Personalized Repeated Measurement Design for Phase I Clinical
Trials
Implements Bayesian phase I repeated measurement design that
accounts for multidimensional toxicity endpoints and longitudinal efficacy
measure from multiple treatment cycles. The package provides flags to
fit a variety of model-based phase I design, including 1 stage models with
or without individualized dose modification, 3-stage models with or without
individualized dose modification, etc. Functions are provided to recommend
dosage selection based on the data collected in the available patient cohorts
and to simulate trial characteristics given design parameters.
Yin, Jun, et al. (2017) <doi:10.1002/sim.7134>.
rjags, arrayhelpers, phase1RMD, MASS, reshape2, dplyr, plyr,
RColorBrewer, gridExtra, kableExtra, knitr

rjags, arrayhelpers, MASS, reshape2, plyr, dplyr,
RColorBrewer, gridExtra, kableExtra, knitr

Repeated Measurement Design for Phase I Clinical Trial
R (>= 3.0.0), coda, boot, rjags, mvtnorm
Implements our Bayesian phase I repeated measurement design that accounts for multidimensional toxicity endpoints from multiple treatment cycles. The package also provides a novel design to account for both multidimensional toxicity endpoints and early-stage efficacy endpoints in the phase I design. For both designs, functions are provided to recommend the next dosage selection based on the data collected in the available patient cohorts and to simulate trial characteristics given design parameters. Yin, Jun, et al. (2017) <doi:10.1002/sim.7134>.

R (>= 3.0.0), coda, boot, rjags, mvtnorm, ggplot2

Phase Plane Analysis of One and Two Dimensional ODE Systems
phaseR is an R package for the qualitative analysis of one
and two dimensional autonomous ODE systems, using phase plane methods.
Programs are available to identify and classify equilibrium points, plot
the direction field, and plot trajectories for multiple initial
conditions. In the one dimensional case, a program is also available to
plot the phase portrait. Whilst in the two dimensional case,
additionally a program is available to plot nullclines. Many example
systems are provided for the user.