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Casey Dunn committed e82d41a

created black and white and color figures, updated pdf

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 # sicb2013
 
+## Background
+
 This repository includes the source code for the analyses presented 
 at the [EDEN](http://edenrcn.com) sponsored symposium ["Understanding First 
 Order Phenotypes: Transcriptomics for Emerging Model Systems"](http://www.sicb.org/meetings/2013/symposia/phenotypes.php) 
 Many thanks to [Joe Felsenstein](http://www.gs.washington.edu/faculty/felsenstein.htm) 
 for helpful discussions about multivariate comparative analyses.
 
+## Use
+
+To run the simulation and analyses, execute the following shell command:
+
+    R CMD BATCH simulation.r
+    
+This will regenerate the pdf file.
+
+## Citations
+
+This code implements the two regularization methods described in:
+
+Bickel, P. J. & Levina, E. Covariance regularization by thresholding. 
+Ann. Statist. 36, 2577–2604 (2008). [doi:10.1214/08-AOS600](http://dx.doi.org/10.1214/08-AOS600)
+
+Luo, X. High Dimensional Low Rank and Sparse Covariance Matrix Estimation via 
+Convex Minimization. arXiv.org (2011). [arxiv](http://arxiv.org/abs/1111.1133)
+
+
 ## License
 
 This program is free software: you can redistribute it and/or modify

File regularization.pdf

Binary file modified.

File regularization_bw.pdf

Binary file added.

File simulation.r

 
 # Set up plotting parameters
 # Color plots
-# mycols <- tim.colors(100)
+mycols <- tim.colors(100)
 # Greyscale plots
-mycols <- gray(1:100 / 100)
+# mycols <- gray(1:100 / 100)
 
 mybreaks <- seq(-1, 1, length.out=101)