How to redo for cutoffs

Retry try11 as cut0:
core fields,
initial params: 1,-1,
disagreement cutoff: 0

RunEM to get .0 files

in R:
change dir to c:\Program Files\R\R2.4.1\paper2
source("showDist.R")
source("scoreDist.R")
chage dir to c:\Program Files\R\R2.4.1\paper2\cut0
showDist("0.EDMU.score")
enter showDist EDMU cutoff (if it is good) in Java

showDist("0.MU.score")
enter showDist MU cutoff (if it is good) in Java

MU and EDMU cutoffs for 0. iteration should be the same (same starting params)

repeat for 1., 2., and validate. iteration steps.

Then do
edmu = scoreDist("validate.EDMU.score")
mu = scoreDist("validate.MU.score")
plot(edmu, type="l", xlim=c(0,0.02), ylim=c(.98,1))
lines(mu)

change cutoffs by changing hard coded variable approx in main (approx line 348)
change default field set in main (approx line 424)

name scoreDists
edmu
mu0 for 0 cutoff
mu1 for 1 cutoff
...
mu5 for 5 cutoff

then use roc.R and run roc() to get ROC curve and AUC for all values.

Otherwise use int(edmu) for AUC and above plot, lines combo.