Package: escalation 0.1.10

Kristian Brock

escalation:A Modular Approach to Dose-Finding Clinical Trials

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) <doi:10.2307/2531628>, the toxicity probability interval (TPI) design by Ji et al. (2007) <doi:10.1177/1740774507079442>, the modified TPI (mTPI) design by Ji et al. (2010) <doi:10.1177/1740774510382799>, the Bayesian optimal interval design (BOIN) by Liu & Yuan (2015) <doi:10.1111/rssc.12089>, EffTox by Thall & Cook (2004) <doi:10.1111/j.0006-341X.2004.00218.x>; the design of Wages & Tait (2015) <doi:10.1080/10543406.2014.920873>, and the 3+3 described by Korn et al. (1994) <doi:10.1002/sim.4780131802>. 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.

Authors:Kristian Brock [aut, cre], Daniel Slade [aut], Michael Sweeting [aut]

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Bug tracker:https://github.com/brockk/escalation/issues

100 exports 0.36 score 118 dependencies 334 downloads

Last updated 8 days agofrom:91d2ff7587

Exports:calculate_probabilitiescheck_dose_selector_consistencycohortcohorts_of_ncontinueconvergence_plotCorrelatedPatientSamplecrystallised_dose_pathsdemand_n_at_dosedont_skip_dosesdose_admissibledose_indicesdose_pathsdose_paths_functiondoses_giveneffeff_at_doseeff_limitempiric_eff_rateempiric_tox_rateenforce_three_plus_threefitfollow_pathget_boinget_boin12get_dfcrmget_dfcrm_titeget_dose_pathsget_empiric_crm_skeleton_weightsget_mtpiget_mtpi2get_potential_outcomesget_random_selectorget_three_plus_threeget_tpiget_trialr_crmget_trialr_crm_titeget_trialr_efftoxget_trialr_nbgget_trialr_nbg_titeget_wages_and_taitgraph_pathsis_randomisinglinear_follow_up_weightmean_prob_effmean_prob_toxmedian_prob_effmedian_prob_toxmodel_framen_at_dosen_at_recommended_dosenum_cohort_outcomesnum_dose_path_nodesnum_dosesnum_effnum_patientsnum_toxparse_phase1_2_outcomesparse_phase1_outcomesPatientSamplephase1_2_outcomes_to_cohortsphase1_outcomes_to_cohortsprob_administerprob_eff_exceedsprob_eff_quantileprob_eff_samplesprob_recommendprob_tox_exceedsprob_tox_quantileprob_tox_samplesrecommended_doseselect_boin_mtdselect_boin12_obdselect_dose_by_cibpselect_mtpi_mtdselect_mtpi2_mtdselect_tpi_mtdselectorselector_factorysimulate_comparesimulate_trialssimulation_functionsimulationssimulations_collectionspread_pathsstack_sims_vertstop_at_nstop_when_n_at_dosestop_when_too_toxicstop_when_tox_ci_coveredsupports_samplingthree_plus_threetoxtox_at_dosetox_limittox_targettrial_durationtry_rescue_doseutilityweight

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