R help - Aug 2011 - Help with aggregate syntax for a multi-column function please.

Dear R-experts:

 

I am using a function called AUC whose arguments are data, time, id, and
dv.
 
data is the name of the dataframe, 
time is the independent variable column name, 
id is the subject id and 
dv is the dependent variable.  
 
The function computes area under the curve by trapezoidal rule, for each
subject id.
 
I would like to embed this in aggregate to further subset by each Cycle,
DoseDayNominal and Drug, but I can't seem to get the aggregate syntax
correct.  All the examples I can find use single column function such as
mean, whereas this AUC function requires four arguments.
 
Could someone kindly show me the syntax?
 
This is what I've tried so far:
 
AUC.DF<- aggregate(PKdata, list(PKdata$Cycle, PKdata$DoseDayNominal,
PKdata$Drug), 
                   function(x,tm,pt,conc) {AUC(x)},
tm="TimeBestEstimate", pt="Pt",
conc="ConcentrationBQLzero" )
 
AUC.DF<- aggregate(PKdata, list(PKdata$Cycle, PKdata$DoseDayNominal,
PKdata$Drug), 
                   function(x) {AUC(x,"TimeBestEstimate",
"Pt",
"ConcentrationBQLzero" )} )
 
AUC syntax is:
args(AUC)
function (data, time = "TIME", id = "ID", dv =
"DV")
 
 
thanks

 

Regards, 

Michael

 


	[[alternative HTML version deleted]]

Michael,

The function aggregate() is not going to work for your situation.  The 
function is applied to the individual columns of the subsetted data, not 
the subsetted data frame as a whole.  The help file reads: "Then, each of 
the variables (columns) in x is split into subsets of cases (rows) of 
identical combinations of the components of by, and FUN is applied to each 
such subset with further arguments in ... passed to it."

If you can rewrite your function so that it is a function with one 
argument, the data frame alone, then using the by() function should give 
you what you need.  Here is a simple example:

df <- data.frame(a=1:5, b=2:6, i=c(1, 1, 1, 2, 2))

junk <- function(df) {
        sum(df$a^2) + prod(df$b)
        }

data.frame(index=sort(unique(df$i)), results=as.vector(by(df[, c("a", 
"b")], df$i, junk)))

Hope this helps.

Jean


`·.,,  ><(((º>   `·.,,  ><(((º>   `·.,,  ><(((º>

Jean V. Adams
Statistician
U.S. Geological Survey
Great Lakes Science Center
223 East Steinfest Road
Antigo, WI 54409  USA



From:
"Michael Karol" <MKarol@syntapharma.com>
To:
<r-help@r-project.org>
Date:
08/02/2011 09:35 AM
Subject:
[R] Help with aggregate syntax for a multi-column function please.
Sent by:
r-help-bounces@r-project.org



Dear R-experts:

 

I am using a function called AUC whose arguments are data, time, id, and
dv.
 
data is the name of the dataframe, 
time is the independent variable column name, 
id is the subject id and 
dv is the dependent variable. 
 
The function computes area under the curve by trapezoidal rule, for each
subject id.
 
I would like to embed this in aggregate to further subset by each Cycle,
DoseDayNominal and Drug, but I can't seem to get the aggregate syntax
correct.  All the examples I can find use single column function such as
mean, whereas this AUC function requires four arguments.
 
Could someone kindly show me the syntax?
 
This is what I've tried so far:
 
AUC.DF<- aggregate(PKdata, list(PKdata$Cycle, PKdata$DoseDayNominal,
PKdata$Drug), 
                   function(x,tm,pt,conc) {AUC(x)},
tm="TimeBestEstimate", pt="Pt",
conc="ConcentrationBQLzero" )
 
AUC.DF<- aggregate(PKdata, list(PKdata$Cycle, PKdata$DoseDayNominal,
PKdata$Drug), 
                   function(x) {AUC(x,"TimeBestEstimate",
"Pt",
"ConcentrationBQLzero" )} )
 
AUC syntax is:
args(AUC)
function (data, time = "TIME", id = "ID", dv =
"DV")
 
 
thanks

 

Regards, 

Michael

 


                 [[alternative HTML version deleted]]

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PLEASE do read the posting guide 
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and provide commented, minimal, self-contained, reproducible code.



	[[alternative HTML version deleted]]

Hi:

Another way to do this is to use one of the summarization packages.
The following uses the plyr package.

The first step is to create a function that takes a data frame as
input and outputs either a data frame or a scalar. In this case, the
function returns a scalar, but if you want to carry along additional
variables in the output, you can replace it with a data frame that
returns the set of variables you want. You don't need to return the
grouping variables, but no harm is done if you do.

# This assumes the existence of a function AUC with the arguments
#  you stated in your post. I presume it returns a scalar value; if not,
# you should modify it to return a data frame instead. It would probably
# be better to modify AUC and call it in ddply() directly, but without the
# function code there's not much one can do...
myAUC <- function(df)
   AUC(df, 'TimeBestEstimate',
'Pt','ConcentrationBQLzero')

library('plyr')
ddply(PKdata, .(Cycle, DoseDayNominal, Drug), myAUC)

This is obviously untested, so caveat emptor. Both plyr and data.table
can accept functions with multiple arguments and do the right thing.
The trick in plyr is to write a function that takes a generic input
object (e.g., a (sub)data frame) and then uses (the variables within)
it to do the necessary calculations. Generally, you want the output of
the function to be compatible with the type of output you want from
the **ply() function. In this case, ddply() means data frame input,
data frame output; alply() would mean array input and list output,
etc.

If this doesn't work, please provide a reproducible example.

HTH,
Dennis

On Tue, Aug 2, 2011 at 7:32 AM, Michael Karol <MKarol at syntapharma.com>
wrote:
> Dear R-experts:
>
>
>
> I am using a function called AUC whose arguments are data, time, id, and
> dv.
>
> data is the name of the dataframe,
> time is the independent variable column name,
> id is the subject id and
> dv is the dependent variable.
>
> The function computes area under the curve by trapezoidal rule, for each
> subject id.
>
> I would like to embed this in aggregate to further subset by each Cycle,
> DoseDayNominal and Drug, but I can't seem to get the aggregate syntax
> correct. ?All the examples I can find use single column function such as
> mean, whereas this AUC function requires four arguments.
>
> Could someone kindly show me the syntax?
>
> This is what I've tried so far:
>
> AUC.DF<- aggregate(PKdata, list(PKdata$Cycle, PKdata$DoseDayNominal,
> PKdata$Drug),
> ? ? ? ? ? ? ? ? ? function(x,tm,pt,conc) {AUC(x)},
> tm="TimeBestEstimate", pt="Pt",
conc="ConcentrationBQLzero" )
>
> AUC.DF<- aggregate(PKdata, list(PKdata$Cycle, PKdata$DoseDayNominal,
> PKdata$Drug),
> ? ? ? ? ? ? ? ? ? function(x) {AUC(x,"TimeBestEstimate",
"Pt",
> "ConcentrationBQLzero" )} )
>
> AUC syntax is:
> args(AUC)
> function (data, time = "TIME", id = "ID", dv =
"DV")
>
>
> thanks
>
>
>
> Regards,
>
> Michael
>
>
>
>
> ? ? ? ?[[alternative HTML version deleted]]
>
> ______________________________________________
> 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.
>