---
title: "Simulation of outbreak data"
author: "Xavier Didelot"
date: '`r Sys.Date()`'
output: html_vignette
vignette: >
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteIndexEntry{Simulation of outbreak data}
  %\usepackage[utf8]{inputenc}
---
```{r echo=F}
knitr::opts_chunk$set(fig.width=6, fig.height=4) 
```

If you want to reproduce exactly the same results as the ones shown in this tutorial, you need to set the seed of your random number generator to zero:
```{r}
library(TransPhylo)
set.seed(0)
```

A pathogen has an effective within-host population size of $N_e=100$ and a generation time $g=1$ day, so that $N_e g=100/365$ year. The offspring distribution is negative binomial with mean equal to the basic reproduction number $R=5$. Both the generation time and the sampling time are Gamma distributed with parameters (10,0.1) which has a mean of 1 year. The density of sampling is $\pi=0.25$. The following commands specify these parameters:
```{r}
neg=100/365
off.r=5
w.shape=10
w.scale=0.1
pi=0.25
```

We simulate an outbreak that starts in 2005 and which and is observed up to 2008:

```{r}
simu <- simulateOutbreak(neg=neg,pi=pi,off.r=off.r,w.shape=w.shape,
                         w.scale=w.scale,dateStartOutbreak=2005,dateT=2008)
```

This simulation contains both the transmission tree between infected hosts and the within-host phylogenetic tree of each host. This can be visualised as a colored phlogenetic tree, where each host is represented by a unique color:

```{r}
plot(simu)
```

The transmission tree can be extracted and plotted separately from the phylogeny:

```{r}
ttree<-extractTTree(simu)
plot(ttree)
```

A more detailed plot can be displayed as follows:

```{r}
plot(ttree,type='detailed',w.shape,w.scale)
```

The phylogenetic tree can be extracted and plotted separately from the transmission tree:

```{r}
ptree<-extractPTree(simu)
plot(ptree)
```

The extracted phylogenetic tree can also be converted into a phylo object from the ape package:

```{r}
library(ape)
p<-phyloFromPTree(ptree)
plot(p)
axisPhylo(backward = F)
```

You can save this tree into a Newick file for further analysis. This is the tree that is used as the starting poit of the tutorial on inference of a transmission tree from a dated phylogeny.

```{r eval=F} 
write.tree(p,'tree.nwk')
```

The content of this Newick file is:

```{r}
write.tree(p,'')
```

This phylogeny is scaled in years, but time is measured only relatively to the 
date of the last sample which is at 0 on the x-axis of the figure above. To use this tree
again we also need to know exactly when was the last sample taken:

```{r}
dateLastSample(simu)
```