Hi,
I propose here a solution that relies on names of elements:
# From a list, with any names
ll=list(v1=1:4,v2=1:2,v3=5:7,v4=9:11,v5=1,v6=rnorm(4))
# Make a copy to be able to change names
ll2=ll
names(ll2)=rep("a",lengh(ll2))
# Use unlist, which "autobuilds" names based on
# previous names and
This is not a bug. It just means that the algorithm sometimes finds an
empty cluster, and as you asked for 34 clusters and it had 33 or less it
stops.
What to do in this situation is currently under discussion, but the advice
given is good: try another set of initial centres.
Please do read t
I was surprised by the following (R 1.8.0):
R> lm.fit = lm(y~x, data.frame(x=1:10, y=1:10))
R> predict(lm.fit, data.frame(x = rep(NA, 10)))
1 2 3 4 5
-1.060998e-314 -1.060998e-314 -1.060998e-314 -1.060998e-314 -1.060998e-314
Hi Thomas,
the matrix V , which produced the anomelous order,is attached as an R
object,
load("V.r")
eigen(V)$values
you'll get the eigen values in reverse order
best regards
Karim
Thomas Lumley wrote:
>
> On Sun, 9 Nov 2003, Karim Elsawy wrote:
>
> > I'm using R 1.7.1 under linux redhat
> > i
On Mon, 10 Nov 2003, Edzer J. Pebesma wrote:
> I was surprised by the following (R 1.8.0):
>
> R> lm.fit = lm(y~x, data.frame(x=1:10, y=1:10))
> R> predict(lm.fit, data.frame(x = rep(NA, 10)))
> 1 2 3 4 5
> -1.060998e-314 -1.060998e
> "Karim" == Karim Elsawy <[EMAIL PROTECTED]>
> on Mon, 10 Nov 2003 08:34:07 + writes:
Karim> Hi Thomas, the matrix V , which produced the
Karim> anomelous order,is attached as an R object,
and it wasn't :
Most binary attachments are *not* allowed on our mailing lists
(for
Hi
Since a stepwise procedure for variable selection (as e.g. in SPSS) for
a LDA is not implemented in R and anyway I cannot be sure, that all the
required assumptions for e.g. a procedure using a statistic based on
wilks' lambda, hold (such as normality and variance homogeneity) I would
like to as
Hi Thomas,
the matrix V , which produced the anomelous order,is attached as a text
file,
V<-matrix(scan("V.dat"),ncol=40,byrow=T)
eigen(V)$values
best regards
karim
Martin Maechler wrote:
>
> > "Karim" == Karim Elsawy <[EMAIL PROTECTED]>
> > on Mon, 10 Nov 2003 08:34:07 + writes
To get the Rdbi/RdbiPgSQL 1.0.1 interface from BioConductor
functional, I would like to suggest some fixes.
Find patches and the updated packages here:
http://mpa.itc.it/markus/tmp/rdbi/
Changes
Rdbi:
- fixed load of RdbiPgSQL (wrong name)
- fixed dbConnectionInfo() (typo)
RdbiPgSQL:
Hello dear listers,
I can't find a way to align the given values labels when using coplot.
The labels always appear like a stair. Is there a way to modify this ?
I searched the help and archives but was unable to find out.
Any help would be much appreciated,
Tito
--
L. Tito de Morais
U
That is not a symmetric matrix so the eigenvalues are potentially complex
and are sorted by modulus. There's an ambiguity in the description for
that case.
In all cases the eigenvectors are in the same order as the eigenvalues.
On Mon, 10 Nov 2003, Karim Elsawy wrote:
> Hi Thomas,
> the matr
Prof Brian Ripley <[EMAIL PROTECTED]> writes:
> That is not a symmetric matrix so the eigenvalues are potentially complex
> and are sorted by modulus. There's an ambiguity in the description for
> that case.
Ah-ha! Thanks, Brian.
I wonder if we should switch to sorting by absolute value in t
I think switching the sort order would probably
break a fair amount of code, and it wouldn't
necessarily be obvious that it had been broken.
For example, I suspect that there is a fair amount
of code that tests if all eigenvalues are positive by
just looking at the last one.
Anyway, consistency
Dear list members,
this is not an R question and forgive me for using the list for irrelevant
questions, but this is the only place I know where I can find some good
statisticians and I need an expert opinion.
There is this power law kinetic model of the form:
M=kt^n
where t is the time, M is the
I want to use the identify command when I have multiple plots on the
same page.
For example if I use:
par(mfrows=c(2,1))
and then:
plot(x1,y1)
plot(x2,y2)
I get two plots on the same page, but if I use identify after this plot
set-up it can't find the data points. I need som
Dear Thomas,
Try Jim Lindsey's R code: http://alpha.luc.ac.be/~jlindsey/
HTH
> Hello
>
>
> I am writing to you regarding your interest in Copula/copulae and it´s
> usage. I am currently studying Copula for my Master thesis and also
> therefore have a large interest in it. Now I am looking for
Using split.screen should enable you to go back to earlier plots, with the
coordinate system you used. I was able to amend the example of
split.screen to identify on the first plot, for example. As far as I
recall this works imperfectly with log axes.
On Mon, 10 Nov 2003, Luke Keele wrote:
> I
Have you looked at the correlation of the parameter estimates?
In S-Plus, this is automatically produced by summary(lm(...)).
There is probably a simple, elegant way to get this in R, but I don't
know it. Therefore, I produced it as follows:
> DF <- data.frame(x=1:12, y=rep(1:6, ea
On Mon, 10 Nov 2003, Christoph Lehmann wrote:
> Hi
> Since a stepwise procedure for variable selection (as e.g. in SPSS) for
> a LDA is not implemented in R and anyway I cannot be sure, that all the
> required assumptions for e.g. a procedure using a statistic based on
> wilks' lambda, hold (such
On Mon, 10 Nov 2003, Spencer Graves wrote:
> Have you looked at the correlation of the parameter estimates?
>
> In S-Plus, this is automatically produced by summary(lm(...)).
> There is probably a simple, elegant way to get this in R, but I don't
> know it. Therefore, I produced i
I agree with Patrick that we should leave the symmetric case alone,
although I did notice that Splus 6.1 says
values: vector of nrow(x) eigenvalues in descending order of modulus.
but does sort the symmetric case by value and not modulus, so the code
that Pat refers to is presuming the docum
On Sun, 9 Nov 2003, Hadley Wickham wrote:
> Does signalCondition() only work within try-catch blocks?
>
> I expected:
>
> testSignal <- function() {
> error <- simpleError("An error!")
> signalCondition(error)
> }
>
> to do the same thing as
>
> testStop <- function() {
> error <-
Hi dear R-listers, I'm trying to fit a 3-level model using lme in R. My
sample size is about 2965 and 3 factors:
year (5 levels), ssize (4 levels), condition (2 levels).
When I issue the following command:
>
lme(var~year*ssize*condition,random=~ssize+condition|subject,data=smp,method
="ML")
I g
Hi, all!
I want to give an object to a function and use the NAME of this object
inside the function to build new objects based on this name.
How do I get the name of an object if I don't pass a string containing
the name but the object itself?
Christoph.
--
Christoph Lange
MPI fuer biologisch
Hi,
is the following possible - in a given session I make a lot of objects
and save when exiting. Usually I note down seperately what each object
is about. Is it possible to attach data to any object which would
essentially be a short note explaining the meaning of it?
Thanks,
-
You probably want
deparse(substitute(object))
See ?substitute.
> -Original Message-
> From: Christoph Lange [mailto:[EMAIL PROTECTED]
> Sent: 10 November 2003 16:06
> To: R Help List
> Subject: [R] Finding the name ob an object
>
>
> Security Warning:
> If you are not sure an attachme
Thanks very much: I typed "?summary.fit" when I meant to type
"?summary.lm", which explains why I didn't find the "cor" argument.
Thanks also for the reference to "?vcov". I didn't see that in the "see
also" section for either "lm" or "summary" or "summary.lm". Might it be
worth added?
Th
The error says you don't have enough memory on your computer.
Unfortunately, the only solution may be to buy more.
-roger
Rodrigo Abt wrote:
Hi dear R-listers, I'm trying to fit a 3-level model using lme in R. My
sample size is about 2965 and 3 factors:
year (5 levels), ssize (4 levels), cond
> f <- function(x)deparse(substitute(x))
> f(pi)
[1] "pi"
answer the question? spencer graves
Christoph Lange wrote:
Hi, all!
I want to give an object to a function and use the NAME of this object
inside the function to build new objects based on this name.
How do I get the name of an object if
Hi,
I'me trying to write a function that will shuffle a vector. At the
moment I'm baically making a vector of randomized indices and then
making a new vector from the original one using these random indices.
However, is there an alternative (more elegant) method to do this? I
tried help.search
Rajarshi Guha wrote:
Hi,
is the following possible - in a given session I make a lot of objects
and save when exiting. Usually I note down seperately what each object
is about. Is it possible to attach data to any object which would
essentially be a short note explaining the meaning of it?
You c
Look at the first lines of plot.default for an example of how to
extract the name of an argument.
HTH,
Giovanni
> Date: Mon, 10 Nov 2003 17:06:17 +0100
> From: Christoph Lange <[EMAIL PROTECTED]>
> Sender: [EMAIL PROTECTED]
> Mail-followup-to: R Help List <[EMAIL PROTECTED]>
> Precedence: list
>
Have you done what the message said?
On Mon, 10 Nov 2003, Rodrigo Abt wrote:
> Hi dear R-listers, I'm trying to fit a 3-level model using lme in R. My
> sample size is about 2965 and 3 factors:
>
> year (5 levels), ssize (4 levels), condition (2 levels).
>
> When I issue the following command:
See ?comment for a built-in method using S3 class attributes.
> -Original Message-
> From: Rajarshi Guha [mailto:[EMAIL PROTECTED]
> Sent: 10 November 2003 16:15
> To: R
> Subject: [R] attaching data to any object
>
>
> Security Warning:
> If you are not sure an attachment is safe to op
Christoph Lange wrote:
Hi, all!
I want to give an object to a function and use the NAME of this object
inside the function to build new objects based on this name.
How do I get the name of an object if I don't pass a string containing
the name but the object itself?
deparse(substitute(x))
Uwe L
On 10 Nov 2003, Rajarshi Guha wrote:
> Hi,
> is the following possible - in a given session I make a lot of objects
> and save when exiting. Usually I note down seperately what each object
> is about. Is it possible to attach data to any object which would
> essentially be a short note explainin
Dear colleagues,
Is there any way of saving an animated plot with R? For instance, any format
that could be read by Microsoft windows media or whatever.
Cheers,
Jesus
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Rajarshi Guha <[EMAIL PROTECTED]> writes:
> Hi,
> I'me trying to write a function that will shuffle a vector. At the
> moment I'm baically making a vector of randomized indices and then
> making a new vector from the original one using these random indices.
>
> However, is there an alternativ
On Mon, 2003-11-10 at 11:32, Uwe Ligges wrote:
> Rajarshi Guha wrote:
>
> > Hi,
> > is the following possible - in a given session I make a lot of objects
> > and save when exiting. Usually I note down seperately what each object
> > is about. Is it possible to attach data to any object which wo
On Mon, 2003-11-10 at 11:28, Rajarshi Guha wrote:
> Hi,
> I'me trying to write a function that will shuffle a vector. At the
> moment I'm baically making a vector of randomized indices and then
> making a new vector from the original one using these random indices.
>
> However, is there an alt
Rajarshi Guha wrote:
Hi,
I'me trying to write a function that will shuffle a vector. At the
moment I'm baically making a vector of randomized indices and then
making a new vector from the original one using these random indices.
However, is there an alternative (more elegant) method to do this
This is probably what you want.
?sample
HTH,
Jim
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623
>>> Rajarshi Guha <[EMAIL PROTECTED]> 11/10/03 11:28AM >>>
Hi,
I'me trying to
help(sample)
-Original Message-
From: [EMAIL PROTECTED] on behalf of Rajarshi Guha
Sent: Tue 11/11/2003 12:28 AM
To: R
Cc:
Subject: [R] shuffling a vector
Hi,
I'me trying to write a function that wil
On Monday 10 November 2003 17:28, Rajarshi Guha wrote:
> Hi,
> I'me trying to write a function that will shuffle a vector. At
> the moment I'm baically making a vector of randomized indices and
> then making a new vector from the original one using these random
> indices.
>
> However, is there
On Mon, 2003-11-10 at 10:28, Rajarshi Guha wrote:
> Hi,
> I'me trying to write a function that will shuffle a vector. At the
> moment I'm baically making a vector of randomized indices and then
> making a new vector from the original one using these random indices.
>
> However, is there an alt
[EMAIL PROTECTED] wrote:
> I'me trying to write a function that will shuffle a vector.
> At the moment I'm baically making a vector of randomized indices
> and then making a new vector from the original one using these
> random indices.
What's your definition of "elegant"? :-)
Isn't this eleg
?sample
> Date: Mon, 10 Nov 2003 11:28:56 -0500
> From: Rajarshi Guha <[EMAIL PROTECTED]>
> Sender: [EMAIL PROTECTED]
> Organization:
> Precedence: list
>
> Hi,
> I'me trying to write a function that will shuffle a vector. At the
> moment I'm baically making a vector of randomized indices an
Dear R supports:
I am trying to install R-1.8.0 on an IBM p630 box (AIX 5.1) for a user.
When I try to run make after I run ./configure, I get the following error:
# make
Target "R" is up to date.
make: 1254-002 Cannot find a rule to create target R from dependencies.
Stop.
make: 1254-004 The
On Mon, 2003-11-10 at 10:51, Marc Schwartz wrote:
> On Mon, 2003-11-10 at 10:28, Rajarshi Guha wrote:
> > Hi,
> > I'me trying to write a function that will shuffle a vector. At the
> > moment I'm baically making a vector of randomized indices and then
> > making a new vector from the original o
Prof Brian Ripley wrote:
>
> This is not a bug. It just means that the algorithm sometimes finds an
> empty cluster, and as you asked for 34 clusters and it had 33 or less it
> stops.
>
> What to do in this situation is currently under discussion, but the advice
> given is good: try another s
On 10 Nov 2003 at 11:14, Rajarshi Guha wrote:
The library Hmisc has a function comment()
doing this.
Kjetil Halvorsen
> Hi,
> is the following possible - in a given session I make a lot of objects
> and save when exiting. Usually I note down seperately what each object
> is about. Is it possib
On 10 Nov 2003 at 17:06, Christoph Lange wrote:
> test <- function(x){
+ return(substitute(x))}
> a <- 3
> test(a)
a
Kjetil Halvorsen
>
> Hi, all!
>
> I want to give an object to a function and use the NAME of this object
> inside the function to build new objects based on this name.
>
Dear Rajarshi,
sample(x) will randomly permute the elements of x.
I hope that this helps,
John
At 11:28 AM 11/10/2003 -0500, Rajarshi Guha wrote:
Hi,
I'me trying to write a function that will shuffle a vector. At the
moment I'm baically making a vector of randomized indices and then
making a
On 10 Nov 2003 at 13:01, Rodrigo Abt wrote:
See?Memory
for how you can get R to use virtual memory.
Kjetil Halvorsen
> Hi dear R-listers, I'm trying to fit a 3-level model using lme in R. My
> sample size is about 2965 and 3 factors:
>
> year (5 levels), ssize (4 levels), condition (2 levels).
Is it normal that it takes a very long time to generate a connection
object on a big character vector?
This takes a very long time to process:
lines <- readLines ("myBigFile.txt")
data <- scan(textConnection(lines), sep = "\t")
against this that is pretty short to process:
data <- scan("myBigFile
Hi. I haven't looked at the source code for textConnection(), but I am
confident that the authors have done a good job, which makes me believe
that you're running out of RAM-memory and that you're starting to swap.
>From ?textConnection:
"An input text connection is opened and the character vecto
On Mon, 10 Nov 2003, Mathieu Drapeau wrote:
> Is it normal that it takes a very long time to generate a connection
> object on a big character vector?
Yes.
> This takes a very long time to process:
> lines <- readLines ("myBigFile.txt")
> data <- scan(textConnection(lines), sep = "\t")
>
> aga
Murad Nayal wrote:
I am running kmeans in a loop for a range of possible cluster numbers.
The error terminates the loop. is there a mechanism by which I can
'trap' the error so that I can rerun kmeans with another set of initial
centers and hence allow the loop to run to completion. something like
An alternative that might alleviate Uwe's scepticism:
Many functions such as the modelling functions have
a "call" component or attribute which is the result of
match.call()
within the function. This makes the resulting object essentially
self-documenting. I find it easier to write functions wi
--- On Mon 11/10, Mathieu Drapeau < [EMAIL PROTECTED] > wrote:
> Is it normal that it takes a very long time to generate a
> connection object on a big character vector?
If the reason you need a text connection is that you are locating
your data via a tag like this:
lines <- readLines( "inp
Hi all:
I've been looking at the boot package to "bootstrap" sample my data in a
particular way. I haven't figured out how to set this up using the boot() command and
thus have resorted to trying to write my own script (although I'd prefer if I could
get boot() to work for this problem!)
I want to investigate possible relationships between two discrete variables. I have
tried a few things but figured you guys might be able to point me at some purpose
built functions.
Our scientists score results of tests which are performed in lets say, 8 positions.
The scores are assigned a
Hola!
I have data in the form of a symmetric distance matrix, in the file I
have recorded only the upper triangular part, with diagonal. The
matrix is 21x21, and the file have row and col names, and some other
information. I am trying to read with the following code (I tried
many variations on
For various reasons, I spent part of my time today looking at sample
size and power calculation tools (don't ask, don't tell...). This
seems to be one area that R is incredibly weak in (well, nearly all
stat packages, except perhaps specialized tools and SAS); sure, there
are a number of function
Hello,
How do I tell R not to place a label on an axis when using the "plot"
command?
Thank you,
Ann Loraine
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e.g.:
plot(1:2, axes=F)
axis(1)
spencer graves
Ann Loraine wrote:
Hello,
How do I tell R not to place a label on an axis when using the "plot"
command?
Thank you,
Ann Loraine
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Ann -
Maybe you are looking for
plot( ..., xlab="", ylab="")
followed by title(xlab="the real x axis label")
title(ylab="the real y axis label", mgp=c(2.5,0.5,0))
This is a construction that I use all, all, all the time.
- tom blackwell - u michigan medica
Scott -
The second argument to boot(), called 'statistic', can be
any user-written function you want to cook up, with additional
arguments being passed to it through the '...' mechanism after
all of the named arguments. (See: `R-intro `Writing your own
functions `The ellipsis argument for det
Paul -
This situation seems like an obvious candidate for a log-linear model.
See the book MASS for details. They're beyond the scope of this list.
Or try help.search("log-linear").
(and ... can you find a way to break lines when sending your email ?)
- tom blackwell - u michigan medical s
Kjetil -
Frankly, your file would be much, much easier to read
if it didn't have a row name at the beginning of each
line. Any chance you can edit it to remove those ?
Then, I think you could read in the numeric data with
just one call to scan:
mat <- matrix(0, 21, 21)
mat[row(mat) >= col(mat
Thanks to you all for your helpful solutions. I particularly like the
simplicity of Gabor's na.omit( sapply(... ) ) formulation, but you've
all given me some ideas to think about.
Thanks again,
Hadley
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