Installation

Installing coala

The current stable version of coala can be installed from CRAN using

install.packages("coala")

Alternatively, you can install the current development version from GitHub using

devtools::install_github("statgenlmu/coala")

this requires that the devtools package is installed. Coala follows a continuous integration approach, so that the master brach of its GitHub repository should always contain a usable version.

Installing additional Simulators

The simulator scrm should work out-of-the-box. The others have to be installed.

ms

Coala can use the simulator ms. It is included in the CRAN package phyclust, which can be installed with

install.packages("phyclust")
activate_ms()

Once phyclust is installed, coala should detect it automatically, so that no further calls to activate_ms are needed. However, coala will by default prefer scrm to ms, because the first does not require temporary files. Raise ms' priority to change that:

activate_ms(priority = 500)

When doing so, make sure that there is enough free space on tempdir() for all temporary files and consider using a tempdir that resides in memory instead of on disc. On modern Linux systems, this can be done by starting R with

TMPDIR=/dev/shm R

msms

If you want to simulate selection, you need to install msms. You need to install Java on your system. Then you need to download the jar file. Coala can do the latter for you, so that a

activate_msms(download = TRUE)

should suffice to use it if Java is installed correctly.

seq-gen

Coala uses seq-gen to simulate finite-site mutation models. On Debian based systems (e.g. Debian, Ubuntu, Linux Mint), it can be installed from the official repos using

apt-get install seq-gen

Coala should detect it automatically after R is restarted.

On other systems, download and extract its last version. Compile it according to the instructions in the package. On Unix systems, you can just execute

cd source
make

You need to provide the path to the created seq-gen binary:

activate_seqgen("path/to/seqgen/source/seq-gen")

Installing additional Summary Statistics

Some summary statistics also need aditional software to be installed. The ones not listed here should always work.

iHH

Coala relies on the R package rehh to calculate iHH and iHS. Install it prior to adding sumstat_ihh to a model:

install.packages("rehh")

Omega

Coala employs OmegaPlus to calculate the Omega statistic. To install it, please follow the instructions on the website and in the package. You then need to provide the path to the binary as binary argument of sumstat_omega.