Man pages for trialr
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... |
