THE BASIC Random Jungle (RJ) README
See "INSTALL" for help on installation
Modified on 11-15-11 by Nick Davis for Mac OS X compilation addendum

1. INTRODUCTION

This directory contains the source code, tests, autobuild files and autobuild
tools for RJ. RJ is a generalized implementation of Random Forests(tm) (RF) by
Leo Breiman and Adele Cutler. In genetics, it is an well established method for
analysing genetic data (i.e. GWA data).

RJ is free software distributed under a GNU-style copyleft.

RF is a powerful machine learning method. Most interesting features [1]:
- Variable selection: Estimates the importance of variables
- Efficiency:         It runs efficiently on large data.
- Missing values:     It has an effective method for estimating missing data.
- Classifier:         It creates classifier for further analyses.
- General. err.:      It generates an internal unbiased estimate of the
                      generalization error as the building progresses.
- Proximities:        It computes proximities between pairs of cases that can be
                      used in clustering, locating outliers, or (by scaling)
                      give interesting views of the data. Can be used as the
                      distance matrix for Multidimensional Scaling (MDS)


2. HISTORY

RJ was initially written by Daniel F. Schwarz of the Institute of Medical
Biometry and Statistics of University of Lubeck in Germany.
He started in the beginning of 2008.


3. GOALS

Create a machine learning tool for analysing data as an equivalent to
alternative statistical methods.

4. DEPS
UBUNTU (packages):
- gcc
- g++
- gfortran
- libtool
- autoconf
- libboost-dev
- zlib1g-dev
- libgsl0-dev
- libxml2-dev

optional:
(make dist)
- texinfo
- texlive

mpi:
- mpi-default-dev
- mpi-default-bin

5. Mac OS X compilation (addendum by Nick Davis)
Random Jungle has been successfully built on Mac OS X Lion (10.7.2).  Homebrew,
a package manager for OS X, was used to install some of the dependencies.
http://mxcl.github.com/homebrew.  Once installed, the following commands will
install the missing dependencies:

brew install gsl
brew install gfortran
brew install boost

To build RJ on Mac OS X, the following configure line can be used:
LDFLAGS="-L/usr/local/homebrew/lib -L/usr/local/homebrew/lib/gcc/i686-apple-darwin11/4.2.1/x86_64" ./configure --with-boost=/usr/local/homebrew/include
(note, replace /usr/local/homebrew above with the location of homebrew.  The
default location is /usr/local)



Sincerely,
Daniel


[1] http://www.stat.berkeley.edu/~breiman/RandomForests/cc_home.htm