This vignette focuses on getting everything together to get this package to run.
There are several packages located on CRAN that skeleSim depends upon. They all currently install automatically during the installation process.
Currently, skeleSim implements coalescent simulations in
fastsimcoal2 and forward-time in
rmetasim dependency is handled via normal package installation.
You must install fastsimcoal2 on your computer yourself. The executable for your operating system (Windows, MacOSX, linux) is available here.
The trick is to make sure that the folder/directory in which the fastsimcoal executable resides is in the search path for your operating system
Helpful instructions for editing the PATH environmental variable for Windows can be found here. On Mac OS or LINUX/UNIX systems, the executable should be placed in the /usr/local/bin folder which is usually a default in the PATH.
If the executable is in your path, skeleSimGUI() looks for it (and other versions if present) and allows you to select among versions on the "FastSimCoal params" tab.
The most up to date version (new bugs and all) of skeleSim is always going to be on github. This is also a place to ask specific questions about skeleSim.
First install the great 'devtools' package. Then,
library(devtools) install_github("christianparobek/skeleSim", build_vignettes = TRUE, force = TRUE)
Once the above has been completed the shiny interface can be run:
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