Description Usage Arguments Value Author(s) References See Also Examples
The PKCOV model is a modification of the method proposed by Piantadosi and Liu (1996) who suggested to use the AUC as covariate for p_T, probability of toxicity, through the logit link. Therefore, the dose-toxicity model is:
logit(p_T(d_k, Δ {z_d}_k, \boldsymbol{β})) = -β_0 + β_1 log(d_k) + β_2 Δ {z_d}_k
where \boldsymbol{β} = (β_1, β_2), β_0 is a constant with β_0 = -beta0mean,
β_1 \sim U(l_1, u_1),
β_2 \sim U(0,5),
beta1mean = c(l_1, u_1)
where default choices are beta0mean = -14.76, beta1mean = c(0, 8.23) and Δ {z_d}_k is the difference between the logarithm of population AUC at dose d_k and z, the logarithm of AUC of the subject at the same dose. Therefore, the default choices for model's priors are given by
betapriors = c(beta0mean = -14.76, l_1 = 0, u_1 = 8.23)
Finally, the PKCOV model has the following stopping rule in toxicity: if
P(p_T(dose) > theta) > prob
then, no dose is suggested and the trial is stopped.
1 2 3 |
y |
A binary vector of patient's toxicity outcomes; TRUE indicates a toxicity, FALSE otherwise. |
doses |
A vector with the doses panel. |
x |
A vector with the dose level assigned to the patients. |
theta |
The toxicity target. |
prob |
The threshold of the posterior probability of toxicity for the stopping rule; defaults to 0.9. |
betapriors |
A vector with the value for the prior distribution of the regression parameters in the model; defaults to betapriors = c(beta0mean, beta1mean), where beta0mean = -14.76 and beta1mean = c(0, 8.23). |
options |
A list with the Stan model's options; the number of chains, how many iterations for each chain and the number of warmup iterations; defaults to options = list(nchains = 4, niter = 4000, nadapt = 0.8). |
auc |
A vector with the computed AUC values of each patient for pktox, pkcrm, pklogit and pkpop; defaults to NULL. |
deltaAUC |
The difference between computed individual AUC and the AUC of the population at the same dose level (defined as an average); argument for pkcov; defaults to NULL. |
p0 |
The skeleton of CRM for pkcrm; defaults to NULL (must be defined only in the PKCRM model). |
L |
The AUC threshold to be set before starting the trial for pklogit, pkcrm and pktox; defaults to NULL (must be defined only in the PKCRM model). |
thetaL |
A second threshold of AUC; must be defined only in the PKCRM model. |
CI |
A logical constant indicating the estimated 95% credible interval; defaults to TRUE. |
A list is returned, consisting of determination of the next recommended dose and estimations of the model. Objects generated by pkcov contain at least the following components:
newDose |
The next maximum tolerated dose (MTD); equals to "NA" if the trial has stopped before the end, according to the stopping rules. |
pstim |
The mean values of estimated probabilities of toxicity. |
p_sum |
The summary of the estimated probabilities of toxicity if CI = TRUE, otherwise is NULL. |
parameters |
The estimated model's parameters. |
Artemis Toumazi artemis.toumazi@gmail.com, Moreno Ursino moreno.ursino@inserm.fr, Sarah Zohar sarah.zohar@inserm.fr
Ursino, M., et al, (2017) Dose-finding methods for Phase I clinical trials using pharmacokinetics in small populations, Biometrical Journal, <doi:10.1002/bimj.201600084>.
Toumazi, A., et al, (2018) dfpk: An R-package for Bayesian dose-finding designs using pharmacokinetics (PK) for phase I clinical trials, Computer Methods and Programs in Biomedicine, <doi:10.1016/j.cmpb.2018.01.023>.
Piantadosi, S. and Liu, G. (1996) Improved designs for dose escalation studies using pharmacokinetic measurements. Statistics in Medicine, 15 (15), 1605-1618.
1 2 3 4 5 6 7 8 9 10 11 | ## Not run:
doses <- c(12.59972,34.65492,44.69007,60.80685,83.68946,100.37111)
theta <- 0.2
AUCs <- c(0.43, 1.4, 5.98, 7.98, 11.90, 3.45)
x <- c(1,2,3,4,5,6)
y <- c(FALSE,FALSE,FALSE,FALSE,TRUE,FALSE)
deltaAUC <- c(0, 1.3, -0.34, -2.7, 0.39, -2.45)
options <- list(nchains = 2, niter = 4000, nadapt = 0.8)
res <- pkcov(y, AUCs, doses, x, theta, deltaAUC, options=options)
## End(Not run)
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