R help - Sep 2009 - apply function across two variables by mult factors

Greetings,

I am attempting to run a function, which produces a vector and  
requires two input variables, across two nested factor levels.  I can  
do this using by(X, list(factor1, factor2), function), however I  
haven't found a simple way to extract the list output into an  
organized vector form.  I can do this using nested loops but it isn't  
exactly an optimal approach.

Thank you for any and all suggestions.  Jon

# example data frame
testDF<-data.frame(
	x=rnorm(12),
	y=rnorm(12),
	f1=gl(3,4),
	f2=gl(2,2,12))

# example function [trivial]
testFun<-function(x){
	X<-abs(x[,1]);
	Y<-abs(x[,2]);
	as.numeric(	paste(round(X), round(Y), sep='.'))
	}

# apply by factor levels but hard to extract values
by(testDF[,1:2], list(testDF$f1, testDF$f2), testFun)

# Loop works, but not efficient for large datasets
testDF$value<-NA
for(i in levels(testDF$f1)){
	for(j in levels(testDF$f2)){
		testDF[testDF$f1==i & testDF$f2==j,]$value<-testFun(testDF[testDF 
$f1==i & testDF$f2==j,1:2])
		}
	}
testDF
sessionInfo()
#R version 2.9.1 Patched (2009-08-07 r49093)
#i386-apple-darwin8.11.1
#
#locale:
#en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
#
#attached base packages:
#[1] stats     graphics  grDevices utils     datasets  methods   base


Jon Loehrke
Graduate Research Assistant
Department of Fisheries Oceanography
School for Marine Science and Technology
University of Massachusetts
200 Mill Road, Suite 325
Fairhaven, MA 02719
jloehrke@umassd.edu
T 508-910-6393
F 508-910-6396


	[[alternative HTML version deleted]]

Hello, 
> -----Original Message-----
> From: r-help-bounces at r-project.org [mailto:r-help-bounces at
r-project.org]
> On Behalf Of Jon Loehrke
> Sent: Wednesday, September 16, 2009 2:23 PM
> To: r-help at r-project.org
> Subject: [R] apply function across two variables by mult factors
> 
> Greetings,
> 
> I am attempting to run a function, which produces a vector and
> requires two input variables, across two nested factor levels.  I can
> do this using by(X, list(factor1, factor2), function), however I
> haven't found a simple way to extract the list output into an
> organized vector form.  I can do this using nested loops but it isn't
> exactly an optimal approach.
> 
> Thank you for any and all suggestions.  Jon
> 
> # example data frame
> testDF<-data.frame(
> 	x=rnorm(12),
> 	y=rnorm(12),
> 	f1=gl(3,4),
> 	f2=gl(2,2,12))
> 
Try this using lapply, split, mapply?  Maybe it is in a nicer output object for
you?

testFun2 <- function(x, y) {
  X <- abs(x);
  Y <- abs(y);
  as.numeric(paste(round(X), round(Y), sep='.'))
}

lapply(split(testDF, list(testDF$f1, testDF$f2)),
       function(x) mapply(testFun2, x[1], x[2]))


> # example function [trivial]
> testFun<-function(x){
> 	X<-abs(x[,1]);
> 	Y<-abs(x[,2]);
> 	as.numeric(	paste(round(X), round(Y), sep='.'))
> 	}
> 
> # apply by factor levels but hard to extract values
> by(testDF[,1:2], list(testDF$f1, testDF$f2), testFun)
> 
> # Loop works, but not efficient for large datasets
> testDF$value<-NA
> for(i in levels(testDF$f1)){
> 	for(j in levels(testDF$f2)){
> 		testDF[testDF$f1==i & testDF$f2==j,]$value<-
> testFun(testDF[testDF
> $f1==i & testDF$f2==j,1:2])
> 		}
> 	}
> testDF
> sessionInfo()
> #R version 2.9.1 Patched (2009-08-07 r49093)
> #i386-apple-darwin8.11.1
> #
> #locale:
> #en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
> #
> #attached base packages:
> #[1] stats     graphics  grDevices utils     datasets  methods   base
> 
> 
> Jon Loehrke
> Graduate Research Assistant
> Department of Fisheries Oceanography
> School for Marine Science and Technology
> University of Massachusetts
> 200 Mill Road, Suite 325
> Fairhaven, MA 02719
> jloehrke at umassd.edu
> T 508-910-6393
> F 508-910-6396
> 
> 
> 	[[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.

Hi Jon,
Here is a suggestion:

foo <- function(x) as.numeric( paste( abs( round( x ) ), collapse =
"." ) )
testDF$value <- apply( testDF[,1:2], 1, foo )
testDF

HTH,
Jorge


On Wed, Sep 16, 2009 at 3:22 PM, Jon Loehrke <jloehrke@umassd.edu> wrote:
> Greetings,
>
> I am attempting to run a function, which produces a vector and
> requires two input variables, across two nested factor levels.  I can
> do this using by(X, list(factor1, factor2), function), however I
> haven't found a simple way to extract the list output into an
> organized vector form.  I can do this using nested loops but it isn't
> exactly an optimal approach.
>
> Thank you for any and all suggestions.  Jon
>
> # example data frame
> testDF<-data.frame(
>        x=rnorm(12),
>        y=rnorm(12),
>        f1=gl(3,4),
>        f2=gl(2,2,12))
>
> # example function [trivial]
> testFun<-function(x){
>        X<-abs(x[,1]);
>        Y<-abs(x[,2]);
>        as.numeric(     paste(round(X), round(Y), sep='.'))
>        }
>
> # apply by factor levels but hard to extract values
> by(testDF[,1:2], list(testDF$f1, testDF$f2), testFun)
>
> # Loop works, but not efficient for large datasets
> testDF$value<-NA
> for(i in levels(testDF$f1)){
>        for(j in levels(testDF$f2)){
>                testDF[testDF$f1==i &
> testDF$f2==j,]$value<-testFun(testDF[testDF
> $f1==i & testDF$f2==j,1:2])
>                }
>        }
> testDF
> sessionInfo()
> #R version 2.9.1 Patched (2009-08-07 r49093)
> #i386-apple-darwin8.11.1
> #
> #locale:
> #en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
> #
> #attached base packages:
> #[1] stats     graphics  grDevices utils     datasets  methods   base
>
>
> Jon Loehrke
> Graduate Research Assistant
> Department of Fisheries Oceanography
> School for Marine Science and Technology
> University of Massachusetts
> 200 Mill Road, Suite 325
> Fairhaven, MA 02719
> jloehrke@umassd.edu
> T 508-910-6393
> F 508-910-6396
>
>
>        [[alternative HTML version deleted]]
>
> ______________________________________________
> 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]]

Try this:

transform(testDF, value = as.numeric(paste(round(abs(x)),
round(abs(y)), sep = ".")))


On Wed, Sep 16, 2009 at 3:22 PM, Jon Loehrke <jloehrke at umassd.edu>
wrote:
> Greetings,
>
> I am attempting to run a function, which produces a vector and
> requires two input variables, across two nested factor levels. ?I can
> do this using by(X, list(factor1, factor2), function), however I
> haven't found a simple way to extract the list output into an
> organized vector form. ?I can do this using nested loops but it isn't
> exactly an optimal approach.
>
> Thank you for any and all suggestions. ?Jon
>
> # example data frame
> testDF<-data.frame(
> ? ? ? ?x=rnorm(12),
> ? ? ? ?y=rnorm(12),
> ? ? ? ?f1=gl(3,4),
> ? ? ? ?f2=gl(2,2,12))
>
> # example function [trivial]
> testFun<-function(x){
> ? ? ? ?X<-abs(x[,1]);
> ? ? ? ?Y<-abs(x[,2]);
> ? ? ? ?as.numeric( ? ? paste(round(X), round(Y), sep='.'))
> ? ? ? ?}
>
> # apply by factor levels but hard to extract values
> by(testDF[,1:2], list(testDF$f1, testDF$f2), testFun)
>
> # Loop works, but not efficient for large datasets
> testDF$value<-NA
> for(i in levels(testDF$f1)){
> ? ? ? ?for(j in levels(testDF$f2)){
> ? ? ? ? ? ? ? ?testDF[testDF$f1==i &
testDF$f2==j,]$value<-testFun(testDF[testDF
> $f1==i & testDF$f2==j,1:2])
> ? ? ? ? ? ? ? ?}
> ? ? ? ?}
> testDF
> sessionInfo()
> #R version 2.9.1 Patched (2009-08-07 r49093)
> #i386-apple-darwin8.11.1
> #
> #locale:
> #en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
> #
> #attached base packages:
> #[1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base
>
>
> Jon Loehrke
> Graduate Research Assistant
> Department of Fisheries Oceanography
> School for Marine Science and Technology
> University of Massachusetts
> 200 Mill Road, Suite 325
> Fairhaven, MA 02719
> jloehrke at umassd.edu
> T 508-910-6393
> F 508-910-6396
>
>
> ? ? ? ?[[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.
>