outbreak

# Load packages
library ("OutbreakTools")

## Loading required package: ggplot2

## Loading required package: network

## network: Classes for Relational Data
## Version 1.13.0 created on 2015-08-31.
## copyright (c) 2005, Carter T. Butts, University of California-Irvine
##                     Mark S. Handcock, University of California -- Los Angeles
##                     David R. Hunter, Penn State University
##                     Martina Morris, University of Washington
##                     Skye Bender-deMoll, University of Washington
##  For citation information, type citation("network").
##  Type help("network-package") to get started.

## Loading required package: knitr

##  OutbreakTools 0.1-14 has been loaded

library ("ggplot2")
library ("ape")
library ("adegenet")

## Loading required package: ade4

## 
##    /// adegenet 2.0.1 is loaded ////////////
## 
##    > overview: '?adegenet'
##    > tutorials/doc/questions: 'adegenetWeb()' 
##    > bug reports/feature requests: adegenetIssues()

library ("adephylo")

## 
## Attaching package: 'adephylo'

## The following object is masked from 'package:ade4':
## 
##     orthogram

# Figure 1: Timeline of horseflu data

# Load data
data ("HorseFlu")

# Create basic figure
figure1 <- plot(HorseFlu, orderBy="yardID", colorBy="yardID",
what="shedding", size=3)

## Warning: `show_guide` has been deprecated. Please use `show.legend`
## instead.

# Customise legends
figure1 <- figure1 + scale_color_discrete("Yard identifier") +
guides(col=guide_legend(ncol = 3))
figure1 <- figure1 + scale_shape("Shedding data", labels=paste("sample",
1:6)) + labs(x="Collection date")

# Display Figure 1
figure1

Figure 1 is blah. blah blah