with FFT -
I am not sure).
Once again, thank you very much for your comments and help.
From: Stefan Evert
To: Moshe Olshansky
Cc: R-devel Mailing List
Sent: Monday, 19 June 2017, 2:23
Subject: Re: [Rd] dist function in R is very slow
> By the way, since the tcrossprod funct
> By the way, since the tcrossprod function in the Matrix package is so fast,
> the Euclidean distance can be computed very fast:
Indeed.
> euc_dist <- function(m) {mtm <- Matrix::tcrossprod(m); sq <- rowSums(m*m);
> sqrt(outer(sq,sq,"+") - 2*mtm)}
There are two reasons why I didn't use this
of magnitude faster than dist).
From: Stefan Evert
To: Moshe Olshansky
Cc: R-devel Mailing List
Sent: Sunday, 18 June 2017, 2:33
Subject: Re: [Rd] dist function in R is very slow
> On 17 Jun 2017, at 08:47, Moshe Olshansky via R-devel
> wrote:
>
> I am visualising h
> On 17 Jun 2017, at 08:47, Moshe Olshansky via R-devel
> wrote:
>
> I am visualising high dimensional genomic data and for this purpose I need to
> compute pairwise distances between many points in a high-dimensional space
> (say I have a matrix of 5,000 rows and 20,000 columns, so the resul
Dear R developers,
I am visualising high dimensional genomic data and for this purpose I need to
compute pairwise distances between many points in a high-dimensional space (say
I have a matrix of 5,000 rows and 20,000 columns, so the result is a
5,000x5,000 matrix or it's upper diagonal).Computi
