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Installation
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.
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
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
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.
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")
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:
install.packages("rehh")
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
.