R help - Aug 2012 - repeating a function across a data frame

Hello everyone.  Like others on this list, I'm new to R, and really not much
of a programmer, so please excuse any obtuse questions!  I'm trying to
repeat a function across all possible combinations of vectors in a data
frame.  I'd hugely appreciate any advice!

Here's what I'm doing:

I have some data: 40 samples, ~460 000 different readings between 1 and 0
for each sample.  I would like to make R spit out a matrix of distances
between the samples.  So far, I have made a function to calculate the
distance between any two samples:

DistanceCalc<-function(x,y){#x and y are both vectors - the entire reading
set for sample x and
#sample y, respectively
  distance<-sqrt(sum((x-y).^2))
  distanceCorrected<-distance/sqrt(length(x))#to force the maximum possible
value to =1
  print(distanceCorrected)
}

The next thing I want to do is to make this function run to compare all
possible combinations of my samples (1vs1, 1vs2, 1vs3...2vs1, 2vs2 etc).  In
python, the only other programming language I have ever used, I would just
use a "for" loop.  I have asked the internet how to do this, but the
overwhelming response seems to be "you don't want to do it like that -
use
the 'apply' functions".  I've tried to use the apply functions,
but I tend
to find that I can only give my DistanceCalc function a single vector (I can
tell it where to find x, but not where to find y, or vice versa).  I've also
found the 'by' and the 'outer' functions, but I'm likewise
failing at making
those work, e.g.
>
distancetable<-outer(DataWithoutBlanks,DataWithoutBlanks,FUN=DistanceCalc)
Error in x - y : non-numeric argument to binary operator

I think this may be because my data has headers and the function is trying
to calculate the difference between the names of my samples, but I don't
know how to correct this.

Would really appreciate your help!

Jen



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Hi

did you find function dist? It seems that it can do directly what you 
want.

Regards
Petr
> 
> Hello everyone.  Like others on this list, I'm new to R, and really not
much
> of a programmer, so please excuse any obtuse questions!  I'm trying to
> repeat a function across all possible combinations of vectors in a data
> frame.  I'd hugely appreciate any advice!
> 
> Here's what I'm doing:
> 
> I have some data: 40 samples, ~460 000 different readings between 1 and 
0
> for each sample.  I would like to make R spit out a matrix of distances
> between the samples.  So far, I have made a function to calculate the
> distance between any two samples:
> 
> DistanceCalc<-function(x,y){#x and y are both vectors - the entire 
reading
> set for sample x and
> #sample y, respectively
>   distance<-sqrt(sum((x-y).^2))
>   distanceCorrected<-distance/sqrt(length(x))#to force the maximum 
possible
> value to =1
>   print(distanceCorrected)
> }
> 
> The next thing I want to do is to make this function run to compare all
> possible combinations of my samples (1vs1, 1vs2, 1vs3...2vs1, 2vs2 etc). 
 In
> python, the only other programming language I have ever used, I would 
just
> use a "for" loop.  I have asked the internet how to do this, but
the
> overwhelming response seems to be "you don't want to do it like
that -
use
> the 'apply' functions".  I've tried to use the apply
functions, but I
tend
> to find that I can only give my DistanceCalc function a single vector (I 
can
> tell it where to find x, but not where to find y, or vice versa).  I've
also
> found the 'by' and the 'outer' functions, but I'm
likewise failing at
making
> those work, e.g.
> 
> > 
distancetable<-outer(DataWithoutBlanks,DataWithoutBlanks,FUN=DistanceCalc)
> Error in x - y : non-numeric argument to binary operator
> 
> I think this may be because my data has headers and the function is 
trying
> to calculate the difference between the names of my samples, but I
don't
> know how to correct this.
> 
> Would really appreciate your help!
> 
> Jen
> 
> 
> 
> --
> View this message in context: http://r.789695.n4.nabble.com/repeating-a-
> function-across-a-data-frame-tp4638643.html
> Sent from the R help mailing list archive at Nabble.com.
> 
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> and provide commented, minimal, self-contained, reproducible code.

As Petr suggests, the dist() function will do much of the work for you. 
For example ...
# example matrix of data
nsamples <- 40
nreadings <- 460000
dat <- matrix(runif(nsamples*nreadings), nrow=nsamples)
# Euclidean distance between the ROWS of dat
distance <- dist(dat)

Jean


JenniferH <jenachobbs@gmail.com> wrote on 08/01/2012 04:42:48
AM:
> 
> Hello everyone.  Like others on this list, I'm new to R, and really not
much
> of a programmer, so please excuse any obtuse questions!  I'm trying to
> repeat a function across all possible combinations of vectors in a data
> frame.  I'd hugely appreciate any advice!
> 
> Here's what I'm doing:
> 
> I have some data: 40 samples, ~460 000 different readings between 1 and 
0
> for each sample.  I would like to make R spit out a matrix of distances
> between the samples.  So far, I have made a function to calculate the
> distance between any two samples:
> 
> DistanceCalc<-function(x,y){#x and y are both vectors - the entire 
reading
> set for sample x and
> #sample y, respectively
>   distance<-sqrt(sum((x-y).^2))
>   distanceCorrected<-distance/sqrt(length(x))#to force the maximum 
possible
> value to =1
>   print(distanceCorrected)
> }
> 
> The next thing I want to do is to make this function run to compare all
> possible combinations of my samples (1vs1, 1vs2, 1vs3...2vs1, 2vs2 etc). 
 In
> python, the only other programming language I have ever used, I would 
just
> use a "for" loop.  I have asked the internet how to do this, but
the
> overwhelming response seems to be "you don't want to do it like
that -
use
> the 'apply' functions".  I've tried to use the apply
functions, but I
tend
> to find that I can only give my DistanceCalc function a single vector (I 
can
> tell it where to find x, but not where to find y, or vice versa).  I've
also
> found the 'by' and the 'outer' functions, but I'm
likewise failing at
making
> those work, e.g.
> 
> > 
distancetable<-outer(DataWithoutBlanks,DataWithoutBlanks,FUN=DistanceCalc)
> Error in x - y : non-numeric argument to binary operator
> 
> I think this may be because my data has headers and the function is 
trying
> to calculate the difference between the names of my samples, but I
don't
> know how to correct this.
> 
> Would really appreciate your help!
> 
> Jen
	[[alternative HTML version deleted]]

Hi Petr and Jean,

thanks very much, problem solved!  Really appreciate your help.

Jennifer



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