jags_picker_2stage: Set up a Two-Stage Binary Outcome Misclassification...

In COMBO: Correcting Misclassified Binary Outcomes in Association Studies

Set up a Two-Stage Binary Outcome Misclassification jags.model Object for a Given Prior

Description

Set up a Two-Stage Binary Outcome Misclassification jags.model Object for a Given Prior

Usage

jags_picker_2stage(
  prior,
  sample_size,
  dim_x,
  dim_z,
  dim_v,
  n_cat,
  Ystar,
  Ytilde,
  X,
  Z,
  V,
  beta_prior_parameters,
  gamma_prior_parameters,
  delta_prior_parameters,
  number_MCMC_chains,
  model_file,
  display_progress = TRUE
)

Arguments

prior	A character string specifying the prior distribution for the \beta, \gamma, and \delta parameters. Options are "t", "uniform", "normal", or "dexp" (double Exponential, or Weibull).
sample_size	An integer value specifying the number of observations in the sample.
dim_x	An integer specifying the number of columns of the design matrix of the true outcome mechanism, X.
dim_z	An integer specifying the number of columns of the design matrix of the first-stage observation mechanism, Z.
dim_v	An integer specifying the number of columns of the design matrix of the second-stage observation mechanism, V.
n_cat	An integer specifying the number of categorical values that the true outcome, Y, and the observed outcomes, Y^* and \tilde{Y}, can take.
Ystar	A numeric vector of indicator variables (1, 2) for the first-stage observed outcome Y*. The reference category is 2.
Ytilde	A numeric vector of indicator variables (1, 2) for the second-stage observed outcome \tilde{Y}. The reference category is 2.
X	A numeric design matrix for the true outcome mechanism.
Z	A numeric design matrix for the first-stage observation mechanism.
V	A numeric design matrix for the second-stage observation mechanism.
beta_prior_parameters	A numeric list of prior distribution parameters for the \beta terms. For prior distributions "t", "uniform", "normal", or "dexp", the first element of the list should contain a matrix of location, lower bound, mean, or shape parameters, respectively, for \beta terms. For prior distributions "t", "uniform", "normal", or "dexp", the second element of the list should contain a matrix of shape, upper bound, standard deviation, or scale parameters, respectively, for \beta terms. For prior distribution "t", the third element of the list should contain a matrix of the degrees of freedom for \beta terms. The third list element should be empty for all other prior distributions. All matrices in the list should have dimensions dim_x X n_cat, and all elements in the n_cat column should be set to NA.
gamma_prior_parameters	A numeric list of prior distribution parameters for the \gamma terms. For prior distributions "t", "uniform", "normal", or "dexp", the first element of the list should contain an array of location, lower bound, mean, or shape parameters, respectively, for \gamma terms. For prior distributions "t", "uniform", "normal", or "dexp", the second element of the list should contain an array of shape, upper bound, standard deviation, or scale parameters, respectively, for \gamma terms. For prior distribution "t", the third element of the list should contain an array of the degrees of freedom for \gamma terms. The third list element should be empty for all other prior distributions. All arrays in the list should have dimensions n_cat X n_cat X dim_z, and all elements in the n_cat row should be set to NA.
delta_prior_parameters	A numeric list of prior distribution parameters for the \delta terms. For prior distributions "t", "uniform", "normal", or "dexp", the first element of the list should contain an array of location, lower bound, mean, or shape parameters, respectively, for \delta terms. For prior distributions "t", "uniform", "normal", or "dexp", the second element of the list should contain an array of shape, upper bound, standard deviation, or scale parameters, respectively, for \delta terms. For prior distribution "t", the third element of the list should contain an array of the degrees of freedom for \delta terms. The third list element should be empty for all other prior distributions. All arrays in the list should have dimensions n_cat X n_cat X n_cat X dim_v, and all elements in the n_cat row should be set to NA.
number_MCMC_chains	An integer specifying the number of MCMC chains to compute.
model_file	A .BUG file and used for MCMC estimation with rjags.
display_progress	A logical value specifying whether messages should be displayed during model compilation. The default is TRUE.

Value

jags_picker returns a jags.model object for a two-stage binary outcome misclassification model. The object includes the specified prior distribution, model, number of chains, and data.

COMBO documentation built on Oct. 30, 2024, 5:07 p.m.