Bayesian Continual Reassessment Method for Phase I
Implements a wide variety of one and two-parameter Bayesian CRM
designs. The program can run interactively, allowing the user to enter outcomes
after each cohort has been recruited, or via simulation to assess operating
The threep3 command also now returns all possible desigin in an object labelled `all.designs' for the user to interrogate further if required
The threep3 command now also returns the average number of patients per dose level and the average number of DLTs per dose level
Designs that use toxicity intervals now return the posterior probability of lying in each interval in the print.bcrm output
seed argument added to allow reproducibility of results
The help files for bcrm and getprior incorrectly specified the parameter `b' as the standard deviation of the lognormal prior. It is actually the variance. Many thanks to Elaidi Reza for spotting this error
New data argument allows specification of doses and toxicities of all previously recruited patients, and the sequential order in which they were entered into the trial. Arguments tox and notox in bcrm are now deprecated.
The dose trajectory and observed toxicities from a single trial can now be plotted using the argument trajectory = TRUE inside plot.bcrm
Stores posterior summaries after each step of an escalation, if a trial is conducted interactivey. These summaries are now returned in the "ndose" componenet of the bcrm object. The component "alpha" is now redundant and has been removed.
Stopping rules have been added, allowing stopping to be based on a maximum sample size, the maximum number to be treated at the final MTD estimate, the precision of the MTD estimate, and a minumum sample size.
Posterior summaries after each recruited cohort can now be plotted using the "each" argument of plot.bcrm.
When simulating, operating characteristics are also now presented by true regions of toxicity risk.
Initial search space for posterior quantiles limited to a grid of size 100
Simulations now run faster, as they use information from identical previous simulations to choose next dose. This is only implemented if nsims<=1000, otherwise the computation time to search previous simulations becomes unmanageable.
Plot and print commands now refer to actual dose labels when they have been given by the user
Output from simulations can now be plotted as histograms using the function plot.bcrm.sim
Implementation of escalation based on posterior toxicity intervals using loss functions, as described in Neuenschwander et al, 2008.
Fixed bug where posterior quantiles are occasionally incorrectly calculated using method="exact". This occurred because the space in which optimize searched for the quantile was sometimes too large and optimize did not find the correct minimum. The new release chooses the interval in which to search based on a preliminary grid search.
Fixed problem with `file' argument, where only the last of the two plots was saved.