[R] by output into data frame

[Peter Ehlers]

On 2012-03-19 15:00, Jorge I Velez wrote:
> Hi David,
>
> Thank you for the reproducible example!
>
> Try
>
>> do.call(rbind, auc_stress)
>    cortisol  amylase
> 2   919.05  6834.80
> 3   728.25 24422.05
> 4  2106.00 25908.35
> 6   636.40 12209.75
> 7  1925.95  4749.25
>
>> do.call(rbind, auc_control)
>    cortisol  amylase
> 2   604.90  2458.00
> 4   587.65 29954.55
> 6   493.60 13833.80
> 7  1211.00  4932.35
>
> HTH,
> Jorge.-


Or with the plyr package:

library(plyr)
ldply(auc_stress)

Peter Ehlers


>
>
> On Mon, Mar 19, 2012 at 5:44 PM, David Perlman<>  wrote:
>
>> I could do this in various hacky ways, but what's the right way?
>>
>> I have a nice application of the by function, which does what I want.  The
>> output looks like this:
>>
>>> auc_stress
>> lab.samples.stress$subid: 2
>>   cortisol amylase
>> 1   919.05  6834.8
>>
>> ---------------------------------------------------------------------------------------------------------------------------
>> lab.samples.stress$subid: 3
>>    cortisol  amylase
>> 11   728.25 24422.05
>>
>> etc.
>>
>> What I want is a data frame roughly like this:
>>
>> subid  cortisol.auc  amylase.auc
>> 2      919.05        6834.8
>> 3      728.25        24422.05
>>
>> etc.
>>
>> What is a nice way to make that happen?
>>
>>
>>
>> Here is the code and data that I am using, which should run directly if
>> you copy and paste it:
>>
>>
>> sanity.check<-read.csv("
>> http://brainimaging.waisman.wisc.edu/~perlman/testdata.csv", header=TRUE,
>> sep = ",")
>> lab.samples<- subset(sanity.check,Sample!='before bed'&  Sample!='morning
>> after')
>> lab.samples$Sample<-factor(lab.samples$Sample)
>> lab.samples.stress<-subset(lab.samples,challenge=='stress')
>> lab.samples.control<-subset(lab.samples,challenge=='control')
>>
>> auc_ground<- function(sub_df) {
>>         print(sub_df)
>>         auc<-sub_df[1,]*0
>>         timedif<-c(60,10,10,10,10,10,10)
>>         for (i in 1:(nrow(sub_df)-1) ) {
>>                 print(c(i,i+1))
>>                 #print(c(values[i],values[i+1]))
>>                 pair_area<-(sub_df[i,]+sub_df[i+1,])*timedif[i]/2
>>                 auc<-auc+pair_area
>>         }
>>         auc
>> }
>>
>> auc_stress<-by(lab.samples.stress[c('cortisol','amylase')],
>> lab.samples.stress$subid, auc_ground, simplify=T)
>> auc_control<-by(lab.samples.control[c('cortisol','amylase')],
>> lab.samples.control$subid, auc_ground, simplify=T)
>>
>>
>> Thanks for your help!
>>
>> P.S. sorry if this question has been answered before, it is nearly
>> impossible to get useful google results on search terms like "by"...  too
>> common word...
>>
>>
>> -dave----------------------------------------------------------------------
>> A neuroscientist is at the video arcade, when someone makes him a $1000 bet
>> on Pac-Man. He smiles, gets out his screwdriver and takes apart the Pac-Man
>> game. Everyone says "What are you doing?" The neuroscientist says "Well,
>> since we all know that Pac-Man is based on electric signals traveling
>> through these circuits, obviously I can understand it better than the other
>> guy by going straight to the source!"
>>
>> ______________________________________________
>> R-help at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>
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>
> ______________________________________________
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.