Linear MINE simulations Files

README for MINE program

You will need java to run the program. If it is not installed you can install it by going to www.java.com

The Jama package class files must be in the Jama folder.
A class file will be provided, however to rebuild this file you can use the java command:
javac Mine.java

The program has 7 inputs in this order:

-Input file name
-Number of experiment loops (each loop is 10 observations) This means using 100 here will produce 1000 individual observations.
-Output file name
-Alpha value
-Start seed
-Iteration seed
-Which method 
	For MINE use "mine"
	For MINE with orthonormal basis use "random"
	For MINE with rotation use "rotation"
	For MINE-like, if none of the above cases fit, this will run.

A sample command line run of the program:
java Mine input.txt 50 output.txt 0.005 123123 10 rotation

This will have 50 experiments for 500 observations with an alpha of 1% (two tailed) and use the Mine with random rotation method.


The input file needs to be in the format

pvalues
sigma
mu0 
precision matrix

A single blank line should be between each of the sections.
The first 3 items must be a single value on each line (pvalues and mu0 are 1xp arrays) and the pxp precision matrix should be written with only a single comma between each value.




Bouffier, Amanda. A MINE Alternative to D-optimal Designs for the Linear Model. MS Thesis. University of Georgia, Athens. 2013

Bouffier A, Arnold J, and Schuttler HB. A MINE Alternative to D-optimal Designs for the Linear Model. Submitted to PLOS One 2014