The current stable version of coala can be installed from CRAN using
Alternatively, you can install the current development version from GitHub using
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.
Coala can use the simulator ms. It is included in the CRAN package phyclust, which can be installed with
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
activate_msms(download = TRUE)
should suffice to use it if Java is installed correctly.
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
Installing additional Summary Statistics
Some summary statistics also need aditional software to be installed. The ones not listed here should always work.
Coala relies on the R package rehh to calculate iHH and iHS. Install it prior to adding sumstat_ihh to a model:
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