[R] counting row repetitions without loop

Waterman, DG (David) david.waterman at diamond.ac.uk
Thu Feb 7 16:18:12 CET 2008


Hi Harold,

Thanks for your suggestion, which worked very well. I had to modify the
pattern as I'm really dealing with larger grids than 10x10 so I needed a
way to distinguish between for example position 1,11 and 11,1. The new
function based on your suggestion runs in ~40% of the time compared with
the original for loop construction, so it's an important saving! For the
record, the new function is essentially as follows:

pixellate <- function(input, xPxNum = 128, yPxNum = 128, gain = 1){
  temp <- matrix(data = 0, ncol = yPxNum, nrow = xPxNum)
  input <- subset(input, x <= xPxNum & x > 0 & y <= yPxNum & y > 0)
#strip illegal pixel values
  input$patt <- input$x + (input$y - 1) * xPxNum #make unique identifier
for each pixel
  counts <- as.data.frame(with(input, table(patt)))
  input <- merge(input, counts, by='patt')
  index <- matrix(c(input$x, input$y), ncol=2) #make an index matrix
  temp[index] <- input$Freq * gain
  temp
}

where input is a data frame consisting of x and y coordinates of events
on a grid, 1 row per event, e.g.

>input
     x   y
1   86  63
2   75  16
3  122  34
4    8  17
5    1   7
6  115  81
7  103 125
8   76  54
9  114 117
10  96  18

...and so on for many rows.

Cheers
David.


-----Original Message-----
From: Doran, Harold [mailto:HDoran at air.org] 
Sent: 06 February 2008 15:03
To: Doran, Harold; Waterman, DG (David); r-help at r-project.org
Subject: RE: [R] counting row repetitions without loop

Sorry, word wrap made that incomprehensible, I think

x  y
4  5
6  7
6  6
7  5
5  7
6  7
4  5
6  7
7  6
5  6
dat <- read.table('clipboard', header=TRUE)

dat$patt <- paste(dat$x,dat$y, sep='')

mm <- as.data.frame(with(dat, table(patt)))

dat <- merge(dat, mm, by='patt')

mat <- matrix(0, ncol=10, nrow=10)

gg <- matrix(c(dat$x, dat$y), ncol=2)

mat[gg] <- dat$Freq 

> -----Original Message-----
> From: r-help-bounces at r-project.org
> [mailto:r-help-bounces at r-project.org] On Behalf Of Doran, Harold
> Sent: Wednesday, February 06, 2008 9:56 AM
> To: Waterman, DG (David); r-help at r-project.org
> Subject: Re: [R] counting row repetitions without loop
> 
> I think this does what you want, but there may be a more efficient way
> 
> x  y
> 4  5
> 6  7
> 6  6
> 7  5
> 5  7
> 6  7
> 4  5
> 6  7
> 7  6
> 5  6
> dat <- read.table('clipboard', header=TRUE) # copy sample data above 
> dat$patt <- paste(dat$x,dat$y, sep='') mm <- as.data.frame(with(dat, 
> table(patt))) dat <- merge(dat, mm,
> by='patt') mat <- matrix(0, ncol=10, nrow=10) gg <- matrix(c(dat$x, 
> dat$y), ncol=2) mat[gg] <- dat$Freq
> 
> > -----Original Message-----
> > From: r-help-bounces at r-project.org
> > [mailto:r-help-bounces at r-project.org] On Behalf Of Waterman, DG
> > (David)
> > Sent: Wednesday, February 06, 2008 9:08 AM
> > To: r-help at r-project.org
> > Subject: [R] counting row repetitions without loop
> > 
> > Hi,
> >  
> > I have a data frame consisting of coordinates on a 10*10 grid, i.e.
> >  
> > > example
> >     x  y
> > 1   4  5
> > 2   6  7
> > 3   6  6
> > 4   7  5
> > 5   5  7
> > 6   6  7
> > 7   4  5
> > 8   6  7
> > 9   7  6
> > 10  5  6
> > 
> > What I would like to do is return an 10*10 matrix
> consisting of counts
> > at each position, so in the above example I would have a
> matrix where,
> > for example, cell [4,5] contains 2 and [6,7] contains 3. At
> the moment
> > I have implemented this using a for loop over the rows of the data 
> > frame, however the data frames I want to process are very
> long so the
> > loop takes many minutes to complete. Can I do this in a
> more efficient
> > way?
> >  
> > Cheers,
> > David
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