Man pages for escalation
A Modular Approach to Dose-Finding Clinical Trials
| 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 |
| 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... |
| continue | Should this dose-finding experiment continue? |
| convergence_plot | Plot the convergence processes from a collection of... |
| CorrelatedPatientSample | A sample of patients that experience correlated events in... |
| crystallised_dose_paths | Dose-paths with probabilities attached. |
| demand_n_at_dose | Demand there are n patients at a dose before condisdering... |
| 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_boin12 | Get an object to fit the BOIN12 model for phase I/II... |
| 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... |
| get_dose_paths | Calculate future dose paths. |
| get_empiric_crm_skeleton_weights | Get posterior model weights for several empiric CRM... |
| 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... |
| 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... |
| get_trialr_efftox | Get an object to fit the EffTox model using the trialr... |
| get_trialr_nbg | Get an object to fit the NBG dose-finding model using the... |
| get_trialr_nbg_tite | Get an object to fit a TITE version of the NBG dose-finding... |
| get_wages_and_tait | Get an object to fit Wages & Tait's model for phase I/II... |
| graph_paths | Visualise dose-paths as a graph |
| is_randomising | Is this selector currently randomly allocating doses? |
| linear_follow_up_weight | Weights for tolerance and toxicity events using linear... |
| 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... |
| 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... |
| parse_phase1_outcomes | Parse a string of phase I dose-finding outcomes to vector... |
| 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... |
| 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 | 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. |
| 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. |
| selector | Dose selector. |
| selector_factory | Dose selector factory. |
| select_tpi_mtd | Select dose by TPI's MTD-choosing algorithm. |
| simulate_compare | Simulate clinical trials for several designs using common... |
| simulate_trials | Simulate clinical trials. |
| simulation_function | Get function for simulating trials. |
| simulations | Simulated trials. |
| simulations_collection | Make an instance of type 'simulations_collection' |
| spread_paths | Spread the information in dose_finding_paths object to a wide... |
| 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... |
| utility | Utility score of each dose. |
| weight | Outcome weights. |
