---
title: "Demo"
author: "Richèl J.C. Bilderbeek"
date: "`r Sys.Date()`"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Demo}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r setup, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
```

## Introduction

![](mcbette_logo.png)

Given a DNA alignment, one wonders which phylogenetic inference model
fits that alignment best. `mcbette` ('Model Comparison using babette') 
can give the answer.

In this example, we use a 'BEAST2' example alignment and compare the fit
of two inference models on that alignment. We'll interpret the finding
in the end, concluding which inference model to use.

## Getting started

First, load `mcbette`:

```{r}
library(mcbette)
```

To use `mcbette`, BEAST2 and the BEAST2 `NS` package must be installed:

```{r}
if (rappdirs::app_dir()$os == "win") {
  message("'mcbette' can only run on Linux and MacOS")
} else if (!beastier::is_beast2_installed()) {
  message(
    "BEAST2 must be installed. ",
    "Tip: use 'beastier::install_beast2()'"
  )
} else if (!mauricer::is_beast2_ns_pkg_installed()) {
  message(
    "The BEAST2 'NS' package must be installed. ",
    "Tip: use 'mauricer::install_beast2_pkg(\"NS\")'"
  )
}
```

If you've just gotten a message that you need to install either
BEAST2 or the BEAST2 NS package, do so. The rest of this
vignette will be empty.

## Method

To run `mcbette`, we need a FASTA file with a DNA alignment in it.
We use one that is present in the `mcbette` package:

```{r}
fasta_filename <- system.file("extdata", "primates.fas", package = "mcbette")
```

Now we have the alignment saved in our FASTA file, we can display it:

```{r}
alignment <- ape::read.FASTA(fasta_filename)
image(alignment)
```

`mcbette` allows one to select the evolutionary model that has the
heighest evidence (aka marginal likelihood) for having generated that 
alignment. For more information how to set up an inference model, 
see the 'Inference models' vignette of the `beautier` package:

```
vignette("beautier", "inference_models")
```

In this example, we compare two evolutionary models on the alignment shown
above. Because the best evolutionary model will likely be used
in Bayesian inference, in this example we will use 'evolutionary model'
and 'inference model' interchangably.

One of the inference models is the default `babette` inference
model. 

```{r}
inference_model_1 <- beautier::create_ns_inference_model()
inference_model_1$site_model$name
```


only differing in their nucleotide substitution model:

  1. JC69: all nucleotides share the same mutation rate. 
     For example, the
     mutation rate from adenine to cytosine is the same as the
     mutation rate from guanine to thymine
  2. GTR: there is a different mutation rate from each nucleotide to each
     other nucleotide

```{r}
if (can_run_mcbette()) {
  # Create the two inference models
  inference_model_1 <- beautier::create_ns_inference_model(
    site_model = beautier::create_jc69_site_model()
  )
  inference_model_2 <- beautier::create_ns_inference_model(
    site_model = beautier::create_gtr_site_model()
  )
  # Shorten the run, by doing a short (dirty, unreliable) MCMC
  inference_model_1$mcmc <- beautier::create_test_ns_mcmc()
  inference_model_2$mcmc <- beautier::create_test_ns_mcmc()

  # Combine the two inference models
  inference_models <- c(list(inference_model_1), list(inference_model_2))

  # Compare the the two inference models
  marg_liks <- est_marg_liks(
    fasta_filename = fasta_filename,
    inference_models = inference_models
  )
  knitr::kable(marg_liks)
}
```

The results are interpreted by `interpret_marg_lik_estimates` as follows:

```{r}
if (can_run_mcbette()) {
  interpret_marg_lik_estimates(marg_liks)
}
```
