Re: [R] ROCR for combination of markers

From: Rasanga Ruwanthi <ruwanthi_kdr_at_yahoo.com>
Date: Thu, 28 Apr 2011 08:15:38 -0700 (PDT)


Many thanks Eik. That was really helpful. I have found ROC function Epi package draws ROC curve for a combination of markers. What I tried was  
library(Epi)

x <- rnorm( 100 )
z <- rnorm( 100 )
w <- rnorm( 100 )

tigol <- function( x ) 1 - ( 1 + exp( x ) )^(-1) y1 <- rbinom( 100, 1, tigol( 0.3 + 3*x + 5*z + 7*w ) )
out=ROC( form = y1 ~ x + z, plot="ROC",MI=FALSE)  
But this function does not produce SE or CI of the AUC or any other statistics. Any suggestion to get these?  
Thanks again
Rasanga

From: Eik Vettorazzi <E.Vettorazzi_at_uke.uni-hamburg.de> Subject: Re: [R] ROCR for combination of markers To: "Rasanga Ruwanthi" <ruwanthi_kdr_at_yahoo.com> Cc: r-help_at_r-project.org
Date: Thursday, 28 April, 2011, 13:11

... and additionally, 'ROC' from the Epi package does the second step all in one.

Am 28.04.2011 13:01, schrieb Eik Vettorazzi:
> Hi Rasanga,
> you may have a look at the 'improveProb' function from the Hmisc
> package. There you can compare the increase in prognostic power for
> several combinations of markers. You can create a ROC curve for a
> combination of markers by using the predicted risks eg. from a logistic
> regression model.
>
> To compare ROC curves of competing markers you can use 'roc.area.test'
> from the 'clinfun' package or 'hanley' from gcl.
>
> hth.
>
>
> Am 27.04.2011 23:17, schrieb Rasanga Ruwanthi:

>> Dear list
>>  
>> I have 5 markers that can be used to detect an infection in combination. Could you please advise me how to use functions in ROCR/ other package to produce the ROC curve for a combination of markers?
>>  
>> I have used the following to get ROC statistics for each marker.
>> pred <- prediction(y$marker1, y$infectn)
>> perf <-performance(pred,"tpr","fpr")
>> plot(perf,ave="threshold",spread.estimate="boxplot")
>>
>> But I want know whether we could get this for more than one marker, so we can look at how good the markers in combination to predict the infection. I'm very grateful for any suggestion/help.
>>  
>> Thanks
>> Rasanga
>>  
>>
>>     [[alternative HTML version deleted]]
>>
>>
>>
>>
>> ______________________________________________
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>
-- 
Eik Vettorazzi
Institut für Medizinische Biometrie und Epidemiologie
Universitätsklinikum Hamburg-Eppendorf

Martinistr. 52
20246 Hamburg

T ++49/40/7410-58243
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Received on Thu 28 Apr 2011 - 15:21:07 GMT

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