McCOILR is an Rcpp wrapper for THE REAL McCOIL software developed by the Greenhouse Lab that estimates complexity of infection and population allele frequencies using SNP data obtained from Sequenom or similar types of SNP assays. It was simply created to aid incorporating COI estimation more easily within distributed computing pipelines, and I claim no ownership over the original source code, and all attribution and acknowledgement should be referred to the original project, and the associated publication. I have simply provided this wrapper in the hope that it might be helpful for others, and have provided a tutorial for basic use.

To view the tutorial please click here.

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/McCOILR")
library(McCOILR)

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