ojwatson / paper

R toolkit for assisting with Imperial College "paper outbreak" practical

paper

What is this?

Paper is a package designed to assist in demonstration of analysis associated to a "paper outbreak" teaching practical. It is a collection of functions designed to ease analaysis of the paper outbreak practical within R. This includes importing and cleaning data from an excel sheet, viewing the infection network, visualising the outbreak as an animation, and calculating the epidemiological parameters associated with the practical.

---

To view the tutorial please click here.

---

In addition, there is an updated google form version of the infection form that went with the practical, which can be located here.

Installing paper

To install the development version from github the package devtools is required.

In order to install devtools you need to make sure you have a working development environment:

1. Windows: Install Rtools. For help on how to install Rtools please see the following guide, paying particular attention to the section about adding Rtools to your system PATH.

In order to find out which version of Rtools you will need to check which version of R you are running. This can be be found out using the sessionInfo() function:

> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

2. Mac: Install Xcode from the Mac App Store.

3. Linux: Install a compiler and various development libraries (details vary across different flavors of Linux).

Once a working development environment is ready, then devtools can be installed from CRAN. If you have not set up which CRAN mirror to use before, then you will be asked to choose your CRAN mirror. Select the cloud mirror.

install.packages("devtools")
library(devtools)

Once devtools is installed it is best to restart our R session. To do this either close RStudio or restart R (ctrl + shift + F10). Once your R session has been restarted the package can be installed and loaded using:

devtools::install_github("OJWatson/paper")
library(paper)

---

Troubleshoot Guide

1. If you are installing the package outside of RStudio or an IDE that enables write access then try launching your IDE as an administrator.

2. When installing the package to a library/shared computer you may see the following error:

"Error in unzip(src, list = TRUE) : 'exdir' does not exist".

This error is related to RStudio failing to handle the network location for installation. A quick fix is to close RStudio and open the directory where you have R installed on your network ("\icnas1.cc.ic.ac.uk/ic001/R/R-3.3.2/bin" - where ic001 is your username). In that directory run R and then install the package by using:

devtools::install_github("OJWatson/paper")

Now, open a new RStudio window and you should be able to load the package, presuming your RStudio session is using your network R library. To troubleshoot this:

.libPaths()
## If the above does not return something that looks like "\\\\icnas1.cc.ic.ac.uk/ic001/R/R-3.3.2/library" then add the library path:
.libPaths("\\\\icnas1.cc.ic.ac.uk/ic001/R/R-3.3.2/library")

---

Asking a question

For bug reports, feature requests, contributions, use github's issue system.