Displaying 20 results from an estimated 600 matches similar to: "Matrix package: writeMM"
2007 Jun 19
1
Matrix library error: "should never happen; please report"
Hi,
I got the following error. Sorry but this time I couldn't reproduce it
with a simple chunk of code:
.TM.repl.i.2col(): drop 'matrix' case ...
Error in .nextMethod(x = x, i = i, j = j) :
'i' has no integer column number should never happen; please report
In addition: Warning messages:
1: Ambiguous method selection for "%*%", target
2007 Jan 26
2
%*% in Matrix objects
Dear R users,
I need to normalize a bunch of row vectors. At a certain point I need to divide a matrix by a vector of norms. I find that the behavior of Matrix objects differs from normal matrix objects. Example the following code examples differ only in xnormed changing from normal to Matrix object:
x = matrix(1:12,3,4)
x = as(x, "CsparseMatrix")
xnorms = sqrt(colSums(x^2))
2016 Apr 20
0
Matrix: How create a _row-oriented_ sparse Matrix (=dgRMatrix)?
>>>>> Henrik Bengtsson <henrik.bengtsson at gmail.com>
>>>>> on Tue, 19 Apr 2016 14:04:11 -0700 writes:
> Using the Matrix package, how can I create a row-oriented sparse
> Matrix from scratch populated with some data? By default a
> column-oriented one is created and I'm aware of the note that the
> package is optimized for
2007 Jan 23
3
[fixed] vectorized nested loop: apply a function that takes two rows
(Extremely sorry, disregard previous email as I hit send before pasting the latest version of the example; this one is smaller too)
Dear R users,
I want to apply a function that takes two vectors as input to all pairs
(combinations (nrow(X), 2))of matrix rows in a matrix.
I know that ideally, one should avoid loops in R, but after reading the docs for
do.call, apply, etc, I still don't know
2007 Jan 23
3
[fixed] vectorized nested loop: apply a function that takes two rows
(Extremely sorry, disregard previous email as I hit send before pasting the latest version of the example; this one is smaller too)
Dear R users,
I want to apply a function that takes two vectors as input to all pairs
(combinations (nrow(X), 2))of matrix rows in a matrix.
I know that ideally, one should avoid loops in R, but after reading the docs for
do.call, apply, etc, I still don't know
2007 Apr 16
1
colSum() in Matrix objects
Hi,
I'd like to simply add column-wise using Matrix objects (Csparse).
It looks like one can apply mosty any base function to these objects
(i.e., apply, colSums), but there is a nasty conversion to traditional
matrix objects if one does that.
Is there any workaround? I can see colSum listed in the help for Class
'CsparseMatrix' , but I wonder whether I'm using the default
2017 Nov 20
2
package check fail on Windows-release only?
I mistakenly left a write in "/tmp" in the rockchalk package (version
1.8.109) that I uploaded last Friday. Kurt H wrote and asked me to fix
today.
While uploading a new one, I became aware of a problem I had not seen.
The version I uploaded last Friday, 1.8.109, has OK status on all
platforms except r-release-windows-ix86+x86_64. I get OK on
oldrel-windows and also on devel-windows.
2016 Apr 19
2
Matrix: How create a _row-oriented_ sparse Matrix (=dgRMatrix)?
Using the Matrix package, how can I create a row-oriented sparse
Matrix from scratch populated with some data? By default a
column-oriented one is created and I'm aware of the note that the
package is optimized for column-oriented ones, but I'm only interested
in using it for holding my sparse row-oriented data and doing basic
subsetting by rows (even using drop=FALSE).
Here is what I
2012 Jan 18
1
kmeans clustering on large but sparse matrix
Hi,
I have a 60k*600k matrix, which exceed the vector length limit of 2^32-1.
But it's rather sparse, only 0.02% has value. So I save is as MarketMatrix
(mm) file, it's about 300M in size. I use readMM in Matrix package to read
it in. If do so, the data type becomes dgTMatrix in 'Matrix' package
instead of the common matrix type.
The problem is, if I run k-means only on part of
2007 May 07
3
like apply(x,1,sum), but using multiplication?
Hi,
I need to multiply all columns in a matrix so something like
apply(x,2,sum), but using multiplication should do.
I have tried apply(x,2,"*")
I know this must be trivial, but I get:
Error in FUN(newX[, i], ...) : invalid unary operator
The help for apply states that unary operators must be quoted. I tried
single quotes too, with the same results.
Thanks,
-Jose
--
Jose
2009 Oct 24
1
operations on sparse matrices, and dense intermediary steps
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Hash: SHA1
Hi,
I'm doing some basic operations on large sparse matrices, for example
getting a row.
it takes close to 30 seconds on a 3Ghz machine, and shots the memory
usage up to the sky.
I suspect there are dense intermediary steps (which, if true would
defeat the purpose of trying to use sparse representaitons).
As much as I try understanding the
2006 Apr 27
3
gmane?
Hi All,
I recently found gmane
http://gmane.org/
It's a system to covert mail to news and back, with the nice property of
keeping
a searchable archive... Very convenient if you are subscribed to many lists
and
don't want to have your mail box cluttered. I use it to read several mailing
lists already, but R is not available there.
I wonder if the admins know about gmane and if they
2007 Jan 23
0
vectorized nested loop: apply a function that takes two rows
Dear R users,
I want to apply a function that takes two vectors as input to all pairs
(combinations (nrow(X), 2))of matrix rows in a matrix.
I know that ideally, one should avoid loops in R, but after reading the docs for
do.call, apply, etc, I still don't know how to write the nested loop in a
vectorized way.
Example data:
x = matrix(rnorm(1000), 100, 100)
zeros = runif(90)
x[]
# this is
2004 Dec 01
2
rank in descending order?
Hi,
Is there any simple solution to get ranks in descending order?
Example,
a <- c(10, 98, 98, 98, 99, 100)
r <- rank(a, ties.method="average")
produces
1 3 3 3 5 6
I would want this instead:
6 5 3 3 3 1
Note that reversing r doesn't work but in small examples.
Thanks,
-Jose
--
jquesada at andrew.cmu.edu Research associate
http://lsa.colorado.edu/~quesadaj Dept. of
2008 Dec 06
1
R vs Python performance-wise
Hi,
Has anyone run any R vs Python (numpy) tests?
I'd love to see what the differences performance-wise are, specially
handling large sparse matrices.
Since both rely on external C code, there might not be much of a
difference.
If you know and use both languages, what are the main differences and what
made you stick to one over another?
I also noticed that there are strong libraries
2016 Jan 04
2
R, AIX 64-bit builds - trying to understand root cause for message: "Error: Line starting 'Package: tools ...' is malformed!"
The bulk is on my forums - the final post for today is:
Results to date:
A. It looks like I am going to need a newer compiler for C - xlc/xlC V11
apparently does not understand this code:
"/data/prj/cran/R-3.2.3/src/main/memory.c", line 2149.31: 1506-046 (S)
Syntax error.
I will have to check if R-devel has different code before asking for
assistence.
+2139 #ifdef
2007 Jul 16
1
R equivalent to Matlab's Bayes net toolbox
Hi,
I'm attending summer School at UCLA (IPAM) on "probabilistics models of
cognition". I have been an R-user since v. 1.4.1, but was trained in the
frequentist tradition (as most psychologists!). I found that all faculty
here use matlab and Murphy's bayes net toolbox. I have not had the need to
use matlab before, and would love to stick to R for graphics models and
2017 Nov 21
0
package check fail on Windows-release only?
>>>>> Paul Johnson <pauljohn32 at gmail.com>
>>>>> on Mon, 20 Nov 2017 14:59:26 -0600 writes:
> I mistakenly left a write in "/tmp" in the rockchalk package (version
> 1.8.109) that I uploaded last Friday. Kurt H wrote and asked me to fix
> today.
> While uploading a new one, I became aware of a problem I had not seen.
2006 Jul 09
1
package:Matrix handling of data with identical indices
In the Matrix package v. 0.995-11 I see that the dgTMatrix
Class for compressed, sparse, triplet-form matrices handles
Identically indexed data instances by summing their values,
e.g.,
library(Matrix)
(Mt <- new("dgTMatrix",
i = as.integer(c(0,0,1,1,4)),
j = as.integer(c(0,1,2,2,4)),
x = as.double(1:5),
Dim = as.integer(c(5,5))))
## 5 x 5 sparse Matrix of class
2006 Jul 09
1
package:Matrix handling of data with identical indices
In the Matrix package v. 0.995-11 I see that the dgTMatrix
Class for compressed, sparse, triplet-form matrices handles
Identically indexed data instances by summing their values,
e.g.,
library(Matrix)
(Mt <- new("dgTMatrix",
i = as.integer(c(0,0,1,1,4)),
j = as.integer(c(0,1,2,2,4)),
x = as.double(1:5),
Dim = as.integer(c(5,5))))
## 5 x 5 sparse Matrix of class