Clinical Trial Designs in 'rstan'

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Documentation for package ‘trialr’ version 0.1.6

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

trialr-package	The 'trialr' package.
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.
binary_prob_success.augbin_2t_1a_fit	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_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_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_fit-class	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.
dose_finding_path_node-class	Class to hold the elements of a single dose-finding analysis residing in a pathway of analyses.
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_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_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
eff_at_dose	Get the number of efficacy events seen at the doses under investigation.
eff_at_dose.efftox_fit	Get the number of efficacy events seen at the doses under investigation.
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.
n_at_dose.dose_finding_fit	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_success.augbin_2t_1a_fit	Calculate the probability of success.
prob_tox_exceeds	Calculate the probability that the rate of toxicity exceeds some threshold
prob_tox_exceeds.dose_finding_fit	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.
total_weight_at_dose.default	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.
tox_at_dose.dose_finding_fit	Get the number of toxicity events seen at the doses under investigation.
trialr	The 'trialr' package.
trialr_simulate	Run a simulation study.
weights_at_dose	Get the weights of patient outcomes at the doses under investigation.
weights_at_dose.crm_fit	Get the weights of patient outcomes at the doses under investigation.
weights_at_dose.default	Get the weights of patient outcomes at the doses under investigation.