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_stresslab.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 $1000 bet on Pac-Man. He smiles, gets out his screwdriver and takes apart the Pac-Man game. Everyone says "What are you doing?" The neuroscientist says "Well, since we all know that Pac-Man is based on electric signals traveling through these circuits, obviously I can understand it better than the other guy by going straight to the source!"
Hi David, Thank you for the reproducible example! Try> do.call(rbind, auc_stress)cortisol amylase 2 919.05 6834.80 3 728.25 24422.05 4 2106.00 25908.35 6 636.40 12209.75 7 1925.95 4749.25> do.call(rbind, auc_control)cortisol amylase 2 604.90 2458.00 4 587.65 29954.55 6 493.60 13833.80 7 1211.00 4932.35 HTH, Jorge.- On Mon, Mar 19, 2012 at 5:44 PM, David Perlman <> wrote:> I could do this in various hacky ways, but what's the right way? > > I have a nice application of the by function, which does what I want. The > output looks like this: > > > auc_stress > lab.samples.stress$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 $1000 bet > on Pac-Man. He smiles, gets out his screwdriver and takes apart the Pac-Man > game. Everyone says "What are you doing?" The neuroscientist says "Well, > since we all know that Pac-Man is based on electric signals traveling > through these circuits, obviously I can understand it better than the other > guy by going straight to the source!" > > ______________________________________________ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. >[[alternative HTML version deleted]]
Thanks for providing a reproducible example.
Using the plyr package you can write your whole computation more compactly:
library(plyr)
library(caTools) #for trapz
auc <- ddply(lab.samples, .(challenge, subid),
function(df) {
df$time <- c(0, seq(60,by=10, len=nrow(df)-1))
summarize(df,
cortisol = trapz(time, cortisol),
amylase = trapz(time, amylase))
})
On Mon, Mar 19, 2012 at 2:44 PM, David Perlman <dperlman@wisc.edu> 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@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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