I am working with about 600 nodes in an Rgraphviz graph. Within this graph
there are, when plotted, about 8 obvious clusters that are highly connected
within them but do not share connections between them. I have a wrapper
function that handles a lot of tasks automatically for me like setting
vario
t; From: r-help-boun...@r-project.org
> > [mailto:r-help-boun...@r-project.org] On Behalf Of William Dunlap
> > Sent: Wednesday, October 20, 2010 10:47 AM
> > To: Duncan Murdoch; Mark Kimpel
> > Cc: r-help@r-project.org
> > Subject: Re: [R] ascii or regex code for alt-e
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 withou
I need to compare gene expression differences between multiple line pairs of
alcohol preferring and non-preferring rat lines. I have 5 such line pairs, 3
are unrelated but two were derived independently from the same parent stock.
For each line, there are 10 samples. I'll be testing multiple genes,
nder and Tina
> Müller, http://stat-computing.org/newsletter/issues/scgn-18-1.pdf.
>
> If you just want to do it, see the examples in
> http://had.co.nz/plyr/plyr-intro-090510.pdf.
>
> Hadley
>
> On Sun, Mar 7, 2010 at 7:03 PM, Mark Kimpel wrote:
> > Is it possible t
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
c
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 "."
ged? Am I doing something wrong? Following is my gcc
version and sessionInfo().
Thanks, Mark
kimpel-desktop ~/my_C: gcc --version
gcc (Ubuntu 4.4.1-4ubuntu8) 4.4.1
Copyright (C) 2009 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warrant
bile & VoiceMail
(317) 399-1219 Skype No Voicemail please
On Tue, Dec 8, 2009 at 11:00 PM, jim holtman wrote:
> Also instead of 'splitting' the data frame, I split the indices and then
> use those to access the information in the original dataframe.
>
>
> On Tue, Dec 8, 20
is case you might find
> characters are faster and more space efficient.
>
> Alternatively, you can have a look at the plyr package which uses some
> tricks to keep memory usage down.
>
> Hadley
>
> On Tue, Dec 8, 2009 at 9:46 PM, Mark Kimpel wrote:
> > Charles, I su
l
(317) 399-1219 Skype No Voicemail please
On Tue, Dec 8, 2009 at 10:22 PM, Charles C. Berry wrote:
> On Tue, 8 Dec 2009, Mark Kimpel wrote:
>
> I'm having trouble using split on a very large data-set with ~1400 levels
>> of
>> the factor to be split. Unfortunately, I
I'm having trouble using split on a very large data-set with ~1400 levels of
the factor to be split. Unfortunately, I can't reproduce it with the simple
self-contained example below. As you can see, splitting the artificial
dataframe of size ~13MB results in a split dataframe of ~ 144MB, with an
in
r wrote:
> On Thu, Nov 12, 2009 at 11:29:50AM -0500, Mark Kimpel wrote:
> > I am using code that previously worked to remove stopwords using package
> "tm".
>
> Thanks for reporting. This is a bug in the removeWords() function in
> tm version 0.5-1 available from CRAN
;
> text.corp <- Corpus(VectorSource(myDocument))
>
> dtm <- DocumentTermMatrix(text.corp, control = params)
>
> dtm
>
> dtm.mat <- as.matrix(dtm)
>
> dtm.mat
>
>
>
>
>
> *From:* Mark Kimpel [mailto:mwkim...@gmail.com]
> *Sent:* Thursday, Nove
I am using code that previously worked to remove stopwords using package
"tm". Even manually adding "the" to the list does not work to remove "the".
This package has undergone extensive redevelopment with changes to the
function syntax, so perhaps I am just missing something.
Please see my simple
I am analyzing an experiment in which time is a factor, represented by
numbers indicating time since last treatment, but in this particular case
there is no reason to think that time has a numeric meaning in the sense
that 24 would be greater than 6. We have no idea which genes will be
increasing o
;> par("oma")
>>
> [1] 0 0 0 0
>
>> par("oma"=c(0,0,2,0))
>> for (i in 1:4) plot(0:1,0:1)
>> mtext(text = "my test plots", side = 3, outer = TRUE)
>>
>>
> Mark Kimpel wrote:
>
>> I'm trying to use mtext to cre
I'm trying to use mtext to create a main title over multiple plots. Below is
a simple self-contained example and my sessionInfo (I should note I've also
tried this with R-2.8.1 with the same results). When I execute the code
chunk below, I get the plots, but no title. I've tried this using the scre
b', 'a \\ b')
> cat(a, "\n")
>
> You can write in this form:
>
> strsplit(a, " .*\\.* ")
>
>
>
> On Thu, Aug 27, 2009 at 10:03 PM, Mark Kimpel wrote:
>
>> I have a vector of gene symbols, some of which have multiple aliases. In
&g
I have a vector of gene symbols, some of which have multiple aliases. In the
case of an alias, they are separated by ' \\\ '.
Here is a real world example, which would represent one element of my
vector:
Eif4g2 /// Eif4g2-ps1 /// LOC678831
What I would like to do is input the vector into a functio
t; In English: substitute the shortest string starting with "[" or "(" and
> ending with "]" or ")" with nothing.
>
> Hope this helps.
> - Phil
>
>
>
>
> On Thu, 20 Aug 2009, Mark Kimpel wrote:
>
> Well, I guess
***
On Thu, Aug 20, 2009 at 11:39 AM, William Dunlap wrote:
>
> > -Original Message-
> > From: r-help-boun...@r-project.org
> > [mailto:r-help-boun...@r-project.org] On Behalf Of Mark Kimpel
> > Sent: Thursday, August 20, 2009 8:31
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 on
er men do." -- B.
F. Skinner
**
On Tue, Aug 18, 2009 at 10:56 AM, Ingo Feinerer wrote:
> On Tue, Aug 18, 2009 at 12:00:07PM +0200, Mark Kimpel wrote:
> > I am familiar with packages that read and write Excel files on both
> Windows
> > and Linux platforms.
&g
I am familiar with packages that read and write Excel files on both Windows
and Linux platforms.
Do any packages provide similar functionality for MS Word files? I have a
lot of text processing to do and the text is embedded in ~200 different Word
files (.doc format Office 2003). All I need to do
il
"The real problem is not whether machines think but whether men do." -- B.
F. Skinner
**
On Thu, Aug 13, 2009 at 6:11 PM, Ingo Feinerer wrote:
> On Thu, Aug 13, 2009 at 03:36:22PM -0400, Mark Kimpel wrote:
> >
I am using the package "tm" for text-mining of abstracts and would like to
use it to find instances of gene names that may contain white space. For
instance "gene regulatory protein 1". The default behavior of tm is to parse
this into 4 separate words, but I would like to use the class constructor
machines think but whether men do."
-- B. F. Skinner
**
On Tue, Jul 21, 2009 at 10:28 AM, Mark Kimpel wrote:
> I have written a wrapper for heatmap.2 called
> heatmap.w.row.and.col.clust which auto-generates breaks using
>
I have written a wrapper for heatmap.2 called
heatmap.w.row.and.col.clust which auto-generates breaks using
breaks<-round((c(seq(from=(-20 * stddev), to=(20 * stddev/20,
digits = 2) #(stddev in this case = 2.5)
This has always worked well in the past but now I am getting an error
that non-fin
If so, install Sun's Java first. apt-get install sun-java6-jdk might do it.
>
> - Godmar
>
>
> On Tue, Jul 7, 2009 at 9:28 PM, Mark Kimpel wrote:
>> Having difficulties getting rJava to install on my Debian Squeeze box.
>> Perused the R-help list and tried some thin
Having difficulties getting rJava to install on my Debian Squeeze box.
Perused the R-help list and tried some things that have worked for
others but not for me. Below is the output of my attempted build, R
CMD javareconf -e, and sessionInfo(). Note I tried the R CMD
javareconf also as root, restart
p; Mobile & VoiceMail
"The real problem is not whether machines think but whether men do."
-- B. F. Skinner
**
On Sat, Jul 4, 2009 at 2:47 PM, Allan Engelhardt wrote:
>
>
> On 04/07/09 18:56, Mark Kimpel wrote:
I am using grep to locate colnames to automate a report build and have
run into a problem when a colname is not found. The use of integer(0)
in a conditional statement seems to be a no no as it has length 0.
Below is a self-contained trivial example. I would like to get
something like "NA" or -1 fo
I'm using R to do some file processing in Linux and am trying to read
in the output of find . -type f -print >
~/Music_Archives_search_problem/ls.output.find.txt
This command yields a text file with each line representing the full
path name of all files in the directory and subdirs. Unfortunately,
r) # do not think the "utils::" is needed
> my.func <- function(x){
> y <- x + 12
> nonsense
> y
> }
>
> my.func(14)
> Error in my.func(14) : object "nonsense" not found
>
> Enter a frame number, or 0 to exit
>
> 1: my.func(14)
&g
pe: mkimpel
"The real problem is not whether machines think but whether men do." -- B.
F. Skinner
**
On Sat, May 30, 2009 at 5:44 AM, Duncan Murdoch wrote:
> [Sent this before completing my last sentence; here's another attemp
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
with
ot;The real problem is not whether machines think but whether men do." -- B.
F. Skinner
**
On Sun, Nov 9, 2008 at 3:59 PM, Vincent Carey 525-2265 <
[EMAIL PROTECTED]> wrote:
> On Sat, 8 Nov 2008, Mark Kimpel wrote:
>
I found the article the "Y of R" in the latest R news to be very
interesting. It is certainly challenging me to learn more about how R works
"under the hood" as the author states. What is less clear to me is whether
this approach is primarily for teaching purposes or has a real world
application. W
Work, & Mobile & VoiceMail
(317) 399-1219 Home
Skype: mkimpel
"The real problem is not whether machines think but whether men do." -- B.
F. Skinner
**
On Fri, Oct 17, 2008 at 11:03 AM, Mark Kimpel <[EMAIL PROT
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',
wrote:
> On Tue, Oct 14, 2008 at 02:34:57PM -0400, Mark Kimpel wrote:
> > 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:
>
> You are wondering wronly.
>
> > * Installing *sou
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
chec
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
li
ype: mkimpel
**
On Sun, Oct 5, 2008 at 10:28 AM, Duncan Murdoch <[EMAIL PROTECTED]>wrote:
> On 05/10/2008 10:08 AM, Mark Kimpel wrote:
>
>> I have a large matrix, each row of which needs lm applied. I am certain
>> than
I have a large matrix, each row of which needs lm applied. I am certain than
I read an article in R-news about this within the last year or two that
discussed the application of lm to matrices but I'll be darned if I can find
it with Google. Probably using the wrong search terms.
Can someone steer
Ouch! I had searched the archives and read over ?par and ?plot, but sure
missed the post of today. Thanks, Mark
On Tue, Aug 5, 2008 at 7:27 PM, Marc Schwartz <[EMAIL PROTECTED]>wrote:
> on 08/05/2008 06:05 PM Mark Kimpel wrote:
>
>> I'm making some plots on the same
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 *
on 07/30/2008 12:54 PM Mark Kimpel wrote:
>
>> I'm running R on Linux and use emacs as my editor. When doing
>> "edit(vignette(foo.vignette))" I would like to invoke emacs rather than
>> the
>> default vi. I am able to manually set this by editing $R_HOME
I'm running R on Linux and use emacs as my editor. When doing
"edit(vignette(foo.vignette))" I would like to invoke emacs rather than the
default vi. I am able to manually set this by editing $R_HOME/etc/Renviron
but would like to avoid doing this with each install. I assume this can be
accomplishe
Where is the link on www.r-project.org or CRAN to download source code for
development versions of packages? This is straightforward for BioConductor
packages but I can't seem to find it for R packages.
Mark
--
Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry
Indiana University Schoo
a draft and send it to
you for comments and input. Ben, if you get such a list of packages
with functions that depend on rgl, send it to me.
Mark
On Thu, Jun 26, 2008 at 7:02 AM, Duncan Murdoch <[EMAIL PROTECTED]> wrote:
> Mark Kimpel wrote:
>>
>> Thanks for the pointers. I th
se
other attached packages:
[1] rgl_0.79 graph_1.18.1
loaded via a namespace (and not attached):
[1] cluster_1.11.11 tools_2.7.1
On Wed, Jun 25, 2008 at 5:25 PM, Duncan Murdoch <[EMAIL PROTECTED]> wrote:
> Mark Kimpel wrote:
>>
>> Ben and Duncan,
>>
>> Thanks for y
rovide? I saw a book
at B&N just last week on openGL. Would that be helpful?
Mark
On Tue, Jun 24, 2008 at 10:54 PM, Ben Bolker <[EMAIL PROTECTED]> wrote:
> Mark Kimpel gmail.com> writes:
>
>>
>> I'm using the command below on an open3d() object to create a
I'm using the command below on an open3d() object to create a shaded
cube. Changes to myScalingFactor do not effect changes in the size of
the cube. What is the correct approach? Mark
shade3d(translate3d(cube3d(identityMatrix() *
myScalingFactor),-6,1,-1),col="green", alpha = 0.2)
--
Mark W. Kim
I'd like to use rgl.surface (or some other function if more
appropriate) to create a horizontal and vertical transparent grey
slice (plane) running through both the x and y origins and extending
across the z axis, i.e. the 3-d equivalent of the normal 2-d
coordinate axes we are all familiar with. T
ile named "~/.R/Makevars" with the
> following line:
>
> PKG_CPPFLAGS = -I/opt/openmpi/include
>
> ... where /opt/openmpi/include/ contains the necessary mpi.h include
> file.
>
> Then, try to recompile.
>
> Hope this helps,
> - Stu
>
>
>
> O
> hist(rt1$p.value, breaks=100, col="mistyrose")
> hist(rt2$p.value, breaks=100, col="mistyrose")
>
>
> --
> Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber
>
>
> Mark K
I'm working with a genomic data-set with ~31k end-points and have
performed an F-test across 5 groups for each end-point. The QA
measurments on the individual micro-arrays all look good. One of the
first things I do in my work-flow is take a look at the p-valued
distribution. it is my understanding
Uninstalling and reinstalling ggobi via Synaptic solved the problem, at
least for the demo data mtcars. Rotation works fine. No crashes on exit.
Thanks for the good advice.
Mark
On Wed, May 7, 2008 at 2:12 PM, Paul Johnson <[EMAIL PROTECTED]> wrote:
> On Tue, May 6, 2008 at 12:32
case.
Ubuntu currently is distributing graphviz 2.16.1
Thanks,
Mark
On Wed, May 7, 2008 at 12:14 AM, Michael Lawrence <[EMAIL PROTECTED]>
wrote:
>
>
> On Tue, May 6, 2008 at 6:06 PM, Mark Kimpel <[EMAIL PROTECTED]> wrote:
>
> > R crashed just after the warnings were
will be no output!
>
>
> ~ If that is the case, we will have to back to having our own copy
> of that routine and so we will end up with two versions - one for
> the old and one for the new and the configuration will endeavor to
> determine which is appropriate.
>
> ~ HTH
&
the RCurl source, and one thing I notice is that
> RCurl/src/curl_base64.c has the 'execute' bit set, and perhaps a sane
> system would not compile it. Try
>
> % chmod -x RCurl/src/curl_base64.c
>
> and then
>
> % R CMD INSTALL RCurl
>
> Martin
>
>
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:
L
Subject pretty much says it all. I am running 64-bit Ubuntu 8.04, i.e. Hardy
Heron, have openmpi installed, and get the following error message with
attempted install of Rmpi. sessionInfo() follows.
Mark
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat
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 ava
Can merge be tricked into merging via rownames as opposed to via contents of
a particular column? I have two data.frames with overlapping, but out of
order, rownames, but no column contents in common and would like to merge
without cbinding the rownames to the data.frames.
Mark
--
Mark W. Kimpel
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
As a medical researcher, I keep tabs on the journals Bioinformatics andd BMC
Bioinformatics. If your package is for "'omics", those are good journals to
look at.
Mark
On Sun, Mar 30, 2008 at 10:02 AM, Peter Dalgaard <[EMAIL PROTECTED]>
wrote:
> Gavin Simpson wrote:
> > On Sun, 2008-03-30 at 15:01
try Rmpi package
On Jan 21, 2008 7:13 PM, markaoki <[EMAIL PROTECTED]> wrote:
> hi,
> Does R have any built-in capabilities that allow one to use in a
> multi-node
> (supercomputer) environment?
>
> For example, MPI'ish commands allowing me to distribute specific R code to
> specific compute node
I'll throw one more idea into the mix. I agree with Bill that a rating
system for respondents is probably not that practical and of not the highest
importance. It also seems like a recipe for creating inter-personal problems
that the list doesn't need.
I do like Bill's idea of a review system for
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