A Modular Approach to Dose-Finding Clinical Trials


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Documentation for package ‘escalation’ version 0.1.8

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escalation-package The 'escalation' package.
as_tibble.derived_dose_selector Cast 'dose_selector' object to 'tibble'.
as_tibble.dose_paths Cast 'dose_paths' object to 'tibble'.
as_tibble.simulations_collection Convert a simulations_collection to a tibble
calculate_probabilities Calculate dose-path probabilities
cohort Cohort numbers of evaluated patients.
cohorts_of_n Sample times between patient arrivals using the exponential distribution.
continue Should this dose-finding experiment continue?
convergence_plot Plot the convergence processes from a collection of simulations.
CorrelatedPatientSample A sample of patients that experience correlated events in simulations.
crystallised_dose_paths Dose-paths with probabilities attached.
demand_n_at_dose Demand there are n patients at a dose before condisdering stopping.
dont_skip_doses Prevent skipping of doses.
doses_given Doses given to patients.
dose_admissible Is each dose admissible?
dose_indices Dose indices
dose_paths Dose pathways
dose_paths_function Get function for calculating dose pathways.
eff Binary efficacy outcomes.
eff_at_dose Number of toxicities seen at each dose.
eff_limit Efficacy rate limit
empiric_eff_rate Observed efficacy rate at each dose.
empiric_tox_rate Observed toxicity rate at each dose.
enforce_three_plus_three Enforce that a trial path has followed the 3+3 method.
escalation The 'escalation' package.
fit Fit a dose-finding model.
follow_path Follow a pre-determined dose administration path.
get_boin Get an object to fit the BOIN model using the BOIN package.
get_boin12 Get an object to fit the BOIN12 model for phase I/II dose-finding.
get_dfcrm Get an object to fit the CRM model using the dfcrm package.
get_dose_paths Calculate future dose paths.
get_empiric_crm_skeleton_weights Get posterior model weights for several empiric CRM skeletons.
get_mtpi Get an object to fit the mTPI dose-finding model.
get_mtpi2 Get an object to fit the mTPI-2 dose-finding model.
get_potential_outcomes Get potential outcomes from a list of PatientSamples
get_random_selector Get an object to fit a dose-selector that randomly selects doses.
get_three_plus_three Get an object to fit the 3+3 model.
get_tpi Get an object to fit the TPI dose-finding model.
get_trialr_crm Get an object to fit the CRM model using the trialr package.
get_trialr_efftox Get an object to fit the EffTox model using the trialr package.
get_trialr_nbg Get an object to fit the NBG dose-finding model using the trialr package.
get_wages_and_tait Get an object to fit Wages & Tait's model for phase I/II dose-finding.
graph_paths Visualise dose-paths as a graph
is_randomising Is this selector currently randomly allocating doses?
mean_prob_eff Mean efficacy rate at each dose.
mean_prob_tox Mean toxicity rate at each dose.
median_prob_eff Median efficacy rate at each dose.
median_prob_tox Median toxicity rate at each dose.
model_frame Model data-frame.
num_cohort_outcomes Number of different possible outcomes for a cohort of patients
num_doses Number of doses.
num_dose_path_nodes Number of nodes in dose-paths analysis
num_eff Total number of efficacies seen.
num_patients Number of patients evaluated.
num_tox Total number of toxicities seen.
n_at_dose Number of patients treated at each dose.
n_at_recommended_dose Number of patients treated at the recommended dose.
parse_phase1_2_outcomes Parse a string of phase I/II dose-finding outcomes to vector notation.
parse_phase1_outcomes Parse a string of phase I dose-finding outcomes to vector notation.
PatientSample A sample of patients to use in simulations.
phase1_2_outcomes_to_cohorts Break a phase I/II outcome string into a list of cohort parts.
phase1_outcomes_to_cohorts Break a phase I outcome string into a list of cohort parts.
prob_administer Percentage of patients treated at each dose.
prob_eff_exceeds Probability that the toxicity rate exceeds some threshold.
prob_eff_quantile Quantile of the efficacy rate at each dose.
prob_eff_samples Get samples of the probability of toxicity.
prob_recommend Probability of recommendation
prob_tox_exceeds Probability that the toxicity rate exceeds some threshold.
prob_tox_quantile Quantile of the toxicity rate at each dose.
prob_tox_samples Get samples of the probability of toxicity.
recommended_dose Recommended dose for next patient or cohort.
selector Dose selector.
selector_factory Dose selector factory.
select_boin12_obd Select dose by BOIN12's OBD-choosing algorithm.
select_boin_mtd Select dose by BOIN's MTD-choosing algorithm.
select_dose_by_cibp Select dose by the CIBP selection criterion.
select_mtpi2_mtd Select dose by mTPI2's MTD-choosing algorithm.
select_mtpi_mtd Select dose by mTPI's MTD-choosing algorithm.
select_tpi_mtd Select dose by TPI's MTD-choosing algorithm.
simulate_compare Simulate clinical trials for several designs using common patients.
simulate_trials Simulate clinical trials.
simulations Simulated trials.
simulations_collection Make an instance of type 'simulations_collection'
simulation_function Get function for simulating trials.
spread_paths Spread the information in dose_finding_paths object to a wide data.frame format.
stack_sims_vert Stack 'simulations_collection' results vertically
stop_at_n Stop when there are n patients in total.
stop_when_n_at_dose Stop when there are n patients at a dose.
stop_when_too_toxic Stop trial and recommend no dose when a dose is too toxic.
stop_when_tox_ci_covered Stop when uncertainty interval of prob tox is covered.
supports_sampling Does this selector support sampling of outcomes?
three_plus_three Fit the 3+3 model to some outcomes.
tox Binary toxicity outcomes.
tox_at_dose Number of toxicities seen at each dose.
tox_limit Toxicity rate limit
tox_target Target toxicity rate
trial_duration Duration of trials.
try_rescue_dose Demand that a rescue dose is tried before stopping is permitted.
utility Utility score of each dose.