---
title: "Bayesian comparison on networks of binary and ordinal variables in two independent samples using the bgmCompare function"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Introducing bgmCompare}
  %\VignetteEngine{knitr::rmarkdown}
bibliography: refs.bib
csl: apa.csl
link-citations: TRUE
---
<style>
body {
text-align: justify}
</style>

## Introduction

This example demonstrates how to use the `bgmCompare` function for Bayesian analysis of the ordinal Markov Random Field (MRF) model in two independent samples.

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  eval = identical(Sys.getenv("BUILD_VIGNETTE"), "true")
)
```


```{r setup}
library(bgms)
```

# Example -- 


## Usage 

```{r usage2, eval=FALSE}
bgmCompare(x,
           y,
           difference_selection = TRUE,
           main_difference_model = c("Collapse", "Constrain", "Free"),
           variable_type = "ordinal",
           reference_category,
           pairwise_difference_scale = 1,
           main_difference_scale = 1,
           pairwise_difference_prior = c("Bernoulli", "Beta-Bernoulli"),
           main_difference_prior = c("Bernoulli", "Beta-Bernoulli"),
           pairwise_difference_probability = 0.5,
           main_difference_probability = 0.5,
           pairwise_beta_bernoulli_alpha = 1,
           pairwise_beta_bernoulli_beta = 1,
           main_beta_bernoulli_alpha = 1,
           main_beta_bernoulli_beta = 1,
           interaction_scale = 2.5,
           threshold_alpha = 0.5,
           threshold_beta = 0.5,
           iter = 1e4,
           burnin = 1e3,
           na.action = c("listwise", "impute"),
           save = FALSE,
           display_progress = TRUE)
```


## Arguments 

- `x`: 

## References