Displaying 20 results from an estimated 700 matches similar to: "bigmemory - extracting submatrix from big.matrix object"
2010 Dec 17
1
[Fwd: adding more columns in big.matrix object of bigmemory package]
Hi,
With reference to the mail below, I have large datasets, coming from various
different sources, which I can read into filebacked big.matrix using library
bigmemory. I want to merge them all into one 'big.matrix' object. (Later, I
want to run regression using library 'biglm').
I am unsuccessfully trying to do this from quite some time now. Can you
please
2010 Aug 11
1
Bigmemory: Error Running Example
Hi,
I am trying to run the bigmemory example provided on the
http://www.bigmemory.org/
The example runs on the "airline data" and generates summary of the csv
files:-
library(bigmemory)
library(biganalytics)
x <- read.big.matrix("2005.csv", type="integer", header=TRUE,
backingfile="airline.bin",
descriptorfile="airline.desc",
2011 Sep 29
1
efficient coding with foreach and bigmemory
I recently learned about the bigmemory and foreach packages and am trying
to use them to help me create a very large matrix. Without those
packages, I can create the type of matrix that I want with 10 columns and
5e6 rows. I would like to be able to scale up to 5e9 rows, or more, if
possible.
I have created a simplified example of what I'm trying to do, below. The
first part of the
2010 Dec 16
0
adding more columns in big.matrix object of bigmemory package
Hi all,
Is there any way I can add more columns to an existing filebacked big.matrix
object.
In general, I want a way to modify an existing big.matrix object, i.e., add
rows/columns, rename colnames, etc.
I tried the following:
> library(bigmemory)
> x =
read.big.matrix("test.csv",header=T,type="double",shared=T,backingfile="test
2012 May 05
2
looking for adice on bigmemory framework with C++ and java interoperability
I work with problems that have rather large data requirements -- typically
a bunch of multigig arrays. Given how generous R is with using memory, the
only way for me to work with R has been to use bigmatrices from bigmemory
package. One thing that is missing a bit is interoperability of bigmatrices
with C++ and possibly java. What i mean by that is API that would allow
read and write filebacked
2010 Apr 23
2
bigmemory package woes
I have pretty big data sizes, like matrices of .5 to 1.5GB so once i need to
juggle several of them i am in need of disk cache. I am trying to use
bigmemory package but getting problems that are hard to understand. I am
getting seg faults and machine just hanging. I work by the way on Red Hat
Linux, 64 bit R version 10.
Simplest problem is just saving matrices. When i do something like
2019 Jul 19
1
difficulty with sanitizer using bigmemory
Dear all,
bigKRLS, which has been on CRAN for a couple of years, had to be pulled
recently due to what seems to be a sanitizer issue stemming from its use of
bigmemory. bigKRLS works fine (we?ve used it ourselves on many different
platforms and have had over 15,000 downloads without an end user reporting
difficulties because of this issue). Unfortunately, we have been unable to
reproduce the
2009 Apr 16
0
Major bigmemory revision released.
The re-engineered bigmemory package is now available (Version 3.5
and above) on CRAN. We strongly recommend you cease using
the older versions at this point.
bigmemory now offers completely platform-independent support for
the big.matrix class in shared memory and, optionally, as filebacked
matrices for larger-than-RAM applications. We're working on updating
the package vignette, and a
2009 Apr 16
0
Major bigmemory revision released.
The re-engineered bigmemory package is now available (Version 3.5
and above) on CRAN. We strongly recommend you cease using
the older versions at this point.
bigmemory now offers completely platform-independent support for
the big.matrix class in shared memory and, optionally, as filebacked
matrices for larger-than-RAM applications. We're working on updating
the package vignette, and a
2009 Jul 20
2
kmeans.big.matrix
Hi,
I'm playing around with the 'bigmemory' package, and I have finally
managed to create some really big matrices. However, only now I
realize that there may not be functions made for what I want to do
with the matrices...
I would like to perform a cluster analysis based on a big.matrix.
Googling around I have found indications that a certain
kmeans.big.matrix() function should
2012 May 09
2
ergm model, nodematch with diff=T
Dear all,
I am new to network analysis, but since I have good data I started to read
about it and learned how to use the ergm and related packages. I generally
get interesting results, but when I run a model including sociality and
selective mixing effects for different groups, the model runs (and
converges) but I get a warning as follows:
mod <- ergm(network ~ edges + gwesp(0, fixed=T) +
2012 Jun 19
1
how to manipulate dput output format
I am reading into Java dput output for a matrix, more specifically for a
file backed big-matrix. I basically need to lift dimnames for a matrix from
dput output. It's no big deal, but the code is very 'hackish' due to the
need to get rid of quotes, endlines, parenthesis, etc. I was wondering if i
could manipulate to an extent dput output with some options that define it,
for example,
2012 Feb 20
1
bigmemory not really parallel
Hi, all,
I have a really big matrix that I want to run k-means on.
I tried:
>data <-
read.big.memory('mydata.csv',type='double',backingfile='mydata.bin',descriptorfile='mydata.desc')
I'm using doMC to register multicore.
>library(doMC)
>registerDoMC(cores=8)
>ans<-bigkmeans(data,k)
In system monitor, it seems only one thread running R. Is
2010 Jan 10
0
problems with bigmemory
Hi all,
I am trying to read a large csv file (~11 Gb - ~900,000 columns, 3000
rows) using the read.big.matrix command from the bigmemory package. I
am using the following command:
x<-read.big.matrix('data.csv', sep=',', header=TRUE, type='char',
backingfile='data.bin', descriptorfile='data.desc')
When the command starts, everything seems to be fine,
2009 Feb 25
3
Using very large matrix
Dear friends,
I have to use a very large matrix. Something of the sort of
matrix(80000,80000,n) .... where n is something numeric of the sort 0.xxxxxx
I have not found a way of doing it. I keep getting the error
Error in matrix(nrow = 80000, ncol = 80000, 0.2) : too many elements specified
Any suggestions? I have searched the mailing list, but to no avail.
Best,
--
Corrado Topi
Global
2007 Feb 09
1
extract submatrix with unique names
Dear list,
I have a table where first 3 columns are identical if the name in the
first column is the same, and
the number in N4 is slightly different for all identical names, like
this:
-------------------------------------------------------------------
29 Mm.1_at 3 + 93649936
30 Mm.1_at 3 + 93649990
31 Mm.1_at 3 + 93649993
32
2009 Oct 30
1
Multicore package: sharing/modifying variable accross processes
Hi,
I want to parallelize some computations when it's possible on multicore
machines.
Each computation produces a big objects that I don't want to store if
not necessary: in the end only the object that best fits my data have to
be returned. In non-parallel mode, a single gloabl object is updated if
the current computation gets a better result than the best previously found.
My plan
2003 Oct 13
2
colnames from submatrix?
Hi R-Wizards:
I've looking through the R docs and have yet to find what I'm looking for
and have tried a few intermediate steps to now avail yet and rather than
spend another few hours looking for the solution, I figured I would post a
message.
I have a matrix (actually a set of them) that I want to pull all the names
of the non-zero columns into a vector/list for further processing:
2009 Dec 24
3
help in merging
Hi All,
I want to "merge" two datasets by column "ID" and I don't want the result to
be sorted by "ID". I am doing the following:
> z = merge(x, y, by = "ID", sort=F)
The result is not sorted by "ID". But (as oppose to what I expected) it is
not even in the original order of either "x" or "y".
Can
2004 Sep 15
2
efficient submatrix extraction
Hi,
I have a matrix of say 1024x1024 and I want to look at it in chunks.
That is I'd like to divide into a series of submatrices of order 2x2.
| 1 2 3 4 5 6 7 8 ... |
| 1 2 3 4 5 6 7 8 ... |
| 1 2 3 4 5 6 7 8 ... |
| 1 2 3 4 5 6 7 8 ... |
...
So the first submatrix would be
| 1 2 |
| 1 2 |
the second one would be
| 3 4 |
| 3 4 |
and so on. That is I want the matrix to be evenly divided