Displaying 20 results from an estimated 1000 matches similar to: "cbind rises floating point exception (PR#2541)"
2003 Apr 22
4
"LAPACK routine DGESDD gave error code -12" with Debian (PR#2822)
Dear All,
Under Debian GNU/Linux La.svd (with method = "dgesdd") sometimes gives the
error
"Error in La.svd(data, nu = 0, nv = min(nrow, ncol), method = "dgesdd") :
LAPACK routine DGESDD gave error code -12"
It seems not to depend on the data per se, but on the relationship between
numbers of rows and columns.
For example, if the number of columns is 100,
2004 Jun 08
0
bootstrap: stratified resampling
Dear All,
I was writing a small wrapper to bootstrap a classification algorithm, but if
we generate the indices in the "usual way" as:
bootindex <- sample(index, N, replace = TRUE)
there is a non-zero probability that all the samples belong to only
one class, thus leading to problems in the fitting (or that some classes will
end up with only one sample, which will be a problem
2004 May 03
1
boxplot.formula with missing values (PR#6846)
If an array has missing values in different rows, plotting using the formul=
a=20
interface can produce errors. Example:
fake.data <- matrix(rep(-100:100, 4),
ncol =3D 4)
par(mfrow =3D c(1,2))
boxplot(fake.data ~ col(fake.data))
abline(h =3D 0, lty =3D 2)
boxplot(as.data.frame(fake.data))
abline(h =3D 0, lty =3D 2)
##### Add the missing data
fake.data[190:200, 1] <-
2003 Jan 21
2
books on categorical data analyses
Dear All,
We are about to purchase the second edition of Agresti's "Categorical Data
Analysis" (my old copy of the first ed. of that wonderful book is falling
apart). I would appreciate suggestions about other comparable books which, if
possible, have examples using R/S code (instead of SAS).
Thanks,
Ram?n
--
Ram?n D?az-Uriarte
Bioinformatics Unit
Centro Nacional de
2003 Sep 16
1
simplifying randomForest(s)
Dear All,
I have been using the randomForest package for a couple of difficult
prediction problems (which also share p >> n). The performance is good, but
since all the variables in the data set are used, interpretation of what is
going on is not easy, even after looking at variable importance as produced
by the randomForest run.
I have tried a simple "variable selection"
2003 Mar 14
0
gls with "crossed heteroscedasticity"
Dear All,
I am using the function gls (in the nlme package) and I would like to fit a
heteroscedastic model, with different variances for each of the levels of two
stratification variables.
In p. 210 of Pinheiro & Bates ("Mixed effects models in S and S-Plus", 2000,
Springer), the authors show the use of the "*" operator. However, that is not
what I want, because it
2003 Oct 06
0
documentation typo in coxph?
Dear All,
I think there is a typo in the documentation for coxph (library survival).
The help says:
eps: convergence threshold. Iteration will continue until the
relative change in the log-likelihood is less than eps.
Default is .0001.
However, if I do "coxph.control()" I get:
> coxph.control()
$eps
[1] 1e-09
So the actual eps being used is not 10-4 but
2006 Jan 09
0
Looking for packages to do Feature Selection and Classifi cation
Hi,
You should also check my msc.features.select from caMassClass package. It
has feature selection algorithm that I found useful in case of mass-spectra
data. It performs individual feature selection and/or removes highly
correlated neighbor features.
Jarek
-----Original Message-----
From: r-help-bounces at stat.math.ethz.ch
[mailto:r-help-bounces at stat.math.ethz.ch]
Sent: Friday, January
2002 Nov 19
1
fexact.c
Dear All,
I am using fexact.c on a C++ program I wrote. To minimize dependencies on
other files (e.g., to not need to include R.h and ctest.h ---now I only
include the R files Boolean.h, Constants.h, and Memory.h), I have re-written
all declarations of Sints as ints and, what is potentially more serious, I
have re-written the line (lines 329 and 330, in fexact.c on R-1.6.1)
/* IMAX is the
2003 Apr 01
2
R function calling: efficiency of different alternatives
Dear all,
I have a piece of code, call it "FA", that will be called thousands of times
in a typical run of function "FB". I can:
a) define FA as a function outside of FB (in the global environment), and call
it;
b) define FA as a function inside the body of FB and call it;
c) "expand inline" FA inside FB.
FA mainly does data frame subsetting, runs svd's, and
2003 Apr 14
5
removing NULL elements from a list
Dear All,
I have a list, where several components are NULL, and I'd like to obtain that
very same list without the NULL components (i.e., I do not want to unlist or
otherwise loose the rest of the list structure). I can do that with a loop,
but how could I do it without a loop?
Thanks,
Ram?n
--
Ram?n D?az-Uriarte
Bioinformatics Unit
Centro Nacional de Investigaciones Oncol?gicas (CNIO)
2006 Feb 14
0
R, AMD Opteron 64, and Rmpi
Dear All,
I found Andy Liaw's suggestion about using a NUMA (instead of SMP) kernel when
running R on amd64 with > 1 CPU
http://finzi.psych.upenn.edu/R/Rhelp02a/archive/35109.html
A couple of questions:
1. Is this still the case with the newer dual-core opterons (e.g., the 275 et
al., families) running Linux (kernel 2.6)?
2. How does this affect using Rmpi (and snow, papply, et al.)
2005 May 05
1
building from source after installing binary package
Dear All,
I've got into the habit of installing R from the precompiled Debian binaries, including many of the packages from the r-cran-* Debian packages, and later building from source (e.g., to link against Goto's BLAS, or to build patched versions, etc). I install the newly built R to the very same place (/usr/lib/R). This allows me to build and update R when I wish, AND provides the
2005 May 06
1
building from source after installing Debian packages
(Apologies for double posting; I sent this to r-help and was suggested that I
ask here which I should probable have done to begin with).
***************
Dear All,
I've got into the habit of installing R from the precompiled Debian binaries,
including many of the packages from the r-cran-* Debian packages, and later
building from source (e.g., to link against Goto's BLAS, or to build
2007 Jan 05
5
eval(parse(text vs. get when accessing a function
Dear All,
I've read Thomas Lumley's fortune "If the answer is parse() you should usually
rethink the question.". But I am not sure it that also applies (and why) to
other situations (Lumley's comment
http://tolstoy.newcastle.edu.au/R/help/05/02/12204.html
was in reply to accessing a list).
Suppose I have similarly called functions, except for a postfix. E.g.
f.1 <-
2006 Oct 18
2
Adding locfit confidence intervals in trelis xyplot
Dear all,
I am trying to include confidence intervals in a xyplot.
This is what I am doing:
xyplot(x ~ y|z, alpha = 1,band = "global",panel = panel.locfit)
(more specifically, in my case x is a binary response from a logistic
regression model)
The output plot was fine but it did not include the confidence intervals
Anyone knows how to do it? (xYplot did not work either)
many thanks
2004 Mar 09
2
levelplot problems !!!
Dear R users,
I have changed my R version to the new 1.8.1 and some problems appears when
using the previous levelplot code.
This is a simple example:
a <-1:10
b <-11:20
j <- rnorm(100)
grid<-expand.grid(a = a, b = b)
levelplot(j~a*b, grid)
Normaly in my previous vs this was suffice to produce the levelplot.
Now, an empty R graphics device appears with the following error
2011 Jul 06
2
wgcna
Hi,
I'm running a tutorial ("Meta-analyses of data from two (or more) microarray data sets"), which use wgcna package. I have an error in the function modulePreservation (it is below).
I'm using R2.13
Can you help me? Do you know, what is happens?
Thanks
Raquel
multiExpr = list(A = list(data=t(badea)),B = list(data=t(mayo)))
# two independent datasets (dim = 13447 x 36)
mp =
2008 Feb 29
1
using zlib (was compress data on read, decompress on write)
Dear All,
I think I am confused about how I'd be able to use zlib starting with
R 2.7.0. I just downloaded the latest development version, built it,
etc, but I am not able to find the zlib.h that, I believe, R should
place somewhere under "where/you/want/R/to/go" (from
--prefix=/where/you/want/R/to/go). There seem to be entry points for
zlib in the binary (e.g., grep -r gzopen ./
2006 Jan 27
1
rbind/cbind unimplemented for raw (RAWSXP) types. (PR#8529)
Full_Name: Hin-Tak Leung
Version: R 2.2.1
OS: x86_64-redhat-linux-gnu
Submission from: (NULL) (131.111.186.92)
rbind/cbind is unimplemented for raw (RAWSXP) types.
I have a working patch implementing the functionality,
to follow.
--please do not edit the information below--
Version:
platform = x86_64-redhat-linux-gnu
arch = x86_64
os = linux-gnu
system = x86_64, linux-gnu
status =
major