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escalation  

A Modular Approach to Dose-Finding Clinical Trials
View on CRAN: Click here


Download and install escalation package within the R console
Install from CRAN:
install.packages("escalation")

Install from Github:
library("remotes")
install_github("cran/escalation")

Install by package version:
library("remotes")
install_version("escalation", "0.1.10")



Attach the package and use:
library("escalation")
Maintained by
Kristian Brock
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2020-03-08
Latest Update: 2024-02-23
Description:
Methods for working with dose-finding clinical trials. We provide implementations of many dose-finding clinical trial designs, including the continual reassessment method (CRM) by O'Quigley et al. (1990) , the toxicity probability interval (TPI) design by Ji et al. (2007) , the modified TPI (mTPI) design by Ji et al. (2010) , the Bayesian optimal interval design (BOIN) by Liu & Yuan (2015) , EffTox by Thall & Cook (2004) ; the design of Wages & Tait (2015) , and the 3+3 described by Korn et al. (1994) . All designs are implemented with a common interface. We also offer optional additional classes to tailor the behaviour of all designs, including avoiding skipping doses, stopping after n patients have been treated at the recommended dose, stopping when a toxicity condition is met, or demanding that n patients are treated before stopping is allowed. By daisy-chaining together these classes using the pipe operator from 'magrittr', it is simple to tailor the behaviour of a dose-finding design so it behaves how the trialist wants. Having provided a flexible interface for specifying designs, we then provide functions to run simulations and calculate dose-paths for future cohorts of patients.
How to cite:
Kristian Brock (2020). escalation: A Modular Approach to Dose-Finding Clinical Trials. R package version 0.1.10, https://cran.r-project.org/web/packages/escalation. Accessed 21 Nov. 2024.
Previous versions and publish date:
0.1.1 (2020-03-08 18:10), 0.1.2 (2020-04-14 17:10), 0.1.3 (2020-05-13 01:40), 0.1.4 (2020-10-18 23:40), 0.1.5 (2023-05-29 20:10), 0.1.8 (2024-02-23 17:50), 0.1.9 (2024-05-22 19:10)
Other packages that cited escalation R package
View escalation citation profile
Other R packages that escalation depends, imports, suggests or enhances
Complete documentation for escalation
Functions, R codes and Examples using the escalation R package
Some associated functions: as_tibble.dose_paths . calculate_probabilities . cohort . cohorts_of_n . continue . crystallised_dose_paths . demand_n_at_dose . dont_skip_doses . dose_admissible . dose_indices . dose_paths . dose_paths_function . doses_given . eff . eff_at_dose . eff_limit . empiric_eff_rate . empiric_tox_rate . enforce_three_plus_three . escalation-package . fit . follow_path . get_boin . get_dfcrm . get_dose_paths . get_empiric_crm_skeleton_weights . get_mtpi . get_mtpi2 . get_random_selector . get_three_plus_three . get_tpi . get_trialr_crm . get_trialr_efftox . get_trialr_nbg . get_wages_and_tait . graph_paths . is_randomising . mean_prob_eff . mean_prob_tox . median_prob_eff . median_prob_tox . model_frame . n_at_dose . n_at_recommended_dose . num_cohort_outcomes . num_dose_path_nodes . num_doses . num_eff . num_patients . num_tox . parse_phase1_2_outcomes . parse_phase1_outcomes . phase1_2_outcomes_to_cohorts . phase1_outcomes_to_cohorts . prob_administer . prob_eff_quantile . prob_recommend . prob_tox_exceeds . prob_tox_quantile . prob_tox_samples . recommended_dose . select_boin_mtd . select_dose_by_cibp . selector . selector_factory . simulate_trials . simulation_function . simulations . spread_paths . stop_at_n . stop_when_n_at_dose . stop_when_too_toxic . stop_when_tox_ci_covered . supports_sampling . three_plus_three . tox . tox_at_dose . tox_limit . tox_target . trial_duration . try_rescue_dose . 
Some associated R codes: boin_selector.R . calculate_probabilities.R . crystallised_dose_paths.R . demand_n_at_dose.R . derived_dose_selector.R . derived_dose_selector_factory.R . dfcrm_selector.R . dont_skip_doses.R . dose_finding_path_node.R . dose_paths.R . eff_tox_selector.R . eff_tox_selector_factory.R . enforce_three_plus_three.R . escalation-package.R . follow_path.R . get_dose_paths.R . get_empiric_crm_skeleton_weights.R . graph_paths.R . helpers.R . interface.R . mtpi2_selector.R . mtpi_selector.R . num_cohort_outcomes.R . num_dose_path_nodes.R . parse_phase1_2_outcomes.R . parse_phase1_outcomes.R . phase1_2_dose_paths.R . phase1_2_outcomes_to_cohorts.R . phase1_2_sim.R . phase1_dose_paths.R . phase1_outcomes_to_cohorts.R . phase1_sim.R . random_dose_selector.R . select_boin_mtd.R . select_dose_by_cibp.R . selector.R . selector_factory.R . simulate_trials.R . simulations.R . spread_paths.R . stop_at_n_selector.R . stop_when_n_at_dose_selector.R . stop_when_too_toxic.R . stop_when_tox_ci_covered.R . three_plus_three.R . three_plus_three_selector.R . tox_selector_factory.R . tpi_selector.R . trialr_crm_selector.R . trialr_efftox_selector.R . trialr_nbg_selector.R . try_rescue_dose.R . wages_tait_selector.R .  Full escalation package functions and examples
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