# A Modular Approach to Dose-Finding Clinical Trials

## Documentation for package ‘escalation’ version 0.2.3

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

## Help Pages

A B C D E F G I L M N P R S T U W

## -- 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

## -- B --

boin12_rds | Tabulate rank-based desirability scores for a BOIN12 trial

## -- C --

calculate_probabilities | Calculate dose-path probabilities
check_dose_selector_consistency | Check the consistency of a dose_selector instance
check_simulations_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.
combo_selector | Dose selector for combinations of treatments
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.
doses_given.boin_comb_selector | Doses given to patients.
doses_given.simulations | Doses given to patients.
dose_admissible | Is each dose admissible?
dose_escalation_table | Plot a table of dose escalation vs de-escalation vs stop decisions
dose_indices | Dose indices
dose_paths | Dose pathways
dose_paths_function | Get function for calculating dose pathways.
dose_strings | Dose strings
dose_string_to_vector | Go from a single multi-treatment dose string to a vector of dose-indices
dose_vector_to_string | Go from a single multi-treatment vector of dose-indices to a dose string

## -- 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.
expand_last_dose_to_cohort | Expand the cohort of the last given dose to at least n patients

## -- 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_boin_comb | Get an object to fit the BOIN COMB model using the BOIN package.
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_combo_indices | Get all combinations of dose indices
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_randomising | Is this selector currently randomly allocating doses?

## -- L --

linear_follow_up_weight | 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.
median_prob_tox.boin_comb_selector | 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_exceeds.boin_comb_selector | Probability that the toxicity rate exceeds some threshold.
prob_tox_quantile | Quantile of the toxicity rate at each dose.
prob_tox_quantile.boin_comb_selector | Quantile of the toxicity rate at each dose.
prob_tox_samples | Get samples of the probability of toxicity.

## -- R --

recommended_dose | Recommended dose for next patient or cohort.
recommended_dose.simulations | 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_comb_mtd | Select dose by BOIN-COMB's MTD-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
stick_on_num_tox | Stay at the current dose when num_tox of num_patients have experienced tox
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 --

unadmit_untested | Make untested and unrecommended doses inadmissible.
utility | Utility score of each dose.

## -- W --

weight | Outcome weights.