Re: [R] Retrieving the 2 row of "dist" computations

From: Jeff08 <jefferyding_at_gmail.com>
Date: Thu, 10 Jun 2010 20:06:08 -0700 (PDT)

Edit:

There is something funky about the code. It definitely returns the right column of the "distance" data, but returns an incorrect row.

Code:

NCols=250
NRows=829
myMat<-matrix(runif(NCols*NRows), ncol=NCols)

d<-dist(myMat)
e<-sort.list(d)
e<-e[1:5]  ##Retrieve minimum 5 distances

k <- 5
res <- matrix(NA, ncol = 2, nrow = k)

ds <- sort(d)
for(i in 1:k) res[i, ] <- which(as.matrix(d) == ds[i], arr.ind = TRUE)[1,]
colnames(res) <- c('row','col')
rownames(res) <- 1:k

res

I have derived the formula for 829 rows, to check if the returned column and row matches the index given by e.

Column # = x, Row # = y. n = 828-(x-2)
index = y+(n+828)(828-n+1)/2

Formula R CODE
##Just checking for row 1

i<-1
y<-res[i,1]
x<-res[i,2]
n<-(828-(x-2))

index1<-(y+(n+828)*(828-n+1)/2)
index2<-e[i]
##index1 should equal index2, but this is not the case
##you can tell that the column is right because index1 & index 2 is close
##(a change in row of 1 shifts the index by 1, but a change in column
## shifts index by ~400 on average)

You can then compare this index to the one given by e[i]

Jorge Ivan Velez wrote:

> 
> Hi there,
> 
> I am sure there is a better way to do it, but here is a suggestion:
> 
> res <- matrix(NA, ncol = 2, nrow = 5)
> for(i in 1:5) res[i, ] <- which(as.matrix(d) == sort(d)[i], arr.ind =
> TRUE)[1,]
> res
> 
> HTH,
> Jorge
> 
> 
> On Wed, Jun 9, 2010 at 11:30 PM, Jeff08 <> wrote:
> 

>>
>> Dear R Gurus,
>>
>> As you probably know, dist calculates the distance between every two rows
>> of
>> data. What I am interested in is the actual two rows that have the least
>> distance between them, rather than the numerical value of the distance
>> itself.
>>
>> For example, If the minimum distance in the following sample run is
>> d[14],
>> which is .3826119, and the rows are 4 & 6. I need to find a generic way
>> to
>> retrieve these rows, for a generic matrix of NRows (in this example
>> NRows=7)
>>
>> NCols=5
>> NRows=7
>> myMat<-matrix(runif(NCols*NRows), ncol=NCols)
>>
>> d<-dist(myMat)
>>
>> 1 2 3 4 5 6
>> 2 0.7202138
>> 3 0.7866527 0.9052319
>> 4 0.6105235 1.0754259 0.8897555
>> 5 0.5032729 1.0789359 0.9756421 0.4167131
>> 6 0.6007685 0.6949224 0.3826119 0.7590029 0.7994574
>> 7 0.9751200 1.2218754 1.0547197 0.5681905 0.7795579 0.8291303
>>
>> e<-sort.list(d)
>> e<-e[1:5] ##Retrieve minimum 5 distances
>>
>> [1] 14 16 4 18 5
>> --
>> View this message in context:
>> http://r.789695.n4.nabble.com/Retrieving-the-2-row-of-dist-computations-tp2249844p2249844.html
>> Sent from the R help mailing list archive at Nabble.com.
>>
>> ______________________________________________
>> 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.
>>
> 
> 	[[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.
> 
> 



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Received on Fri 11 Jun 2010 - 03:46:46 GMT

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