MAPprior_bin: Analysis for binary data using the MAP Prior approach

In pavlakrotka/NCC: Simulation and Analysis of Platform Trials with Non-Concurrent Controls

Analysis for binary data using the MAP Prior approach

Description

This function performs analysis of binary data using the Meta-Analytic-Predictive (MAP) Prior approach. The method borrows data from non-concurrent controls to obtain the prior distribution for the control response in the concurrent periods.

Usage

MAPprior_bin(
  data,
  arm,
  alpha = 0.025,
  opt = 2,
  prior_prec_tau = 4,
  prior_prec_eta = 0.001,
  n_samples = 1000,
  n_chains = 4,
  n_iter = 4000,
  n_adapt = 1000,
  robustify = TRUE,
  weight = 0.1,
  check = TRUE,
  ...
)

Arguments

data	Data frame with trial data, e.g. result from the datasim_bin() function. Must contain columns named 'treatment', 'response' and 'period'.
arm	Integer. Index of the treatment arm under study to perform inference on (vector of length 1). This arm is compared to the control group.
alpha	Double. Decision boundary (one-sided). Default=0.025
opt	Integer (1 or 2). If opt==1, all former periods are used as one source; if opt==2, periods get separately included into the final analysis. Default=2.
prior_prec_tau	Double. Precision parameter (1/\sigma^2_{\tau}) of the half normal hyperprior, the prior for the between study heterogeneity. Default=4.
prior_prec_eta	Double. Precision parameter (1/\sigma^2_{\eta}) of the normal hyperprior, the prior for the hyperparameter mean of the control log-odds. Default=0.001.
n_samples	Integer. Number of how many random samples will get drawn for the calculation of the posterior mean, the p-value and the CI's. Default=1000.
n_chains	Integer. Number of parallel chains for the rjags model. Default=4.
n_iter	Integer. Number of iterations to monitor of the jags.model. Needed for coda.samples. Default=4000.
n_adapt	Integer. Number of iterations for adaptation, an initial sampling phase during which the samplers adapt their behavior to maximize their efficiency. Needed for jags.model. Default=1000.
robustify	Logical. Indicates whether a robust prior is to be used. If TRUE, a mixture prior is considered combining a MAP prior and a weakly non-informative component prior. Default=TRUE.
weight	Double. Weight given to the non-informative component (0 < weight < 1) for the robustification of the MAP prior according to Schmidli (2014). Default=0.1.
check	Logical. Indicates whether the input parameters should be checked by the function. Default=TRUE, unless the function is called by a simulation function, where the default is FALSE.
...	Further arguments passed by wrapper functions when running simulations.

Details

The MAP approach derives the prior distribution for the control response in the concurrent periods by combining the control information from the non-concurrent periods with a non-informative prior.

The model for the binary response y_{js} for the control patient j in the non-concurrent period s is defined as follows:

g(E(y_{js})) = \eta_s

where g(\cdot) denotes the logit link function and \eta_s represents the control log odds in the non-concurrent period s.

The log odds for the non-concurrent controls in period s are assumed to have a normal prior distribution with mean \mu_{\eta} and variance \tau^2:

\eta_s \sim \mathcal{N}(\mu_{\eta}, \tau^2)

For the hyperparameters \mu_{\eta} and \tau, normal and half-normal hyperprior distributions are assumed, with mean 0 and variances \sigma^2_{\eta} and \sigma^2_{\tau}, respectively:

\mu_{\eta} \sim \mathcal{N}(0, \sigma^2_{\eta})

\tau \sim HalfNormal(0, \sigma^2_{\tau})

The MAP prior distribution p_{MAP}(\eta_{CC}) for the control response in the concurrent periods is then obtained as the posterior distribution of the parameters \eta_s from the above specified model.

If robustify=TRUE, the MAP prior is robustified by adding a weakly-informative mixture component p_{\mathrm{non-inf}}, leading to a robustified MAP prior distribution:

p_{rMAP}(\eta_{CC}) = (1-w) \cdot p_{MAP}(\eta_{CC}) + w \cdot p_{\mathrm{non-inf}}(\eta_{CC})

where w (parameter weight) may be interpreted as the degree of skepticism towards borrowing strength.

In this function, the argument alpha corresponds to 1-\gamma, where \gamma is the decision boundary. Specifically, the posterior probability of the difference distribution under the null hypothesis is such that: P(p_{treatment}-p_{control}>0) \ge 1-alpha. In case of a non-informative prior this coincides with the frequentist type I error.

Value

List containing the following elements regarding the results of comparing arm to control:

• p-val - posterior probability that the log-odds ratio is less than zero

• treat_effect - posterior mean of log-odds ratio

• lower_ci - lower limit of the (1-2*alpha)*100% credible interval for log-odds ratio

• upper_ci - upper limit of the (1-2*alpha)*100% credible interval for log-odds ratio

• reject_h0 - indicator of whether the null hypothesis was rejected or not (p_val < alpha)

Author(s)

Katharina Hees

References

Robust meta-analytic-predictive priors in clinical trials with historical control information. Schmidli, H., et al. Biometrics 70.4 (2014): 1023-1032.

Applying Meta-Analytic-Predictive Priors with the R Bayesian Evidence Synthesis Tools. Weber, S., et al. Journal of Statistical Software 100.19 (2021): 1548-7660.

Examples

trial_data <- datasim_bin(num_arms = 3, n_arm = 100, d = c(0, 100, 250),
p0 = 0.7, OR = rep(1.8, 3), lambda = rep(0.15, 4), trend="stepwise")

MAPprior_bin(data = trial_data, arm = 3)

pavlakrotka/NCC documentation built on April 17, 2025, 3:11 a.m.