All functions

as_tibble(<dose_paths>)

Cast dose_paths object to 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?

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.

dose_admissible()

Is each dose admissible?

dose_indices()

Dose indices

dose_paths()

Dose pathways

dose_paths_function()

Get function for calculating dose pathways.

doses_given()

Doses given to patients.

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-package

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_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_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.

n_at_dose()

Number of patients treated at each dose.

n_at_recommended_dose()

Number of patients treated at the recommended dose.

num_cohort_outcomes()

Number of different possible outcomes for a cohort of patients

num_dose_path_nodes()

Number of nodes in dose-paths analysis

num_doses()

Number of doses.

num_eff()

Total number of efficacies seen.

num_patients()

Number of patients evaluated.

num_tox()

Total number of toxicities seen.

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.

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_quantile()

Quantile of the efficacy rate at each dose.

prob_recommend()

Probability of recommendation

prob_tox_exceeds() prob_eff_exceeds()

Probability that the toxicity rate exceeds some threshold.

prob_tox_quantile()

Quantile of the toxicity rate at each dose.

prob_tox_samples() prob_eff_samples()

Get samples of the probability of toxicity.

recommended_dose()

Recommended dose for next patient or cohort.

select_boin_mtd()

Select dose by BOIN's MTD-choosing algorithm.

select_dose_by_cibp()

Select dose by the CIBP selection criterion.

selector()

Dose selector.

selector_factory()

Dose selector factory.

simulate_trials()

Simulate clinical trials.

simulation_function()

Get function for simulating trials.

simulations()

Simulated trials.

spread_paths()

Spread the information in dose_finding_paths object to a wide data.frame format.

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 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.