plotAcceptanceRates: Plot acceptance rates

In batchmix: Semi-Supervised Bayesian Mixture Models Incorporating Batch Correction

Plot acceptance rates

Description

Plot the acceptance rates for the parameters sampled in a Metropolis-Hastings step. Aiming for acceptance rates in [0.2, 0.5] for the class means, the batch effect on location and scale is a good rule of thumb. The class covariance should be in [0.35, 0.8] based on the authors' experience. The class degree of freedom appears to be prone to high acceptance rates, but aim to keep this above 0.2 at a minimum.

Usage

plotAcceptanceRates(mcmc_lst)

Arguments

mcmc_lst

The output of the “runMCMCChains“ function.

Value

A ggplot object of the boxplots of acceptance rates for each parameter across chains.

Examples

# Data in a matrix format
X <- matrix(c(rnorm(100, 0, 1), rnorm(100, 3, 1)), ncol = 2, byrow = TRUE)

# Initial labelling
labels <- c(
  rep(1, 10),
  sample(c(1, 2), size = 40, replace = TRUE),
  rep(2, 10),
  sample(c(1, 2), size = 40, replace = TRUE)
)

fixed <- c(rep(1, 10), rep(0, 40), rep(1, 10), rep(0, 40))

# Batch
batch_vec <- sample(seq(1, 5), replace = TRUE, size = 100)

# Sampling parameters
R <- 500
thin <- 10
n_chains <- 4

# MCMC samples and BIC vector
mcmc_lst <- runMCMCChains(X, n_chains, R, thin, batch_vec, "MVN",
  initial_labels = labels,
  fixed = fixed
)

# Plot the acceptance rate of each parameter in the 4 chains
plotAcceptanceRates(mcmc_lst)

batchmix documentation built on May 29, 2024, 2:14 a.m.