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_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

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.

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_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.