[R] Better way to find distances between points in a set?

[Charles C. Berry]

On Wed, 10 Dec 2008, cgw at witthoft.com wrote:

>
>   Hah!
>   I  DID do my homework first. From now on I guess I'll have to post the
>   complete list of trails I followed before deciding
>   I was lost. That appears to be the only way to stave off the Harpies.
>   So, before I posted, and before I even wrote my toy script, I found and read
>   thru  the  help file for dist(). If in fact dist() does what I want, I
>   couldn't see that from either the description or the example. Or from an
>   example I tried myself.
>   Remember:  my Euclidean distance requires first finding the difference
>   between the orthogonal components of the two points, i.e.
>   (x1-x2) and (y1-y2) and then calculating the Pythagorean of those values.
>   Just getting distances between the actual elements of my matrix (x and y
>   components) isn't the same. And, yes, I tried 'euclidean' .
>   So I would be greatful indeed if someone could confirm that, for a matrix as
>   I described, where each row contains the coordinates of a single point, that
>   dist() can be convinced to return the geometric euclidean distances.
>   Or that it can't.

Carl,

Since you did your homework, you saw this:

From the dist man page:

 	dist(x, method = "euclidean", diag = FALSE, upper = FALSE, p = 2)
[...]
 	euclidean:
 		Usual square distance between the two vectors (2 norm).
---

If you did not appreciate that these 'two vectors' are two rows of 
your matrix, this would have shown you that they are:

 	all.equal( as.vector(alldist), as.vector(alldist3) )

(the 'as.vector' calls strip off attributes like dimnames, so the focus is 
solely on the distances )

Chuck

>   Carl
>   PS I also found which and which.max all by myself! ^_^
>   Dec 9, 2008 11:52:46 PM, cberry at tajo.ucsd.edu wrote:
>   ===========================================
>   The 'better way' to do almost anything starts with a reading of the
>   _posting guide_, which reminds you to
>   Do your homework before posting [Reasons whyfor deleted]]
>   Â  Â * Do help.search("keyword") and apropos("keyword") with different
>   keywords (type this at the R prompt).
>   [other homework items deleted]
>   So, to start with you would have tried:
>   help.search('distance')
>   HA! This leads to
>   dist {stats} Distance Matrix Computation
>   Well, doesn't that sound promising??
>   > alldist3 <- as.matrix( dist( cv ) )
>   > which( alldist3 == max( alldist3 ), arr.ind=TRUE )
>   Oh yes, if you are too lazy to look up the posting guide URL, the function
>   help.request() will open it for you when you admit that you haven't yet
>   read it (or lead you thru the further steps to prepare a question to this
>   list if you say that you have read it).
>   HTH,
>   Chuck
>   On Tue, 9 Dec 2008, Carl Witthoft wrote:
>   > I was playing around a bit to see how I could find the two points in a set
>   of
>   > points (or ordered pairs) Â furthest from each other.
>   >
>   > Here's what I did:
>   > 1) created a Nrow by 2col matrix, so each row contains an x,y coordinate
>   > pair.
>   >
>   > 2) fed the matrix to a nested mapply (cv is my matrix):
>   >
>   > mapply(function(k,l) mapply(function(x,y,a,b)
>   > + sqrt((x-a)^2+(y-b)^2),cv[,1],cv[,2],k,l),cv[,1],cv[,2])->alldist
>   >
>   > Then I just did which.max(alldist) and found the original two points by
>   > figuring out what row, col the results of which.max referred to.
>   >
>   > So, what's a better, or cleaner way to do all this? Â That is, is there a
>   > function in some package that will do anything like my nested mapply
>   thing,
>   > and is there a better tool than which.max for locating a position in a
>   > matrix?
>   >
>   > thanks
>   > Carl
>   >
>   > ______________________________________________
>   > 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.
>   >
>   >
>   Charles C. Berry                            (858) 534-2098
>   Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Dept of
>   Family/Preventive Medicine
>   E mailto:cberry at tajo.ucsd.edu            UC San Diego
>   http://famprevmed.ucsd.edu/faculty/cberry/ Â La Jolla, San Diego 92093-0901
> ______________________________________________
> 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.
>

Charles C. Berry                            (858) 534-2098
                                             Dept of Family/Preventive Medicine
E mailto:cberry at tajo.ucsd.edu	            UC San Diego
http://famprevmed.ucsd.edu/faculty/cberry/  La Jolla, San Diego 92093-0901