Clinical Trial Designs in 'RStan'


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Documentation for package ‘trialr’ version 0.0.7

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trialr-package Clinical Trial Designs in 'RStan'
as.data.frame.crm_fit Convert crm_fit object to 'data.frame'.
as.data.frame.efftox_fit Convert efftox_fit object to 'data.frame'.
BebopInPeps2 Stan model for BEBOP implementation in PePS2 clinical trial
crm_fit Class of model fit by 'trialr' using the CRM dose-finding design.
crm_fit-class Class of model fit by 'trialr' using the CRM dose-finding design.
crm_params Container class for parameters to fit the CRM models in trialr.
crm_params-class Container class for parameters to fit the CRM models in trialr.
crm_process Process RStan samples from a CRM model
df_parse_outcomes Parse a string of dose-finding trial outcomes to binary vector notation.
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_fit Class of model fit by 'trialr' using the EffTox dose-finding design.
efftox_fit-class Class of model fit by 'trialr' using the EffTox dose-finding design.
efftox_get_tox Get the Prob(Tox) for Prob(Eff) and utility pairs
efftox_parameters_demo Get parameters to run the EffTox demo
efftox_params Container class for parameters to fit the EffTox model in trialr.
efftox_params-class Container class for parameters to fit the EffTox model in trialr.
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
gather_samples.crm_fit Extract tall data.frame of posterior prob_tox samples.
gather_samples.efftox_fit Extract tall data.frame of posterior variable samples.
model_BebopInPeps2 Stan model for BEBOP implementation in PePS2 clinical trial
model_EffTox Stan model for EffTox dose-finding design
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
plot.crm_fit Plot an crm_fit
plot.efftox_fit Plot an efftox_fit
print.crm_fit Print crm_fit object.
print.efftox_fit Print efftox_fit object.
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_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_crm Fit a CRM model
stan_efftox Fit an EffTox model
stan_efftox_demo Fit the EffTox model presented in Thall et al. (2014)
stan_files Stan file locations
summary.crm_fit Obtain summary of an crm_fit
summary.efftox_fit Obtain summary of an efftox_fit
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'