Powered By Bing

Pan Lab: Software

 

  • In many phase I trials, the design goal is to find the dose associated with a certain target toxicity rate. In some trials, the goal can be to find the dose with a certain weighted sum of rates of various toxicity grades. For others, the goal is to find the dose with a certain mean value of the continuous response. This UnifiedDoseFinding package provides the setup and calculations needed to run a dose-finding trial with non-binary endpoints and performs simulations to assess the design's operating characteristics under various scenarios. Three dose-finding designs are included in this package: unified phase I design (Ivanova et al. (2009) <doi:10.1111/j.1541-0420.2008.01045.x>), Quasi-CRM/Robust-Quasi-CRM (Yuan et al. (2007) <doi:10.1111/j.1541-0420.2006.00666.x>, Pan et al. (2014) <doi:10.1371/journal.pone.0098147>) and generalized BOIN design (Mu et al. (2018) <doi:10.1111/rssc.12263>). The toxicity endpoints can be handled with these functions including equivalent toxicity score (ETS), total toxicity burden (TTB), general continuous toxicity endpoints, with incorporating ordinal grade toxicity information into the dose-finding procedure. These functions allow customization of design characteristics to vary sample size, cohort sizes, target dose-limiting toxicity (DLT) rates, discrete or continuous toxicity score, and incorporate safety and/or stopping rules. The package can be downloaded from https://cran.r-project.org/web/packages/UnifiedDoseFinding/index.html.
  • An R package MinEDfind containing functions for the implementation and simulation of a Bayesian nonparametric two-stage design for minimum effective dose-finding can be downloaded from the https://cran.r-project.org/web/packages/MinEDfind/index.html. For Windows, the MinEDfind library can be downloaded from within R GUI by clicking on Packages/Install package(s), choose a mirror site, and locating MinEDfind. Questions regarding the R code, the literature, and the application of MinEDfind are welcome. An R Shiny App for this method can be found here (https://sjbiostat.shinyapps.io/mined/).
  • An R package Keyboard containing functions for the implementation and simulation of two phase I model-assisted maximum tolerated dose (MTD)-finding designs for single-agent and combination trials, and one biological dose (OBD)-finding phase I/II design. The package can be downloaded from https://cran.r-project.org/web/packages/Keyboard/index.html. R Shiny App for the single and combination trials can be found at www.trialsdesign.org.
  • An R Shiny App for Robust Bayesian model-averaging continual reassessment method (BMA-CRM) can be found at www.trialsdesign.org.

 

Back to Top