check_and_fix_chains_2stage {COMBO} R Documentation

## Check Assumption and Fix Label Switching if Assumption is Broken for a List of MCMC Samples

### Description

Check Assumption and Fix Label Switching if Assumption is Broken for a List of MCMC Samples

### Usage

check_and_fix_chains_2stage(
n_chains,
chains_list,
pistarjj_matrix,
pitildejjj_matrix,
dim_x,
dim_z,
dim_v,
n_cat
)


### Arguments

 n_chains An integer specifying the number of MCMC chains to compute over. chains_list A numeric list containing the samples from n_chains MCMC chains. pistarjj_matrix A numeric matrix of the average conditional probability P(Y^* = j | Y = j, Z) across all subjects for each MCMC chain, obtained from the pistar_by_chain function. pitildejjj_matrix A numeric matrix of the average conditional probability P( \tilde{Y} = j | Y^* = j, Y = j, V) across all subjects for each MCMC chain. Rows of the matrix correspond to MCMC chains, up to n_chains. Obtained from the pitilde_by_chain function. dim_x The number of columns of the design matrix of the true outcome mechanism, X. dim_z The number of columns of the design matrix of the first-stage observation mechanism, Z. dim_v The number of columns of the design matrix of the second-stage observation mechanism, V. n_cat The number of categorical values that the true outcome, Y, and the observed outcome, Y* can take.

### Value

check_and_fix_chains returns a numeric list of the samples from n_chains MCMC chains which have been corrected for label switching if the following assumption is not met: P(Y^* = j | Y = j, Z) > 0.50 \forall j.

[Package COMBO version 1.1.0 Index]