---
title: "Simulating trees for ape"
author: "Paul Staab"
date: "`r Sys.Date()`"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{scrm-TreesForApe}
  %\VignetteEngine{knitr::rmarkdown}
  %\usepackage[utf8]{inputenc}
---

```{r echo=FALSE}
set.seed(40)
```

The trees in 'newick' format produced by __scrm's__ `-T` option are compatible 
with the `read.tree` function from package 'ape'. This quick example shows how
we can exploid this to visualize the Ancestral Recombination Graph (ARG) 
simulated with __scrm__.


First, we call __scrm__ to simulate the ARG:

```{r}
library(scrm)
sum_stats <- scrm('5 1 -r 1.5 100 -T')
sum_stats$trees[[1]]
```

Now we can convert the trees into ape's internal format using `read.tree`:
```{r}
library(ape)
trees <- read.tree(text = paste0(sum_stats$trees[[1]]))
trees
```

And -- for example -- print the trees:
```{r, fig.align='center'}
plot(trees, no.margin = TRUE)
```