Function reference • trialr

All functions
`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 Binary method in single arm trials with two post-baseline tumour assessments.
`augbin_fit()`	Class used by trialr to fit Wason & Seaman's Augmented Binary method.
`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 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_path_analysis()`	Fit a CRM model to the incrementally observed outcomes on a trial pathway.
`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 vector notation.
`dose_finding_fit()`	Class of dose-finding model fit by trialr using Stan.
`dose_finding_path_node()`	Class to hold the elements of a single dose-finding analysis residing in a pathway of analyses.
`eff_at_dose()`	Get the number of efficacy events seen at the doses under investigation.
`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 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_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 a trial pathway.
`efftox_priors()`	Simple class to hold prior hyperparameters for the EffTox model.
`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 investigation.
`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 measurements.
`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 distribution.
`prob_success()`	Calculate the probability of success.
`prob_tox_exceeds()`	Calculate the probability that the rate of toxicity exceeds some threshold
`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 data.frame format.
`stan_augbin()`	Fit Wason & Seaman's Augmented Binary model for tumour response.
`stan_augbin_demo()`	Simple helper function to demonstrate fitting of an Augmented Binary model.
`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 al. (2003).
`stan_nbg()`	Fit a Neuenschwander, Branson & Gsponer logit dose-finding model
`stan_peps2()`	Fit the P2TNE model developed for the PePS2 trial to some outcomes.
`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 investigation.
`tox_at_dose()`	Get the number of toxicity events seen at the doses under investigation.
`trialr-package`	The 'trialr' package.
`trialr_simulate()`	Run a simulation study.
`weights_at_dose()`	Get the weights of patient outcomes at the doses under investigation.

Reference

All functions