Jaatha's README
===============

Jaatha is a fast parameter estimation method primarily designed for Evolutionary
Biology. The method is described in 

> Mathew, L. A., Staab, P. R., Rose, L. E. and Metzler, D. (2013), 
> [Why to account for finite sites in population genetic studies and 
> how to do this with Jaatha 2.0][1]. Ecology and Evolution.

Practical instructions for running Jaatha are provided in the 
[The Jaatha HowTo][2]. Instructions how to use Jaatha with a non-standard 
simulation method are given in the [Custom Simulation Method HowTo][3].


Installation
------------

## From CRAN:
To install the current stable version of jaatha from CRAN, simply type

install.packages('jaatha')

in R.

## Development version from GitHub  
You can download and build the development version from GitHub following the
commands: 

# Install Jaatha's dependencies from CRAN
Rscript -e "install.packages(c('Rcpp', 'ape', 'doMC', 'RUnit'))"

# Download Jaatha from GitHub
git clone https://github.com/paulstaab/jaatha.git
cd jaatha

# And build the package using the Makefile
make

Afterwards you can install the created package with 
R CMD INSTALL jaatha_x.y.tar.gz


Usage
-----

Please refer to the [The Jaatha HowTo][2] for usage information.


Links
-----

[1]: http://onlinelibrary.wiley.com/doi/10.1002/ece3.722/abstract
[2]: http://evol.bio.lmu.de/_statgen/software/jaatha/jaatha_howto.pdf
[3]: http://evol.bio.lmu.de/_statgen/software/jaatha/custom_simulator_howto.pdf

* [Jaatha's Homepage](http://evol.bio.lmu.de/_statgen/software/jaatha)
* [Source Code on GitHub](https://github.com/paulstaab/jaatha)
* [Bug tracker](https://github.com/paulstaab/jaatha/issues)
* [Jaatha's page on CRAN](http://cran.r-project.org/web/packages/jaatha/index.html)
