titesim {dfcrm}

TITE-CRM Simulator

Description

titesim is used to generate simulation replicates of phase I trial using the TITE-CRM under a specified dose-toxicity configuration.

Usage

titesim(PI, prior, target, n, x0, nsim = 1, restrict = TRUE, obswin = 1,
tgrp = obswin, rate = 1, accrual = "fixed", surv = "uniform", scheme =
"linear", count = TRUE, method = "bayes", model = "empiric", intcpt = 3,
scale = sqrt(1.34), seed = 1009)

Arguments

PI

A vector of the true toxicity probabilites associated with the doses.

prior

A vector of initial guesses of toxicity probabilities associated with the doses. Must be of same length as PI.

target

The target DLT rate.

n

Sample size of the trial.

x0

The initial design. For one-stage TITE-CRM, it is a single numeric value indicating the starting dose. For two-stage TITE-CRM, it is a non-decreasing sequence of dose levels of length n.

nsim

The number of simulations. Default is set at 1.

restrict

If TRUE, restrictions apply during the trials to avoid (1) skipping doses in escalation and (2) escalation immediately after a toxic outcome (i.e., incoherent escalation). If FALSE, dose assignments are purely model-based.

obswin

The observation window with respect to which the MTD is defined.

tgrp

The minimum waiting time between two dose cohorts at the initial stage. Default is set as obswin, i.e., complete follow-up in all current patients is required before escalation to the next dose group. This argument is used only in two-stage TITE-CRM.

rate

Patient arrival rate: Expected number of arrivals per observation window. Example: obswin=6 and rate=3 means expecting 3 patients arrive in 6 time units.

accrual

Patient accrual scheme. Default is “fixed” whereby inter-patient arrival is fixed. Alternatively, use “poisson” to simulate patient arrivals by the Poisson process.

surv

Distribution for time-to-toxicity. Default is “uniform” where toxicity, if occurs, occurs uniformly on the interval [0,obswin]. Other survival distributions including exponential and Weibull are to be made available.

scheme

A character string to specify the method for assigning weights. Default is “linear”. An adaptive weight is specified by “adaptive”.

count

If TRUE, the number of the current simulation replicate will be displayed.

method

A character string to specify the method for parameter estimation. The default method “bayes” estimates the model parameter by the posterior mean. Maximum likelihood estimation is specified by “mle”.

model

A character string to specify the working model used in the method. The default model is “empiric”. A one-parameter logistic model is specified by “logistic”.

intcpt

The intercept of the working logistic model. The default is 3. If model=“empiric”, this argument will be ignored.

scale

Standard deviation of the normal prior of the model parameter. Default is sqrt(1.34).

seed

Seed of the random number generator.

Value

An object of class “sim” is returned, consisting of the operating characteristics of the design specified.

For a “sim” object with nsim=1, the time component of individual subjects in the simulated trial is available via the values arrival, toxicity.time, and toxicity.study.time which respectively contain patients' arrival times, times-to-toxicity, and the times-to-toxicity per study time.

For a “sim” object with nsim>1, the time component of the design is summarized via the value Duration, which is the duration of the simulated trials, computed by adding the arrival time of the last patient and obswin.

All “sim” objects contain at least the following components:

PI

True toxicity rates.

prior

Initial guesses of toxicity rates.

target

The target probability of toxicity at the MTD.

n

Sample size.

x0

The initial design.

MTD

Distribution of the MTD estimates. If nsim=1, this is a single numeric value of the recommended MTD of in simulated trial.

level

Average number of patients treated at the test doses. If nsim=1, this is a vector of length n indicating the doses assigned to the patients in the simulated trial.

tox

Average number of toxicities seen at the test doses. If nsim=1, this is a vector of length n indicating the toxicity outcomes of the patients in the simulated trial.

beta.hat

The estimates of the model parameter throughout the simulated trial(s). The dose assignment of the jth patient in each trial corresponds to the jth element in each row.

final.est

The final estimates of the model parameter of the simulated trials.

References

Cheung, Y. K. and Chappell, R. (2000). Sequential designs for phase I clinical trials with late-onset toxicities. Biometrics 56:1177-1182.

Cheung, Y. K. (2005). Coherence principles in dose-finding studies. Biometrika 92:863-873.

Cheung, Y. K. (2011). Dose Finding by the Continual Reassessment Method. New York: Chapman & Hall/CRC Press.

See Also

crmsim, titecrm.

Examples

PI <- c(0.10, 0.20, 0.40, 0.50, 0.60, 0.65)
prior <- c(0.05, 0.10, 0.20, 0.35, 0.50, 0.70)
target <- 0.2
x0 <- c(rep(1,3), rep(2,3), rep(3,3), rep(4,3), rep(5,3), rep(6,9))

# Generate a single replicate of two-stage TITE-CRM trial of size 24
foo <- titesim(PI, prior, target, 24, x0, obswin=6, rate=4, accrual="poisson")
## Not run: plot(foo, ask=T)  # summarize trial graphically

# Generate 10 replicates of TITE-CRM trial of size 24
foo10 <- titesim(PI, prior, target, 24, 3, nsim=10, obswin=6, rate=4, accrual="poisson")

foo10