Displaying 20 results from an estimated 1000 matches similar to: "fastest way to compute the squared Euclidean distance between two vectors in R"
2007 Feb 21
2
how much performance penalty does this incur, scalar as a vector of one element?
I have been comparing R with other languages and systems. One peculiar feature of R is there is no scalar. Instead, it is just a vector of length one. I wondered how much performance penalty this deign cause, particular in situations with many scalars in a program. Thanks.
Jason Liao, http://www.geocities.com/jg_liao
Associate Professor of Biostatistics
Drexel University School of Public
2006 Aug 24
4
extremely slow recursion in R?
I recently coded a recursion algorithm in R and ir ran a few days
without returning any result. So I decided to try a simple case of
computing binomial coefficient using recusrive relationship
choose(n,k) = choose(n-1, k)+choose(n-1,k-1)
I implemented in R and Fortran 90 the same algorithm (code follows).
The R code finishes 31 minutes and the Fortran 90 program finishes in 6
seconds. So the
2006 Oct 03
3
Linking R with Fortran 90: make: m2c: Command not found
Following the setup in Prof.Duncan Murdoch's page, I have successfully compiled the DLL for one Fortran 95 program using Gfortran and got 300 times speed boost. For the second set of fortran programs, However, I have this error message
R CMD SHLIB -o jiangang kdtree2.f90 jian.f90 gang.f90
m2c -o jian.o jian.mod
make: m2c: Command not found
make: *** [jian.o] Error 127
Can anyone
2007 Nov 06
3
help needed: taking a function out of a package and it can not find some funtions
I tried to modify the R function bw.SJ (from the stats package) for my own use. But if I just get the source code and run directly (without any modification), it can no longer find some key functions called within it. I understand this has something to do with searching path which I do not understand well. Can anyone tell me how to modify the source code of an R function and still make it part of
2007 Nov 06
3
help needed: taking a function out of a package and it can not find some funtions
I tried to modify the R function bw.SJ (from the stats package) for my own use. But if I just get the source code and run directly (without any modification), it can no longer find some key functions called within it. I understand this has something to do with searching path which I do not understand well. Can anyone tell me how to modify the source code of an R function and still make it part of
2001 Sep 04
2
fastest way to multiply each column of a matrix by a single vlaue
Let A be a m by n matrix and b a length n vector. What is the fastest
vectorized code for doing
for(j in 1:n) A[, j] <- A[, j]/b[j] ?
solution 1:
t(t(A)/b)
solution 2:
B <- matrix( rep(b, m), byrow=T, nrow=m )
A/B
anything else?
I have a program that uses this kind of operation million of times and
I appreciate your input.
Thanks.
Jason Liao
=====
Jason G. Liao
Department of
2003 Mar 05
8
how to find the location of the first TRUE of a logical vector
without having to check the vector element by element? Thanks a lot!
Jason
=====
Jason G. Liao, Ph.D.
Division of Biometrics
University of Medicine and Dentistry of New Jersey
335 George Street, Suite 2200
New Brunswick, NJ 08903-2688
phone (732) 235-8611, fax (732) 235-9777
http://www.geocities.com/jg_liao
2005 Apr 18
2
when can we expect Prof Tierney's compiled R?
I am excited to learn that Prof. Tierney is bringing to us compiled R.
I would like to learn when it will be available. This information will
be useful in scheduling some of my projects. Thanks.
Jason
Jason Liao, http://www.geocities.com/jg_liao
Dept. of Biostatistics, http://www2.umdnj.edu/bmtrxweb
University of Medicine and Dentistry of New Jersey
683 Hoes Lane West, Piscataway‚ NJ 08854
2008 Jul 14
5
A question about using function plot
Hello, everyone! I have spent two hours to get what I wanted in a simple situation and have not been successful. The set up is extremely simple
x = c(1,2,4,8)
y = c(1,2,3,4)
plot(x, y)
What I need, however, is for the 4 points of 1,2,4,8 to be spaced evenly, not by their numerical scale. Also, there should not be any other values such as 5,6,7 marked on the axis.
So I tried the following
x =
2006 May 10
3
new package error message
My coauthor made a new R package GeneLogit (100% R code) which installs
ok on R 2.3 on Windows. But when I type
library(GeneLogit)
it gave the error message
Error in library(GeneLogit) : 'GeneLogit' is not a valid package --
installed < 2.0.0?
It runs on R 1.9.0 just fine. It seems that others have encountered
same problem but no solution is found by googling
How can I fix this
2001 Apr 09
4
fastest R platform
Hello, everyone! I picked up R several months ago and have adopted it
as my choice for statistical programming. Coming from a Java
background, I can honestly say that R is not only free, it is better
tha S-plus: the lexical scope in R makes it very simple to simulate
Java's object model. For this, I encourage everyone to read the artcle:
Robert Gentleman and Ross Ihaka (2000) "Lexical
2003 Jul 23
5
Dismal R performance of Athlon moble CPU?
I have been using a laptop computer of Pentium III 1.13 Ghz. I heard
that AMD's Athlon has excellent floating point capacity. So I bought a
Athlon 2200+ laptop yesterday. I expected that new Athlon 2200+ will be
twice as fast as the P III 1.13 GB. I ran a R simulation program and
the new computer is only 30% faster, in fact slightly slower than a
Celeron 1.50 GB laptop. I am very disappointed
2006 Nov 29
1
An example of using rJava
I have received a few private emails asking for some simple
demonstration of calling Java code from R using the rJava package
(which can be installed directly inside R). Here is one example for
convolving two vectors (an example in the R manual about linking C with
R).
First write a Java program
public class my_convolve
{
public static double[] convolve(double[] a, double[] b)
2002 Feb 01
4
ROC curves using R
I did some serach around. It seems that ROC curve computation is not
supported on R. Anyone has some leads? Thanks.
Jason
=====
Jason G. Liao, Ph.D.
Division of Biometrics
UMDNJ School of Public Health
335 George Street, Suite 2200
New Brunswick, NJ 08903-2688
phone (732) 235-9748, fax (732) 235-9777
http://www.geocities.com/jg_liao
__________________________________________________
Great
2002 Oct 30
2
two small wishes for R
1. allows underscore as part of a variable name
2. Uses C or Java style comments mark.
Jason
=====
Jason G. Liao, Ph.D.
Division of Biometrics
University of Medicine and Dentistry of New Jersey
335 George Street, Suite 2200
New Brunswick, NJ 08903-2688
phone (732) 235-8611, fax (732) 235-9777
http://www.geocities.com/jg_liao
__________________________________________________
HotJobs - Search
2004 Sep 08
1
64 bit R slower than 32 bit R on Sun Sparc Solaris?
Hello, everyone! I guess no one is still using R on Sun Sparc these
days. But our department has a (pretty new) two-CPU Sun server. We
recently compiled R as a 64 bit application and expected a performance
boost. But it runs 25-30% slower than the 32 bit version of R. Anyone
knows why this is so? Thanks!
Jason
=====
Jason Liao, http://www.geocities.com/jg_liao
Dept. of Biostatistics,
2001 Dec 19
2
how to get unique vectors
First, happy holidays, everyone! Thanks to the R team for bringing out
1.4 before the new year.
I have 10000 integer triplets stored in A[1:10000, 1:3]. I would like
to find the unique triplets among the 10000 ones with possible
duplications. What is the easiest way for this. I know the function
unique(), which apply to a vector, not the 10000*3 array in my problem.
Thanks in advance.
Jason
2001 May 01
2
6 times faster by eliminating apply
This is some kind of follow-up to my previous posts. I have further
improved the speed of my program 6 times by eliminating all the
apply(). It turns out that apply is slow, is slower than direct loop,
it is an order slower than a matrix operation alternative.
Here is one example. The first apply version runs 19 seconds, the
second loop version runs 13 seconds, the third matrix version runs 1
2004 Aug 12
4
truly object oriented programming in R
Good morning! I recently implemented a KD tree in JAVA for faster
kernel density estimation (part of the code follows). It went well. To
hook it with R, however, has proved more difficult. My question is: is
it possible to implement the algorithm in R? My impression seems to
indicate no as the code requires a complete class-object framework that
R does not support. But is there an R package or
2001 Apr 17
1
fastest R platform: follow-up and summary
The following runs in an eyeblink on my 700Mhz Thinkpad T-20 (256 MB RAM)
with Windows NT:
var(matrix(rnorm(4000000),ncol=4,nrow=1000000))
This also has the virtue of being quite readable. You could allow an
arbitrary covariance matrix and mean vector and it increases the time
slightly, but still only about 5 seconds.
Regarding performance, having tons of RAM is crucial. My Windows NT and the