinary_params | Parameters to be passed to the ThallHierachicalBinary model in Stan
trialr | Clinical Trial Designs in 'RStan'