vtPost: Postetrior sampling for given observed samples

In visit: Vaccine Phase I Design with Simultaneous Evaluation of Immunogenicity and Toxicity

Postetrior sampling for given observed samples

Description

Call STAN to draw posterior samples of the joint distribution of immunogenicity rate and toxicity risk

Usage

vtPost(obs.y, prob.mdl = c("NONPARA", "NONPARA+", "PARA", "PARA+"),
  priors = NULL, ..., nsmp = 4000, prior.const = 0.5)

Arguments

obs.y	Observed data matrix with l rows and 4 columns. Row k in the matrix represents the observed data from dose level k. The columns are column 1: number of patient with no DLT, no immune response column 2: number of patient with no DLT, immune response column 3: number of patient with DLT, no immune response column 4: number of patient with DLT, immune response
prob.mdl	Option of the probability models: NONPARA: non-parametric+ model NONPARA+: non-parametric model PARA: partially parametric model PARA+: partially parametric+ model Default value is NONPARA. See visit for details.
priors	A class VTPRIOR object created by vtPriorPar for PARA and PARA+ model.
...	additional parameters for package rstan's sampling method. These options include warmup, thin, algorithm. See rstan::sampling for details.
nsmp	number of iterations
prior.const	Specify \alpha for a Beta(\alpha, \alpha) prior. The Beta prior is used for NONPARA and NONPARA+ models. Default value 0.5.

Value

A class VTPOST matrix of posterior samples with nsmp rows and 4 columns. Columns 1-4 correspond to\theta^{(l)}_{00}, \theta^{(l)}_{01}, \theta^{(l)}_{10}, \theta^{(l)}_{11}. See visit for details about \theta's.

Examples

obs.y    <- rbind(c(5, 2, 0, 0), c(3, 4, 0, 0), c(1, 6, 0, 0))
prior <- vtPriorPar(prior.y = NULL, tau = c(0.1, 0.3, 0.6), sdalpha=10, sdrho=10, vtheta=NULL)
rst.post <- vtPost(obs.y, priors = prior, warmup = 100, prob.mdl = "PARA", nsmp = 200)

visit documentation built on Aug. 9, 2023, 5:08 p.m.