[R] Sampling the Distance Matrix

[Lorenzo Isella]

On Thu, Sep 24, 2015 at 01:30:02PM -0700, David Winsemius wrote:
>
>On Sep 24, 2015, at 12:36 PM, Lorenzo Isella wrote:
>
>> Hi,
>> And thanks for your reply.
>> Essentially, your script gets the job done.
>> For instance, if I run
>>
>> mm <- cbind(5/(1:5), -2*sqrt(1:5))
>> dst <- dist(mm)
>> dst2 <- as.matrix(dst)
>> diag(dst2) <- NA
>> idx <- which(apply(dst2, 1, function(x) all(na.omit(x)>.9)))
>>
>> then it correctly detects the first two rows, where all the values are
>> larger than 0.9.
>> In other words, it detects the points that are at least 0.9 units away
>> from *all* the other points.
>> My other question (I did not realize this until I got your answer) is
>> the following: I have the distance matrix of a set of N points.
>> You gave me an algorithm two find all the points that are at least 0.9
>> units away from any other points.
>> However, in some cases, for me it is OK even a weaker condition: find
>> a subset of k points (with k tunable) whose distance *from each other*
>> is greater than 0.9 units (even if their distance from some other
>> points may be smaller than 0.9).
>
>If I understand ..... Make a matrix of unique combinations, then apply by rows to get the qualifying columns that satisfy the distance criterion:
>
>mtxcomb <- combn(1:20, 5)
>goodcls <- apply(mtxcomb , 2, function(idx) all( dist( cbind( x[idx], y[idx]) ) > 0.9))
>mtxcomb [ , goodcls]
>
>In my sample it was around 9% of the total 5 item combinations.
>
>snipped a lot of output:
>.....
>    [,1440] [,1441]
>[1,]      12      13
>[2,]      13      16
>[3,]      16      17
>[4,]      19      19
>[5,]      20      20
>> dim( mtxcomb)
>[1]     5 15504
>

Hi,
Thanks for your reply.
I think I am getting there, but when I run your commands, I get this
error message

Error in cbind(x[idx], y[idx]) : object 'x' not found

Any idea why? Should I combine those 3 lines with something else?
Cheers

Lorenzo