A Modular Approach to Dose-Finding Clinical Trials

Documentation for package ‘escalation’ version 0.1.10

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The 'escalation' package.

-- A --

as_tibble.dose_paths	Cast 'dose_paths' object to 'tibble'.
as_tibble.selector	Cast 'dose_selector' object to 'tibble'.
as_tibble.simulations_collection	Convert a simulations_collection to a tibble

-- C --

calculate_probabilities	Calculate dose-path probabilities
check_dose_selector_consistency	Check the consistency of a dose_selector instance
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.

-- D --

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.

-- E --

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.

-- F --

fit	Fit a dose-finding model.
follow_path	Follow a pre-determined dose administration path.

-- G --

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_dfcrm_tite	Get an object to fit the TITE-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_crm_tite	Get an object to fit the TITE-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_trialr_nbg_tite	Get an object to fit a TITE version of the NBG dose-finding model using trialr
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

-- I --

Is this selector currently randomly allocating doses?

-- L --

Weights for tolerance and toxicity events using linear function of time

-- M --

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.

-- N --

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.

-- P --

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.

-- R --

Recommended dose for next patient or cohort.

-- S --

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?

-- T --

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.

-- U --

Utility score of each dose.

-- W --

Outcome weights.