R: Clinical Trial Designs in 'rstan'

# Clinical Trial Designs in 'rstan'

## Documentation for package ‘trialr’ version 0.1.6

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## 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.