Installation

Installing the package

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.

Installing optional external software

Installing 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.

Installing 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.