Displaying 20 results from an estimated 20000 matches similar to: "how to model a numeric factor as a non-ordinal factor"
2009 Aug 20
5
help with regular expressions in R
I'm having trouble achieving the results I want using a regular expression.
I want to eliminate all characters that fall within square brackets as well
as the brackets themselves, returning an "". I'm not sure if it's R's use of
double slash escapes or something else that is tripping me up. If I only use
one slash I get
1: '\[' is an unrecognized escape in a
2008 Oct 17
1
how to list variables enclosed in an environment
I'm having trouble with a Bioconductor package, an variable expected in an
environment does not seem to be there. As part of my investigation of the
problem (most likely on my end) I'd like to list the variables contained in
an environment. If you have an environment loaded, lets call it "pkgEnv',
how does one find what it does contain? Mark
2008 Sep 24
1
splitting strings efficiently
I have a very long list of strings. Each string actually contains multiple
values separated by a semi-colon. I need to turn each string into a vector
of the values delimited by the semi-colons. I know I can do this very
laboriously by using loops, nchar, and substr, but it is terribly slow. Is
there a basic R function that handles this situation? If not, is there
perhaps a faster way to do it than
2008 May 06
3
rggobi is crashing R-2.7.0
I am running 64-bit Ubuntu 8.04 and when I invoke rggobi the interactive
graph displays but R crashes. See my sessionInfo() and a short example
below. Ggobi and rggobi installed without complaints. Mark
> sessionInfo()
R version 2.7.0 Patched (2008-05-04 r45620)
x86_64-unknown-linux-gnu
locale:
2009 Sep 16
4
2.10.0 Under development (unstable) (2009-09-15 r49711) just built segfaults on Debian Squeeze
I just downloaded R-devel and when loaded it immediately segfaults. I'm not
sure how much or what sort of diagnostic info and can provide, but below is
my build script, my console output, and the output of uname -r. I am
currently dependent on the development version of a package, so I'd like to
get R-devel up and running if possible. I am sure there is more info I can
provide, but before
2008 Apr 03
1
getting serial anovas from a complex lm object obtained with a matrix of responses
I have fit a model to ~20k different genes and would now like to extract the
p-val for one of the effects, again for each individual gene.
My model code is:
mod <- lm(myResponseMatrix~ Time)
Were I to do this with a response vector rather than matrix, the following
would work:
anovaResult<- anova(mod)
With a more complex lm object, such as that generated above, it seems anova
is trying to
2008 Mar 05
4
vertex labels in igraph from adjacency matrix
I am getting some unexpected results from some functions of igraph and
it is possible that I am misinterpreting the vertex numbers. Eg., the
max betweenness measure seems to be from a vertex that is not connected
to a single other vertex. Below if my code snippet:
require(igraph)
my.graph <- graph.adjacency(adjmatrix = my.adj.matrix, mode=c("undirected"))
most.between.vert <-
2008 Mar 12
2
subset list based on logical within element flag
I have a very long list that I'd like to subset based on a logical value
within each element. Example below. I'd like to get just those list
elements for further study whose $sig.cor slot is TRUE. In this example,
I'd only want element [[2]].
Should be simple, I know. How can I do this? Thanks, Mark
> gene.pair.tf.lst
[[1]]
[[1]]$gene.pair
[1] "Lgals1:Pxmp2"
2008 Mar 07
1
confused about CORREP cor.LRtest
After some struggling with the data format, non-standard in
BioConductor, I have gotten cor.balance in package CORREP to work. My
desire was to obtain maximum-likelihood p-values from the same data
object using cor.LRtest, but it appears that this function wants
something different, which I can't figure out from the documentation.
Briefly, my dataset consists of 36 samples from 12
2007 Aug 03
2
RSPython won't load in R 2.6.0 under Linux
I can compile RSPython without difficulty, been when I try to load it, I
get the error messages below. Also below are some cryptic warnings I get
on R boot (in case these are pertinent) and my sessionInfo().
Any help is appreciated. Thanks, Mark
Warning messages:
1: In .updateMethodsInTable(fdef, where, attach) :
Couldn't find methods table for "conditional", package
2009 May 30
2
'options=utils::recover' not working in .Rprofile or within R
For years I have been using options(error = recover) either in .Rprofile or
from within R for debugging purposes. The functionality of this appears to
have changed and I can't recover it (no pun intended) using the ?options
help page. How can I get the old functionality back, particularly from
within .Rprofile? A specific line entry would be appreciated. An example,
the help page, and
2010 Mar 07
2
vectorizing ANOVA over a vectorized linear model
Is it possible to vectorize anova over the output of a vectorized lm? I
have a gene expression matrix with each row being a gene and columns for
samples. There are several factors with interactions. I can get p values by
looping over the matrix with lm and anova, but I would like to make this as
computationally efficient as possible. I am able to vectorize the lm
command, but when I try to use
2010 Oct 20
2
ascii or regex code for alt-enter for Excel
I need to write a table that can be opened in Excel or OpenOffice such that
there are newlines embedded within cells.
After much Googling and futzing, I can't figure out how to do this. The way
to do this within Excel is alt-Enter and I've tried '/n', '/n/r', '/r/n' per
some web suggestions without luck.
Anybody know what character or ASCII code to use for this?
2008 Oct 07
1
using assign with lists
I am performing many permutations on a data-set with each permutation
producing a variable number of results. I thought that the best way to keep
track of all this in one object would be with a list ('res.lst'). To address
these variable results for each permutation I attempted to construct this
list using 'assign'. There is even more nesting than indicated below, but
this is a
2008 May 03
4
interactive rotatable 3d scatterplot
I would like to create a 3d scatterplot that is interactive in the sense
that I can spin it on its axes to better visualize some PCA results I have.
What are the options in R? I've looked at RGL and perhaps it will suffice
but it wasn't apparent from the documentation I found.
Any demo scripts available for a package that will work?
Mark
--
Mark W. Kimpel MD ** Neuroinformatics **
2008 Aug 05
2
creating overall title for plots made with par(mfrow=c(2,2))
I'm making some plots on the same page and would like to include an overall
title instead of individual main titles as they are similar and their x and
y axis labels are sufficient to distinguish them.
Is there a way to assign an overall "main" to this page of plots?
Mark
--
Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry
Indiana University School of Medicine
15032
2008 Oct 14
1
XML_1.98-0 fails to build on Debian Lenny with gcc 4.3.2 and R-beta 2.8.0
Subject pretty much says it all. Wonder if there is there is some code in
XML that the new gcc doesn't like? See output below:
* Installing *source* package 'XML' ...
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking
2008 Jun 03
2
benchmarking R installations
Recently I posted to this list with a question about using the Intel 10.1
compilers in building R and one response was basically, "why in the heck
would you want to do that?" The answer is that my sysadmin believes that
there will be a performance boost with the Intel vs. Gnu compilers on our
Linux cluster, of which I am one of many users. Wanting to be a good citizen
and use my machine
2010 Jan 07
1
regex question on escaping "." (and a couple other regex questions as well)
I have an example where escaping "." does not seem to be behaving
consistently, but perhaps it is due to my misunderstanding. Could someone
explain to me why the below produces the output it does?
It seems to me that in the second example, where I am being more precise
about specifying that a "." (dot) should be between the numbers, should
produce the same output as the first
2007 Oct 30
6
trouble installing building packages from source using R 2.6.0 on Ubuntu Gutsy AMD64
I have recently upgraded to Ubuntu Gutsy and, for the first time, am
using a 64-bit installation. After failing miserably to install R from
source, not a problem for me in the past with a 32-bit install, I went
the route of using the Debian Etch build. This went smoothly, but I am
unable to update my numerous R and BioConductor packages, getting
non-zero exit status errors on each package. Is