This document shows the basics of applying our Bayesian model-based
clustering/classification with joint batch correction in `R`

. It shows how to
generate some toy data, apply the model, assess convergence and process outputs.

We simulate some data using the `generateBatchData`

function.

```
library(ggplot2)
library(batchmix)
# Data dimensions
N <- 600
P <- 4
K <- 5
B <- 7
# Generating model parameters
mean_dist <- 2.25
batch_dist <- 0.3
group_means <- seq(1, K) * mean_dist
batch_shift <- rnorm(B, mean = batch_dist, sd = batch_dist)
std_dev <- rep(2, K)
batch_var <- rep(1.2, B)
group_weights <- rep(1 / K, K)
batch_weights <- rep(1 / B, B)
dfs <- c(4, 7, 15, 60, 120)
my_data <- generateBatchData(
N,
P,
group_means,
std_dev,
batch_shift,
batch_var,
group_weights,
batch_weights,
type = "MVT",
group_dfs = dfs
)
```

This gives us a named list with two related datasets, the `observed_data`

which includes batch effects and the `corrected_data`

which is batch-free. It
also includes `group_IDs`

, a vector indicating class membership for each item,
`batch_IDs`

, which indicates batch of origin for each item, and `fixed`

,
which indicates which labels are observed and fixed in the model. We pull these
out of the names list in the format that the modelling functions desire them.

```
X <- my_data$observed_data
true_labels <- my_data$group_IDs
fixed <- my_data$fixed
batch_vec <- my_data$batch_IDs
alpha <- 1
initial_labels <- generateInitialLabels(alpha, K, fixed, true_labels)
```

Given some data, we are interested in modelling it. We assume here that the set of observed labels includes at least one example of each class in the data.

```
# Sampling parameters
R <- 1000
thin <- 50
n_chains <- 4
# Density choice
type <- "MVT"
# MCMC samples and BIC vector
mcmc_output <- runMCMCChains(
X,
n_chains,
R,
thin,
batch_vec,
type,
initial_labels = initial_labels,
fixed = fixed
)
```

We want to assess two things. First, how frequently the proposed parameters in the Metropolis-Hastings step are accepted:

```
plotAcceptanceRates(mcmc_output)
```

Secondly, we want to asses how well our chains have converged. To do this we plot the `complete_likelihood`

of each chain. This is the quantity most relevant to a clustering/classification, being dependent on the labels. The `observed_likelihood`

is independent of labels and more relevant for density estimation.

```
plotLikelihoods(mcmc_output)
```

We see that our chains disagree. We have to run them for more iterations. We use the `continueChains`

function for this.

```
R_new <- 9000
# Given an initial value for the parameters
new_output <- continueChains(
mcmc_output,
X,
fixed,
batch_vec,
R_new,
keep_old_samples = TRUE
)
```

To see if the chains better agree we re-plot the likelihood.

```
plotLikelihoods(new_output)
```

We also re-check the acceptance rates.

```
plotAcceptanceRates(new_output)
```

This looks like several of the chains agree by the 5,000th iteration.

We process the chains, acquiring point estimates of different quantities.

```
# Burn in
burn <- 5000
# Process the MCMC samples
processed_samples <- processMCMCChains(new_output, burn)
```

For multidimensional data we use a PCA plot.

```
chain_used <- processed_samples[[1]]
pc <- prcomp(X, scale = T)
pc_batch_corrected <- prcomp(chain_used$inferred_dataset)
plot_df <- data.frame(
PC1 = pc$x[, 1],
PC2 = pc$x[, 2],
PC1_bf = pc_batch_corrected$x[, 1],
PC2_bf = pc_batch_corrected$x[, 2],
pred_labels = factor(chain_used$pred),
true_labels = factor(true_labels),
prob = chain_used$prob,
batch = factor(batch_vec)
)
plot_df |>
ggplot(aes(
x = PC1,
y = PC2,
colour = true_labels,
alpha = prob
)) +
geom_point()
```

```
plot_df |>
ggplot(aes(
x = PC1_bf,
y = PC2_bf,
colour = pred_labels,
alpha = prob
)) +
geom_point()
```

```
test_inds <- which(fixed == 0)
sum(true_labels[test_inds] == chain_used$pred[test_inds]) / length(test_inds)
```

```
## [1] 0.806383
```