recognize if it's a format
I've seen.
efg
Earl F. Glynn
Scientific Programmer
Stowers Institute for Medical Research
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PLEASE do read the posting guide http://www.R
them easily with many
editors.]
efg
Earl F. Glynn
Stowers Institute for Medical Research
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
FC01=100
FC02=50
FC10=50
[OdorNames]
port0=None
port1=None
[Map]
port0=0,0,0,0,0,0,0,0,0,0,0,0
port1=0,0,0,0,0,0,0,0,0,0,0,0
port2=0,0,0,0,0,0,0,0,0,0,0,0
= = = = =
Thanks again, Gabor!
efg
Earl F. Glynn
Scientific Programmer
Stowers Institute for Medical Research
a package, that reads .INI files into an R list, or other data
structure.
Any suggestions, or do I need to write my own?
efg
Earl F. Glynn
Stowers Institute for Medical Research
__
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x86_64, linux-gnu
status
major 2
minor 4.1
year 2006
month 12
day18
svn rev40228
language R
version.string R version 2.4.1 (2006-12-18)
efg
Earl F. Glynn
Stowers Institute for Medical Research
I'm not sure where you're getting the venn package. I don't find venn in
either of these places:
- http://cran.r-project.org/src/contrib/PACKAGES.html
- http://www.bioconductor.org/packages/release/Software.html
In case this helps, here are some notes about creating Venn Diagrams using
the
efg
Earl F. Glynn
Stowers Institute for Medical Research
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and provide commented, minimal
(TimeStamp) - double
# This seems to work, but is too ugly:
TimeStamp[2]*2^32 + (2^32 + TimeStamp[1])
[1] 8278173569
Can anyone suggest a better way?
Thanks for any suggestions.
efg
Earl F. Glynn
Stowers Institute for Medical Research
__
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Alan E. Davis [EMAIL PROTECTED] wrote in message
news:[EMAIL PROTECTED]
I have been trying to visualize times of lowest tides, month by month.
I have tide predictions with times either in unix time or a text
format, and heights in feet or meters. I had been able to derive the
clock times of
Torsten Hothorn [EMAIL PROTECTED] wrote in message
news:[EMAIL PROTECTED]
The October 2006 issue of R News is now available on CRAN under the
Documentation/Newsletter link.
Direct links are useful:
R News
http://cran.r-project.org/doc/Rnews/
April 2007 Issue:
This example isn't quite what you're asking for, but perhaps it's a starting
point:
http://addictedtor.free.fr/misc/gabor/
Earl F. Glynn
Stowers Institute
Robert Biddle [EMAIL PROTECTED] wrote in message
news:[EMAIL PROTECTED]
I am doing some work that involves plotting points of interest
-GaussQuadrature.html
efg
Earl F. Glynn
Scientific Programmer
Stowers Institute for Medical Research
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PLEASE do read the posting guide http://www.R-project.org/posting
in your
data:
http://research.stowers-institute.org/efg/R/Statistics/MixturesOfDistributions/index.htm
efg
Earl F. Glynn
Stowers Institute for Medical Research
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0 894 362 109.63158 3.197160 6
4 0 642 432 135.81734 12.401344 4
1 0 524 244 213.41795 7.184821 1
efg
Earl F. Glynn
Stowers Institute for Medical Research
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If you don't have too much noise, the peaks in the derivative curves can be
used:
See:
http://research.stowers-institute.org/efg/R/Statistics/MixturesOfDistributions/index.htm
efg
Earl F. Glynn
Scientific Programmer
Stowers Institute for Medical Research
[EMAIL PROTECTED] wrote in message
Earl F. Glynn
Stowers Institute for Medical Research
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R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self
Georg Hoermann [EMAIL PROTECTED] wrote in message
news:[EMAIL PROTECTED]
Peter Dalgaard wrote:
Earl F. Glynn wrote:
Thanks a lot for the help. I will post the script when its ready
(an introduction for our biology students to time series, just 8 hours)
I've been working with one of our labs
) :
there is no package called 'DNAcopy'
[1] FALSE
In the 2nd 100 many packages seem to be affected by the Maximal number of
DLLs reached...
I didn't bother trying to process packages 201 through 957.
efg
Earl F. Glynn
Scientific Programmer
Bioinformatics
Stowers
by the biocLite procedure.
FWIW:
length(pkgs)
[1] 957
Thanks for any suggestions.
efg
Earl F. Glynn
Scientific Programmer
Stower Institute
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PLEASE do read the posting guide http
will be 1/frequency:
cat(Corresponding period\n)
print(1/maxfreq)
par(oldpar)
efg
Earl F. Glynn
Scientific Programmer
Stowers Institute
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PLEASE do read the posting guide
Bill,
I like to use Windows Explorer to find folders and then launch R with the
selected folder as the working directory.
I put some notes online about this:
http://research.stowers-institute.org/efg/R/TechNote/WindowsExplorerWorkingDirectory/index.htm
efg
Bill Shipley [EMAIL PROTECTED] wrote
The following example shows how to get/display the county names:
library(maps)
# Get County Data
m - map('county', 'colorado', plot=FALSE)
names(m)
m$names # State,County names
# The names appear to be in alphabetical order by state, e.g.:
m$names[1:3]
[1] colorado,adamscolorado,alamosa
Duncan Murdoch [EMAIL PROTECTED] wrote in message
news:[EMAIL PROTECTED]
On 12/11/2006 2:21 PM, Earl F. Glynn wrote:
Dieter Menne [EMAIL PROTECTED] wrote in message
news:[EMAIL PROTECTED]
Aimin Yan aiminy at iastate.edu writes:
I want to set default directory for R when I start R.
How
-2.4.0\\bin\\Rgui.exe
http_proxy=http://proxy01:8080 http_proxy_user=ask
---
The above was the exported registry key from what I set manually using
RegEdit. I used simply R instead of Run R, like you suggested.
efg
Earl F. Glynn
Bioinformatics
Stowers Institute for Medical Research
interface. I've never studied the source code -- that's been on
my to do list for months --, but I'm guessing it uses RCOm, like
Hans-Peter suggested. Nevertheless, Tom's example above may also be quite
useful.
efg
Earl F. Glynn
Scientific Programmer
Stowers Institute for Medical Research
with this
kind of FCS data here:
http://research.stowers-institute.org/efg/ScientificSoftware/Utility/FCSExtract/index.htm
efg
Earl F. Glynn
Scientific Programmer
Stowers Institute for Medical Research
Horacio Castellini [EMAIL PROTECTED] wrote in message
news:[EMAIL PROTECTED]
Hi all, excuse me
)
efg
Earl F. Glynn
Scientific Programmer
Stowers Institute for Medical Research
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide
(ellipse)
?plotcorr
Look at the third example for the color plot.
Earl F. Glynn
Bioinformatics
Stowers Institute for Medical Research
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PLEASE do read the posting guide http
] 0x00x 0x10x12345678 0x7FFF
as.numeric(y)
[1] 0 65535 65536 305419896 2147483647
efg
Earl F. Glynn
Scientific Programmer
Stowers Institute for Medical Research
__
R-help@stat.math.ethz.ch mailing list
for any insight about this.
efg
Earl F. Glynn
Scientific Programmer
Stowers Institute for Medical Research
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting
Dieter Menne [EMAIL PROTECTED] wrote in message
news:[EMAIL PROTECTED]
Earl F. Glynn efg at stowers-institute.org writes:
This toy problem is exactly what the warning is for:
Warning
Do not use nls on artificial zero-residual data.
Add some noise and try again.
Thank you!
I had adapted
Berton Gunter [EMAIL PROTECTED] wrote in message
news:[EMAIL PROTECTED]
Or, maybe there's something I don't understand about the
algorithm being used.
Indeed! So before making such comments, why don't you try to learn about
it?
Doug Bates is a pretty smart guy, and I think you do him a
If I want to have a long vector of coefficients, A, (perhaps dozens) how can
I use D to compute partial derivatives?
Thanks for any help with this.
efg
Earl F. Glynn
Scientific Programmer
Stowers Institute for Medical Research
__
R-help
axis are the shades of gray. The original gold
rectangle is at the upper right.
So, given a starting color, you have a number of shades (various
saturations and values) with the same color hue.
I hope this helps.
efg
Earl F. Glynn
Scientific Programmer
Stowers Institute for Medical
, outer=TRUE)
par(oldpar)
efg
Earl F. Glynn
Scientific Programmer
Bioinformatics
Stowers Institute for Medical Research
__
R-help@stat.math.ethz.ch mailing list
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PLEASE do read the posting guide! http://www.R
F. Glynn
Stowers Insititute for Medical Research
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Earl F. Glynn [EMAIL PROTECTED] wrote in message
news:[EMAIL PROTECTED]
Sorry, I mixed up some code in Example #3. Here is a correction:
boxplot.meansd - list(stats = bp.limits,
n = length(len),
boxplot.meansd - list(stats = boxplot.limits,
n
Prof Brian Ripley [EMAIL PROTECTED] wrote in message
news:[EMAIL PROTECTED]
On Wed, 8 Mar 2006, Liaw, Andy wrote:
So now is a very good time for
people to offer further information/suggestions for that chapter.
This may be useful:
Mark Bravington, Debugging Without (Too Many) Tears, R News,
Erin Hodgess [EMAIL PROTECTED] wrote in message
news:[EMAIL PROTECTED]
I am currently saving the R screen as WMF files and inserting them
into PowerPoint. While this works, it seems that there
might be a simpler method.
Does anyone have any suggestions for the Power Point, please?
Instead
Sean Davis [EMAIL PROTECTED] wrote in message
news:[EMAIL PROTECTED]
I need urgently your assistance!!!
I need a global variable in R. The variable ought to be known for every
functions and subfunctions. It is only to comparison purposes of the
numeric algorithms. Is there a possibility?
Don MacQueen [EMAIL PROTECTED] wrote in message
news:[EMAIL PROTECTED]
I have found this little function useful when trying to choose colors:
FWIW: To choose colors, this page
http://research.stowers-institute.org/efg/R/Color/Chart/index.htm
and PDF
Martin Maechler [EMAIL PROTECTED] wrote in message
news:[EMAIL PROTECTED]
The clue is to transform correlations to dissimilarities.
. . .
and then use hclust(), agnes(), pam(), [the latter two from
package 'cluster'], ...
with 'Dx' as dissimilarity
Perhaps this TechNote may be of interest:
Bill Hunsicker [EMAIL PROTECTED] wrote in message
news:[EMAIL PROTECTED]
R-help,
I would like to place nine (3X3) plots per page. I am not properly
implement mfrow(3,3) in the script below:
Does this help?
jpeg(3x3.jpg)
oldpar - par( mfcol=c(3,3) )
plot(1)
plot(2)
plot(3)
plot(4)
plot(5)
I had a similar problem when I posted this recently:
RODBC and Excel: Wrong Data Type Assumed on Import
http://tolstoy.newcastle.edu.au/~rking/R/help/05/11/14938.html
My conclusion was: Being lucky shouldn't be part of processing Excel
files, which is the case when RODBC is used.
This reply
Dieter Menne [EMAIL PROTECTED] wrote in message
news:[EMAIL PROTECTED]...
Jose Claudio Faria joseclaudio.faria at terra.com.br writes:
Looks like a missing file in uses. I compiled it under Delphi 5, and it
looks
like the variants are no longer included in my uses.
Try to find out via help
Gabor Grothendieck [EMAIL PROTECTED] wrote in message
news:[EMAIL PROTECTED]
You could try using the COM interface rather than the ODBC
interface. Try code such as this:
library(RDCOMClient)
xls - COMCreate(Excel.Application)
xls[[Workbooks]]$Open(MySpreadsheet.xls)
sheet -
Kevin Wright [EMAIL PROTECTED] wrote in message
news:[EMAIL PROTECTED]
From my experience (somewhat of a guess):
Excel uses the first 16 rows of data to determine if a column is numeric
or
character. The data type which is most common in the first 16 rows will
then
be used for the whole
of Plasmid
NA.
Thanks for any help with this.
efg
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Earl F. Glynn
Scientific Programmer
Bioinformatics Department
Stowers Institute for Medical Research
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PLEASE do read
t c [EMAIL PROTECTED] wrote in message
news:[EMAIL PROTECTED]
I wish to obtain the right-most n characters of a character string? What
is the appropriate function?
substr will work:
x - c(abcd, xyz)
N - 2
substr(x, nchar(x)-N+1, nchar(x))
[1] cd yz
N - 3
substr(x, nchar(x)-N+1,
From
http://www.stowers-institute.org/ScientistsSought/ScientistsSought.asp#positions
Programmer/Analyst
The Stowers Institute for Medical Research has an opening for a
Programmer/Analyst to support scientific data analysis and assist with
computational biology tasks.
Responsibilities
ecatchpole [EMAIL PROTECTED] wrote in message
news:[EMAIL PROTECTED]
Earl,
I don't think that's a bug. Try
pdf(font5.pdf, onefile=FALSE)
and similarly for postscript().
Mea culpa. The onefile=FALSE wasn't necessary (and caused Ghostscript not to
open the postscript file).
The 2nd page was
table and a second unexpected page with only the clubs suite symbol (167)
in the middle of the plot. I'd call this a bug, but I guess I haven't read
all the documentation about this yet.
efg
Earl F. Glynn
Scientific Programmer
Stowers Institute for Medical Research
font5.R
==
ShowFont5
letters as the plot character:
par(font=5)
# Use Greek letter for plot characters from font=5
plot(0:1, 0:1, axes=F, type=n, xlab=, ylab=,
main=Greek plotting characters)
box()
points(runif(100), runif(100), pch=c(65:90, 97:122))
--
efg
Earl F. Glynn
Scientific Programmer
Stowers Institute
Ashish Ranpura [EMAIL PROTECTED] wrote in message
news:[EMAIL PROTECTED]
I still don't know how to draw
each of the three line segments I need).
See ?segments
Could you post a small toy problem so we can see exactly what segements
you're wanting to draw?
efg
This technote explains the margin area (mar) and how to modify it to control
white space around a graphic:
http://research.stowers-institute.org/efg/R/Graphics/Basics/mar-oma/index.htm
When you have multiple figures on a graphic, you may also want to learn to
control the outer margin area (oma),
Chris Wallace [EMAIL PROTECTED] wrote in message
news:[EMAIL PROTECTED]
how about
plot(..., xlab=)
title(xlab=label text, line=2)
Yes, Chris, I like your idea, especially when I can fix both X and Y axes
at the same time:
plot(0, xlab=,ylab=)
title(xlab=X axis, ylab=Y axis, line=2)
I'd
Berton Gunter [EMAIL PROTECTED] wrote in message
news:[EMAIL PROTECTED]
Failing that, (how) can this be done for Windows (XP or 2000, say) ?
Take a look at the Windows GetDeviceCaps API call
http://msdn.microsoft.com/library/default.asp?url=/library/en-us/gdi/devcons_88s3.asp
Parameters that
Márcio de Medeiros Ribeiro [EMAIL PROTECTED] wrote in message
news:[EMAIL PROTECTED]...
My big problem is that my program reads the image before that its
complete by the png() function. For instance, my graphic image has
1000Kb. When R saves it into the hard disk, my Java program reads the
file
/platform/shell/reference/functions/shbrowseforfolder.asp
Using the Shell API function SHBrowseForFolder()
http://community.borland.com/article/0,1410,17008,00.html
efg
--
Earl F. Glynn
Bioinformatics
Stowers Institute for Medical Research
__
R-help
Dirk Eddelbuettel [EMAIL PROTECTED] wrote in message
news:[EMAIL PROTECTED]
The R-help (!!) list is available via Gmane.org, a fabulous service that
archives, redirects, displays, ... a gazillion mailing lists. Among them
are
are r-help, r-devel, and several r-sig-* lists. See the top of
, col.names=T, file=y.csv)
Error in write.table(..., col.names = NA, sep = ,, qmethod = double) :
col.names = NA makes no sense when row.names = FALSE
Thanks for any insight about this.
efg
--
Earl F. Glynn
Bioinformatics
Stowers Institute
__
R-help
(greenred.colors(64))
# Method 4
library(marray)
pal - maPalette(low=green, high=red,mid=black)
maColorBar(seq(-2,2, 0.2), col=pal, horizontal=TRUE, k=0)
maColorBar(seq(-2,2, 0.1), col=pal, horizontal=TRUE, k=0)
efg
--
Earl F. Glynn
Scientific Programmer
Stowers Institute for Medical Research
Jan Verbesselt [EMAIL PROTECTED] wrote in message
news:[EMAIL PROTECTED]
Dear R-helpers,
Is it possible to create a type of 'movie' in R based on the output of
several figures (e.g., jpegs) via the plot() function. I obtained dynamic
results with the plotting function and would like to save
(5,4,4,2) + 0.1 and can be reduced.
For example:
par(mfrow=c(4,4), mar=c(3,3,0,0))
for (i in 1:16)
{
plot(0:10)
}
efg
--
Earl F. Glynn
Bioinformatics Department
Stowers Institute for Medical Research
__
R-help@stat.math.ethz.ch mailing list
https
The Partek package (www.partek.com) allows only two selections for Multiple
Test Correction: Bonferroni and Dunn-Sidak. Can anyone suggest why Partek
implemented Dunn-Sidak and not the other methods that R has? Is there any
particular advantage to the Dunn-Sidak method?
R knows about these
)]
MyData
col3 col1 col2
1312
2423
3534
--
efg
Earl F. Glynn
Bioinformatics
Stowers Institute for Medical Research
__
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PLEASE do read
Milos Zarkovic [EMAIL PROTECTED] wrote in message
news:[EMAIL PROTECTED]
I believe that FFT is not appropriate. However Lomb-Scargle periodogram
could be used.
This may interest you:
(Preprint of submitted paper)
Detecting periodic patterns in unevenly spaced gene expression time series
using
In R 2.0.1
p.adjust.methods
[1] holm hochberg hommel bonferroni fdrnone
In R 2.1.0
p.adjust.methods
[1] holm hochberg hommel bonferroni BH BY
fdr
[8] none
One might conclude that two new methods BH and BY were added. BUT,
there's a clue in one of the
how it formats the output.
Marc Schwartz [EMAIL PROTECTED] wrote in message
news:[EMAIL PROTECTED]
On Tue, 2005-05-31 at 17:14 -0500, Earl F. Glynn wrote:
Why isn't the number of NA's just 2 instead of the 2.000 shown
above?
The same number of decimal places is used throughout a vector
I'm
Example:
set.seed(19)
summary( c(NA, runif(10,1,100), NaN) )
Min. 1st Qu. MedianMean 3rd Qu.Max.NA's
7.771 24.850 43.040 43.940 63.540 83.830 2.000
Why isn't the number of NA's just 2 instead of the 2.000 shown above?
efg
Luis Ridao Cruz [EMAIL PROTECTED] wrote in message
news:[EMAIL PROTECTED]
R-help,
I have lloked in the archives found no answer to how to round the line
joint.
I have usedthe arguments lnd, ljoin in par but I get no differences in
the plotting.
x=1:10
par(ljoin=round,lend=round)
Jeff D. Hamann [EMAIL PROTECTED] wrote in message
news:[EMAIL PROTECTED]
After trying to find if there was a color picker in the FAQs and the help,
I thought I would send a post here. I was overwhelmed with all the
wonderful color choices R has predefined (discovered after typing in
colors())
==
Thanks for any help in clarifying this R subtilty.
efg
--
Earl F. Glynn
Scientific Programmer
Stowers Institute for Medical Research
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PLEASE do read
Thomas Lumley [EMAIL PROTECTED] wrote in message
news:[EMAIL PROTECTED]
Yes, and convertColor in R-devel does quite a few of these (XYZ
tristimulus space; CIE Lab and Luv; sRGB, Apple RGB and roll-your-own
RGB based on chromaticities of the primaries; and chromatic adaptation for
changing the
dependent.
I suggest as.numeric should perform the unsigned conversion on all
systems. What am I missing?
efg
--
Earl F. Glynn
Scientific Programmer
Bioinformatics Department
Stowers Institute for Medical Research
__
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Duncan Murdoch [EMAIL PROTECTED] wrote in message
news:[EMAIL PROTECTED]
Seems to me the conversion from hex to decimal should be system
independent
(and makes working with colors much more convenient). Why isn't this
system
independent now?
Presumably because nobody thought it was
Thomas Lumley [EMAIL PROTECTED] wrote in message
news:[EMAIL PROTECTED]
The convertColor function in R 2.1.0 provides colorspace conversion,
including hex.
#ff0080 isn't a number, it's a colour (or perhaps a color). If it were
converted to numeric form it would be a vector of three numbers,
Mulholland, Tom [EMAIL PROTECTED] wrote in message
news:[EMAIL PROTECTED]
Since I was only concentrating on colour issues and not on your specific
problem I was just showing the possibilities.
Does this code help
n - 5
par(mfrow = c(2,2))
palette(default)
barplot(1:25,col = 1:25)
when a new figure is created? (without using dummy blank placeholder plots)
The example above is only for discussion. I really want to do this in a
loop
and create 5 plots per figure, and repeat this for many pages in a PDF file.
Thanks for any insight on this.
efg
--
Earl F. Glynn
Scientific
Paul Murrell [EMAIL PROTECTED] wrote in message
news:[EMAIL PROTECTED]...
Does this do what you want?
layout(rbind(c(1, 2, 3),
c(0, 4, 0)))
plot(1:10, main=Plot 1)
plot(1:20, main=Plot 2)
plot(1:30, main=Plot 3)
plot(1:40, main=Plot 4)
# new page!
plot(1:40, main=Plot 5)
Perhaps I can ask a more focused question:
Earl F. Glynn [EMAIL PROTECTED] wrote in message
news:[EMAIL PROTECTED]
I want to get some simple logic regression examples to work before
exploring a hard problem.
..
logicfit - logreg(resp=Y, bin=X,
type = REGRESSION.TYPE-2
with the internal data structures that are present here?
Thanks for any help with this.
efg
--
Earl F. Glynn
Scientific Programmer
Bioinformatics Department
Stowers Institute for Medical Research
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman
is reasonable. (GIFs with drawings would be even better than
BMPs. I guess I could try PNGs.)
With the GIF/LZW patent issue now in the past, why not have a GIF driver and
even support creation/display of some simple animated GIFs in R?
Earl F. Glynn
Scientific Programmer
Stowers Institute
Duncan Murdoch [EMAIL PROTECTED] wrote in message
news:[EMAIL PROTECTED]
On Tue, 8 Feb 2005 11:35:22 -0600, Earl F. Glynn
[EMAIL PROTECTED] wrote :
In what version of R? I just tried in 2.01 and R-patched, and it was
fine. Maybe the problem is your viewer?
Sorry.
I thought I was using R
, how I can I call R from Delphi using R(COM)? Something seems to be
missing.
Duncan Murdoch's suggestion about direct calls to R.dll looks interesting,
but a complete working example would be nice.
Thanks for any help with this.
efg
Earl F. Glynn
Scientific Programmer
Stowers Institute
the long double type and the
computations you'd like to do.
efg
Earl F. Glynn
Stowers Institute for Medical Research
=
Sebastian Kaiser [EMAIL PROTECTED] wrote in message
news:[EMAIL PROTECTED]
Hello Everybody in order to get some needed results out of my function i
need to get my besselI
like. Just
drop me an E-mail.
efg
Earl F. Glynn
Scientific Programmer
Bioinformatics Department
Stowers Institute for Medical Research
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