On Fri, 1 Sep 2006, Hrishikesh Rajpathak wrote:
Hi,
I am a newbie to R and trying to implement parallelism in R. I am
currently using R-2.3.1, and Cygwin to run R on Windows xp.
Did you build R under Cygwin (which is not a supported platform), or are
you running a native Windows
On Wed, 30 Aug 2006, Hans-Joerg Bibiko wrote:
If you are using 'only' English then
str - dog
strsplit(str,NULL)[[1]]
works perfectly and it is fast.
It does also work 'perfectly' and fast in 'Unicode' in all major European
and CJK languages (and many others): extending the iconv example
On Fri, 1 Sep 2006, Prof Brian Ripley wrote:
On Thu, 31 Aug 2006, Jeff D. Hamann wrote:
I've been trying to get some code to run on a 64-bit FreeBSD machine running
R : Copyright 2006, The R Foundation for Statistical Computing
Version 2.3.0 (2006-04-24)
ISBN 3-900051-07-0
and
One solution is to simulate the population by repeating each row
weight number of times. This is inefficient. It may create a very
large dataset for a large sample survey. But some of graphs and other
things may turn out to your liking, depending upon how the functions are
written.
Anupam.
Rick
Estimados,
Quisiera saber cuanto es el tamaño máximo de datos contenidos en mi base de
datos, que el software R puede llegar a procesar y soporta.
De antemano agradezco y envió un cordial saludo.
Marcela Corrales
CPData Optimum
[[alternative HTML version deleted]]
Peter Dalgaard wrote
Is this floating point bound? (When you say 30 factors does that mean
30 parameters or factors representing a much larger number of groups).
If it is integer bound, I don't think you can do much better than
increase CPU speed and - note - memory bandwidth (look for
Hi,
I am trying to convert a variable a = sample(1:3,100,rep = T) represents
choices into a 3X100 dummy varible b with corresponding element set to 1
otherwise 0.
eg.
a: 1 3 2 1 2 3 1 1
b: 1 0 0 1 0 0 1 1..
0 0 1 0 1 0 0 0...
0 1 0 0 0 1 0 0...
Is there something like b[a] =1
(a==1)*1
or ifelse(a == 1, 1, 0)
---
Jacques VESLOT
CNRS UMR 8090
I.B.L (2ème étage)
1 rue du Professeur Calmette
B.P. 245
59019 Lille Cedex
Tel : 33 (0)3.20.87.10.44
Fax : 33 (0)3.20.87.10.31
http://www-good.ibl.fr
Try using outer:
outer(1:3, a, ==)+0
On 8/31/06, z s [EMAIL PROTECTED] wrote:
Hi,
I am trying to convert a variable a = sample(1:3,100,rep = T) represents
choices into a 3X100 dummy varible b with corresponding element set to 1
otherwise 0.
eg.
a: 1 3 2 1 2 3 1 1
b: 1 0 0 1 0 0 1
Here is an additional way:
model.matrix(~ factor(a) - 1)
On 9/1/06, Gabor Grothendieck [EMAIL PROTECTED] wrote:
Try using outer:
outer(1:3, a, ==)+0
On 8/31/06, z s [EMAIL PROTECTED] wrote:
Hi,
I am trying to convert a variable a = sample(1:3,100,rep = T) represents
choices into a
what about:
b - rbind(1*(a==1),1*(a==2),1*(a==3))
z s wrote:
Hi,
I am trying to convert a variable a = sample(1:3,100,rep = T) represents
choices into a 3X100 dummy varible b with corresponding element set to 1
otherwise 0.
eg.
a: 1 3 2 1 2 3 1 1
b: 1 0 0 1 0 0 1 1..
0
Hallo
probably there are other options but
outer(1:3,a, ==)*1
can do what you want.
HTH
Petr
On 31 Aug 2006 at 22:41, z s wrote:
Date sent: Thu, 31 Aug 2006 22:41:27 +0800 (CST)
From: z s [EMAIL PROTECTED]
To: r-help@stat.math.ethz.ch
On Fri, 1 Sep 2006, [EMAIL PROTECTED] wrote:
Peter Dalgaard wrote
Is this floating point bound? (When you say 30 factors does that mean
30 parameters or factors representing a much larger number of groups).
If it is integer bound, I don't think you can do much better than
increase CPU
In the process of checking a package, I get the warning
Foreign function calls without 'PACKAGE' argument:
.Call(tr, ...)
.Call(trProd, ...)
See section 'System and foreign language interfaces' of the 'Writing R..
These functions are called using the wrappers
trX - function(x, package=gRcox)
Søren Højsgaard [EMAIL PROTECTED] writes:
In the process of checking a package, I get the warning
Foreign function calls without 'PACKAGE' argument:
.Call(tr, ...)
.Call(trProd, ...)
See section 'System and foreign language interfaces' of the 'Writing R..
These functions are called
On Fri, 1 Sep 2006, Prof Brian Ripley wrote:
On Fri, 1 Sep 2006, Hrishikesh Rajpathak wrote:
Hi,
I am a newbie to R and trying to implement parallelism in R. I am
currently using R-2.3.1, and Cygwin to run R on Windows xp.
Did you build R under Cygwin (which is not a supported
Yo no soy experto en estos asuntos pero creo que no
haya una respuesta a su pregunta.
No es que R no tenga tamaño máximo de datos que pueda
llegar a procesar, pero ese tamaño depende de el hardware
(las caracteristica de su computadora) y el software
(el sistema operativo no es fijo, como R
Hi,
I output multiple grid-package-based plots to the postscript device.
Because the graphics are complicated and consists of a lot of datapoints
(~200'000) the files become really big. To avoid this big files and to
shorten the creation, I currently print the plots to the png device and
manually
On 8/31/2006 10:40 PM, Kimpel, Mark William wrote:
I installed GSView and the file opens correctly and the output is as is
should be. As you suggest, this must be a bug in Adobe CS2 Illustrator
and Photoshop.
It could conceivably still be our bug, but I'd like to hear what Adobe
tech support
On 1 Sep 2006, at 08:22, Prof Brian Ripley wrote:
On Wed, 30 Aug 2006, Hans-Joerg Bibiko wrote:
If you are using 'only' English then
str - dog
strsplit(str,NULL)[[1]]
works perfectly and it is fast.
It does also work 'perfectly' and fast in 'Unicode' in all major
European
and CJK
At 17:04 31/08/2006, Marcela Corrales wrote:
Estimados,
Quisiera saber cuanto es el tamaño máximo de datos contenidos en mi base de
datos, que el software R puede llegar a procesar y soporta.
Marcela, you will get more help if you
(a) post in English
(b) give us more information about your
On Fri, 1 Sep 2006, Duncan Murdoch wrote:
On 8/31/2006 10:40 PM, Kimpel, Mark William wrote:
I installed GSView and the file opens correctly and the output is as is
should be. As you suggest, this must be a bug in Adobe CS2 Illustrator
and Photoshop.
It could conceivably still be our
Prof Brian Ripley wrote
Probably not, but you have the ability to profile in R and find out.
Thanks. This is certainly something I could check, and I shall do so.
Some more comments;
1) The Fortran code that underlies glm is that of lm.fit that only makes
use of level-1 BLAS and
On Fri, 1 Sep 2006, [EMAIL PROTECTED] wrote:
Prof Brian Ripley wrote
3) As I recall, you were doing model selection via AIC on 20,000
observations. You might want to think hard about that, since AIC is
designed for good prediction. I would do model exploration on a much
Continuing to try to customize my environment for using R under
Windoze, I experimented with installing a package from CRAN in a
local library ``Lib''.
I created the directory ``Lib'' in the folder in which R starts,
and then executed
install.packages(abind,lib=Lib)
Everything went
Prof Brian Ripley wrote:
I would not have expected glm to be more than say 5x slower than lm if
CPU
cycles and not memory were the limiting factor. In that case more RAM
might be all you need.
The ratio between glm and lm might well be about 5x, but that's still a
big difference for us.
On Fri, 1 Sep 2006, [EMAIL PROTECTED] wrote:
Prof Brian Ripley wrote:
I would not have expected glm to be more than say 5x slower than lm if
CPU
cycles and not memory were the limiting factor. In that case more RAM
might be all you need.
The ratio between glm and lm might well be
Perfect, the apply was exactly what I was after, just wasn't clicking
with me, and I overlooked the cumprod ... sweet !
Thanks to all for pushing me down the right path!
Dirk Eddelbuettel [EMAIL PROTECTED]
08/31/2006 05:03 PM
To
[EMAIL PROTECTED]
cc
r-help@stat.math.ethz.ch
Subject
Sam Ferguson wrote:
Hi useRs -
I was wondering if anyone out there can tell me where to find R-code
to do mixes of tables and graphics. I am thinking of something
similar to this:
http://yost.com/information-design/powerpoint-corrupts/
or like the excel routines people are
This warning is indeed really an error, but do you want all your downloads
to fail just because one does? install.packages() behaves the same way on
Unices.
I was not aware that this works with relative paths for any version of R.
Try using a full path, which always works for me.
If indeed
Hi Rolf,
Rolf Turner wrote:
Continuing to try to customize my environment for using R under
Windoze, I experimented with installing a package from CRAN in a
local library ``Lib''.
I created the directory ``Lib'' in the folder in which R starts,
and then executed
On Fri, 1 Sep 2006, Hans-Peter wrote:
Hi,
I output multiple grid-package-based plots to the postscript device.
Because the graphics are complicated and consists of a lot of datapoints
(~200'000) the files become really big. To avoid this big files and to
shorten the creation, I currently
I've been unable to solve this problem using all sorts of variants of
trellis.par.set, or par.settings within xyplot.
I need this plot not to be transparent, so when I drop the .ps into
LaTeX it shows up on my black slides.
thanks.
nathan
traj.female-read.delim(d:\TRAfemales.dat, header =
Hi Catherine,
Not sure if you got any answers yet. This is a Mac issue, so a better
mailing list
is R-SIG-Mac. For now we can take it offline.
Can you tell me how you installed R? What exactly does show up in the
R Console?
Rob
On Aug 31, 2006, at 5:52 AM, Catherine Carter wrote:
Hi
On 31-Aug-06 Sam Ferguson wrote:
Hi useRs -
I was wondering if anyone out there can tell me where to find
R-code to do mixes of tables and graphics. I am thinking of
something similar to this:
http://yost.com/information-design/powerpoint-corrupts/
or like the excel routines people are
Dear R-list members,
I have a problem with translating a mathematica script into R. The whole
script is at the end of the email (with initial values for easy
reproduction) and can be pasted directly into R. The problematic part
(which is included below of course) is
--- Original Mathematica
(Ted Harding) wrote:
On 31-Aug-06 Sam Ferguson wrote:
Hi useRs -
I was wondering if anyone out there can tell me where to find
R-code to do mixes of tables and graphics. I am thinking of
something similar to this:
http://yost.com/information-design/powerpoint-corrupts/
or like the excel
XLSolutions Corporation (www.xlsolutions-corp.com) R/Splus Advanced
programming course taught the R Development Core Team is almost full!
(1) R/Splus Advanced Programming --- by the R Development Core Team
Guru!
http://www.xlsolutions-corp.com/Radv.htm
Thomas == Thomas Koenig [EMAIL PROTECTED]
on 31 Aug 2006 18:36:57 +0200 writes:
Thomas I encounter a problem with method dispatch with S4
Thomas classes, using the 'sealed' parameter in setClass.
[...]
[...]
Thomas Tried on R 2.3.1 and R
Is this a candidate for R's package of wise quotes (whose name I've
forgotten and can't find at the moment)?
The point here is that all but the most
uselss variables will measurably improve the fit in large problems with
few variables.
--
Brian D. Ripley, [EMAIL PROTECTED]
Hello,
I am in Win-XP R:2.3.0
latest rtools and Perl - of today
I got Rcmdr.HH source code and tried to compile it myself
copy all directory to R/R-2.3.0/src/library/Rcmdr.HH
from R/R-2.3.0/src/library
I typed:
..\..\bin\R CMD build --force --binary --auto-zip Rcmdr.HH
* checking for file
fortunes maintained by Achim Zeileis [EMAIL PROTECTED]
Berton Gunter wrote:
Is this a candidate for R's package of wise quotes (whose name I've
forgotten and can't find at the moment)?
The point here is that all but the most
uselss variables will measurably improve the fit in large problems
The LaTeX or other solutions suggested are probably best, but here is a
way to do it using only R base graphics (the below code is to get you
started, some graphical parameters need to be set to get the spacing to
look better):
tmp - structure(list(Cancer = structure(as.integer(c(19, 23, 22, 13,
Hi there
I am very new to R so dont know much about the programming side of thing yet.
I've worked out how to input a data matrix, create distance matrices and print
them to an external file but only for one data matrix at a time.
I actually have a batch of data matrices for which I want to
Dear all,
I wish to thank Christoph Buser and John Wilkinson for their input, and
especially John his examples and for for pointing me to the thread
'Doubt about nested aov output' where the rat-example was hiding...:
I have some data which consists of time series for a number of sites. It
appears that there is not much autocorrelation in the data and I have
fitted a cubic for each site using lm. I would like to obtain a lattice
plot with one panel for each site and showing the original data, and the
Prof. Brian Ripley solved the problem. He wrote:
I was not aware that this works with relative paths for any version
of R. Try using a full path, which always works for me.
I tried it using a full path, and bingo! It worked
like a charm.
Under Unix the relative path
Just have to use a 'for' loop;
for (i in list.files()){
x - read.table(i) # read in the next file (this is in 'i')
compute write your distance matrix.
}
On 9/1/06, Ffenics [EMAIL PROTECTED] wrote:
Hi there
I am very new to R so dont know much about the programming side of
install.packages() in R 2.4.0 will make a full path out of a relative
path, to avoid any confusion. (normalizePath is a good way to do that,
BTW).
On Fri, 1 Sep 2006, Rolf Turner wrote:
Prof. Brian Ripley solved the problem. He wrote:
I was not aware that this works with relative paths
Please use Rcmd INSTALL --build and see if that works for you. It is how
Uwe Ligges and I build the public repositories.
On just Rcmd INSTALL if you don't want to distribute it.
(R CMD and Rcmd are the same thing, and I prefer the older form which is
more efficient.)
On Fri, 1 Sep 2006, R
These are the commands I used
Rcmd check Rcmdr.HH ## detailed checks
Rcmd build Rcmdr.HH ## tar.gz
R CMD INSTALL --build Rcmdr.HH ## installs and builds .zip
__
R-help@stat.math.ethz.ch mailing list
On 9/1/06, David Scott [EMAIL PROTECTED] wrote:
I have some data which consists of time series for a number of sites. It
appears that there is not much autocorrelation in the data and I have
fitted a cubic for each site using lm. I would like to obtain a lattice
plot with one panel for each
I am interested in plotting histograms for the following data
Isoform
Tumor_65_198
Tumor_50_192
Tumor_80_167
Tumor_80_204
Tumor_95_197
Tumor_70_189
Tumor_90_202
Tumor_40_177
Tumor_60_21
Tumor_70_174
Tumor_70_147
Tumor_50_5
ABCC4-2007
1
1
1
6
1
9
10
1
2
0
10
1
It is the same issue. Martin's reply was for a specific value of 'a': the
factor is gamma(a).
Please do study the help page for pgamma (as the posting guide did ask you
to), as it has all the details.
Note that the Mathematica version can easily lead to representation
difficulties for even
Your data seems to have come through messed up but lets
assume you have a data frame with one column per tumor.
The convert your data to stacked form and call histogram:
DF - data.frame(T1 = 1:10, T2 = 6:15)
library(lattice)
histogram(~ values | ind, stack(DF))
On 9/1/06, Nair, Murlidharan T
The apply with the cumprod was exactly what I was after. The apply just
wasn't clicking with me, and I had overlooked the cumprod. Thanks to all
for pushing me down the right path!
Actually, what I am ultimately after is a way to link this series, without
having to use a for loop ( the only
On 1 September 2006 at 14:30, [EMAIL PROTECTED] wrote:
| The apply with the cumprod was exactly what I was after. The apply just
| wasn't clicking with me, and I had overlooked the cumprod. Thanks to all
| for pushing me down the right path!
|
| Actually, what I am ultimately after is a way
Dear R helpers,
To illustrate my problem, here is a simplified example. I want to write
a table to a file similar to:
x a
1 4,5
2 8,9,10
Note the length of elements of a is 2 and 3 respectively. This can be
created by, for
I am fittling a spline to a variable in a regression model, I am then using
the predict.glm funtion to make some predictions. When I use bs to fit the
spline I don't have any problems using the predict.glm function however when
I use ns I get the following error:
Error in model.frame(formula,
That is choice !I'm starting to love this language. Thank-you !
Dirk Eddelbuettel [EMAIL PROTECTED]
09/01/2006 02:59 PM
To
[EMAIL PROTECTED]
cc
r-help@stat.math.ethz.ch
Subject
Re: [R] cumulative growth rates indexed to a common starting point over n
series of observations
What about
x - 1:2
a - list(c(4,5),c(8,9,10)) # Which is the way you *should*
# have constructed a!
ddd - data.frame(x=x,a=I(unlist(lapply(a,paste,collapse=,
write.table(ddd,file=ddd.out,quote=FALSE,row.names=FALSE)
Hi wizards, I have seen the function svd of R for singular value
decomposition, but I need to computes the ``economy size'' or ``thin''
singular value decomposition of a matrix in R. Somebody knows how to
do that?. Thanks in advance.
--
Web Page
http://geocities.com/lord_tyranus_96/
dear group,
i have 100 files starting with 'hsa-*'.
ex. file:
fruit p-value
apple 0.0003
orange 0.004
kiwi 0.0003
peach 0.0004
I want to read all these files and create a single
matrix. here each file may have different fruit names.
in the matrix i want to have a
Your data seems to have come through messed up but lets
assume you have a data frame with one column per tumor.
The convert your data to stacked form and call histogram:
DF - data.frame(T1 = 1:10, T2 = 6:15)
library(lattice)
histogram(~ values | ind, stack(DF))
Or with ggplot and reshape:
Yes, the code does the job. Thanks, Zhu Wang
Rolf Turner wrote:
What about
x - 1:2
a - list(c(4,5),c(8,9,10)) # Which is the way you *should*
# have constructed a!
ddd - data.frame(x=x,a=I(unlist(lapply(a,paste,collapse=,
I have some data which consists of time series for a number of sites. It
appears that there is not much autocorrelation in the data and I have
fitted a cubic for each site using lm. I would like to obtain a lattice
plot with one panel for each site and showing the original data, and the
On 1 September 2006 at 14:59, Dirk Eddelbuettel wrote:
|
| On 1 September 2006 at 14:30, [EMAIL PROTECTED] wrote:
| | The apply with the cumprod was exactly what I was after. The apply just
| | wasn't clicking with me, and I had overlooked the cumprod. Thanks to all
| | for pushing me down
Thanks ../Murli
-Original Message-
From: hadley wickham [mailto:[EMAIL PROTECTED]
Sent: Friday, September 01, 2006 5:08 PM
To: Gabor Grothendieck
Cc: Nair, Murlidharan T; r-help@stat.math.ethz.ch
Subject: Re: Re: [R] histograms
Your data seems to have come through messed up but lets
Yes I do. I was still scratching my head still trying to figure out why
I couldn't get my actual #s to match the example from the random series.
This now matches my brute force calcs.
btw:
Also had a former colleague and good friend suggest this could be done
using ranges. Which opened my
A simple for loop would do it:
x - 1:2; a - list(4:5, 8:10) # test data
cat(x a\n, file = ) # only if you want a header
for(i in seq(along = x)) cat(x[i], a[[i]], \n, file = )
On 9/1/06, Zhu Wang [EMAIL PROTECTED] wrote:
Dear R helpers,
To illustrate my problem, here is a simplified
R's svd does this by default (at least according to Wikipedia's
definition). Take a closer look at the help page, and in particular 'nu'
and 'nv'.
On Fri, 1 Sep 2006, Lord Tyranus wrote:
Hi wizards, I have seen the function svd of R for singular value
decomposition, but I need to computes
Apparently I missed cat. Thanks. Zhu Wang
Gabor Grothendieck wrote:
A simple for loop would do it:
x - 1:2; a - list(4:5, 8:10) # test data
cat(x a\n, file = ) # only if you want a header
for(i in seq(along = x)) cat(x[i], a[[i]], \n, file = )
On 9/1/06, Zhu Wang [EMAIL PROTECTED] wrote:
Your example is not actually a regression, and not reproducible. Here is
one that is both:
fm1 - lm(weight ~ ns(height, df = 5), data = women)
predict(fm1, newdata=women[1,], se=TRUE)
Error: variable 'ns(height, df = 5)' was fitted with class nmatrix.5 but
class nmatrix.1 was supplied
In
On Fri, 1 Sep 2006, Deepayan Sarkar wrote:
On 9/1/06, David Scott [EMAIL PROTECTED] wrote:
I have some data which consists of time series for a number of sites. It
appears that there is not much autocorrelation in the data and I have
fitted a cubic for each site using lm. I would like to
First Graphic in the initial posting: I think this graphic need to be scaled in
a manner so it can be interpreted correctly while going across rows, columns,
and
non-contguous cells, or the correct interpretation and way to read this
provided. For example, in the last row one has to read the
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