---
title: "Phage"
author: "Scott A. Handley"
date: "4 December 2015"
output: html_document
---

```{r}
# Set your working directory
setwd("~/Dropbox/presentations/2015_Africa_virology")

```

```{r}
# Install and load required libraries
install.packages("vegan")
library("vegan")
install.packages("rich")
library("rich")

```

```{r}
# Myoviridae
myo <- read.table("myo.txt")

# Podoviridae
podo <- read.table("podo.txt")

# Siphoviridae
sipho <- read.table("sipho.txt")

# All caudovirales
caudo <- read.table("caudo.txt")

```


```{r}
# Normalize the data
myo.total <- decostand(myo, method="total")
podo.total <- decostand(podo, method="total")
sipho.total <- decostand(sipho, method="total")
caudo.total <- decostand(caudo, method="total")

```

```{r}
# Calculate rarefaction curves
rarc.myo <- rarc(myo.total, nrandom=99)
rarc.podo <- rarc(podo.total, nrandom=99)
rarc.sipho <- rarc(sipho.total, nrandom=99)
rarc.caudo <- rarc(caudo.total, nrandom=99)

```

```{r}
# Plot and customize rarefaction curves

plot(rarc.myo)

# plot(rarc.caudo$richness, type="s", lwd=4, col="firebrick3", ylab="Richness", main="Caudovirales comparison")
# lines(rarc.sipho$richness, type="s", lwd=4, col="steelblue")
# lines(rarc.myo$richness, type="s", lwd=4, col="forestgreen")
# lines(rarc.podo$richness, type="s", lwd=4, col="orange")

```