Displaying 20 results from an estimated 1000 matches similar to: "reading a "sparse" matrix into R"
2004 Jul 09
3
Can R read data from stdin?
Is there anyway I can write a script which feed input datasource from stdin
and let R process it (maybe frequency report) then output the report to
stdout?
I can't seem to find much info on documentation or FAQ on this topic.
Thanks!
Soichi Hayashi
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confidential,
2013 Mar 04
4
enabling reproducible research & R package management & install.package.version & BiocLite
Hi,
In support of reproducible research at my Institute, I seek an approach to re-creating the R environments in which an analysis has been conducted.
By which I mean, the exact version of R and the exact version of all packages used in a particular R session.
I am seeking comments/criticism of this as a goal, and of the following outline of an approach:
=== When all the steps to an workflow
2012 Apr 19
2
Dependency-aware scripting tools for R
There are numerous tools like scons, make, ruffus, ant, rake, etc.
that can be used to build complex pipelines based on task
dependencies. These tools are written in a variety of languages, but
I have not seen such a thing for R. Is anyone aware of a package
available? The goal is to be able to develop robust bioinformatic
pipelines driven by scripts written in R.
Thanks,
Sean
2004 Jul 07
1
lost messages
I've posted a message twice to this list, and never seen it appear yet
... perhaps this one will go through ... ?
--
Aaron J. Mackey, Ph.D.
Dept. of Biology, Goddard 212
University of Pennsylvania email: amackey at pcbi.upenn.edu
415 S. University Avenue office: 215-898-1205
Philadelphia, PA 19104-6017 fax: 215-746-6697
2002 Feb 14
2
RFC: "R::Wrapper" perl module
If I actually finished writing this module, would any of you use it?
Would you wish it did something else/different than what's described
below? Any comments or suggestions on its proposed usage, intent, or
syntax are welcome! (An alternative, better name would also be
appreciated) -Aaron
NAME
R::Wrapper - Wrapper around the RS-Perl R module
SYNOPSIS
#!/usr/bin/perl -w
2014 May 22
1
citEntry handling of encoded URLs
The following citEntry includes a url with %3A and other encodings
citEntry(entry="article",
title = "Software for Computing and Annotating Genomic Ranges",
author = personList( as.person("Michael Lawrence" )),
year = 2013,
journal = "{PLoS} Computational Biology",
volume = "9",
issue =
2008 Sep 11
2
database table merging tips with R
I have not devoted time to setting up ROracle since binaries are not available and it seems to require some effort to compile (see http://cran.r-project.org/web/packages/ROracle/index.html). On the other hand, RODBC worked more or less magically once I set up the data sources.
What is your success using ROracle and why would it be preferable to RODBC ?
-Avram
On Thursday, September 11,
2009 Jul 10
2
error: optim(rho, n2ll.rho, method = method, control = control, beta = parm$beta, : initial value in 'vmmin' is not finite
I am trying to use the lnam autocorrelation model from the SNA package. I have it running for smaller adjacency matrices (<1,500) it works just fine but when my matrices are bigger 4000+. I get the error:
> lnam1_01.adj<- lnam(data01$adopt,x01,ec2001.csr)
Error in optim(rho, n2ll.rho, method = method, control = control, beta = parm$beta, :
initial value in 'vmmin' is not
2010 May 03
1
How to generate Mackey-Glass time series with "ddesolve" package?
I could use some help generating a time series for the Mackey-Glass equation: dx/dt = 0.2 x(t-tau)/(1 + x(t-tau)^10) - 0.1 x(t) for the case there tau = 17. I tried the "ddesolve" package but the dde(...) function seems to hang, not producing anything. Can someone show me the R script how to do this?
- Mike Beddo
[[alternative HTML version deleted]]
2011 Jun 21
1
working with sparse matrix
Hi, I have a 500x 53380 sparse matrix and I am trying to dichotomize it.
Under sna package I have found event2dichot yet it doesnt recognize sparse
matrix and requires adjacency matrix or array. I tried to run a simple loop
code
for (i in 1:500)
for (j in 1:53380)
if (matrix[i,j]>0) matrix[i,j]=1
yet this takes a lot of time to run, I mean it has been last two hours and
it is stil running.
2009 Apr 06
2
Bonpower Crashes Trying Sparse Matrix (Igraph)
Hello All,
I have been trying to do bonpow for a while now.Bonpow works for few graphs
and for few others it goes out of memory.
I did see reply to one of the posting Alph Centrality Crashed in Igraph
memory error.
The solution in the posting was to use sparse matrix. This is the link of
the message.
http://lists.gnu.org/archive/html/igraph-help/2008-04/msg00071.html
I was able to obtain
2006 Jan 27
3
e1071: using svm with sparse matrices (PR#8527)
Full_Name: Julien Gagneur
Version: 2.2.1
OS: Linux (Suse 9.3)
Submission from: (NULL) (194.94.44.4)
Using the SparseM library (SparseM_0.66)
and the e1071 library (e1071_1.5-12)
I fail using svm method with a sparse matrix. Here is a sample example.
I experienced the same problem under Windows.
> library(SparseM)
[1] "SparseM library loaded"
> library("e1071")
2007 Dec 11
4
EL5.1 client problems
Hi all,
I attempted to add an EL5.1 client to our puppet server (EL5), and after
signing the client cert, got the error "Certificates were not trusted:
hostname not match with the server certificate"
I found the mailing list discussion and the relevant page:
http://www.reductivelabs.com/trac/puppet/wiki/RubySSL-2007-006
As far as I can tell, my puppermaster''s cert CN matches
2009 Feb 19
2
an S idiom for ordering matrix by columns?
There's got to be a better way to use order() on a matrix than this:
> y
2L-035-3 2L-081-23 2L-143-18 2L-189-1 2R-008-5 2R-068-15 3L-113-4
3L-173-2
398 1 1 2 2 1 1 2
2
857 1 1 2 2 1 2 2
2
911 1 1 2 2 1 2 2
2
383 1 1
2004 Aug 31
2
Sparse Matrices in R
I have data in i,j,r format,
where r is the value in location A[i,j] for some imaginary matrix A.
I need to build this matrix A, but given the sizes of i and j, I believe that using a sparse format would be most adequate.
Hopefully this will allow me to perform some basic matrix manipulation such as multiplication, addition, rowsums, transpositions, subsetting etc etc.
Is there any way
2008 Sep 30
1
wpi driver freeze on boot
I've got a HP dv8000 laptop. Setting up the wpi driver for wireless freezes
the system on boot with the following error:
wpi0 requested unsupported memory range
wpi0: could not allocate memory resource
It lists a pcbi device (pcbi4 i think) and an actual memory range, but since I
have to reboot using kernel.old the /var/run/dmesg.boot is wiped with the
info. Is there anyway to grab the
2009 Sep 19
2
Use of R in Schools
I am looking for information on experimentation with the use
of R in the teaching of statistics and science in schools. Any
leads would be very welcome. I am certain that there is such
experimentation.
I've made this inquiry on r-sig-teaching, with no response.
John.
John Maindonald email: john.maindonald at anu.edu.au
phone : +61 2 (6125)3473 fax : +61 2(6125)5549
Centre
2004 Aug 05
1
Using pipe for input data
Hi.
I have asked this question before and Aaron J. Mackey and Tony Plate gave me
some great insight but I still can't figure out how to do what I am trying
to accomplish. So let me ask again...
What I am trying to do is to make R read data from pipe (stdin).
Say I have following files on my directory
my.dat
apple 1
orange 2
grape 3
my.R
d <- read.table(
2001 Feb 11
6
embedding R?
My apologies if this is a FAQ, I searched the mailing list archives before
posting.
Background: I am a long time user of SPlus, and a recent user of R. My
work normally involves converting the raw output of something interesting
into data to be analyzed in S/R, for which I use Perl extensively. I then
import the data into S/R, perform the analyses I need, dumping the values
into a new file,
2005 Apr 18
2
Construction of a large sparse matrix
Dear List:
I'm working to construct a very large sparse matrix and have found
relief using the SparseM package. I have encountered an issue that is
confusing to me and wonder if anyone may be able to suggest a smarter
solution. The matrix I'm creating is a covariance matrix for a larger
research problem that is subsequently used in a simulation. Below is the
latex form of the matrix if