dfcomb

Help for package dfcomb const macros = { "\\R": "\\textsf{R}", "\\mbox": "\\text", "\\code": "\\texttt"}; function processMathHTML() { var l = document.getElementsByClassName('reqn'); for (let e of l) { katex.render(e.textContent, e, { throwOnError: false, macros }); } return; } Package {dfcomb} Contents dfcomb-package CombIncrease_next CombIncrease_sim Type: Package Title: Phase I/II Adaptive Dose-Finding Design for Combination Studies Version: 3.1-5 Date: 2026-03-02 Copyright: src/arms.c and src/arms.h are copyright Wally Gilks. All other files are copyright Sanofi-Aventis R&D, Institut de Recherches Internationales Servier and Institut national de la sante et de la recherche medicale. Description: Phase I/II adaptive dose-finding design for combination studies where toxicity rates are supposed to increase with both agents. License: GPL-3 Depends: R (≥ 3.2.3) LinkingTo: BH (≥ 1.55), Rcpp, RcppProgress (≥ 0.2.1) NeedsCompilation: yes Packaged: 2026-03-02 10:38:23 UTC; jjourdan Author: Marie-Karelle Riviere [aut], Jacques-Henri Jourdan [aut, cre] Maintainer: Jacques-Henri Jourdan <jacques-henri.jourdan@cnrs.fr> Repository: CRAN Date/Publication: 2026-03-02 11:50:03 UTC Phase I/II Adaptive Dose-Finding Design for Combination Studies Description Phase I/II adaptive dose-finding design for combination studies where toxicity rates are supposed to increase with both agents. Details The DESCRIPTION file: Package: dfcomb Type: Package Title: Phase I/II Adaptive Dose-Finding Design for Combination Studies Version: 3.1-5 Date: 2026-03-02 Authors@R: c(person(given = "Marie-Karelle", family = "Riviere", role = "aut"), person(given = "Jacques-Henri", family = "Jourdan", role = c("aut", "cre"), email = "jacques-henri.jourdan@cnrs.fr")) Copyright: src/arms.c and src/arms.h are copyright Wally Gilks. All other files are copyright Sanofi-Aventis R&D, Institut de Recherches Internationales Servier and Institut national de la sante et de la recherche medicale. Description: Phase I/II adaptive dose-finding design for combination studies where toxicity rates are supposed to increase with both agents. License: GPL-3 Depends: R (>= 3.2.3) LinkingTo: BH (>= 1.55), Rcpp, RcppProgress (>= 0.2.1) NeedsCompilation: yes Author: Marie-Karelle Riviere [aut], Jacques-Henri Jourdan [aut, cre] Maintainer: Jacques-Henri Jourdan <jacques-henri.jourdan@cnrs.fr> Index of help topics: CombIncrease_next Combination determination with logistic model CombIncrease_sim Combination design Simulator using Logistic model dfcomb-package Phase I/II Adaptive Dose-Finding Design for Combination Studies Author(s) Marie-Karelle Riviere [aut], Jacques-Henri Jourdan [aut, cre] Maintainer: Jacques-Henri Jourdan <jacques-henri.jourdan@cnrs.fr> References Riviere MK, Yuan Y, Dubois F, Zohar S (2014). A Bayesian dose-finding design for drug combination clinical trials based on the logistic model. Pharm Stat, 13, 4:247-57. Combination determination with logistic model Description CombIncrease_next is used to determine the next or recommended combination in a phase I combination clinical trial using the design proposed by Riviere et al. entitled "A Bayesian dose-finding design for drug combination clinical trials based on the logistic model". Usage CombIncrease_next(ndose_a1, ndose_a2, target, target_min, target_max, prior_tox_a1, prior_tox_a2, cohort, final, pat_incl, dose_adm1, dose_adm2, tite=FALSE, toxicity, time_full=0, time_tox=0, time_follow=0, c_e=0.85, c_d=0.45, c_stop=0.95, c_t=0.5, c_over=0.25, cmin_overunder=2, cmin_mtd=3, cmin_recom=1, early_stop=1, alloc_rule=1, nburn=2000, niter=5000) Arguments ndose_a1 Number of dose levels for agent 1. ndose_a2 Number of dose levels for agent 2. target Toxicity (probability) target. target_min Minimum of the targeted toxicity interval. target_max Maximum of the targeted toxicity interval. prior_tox_a1 A vector of initial guesses of toxicity probabilities associated with the doses of agent 1. Must be of length ndose_a1 . prior_tox_a2 A vector of initial guesses of toxicity probabilities associated with the doses of agent 2. Must be of length ndose_a2 . cohort Cohort size. final A boolean with value TRUE if the trial is finished and the recommended combination for further phases should be given, or FALSE (default value) if the combination determination is performed for the next cohort of patients. pat_incl Current number of patients included. dose_adm1 A vector indicating the dose levels of agents 1 administered to each patient included in the trial. Must be of length pat_incl . dose_adm2 A vector indicating the dose levels of agents 2 administered to each patient included in the trial. Must be of length pat_incl . tite A boolean indicating if the toxicity is considered as a time-to-event outcome (TRUE), or as a binary outcome (default value FALSE). toxicity A vector of observed toxicities (DLTs) for each patient included in the trial. Must be of length pat_incl . This argument is used/required only if tite=FALSE. time_full Full follow-up time window. This argument is used only if tite=TRUE. time_tox A vector of times-to-toxicity for each patient included in the trial. If no toxicity was observed for a patient, must be filled with +Inf. Must be of length pat_incl . This argument is used/required only if tite=TRUE. time_follow A vector of follow-up times for each patient included in the trial. Must be of length pat_incl . This argument is used/required only if tite=TRUE. c_e Probability threshold for dose-escalation. The default value is set at 0.85. c_d Probability threshold for dose-deescalation. The default value is set at 0.45. c_stop Probability threshold for early trial termination. The default value is set at 0.95. c_t Probability threshold for early trial termination for finding the MTD (see details). The default value is set at 0.5. c_over Probability threshold to control over-dosing (see details). cmin_overunder Minimum number of cohorts to be included at the lowest/highest combination before possible early trial termination for over-toxicity or under-toxicity (see details). The default value is set at 2. cmin_mtd Minimum number of cohorts to be included at the recommended combination before possible early trial termination for finding the MTD (see details). The default value is set at 3. cmin_recom Minimum number of cohorts to be included at the recommended combination at the end of the trial. The default value is set at 1. alloc_rule Interger (1, 2, or 3) indicating which allocation rule is used (see details). The default value is set at 1. early_stop Interger (1, 2, or 3) indicating which early stopping rule is used (see details). The default value is set at 1. nburn Number of burn-in for HMC. The default value is set at 2000. niter Number of iterations for HMC. The default value is set at 5000. Details Allocation rule: alloc_rule=1 (Riviere et al 2014): If P(toxicity probability at combination (i,j) < target ) > c_e : among combinations in the neighborhood (-1, +1), (0, +1), (+1, 0), (+1, -1), choose the combination with a higher estimated toxicity probability than the current combination and with the estimated toxicity probability closest to target . If P(toxicity probability at combination (i,j) > target ) > 1- c_d : among neighborhood (-1, +1), (-1, 0), (0, -1), (+1, -1), choose the combination with a lower estimated toxicity probability than the current combination and with the estimated toxicity probability closest to target . Otherwise, remain on the same combination. alloc_rule=2 : Among combinations already tested and combinations in the neighborhood (-1, 0), (-1, +1), (0, +1), (+1, 0), (+1, -1), (0, -1), (-1, -1) of a combination tested, choose the combination with the highest posterior probability to be in the targeted interval [ target_min , target_max ] while controling overdosing i.e. P(toxicity probability at combination (i,j) > target_max ) < c_over . alloc_rule=3 : Among combinations in the neighborhood (-1, 0), (-1, +1), (0