[R] PAMR package question: How to plot Estimated probabilities for the training data and test data

From: Waverley <waverley.paloalto_at_gmail.com>
Date: Tue, 01 Apr 2008 14:54:35 -0700

Hi,

 I have tried some time trying to figure out how to use pamr to plot multiclass  Estimated probabilities for the training data and test data?

 Specifically, how to recreate the PAMR publication on PNAS with  Tibshrani et al. The publication is as attached. The plot I want to  do is Figure 5.

 I have downloaded the pamr package and the function which gives  similar plot is pamr.plotcvprob but this is different from plot  estimated probability.

 There is one function pamr.xl.plotcvprob.compute sounds like the one  I am looking for but it is internal function and is not supposed to be  called by user.

 Any R guru or expression analysis guru who are familiar with pamr can help me?

 Given saying that, I hope pamr author can make a public function to  plot this like the figure 5 in their PNAS paper. After they should  encourage user to recreate their nice work through easy APIs.

 Thanks.

 --
 Waverley @ Palo Alto

-- 
Waverley @ Palo Alto

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