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

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

## Introduction

![](beastier_logo.png)

This vignette demonstrates how to use `beastier`.

First, load the library:

```{r load_beastier, results='hide', warning=FALSE, error=FALSE, message=FALSE}
library(beastier)
```

Also, we'll load the `testthat` library, to verify the statements in this vignette:

```{r load_testthat}
library(testthat)
```

To run BEAST2, we need to create a BEAST2 options structure`. We will use
a supplied BEAST2 XML file. For the rest, we'll use the default options:

```{r}
beast2_options <- create_beast2_options(
  input_filename = get_beastier_path("2_4.xml")
)
names(beast2_options)
```


Before running BEAST2, the BEAST2 input file must exist,
and we expect no output file to be created just yet:

```{r}
expect_true(file.exists(beast2_options$input_filename))
expect_false(file.exists(beast2_options$output_state_filename))
```

We can run `beastier` now, if BEAST2 is installed. Because BEAST2 needs
to be installed by the user, this vignette checks if it is installed in every step:

```{r}
if (is_beast2_installed()) {
  output <- run_beast2_from_options(beast2_options)
}
```

If `beastier` has run BEAST2, the BEAST2 output can be shown:

```{r}
if (is_beast2_installed()) {
  print(output)
}
```

If `beastier` has run BEAST2, the MCMC's final state will be saved to a file: 

```{r}
if (is_beast2_installed()) {
  expect_true(file.exists(beast2_options$output_state_filename))
  file.remove(beast2_options$output_state_filename)
}
beastier::remove_beaustier_folders()
```

This final state can be used to continue the run.
