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. |