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'. |

as.mcmc.list.crm_fit | Convert 'crm_fit' to instance of 'mcmc.list' |

as.mcmc.list.efftox_fit | Convert 'efftox_fit' to instance of 'mcmc.list' |

as_tibble.augbin_2t_1a_fit | Cast 'augbin_2t_1a_fit' object to 'tibble'. |

as_tibble.dose_finding_paths | Cast 'dose_finding_paths' object to 'tibble'. |

augbin_2t_1a_fit | Class used by 'trialr' to fit Wason & Seaman's Augmented... |

augbin_fit | Class used by 'trialr' to fit Wason & Seaman's Augmented... |

binary_prob_success | Calculate the binary probability of success. |

careful_escalation | Dose selection function that practices careful escalation. |

closest_to_target | Get index of element in vector with value closest to a target |

crm_codified_dose_logistic | Calculate codified CRM doses. |

crm_dtps | Calculate dose-transition pathways for a CRM study |

crm_fit-class | Class of model fit by 'trialr' using the CRM dose-finding... |

crm_params-class | Container class for parameters to fit the CRM models in... |

crm_path_analysis | Fit a CRM model to the incrementally observed outcomes on a... |

crm_prior_beliefs | Get the prior beliefs for a CRM trial scenario. |

crm_process | Process RStan samples from a CRM model. |

df_parse_outcomes | Parse a string of dose-finding trial outcomes to binary... |

dose_finding_fit-class | Class of dose-finding model fit by 'trialr' using Stan. |

dose_finding_path_node-class | Class to hold the elements of a single dose-finding analysis... |

eff_at_dose | Get the number of efficacy events seen at the doses under... |

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_dtps_to_dataframe | Calculate dose-transition pathways for an EffTox study |

efftox_fit-class | Class of model fit by 'trialr' using the EffTox dose-finding... |

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-class | Container class for parameters to fit the EffTox model in... |

efftox_parse_outcomes | Parse a string of EffTox outcomes to binary vector notation. |

efftox_path_analysis | Fit an EffTox model to the incrementally observed outcomes on... |

efftox_priors | Simple class to hold prior hyperparameters for the EffTox... |

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 |

get_efftox_priors | Get normal prior hyperparameters for the EffTox model. |

n_at_dose | Get the number of patients treated at the doses under... |

parse_dose_finding_outcomes | Parse a string of dose-finding trial outcomes. |

parse_eff_tox_dose_finding_outcomes | Parse a string of phase I/II dose-finding trial outcomes. |

peps2_get_data | Get data to run the PePS2 trial example |

peps2_process | Process RStan samples from a BEBOP model fit to PePS2 data |

plot.crm_fit | Plot an crm_fit |

plot.efftox_fit | Plot an efftox_fit |

predict.augbin_2t_1a_fit | Predict probability of success for given tumour size... |

print.augbin_fit | Print augbin_fit object. |

print.crm_fit | Print crm_fit object. |

print.efftox_fit | Print efftox_fit object. |

print.nbg_fit | Print nbg_fit object. |

prior_predictive_augbin_2t_1a | Sample data from the Augmented Binary model prior predictive... |

prob_success | Calculate the probability of success. |

prob_tox_exceeds | Calculate the probability that the rate of toxicity exceeds... |

ranBin2 | Sample pairs of correlated binary events |

rlkjcorr | Sample LKJ correlation matrices. |

spread_paths | Spread the information in dose_finding_paths object to a wide... |

stan_augbin | Fit Wason & Seaman's Augmented Binary model for tumour... |

stan_augbin_demo | Simple helper function to demonstrate fitting of an Augmented... |

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_hierarchical_response_thall | Fit the hierarchical response model described by Thall _et... |

stan_nbg | Fit a Neuenschwander, Branson & Gsponer logit dose-finding... |

stan_peps2 | Fit the P2TNE model developed for the PePS2 trial to some... |

summary.crm_fit | Obtain summary of an crm_fit |

summary.efftox_fit | Obtain summary of an efftox_fit |

total_weight_at_dose | Get the total weight of patient outcomes at the doses under... |

tox_at_dose | Get the number of toxicity events seen at the doses under... |

trialr-package | The 'trialr' package. |

trialr_simulate | Run a simulation study. |

weights_at_dose | Get the weights of patient outcomes at the doses under... |

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