[R] return only pairwise correlations greater than given value

[B77S]

This is probably not the prettiest or most efficient function ever, but this
seems to do what I wanted.


spec.cor <- function(dat, r, ...){
	
	require("reshape")
	
	d1 <- data.frame(cor(dat))
	d2 <- melt(d1)
	d2[,3] <- rep(rownames(d1), nrow(d2)/length(unique(d2[,1])))
	d2 <- d2[,c("variable", "V3", "value")]
	colnames(d2) <- c("V1", "V2", "value")
	d2 <- d2[with(d2, which(V1 != V2, arr.ind=T)), ]
	d2 <- d2[which(d2[,3] >=r | d2[,3] <= -r, arr.ind=T),]
	d2[,1:2] <- t(apply(d2[,1:2], MARGIN=1, function(x) sort(x)))
	d2 <- unique(d2)	
	
	return(d2)
}



data(mtcars)


> spec.cor(mtcars[,2:5], .6)
Using  as id variables
    V1   V2      value
2  cyl disp  0.9020329
3  cyl   hp  0.8324475
4  cyl drat -0.6999381
7 disp   hp  0.7909486
8 disp drat -0.7102139



I'm not sure how to make melt() quit giving the "Using  as id variables"
warning, but I don't really care either.






B77S wrote:
> 
> Thanks Michael, 
> 
> I just started on the following code (below), and realized I should ask,
> as this likely exists already. 
> 
> basically what I'd like is for the function to return (basically) what you
> just suggested, plus the names of the two variables (I suppose pasted
> together would be good). 
> 
> I hope that is clear, and obviously I didn't get so far as to add the
> names to the output.
> 
> # 
> sig.cor <- function(dat, r, ...){
> 
> cv2 <- data.frame(cor(dat))
> var.names <- rownames(cv2)
> 
> list.cv2 <- which(cv2 >=r | cv2 <= -r, arr.ind=T)
> cor.r <- cv2[list.cv2[which(list.cv2 [,"row"]!=list.cv2 [,"col"]),]]
> cor.names <- var.names[list.cv2[which(list.cv2 [,"row"]!=list.cv2
> [,"col"]),]]
> 
> 	
> return(cor.r)
> 
> }
> 
> 
> data(mtcars)
> sig.cor(mtcars[,2:5], .90)
> 
> 
> #> sig.cor(mtcars[,2:5], .90)
> #[1] 0.9020329 0.9020329
> 
> 
> # Ideally this would look likt this:
> 
> cyl-disp
> 0.9020329
> 
> 
> 
> 
> 
> 
> Michael Weylandt wrote:
>> 
>> What exactly do you mean "returns" them? More generally I suppose,
>> what do you have in mind to do with this?
>> 
>> You could do something like this:
>> 
>> BigCorrelation <- function(X){
>> 
>>      return(which(abs(cor(X)) > 0.9, arr.ind = T))
>> }
>> 
>> but it hardly seems worth its own function call.
>> 
>> On Thu, Nov 17, 2011 at 12:42 AM, B77S <bps0002@> wrote:
>>> Hello,
>>>
>>>  I would like to find out if a function already exists that returns only
>>> pairwise correlations above/below a certain threshold (e.g, -.90, .90)
>>>
>>> Thank you.
>>>
>>>
>>>
>>> --
>>> View this message in context:
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>>> Sent from the R help mailing list archive at Nabble.com.
>>>
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>> 
>> ______________________________________________
>> R-help@ mailing list
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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.
>> 
> 


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