[R] Better way to find distances between points in a set?
Charles C. Berry
cberry at tajo.ucsd.edu
Wed Dec 10 23:12:30 CET 2008
On Wed, 10 Dec 2008, Stavros Macrakis wrote:
> On Tue, Dec 9, 2008 at 11:52 PM, Charles C. Berry <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]]...
>> 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).
> Charles, I am distressed by the nasty tone of your note.
Well, I am sorry that my reply caused you distress.
I try to provide useful answers. And I often do the 'homework' in the
posting guide before responding to be sure I provide useful answers.
Sometimes my 'reward' for a post is to receive off-list requests for
further help that the 'asker' could have easily worked out by following
the 'Do your homework' steps. And I sometimes get those requests even when
I point to the excellent self-help resources in my original post.
I welcome advice on how to do a better job and do so in a gentler, kinder
manner, but I'd like to maintain a focus on strongly encouraging the use
of help.request(), the posting guide, and all of the other resources that
are already available.
> Though I certainly
> agree that poor queries on this list are an annoyance, and that the posting
> guide gives useful advice on what to do before posting, I don't think that
> poor queries are a reason to presume bad faith for any but the most flagrant
> correspondents ("here is my problem set, solve it for me"). And though I
> have not been on this list very long, I have been answering questions on
> other lists like this for a long time.
> What's more, it seems to me that Witthoft has a legitimate problem.
To which I provided a solution and to which Carl responded asking for
I responded to that post too - and I'll admit that it could reasonably be
seen as having a 'snarky' tone - but Carl will know when he reads it what
he asked to know.
> to solve it myself, and here is what I come up with:
> test <- matrix(rnorm(20),ncol=2)
> => Error, though which supports arr.ind, which.max doesn't
> Yes, that is documented, but it violates reasonable expectations.
> => 21 oops, that is a vector index; what about arr.ind?
> Apparently the dist class (return class of dist fnc.)
> doesn't act as an array here (and which/arr.ind is
> happy to treat a vector as an array without warning).
> Is this a problem in dist, or a problem in which?
> So how do I map back from 21 to 3,7? Nothing obvious.
> ? `[`, ? array, and ? dist don't seem to help.
> So let's convert to a matrix explicitly:
> => row col
> [1,] 21 1
> Hmm, that's not right; apparently the == flattened the
> dist class into its base vector, which which/arr.ind
> helpfully (?) treated as a matrix.
> => row col
> 7 7 3
> 3 3 7
> Finally getting useful results; but converting to the array
> added in the upper triangular part... oh, well, we need to
> choose *which* maximum anyway.
OK, so I stopped with the response you just gave and didn't take that next
step to tell Carl to use upper.tri():
which( upper.tri( dist(x) ) &
but help.search("upper") gets it easily enough. So does
> So, as Witthoft said: what's a better, or cleaner way to do all this?
So I gave him my version of a better, cleaner way. If there is a still
better and even cleaner way, I'd be delighted to see it.
Carl did not ask any of the questions you listed below. And I didn't see
anything in his post that implied he wanted answers to them.
> why aren't R's operators more regular in their behavior? Why doesn't
> arr.ind work for which.max? Why doesn't dist(x)==1 return an object of the
> same shape as the original dist (as matrix(...)==1 would have), but instead
> flatten it? Where does one find the function that maps from a list of array
> indices to the corresponding vector index and vice versa?
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
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