Updated Instructions

RunEM updated to take output directory and compare to regular M/U estimation.

java paper2.em.RunEM -Xmx1024m -v -o try11

1. It will load data from database where half=0 (excluding isDup=1 in random tables).
2. Use initial parameters to score records.

3. Output i.EDMU.score and i.MU.score files for iteration i.
4. Require input of a cutoff for EDMU and MU parameter recalculation.
5. Update the parameters based on the cutoff.

6. continue steps 3-5 for each iteration.
7. validate using half=1 and print validate.EDMU.score and validate.MU.score files

To find correct cutoffs, use showDist.R. (showDist("0.EDMU.score"))
To check FP/FN, use scoreDist.R. (scoreDist("0.EDMU.score"))

showDist shows density of all scores and outputs minimum near score mean.
scoreDist shows densities of divided scores (by table) and outputs minimum error rate.

To save PDFs of cutoff and distribution iterations, use printDist.R (printDist("try11"))