Hi.
I'm having difficulty following the advice given in help(Recall).
Consider the two
following toy functions:
f1 - function(n){
if(length(n)1){return(sapply(n,f1))}
matrix(n,n,n)
}
f2 - function(n){
if(length(n)1){return(sapply(n,Recall))}
matrix(n,n,n)
}
f1() works as desired (that
At 16:13 29.03.2005 -0800, Thomas Lumley wrote:
On Wed, 30 Mar 2005, Heinz Tuechler wrote:
Dear all,
Last December there was a thread regarding the famous FAQ 7.21 How can I
turn a string into a variable? and asking what people want to do with
these strings.
My, certainly trivial
At 09:32 30.03.2005 +0200, Heinz Tuechler wrote:
At 16:13 29.03.2005 -0800, Thomas Lumley wrote:
On Wed, 30 Mar 2005, Heinz Tuechler wrote:
Dear all,
Last December there was a thread regarding the famous FAQ 7.21 How can I
turn a string into a variable? and asking what people want to do with
Hallo all,
can somebody tell me if is possible use the locfit function like a
semiparametric model. I need to use two explicative variables and one of them
is a dummy variable.
Thanks Michele
-
Giochi, Rubrica
Scaricalo ora!
Dear all,
I am looking at habituation of dogs trotting on a treadmill.
I record the ground reaction force and I analyze it with several discrete variables (maximum, minimum,...)
For each variable, I get between 40 and 50 data per sample.
I record data at time 1 min, 2 min, and 4 min a day,
How much memory is free when R fails (e.g., what does top show while trying
to run your clustering)? If there's still a sizeable amount of free memory you
may have to look into the system limits, maximum data segment size in
particular. Many Linux distros have it set to unlimited but default
Dear all,
I am trying to wrap up a package. On entering
R CMD check, I get the following error messages:
[...]
* checking S3 generic/method consistency ... WARNING
Error in .try_quietly({ : Error in library(package, lib.loc = lib.loc,
character.only = TRUE, verbose = FALSE) :
since you measure the same dog several times its measurements are
correlated and you should take this into account in your analysis
(i.e., aov() is not appropriate in this case). Probably you could
find functions lme() and gls() in the nlme package very useful
for your problem and for which a
Hello
I am running R 2.0.1 on Windows, I am attempting to use Frank Harrell's
'fastbw' function (from the Design library), but I get an error that the
fit was not created with a Design library fitting function; yet when I
go to the help for fastbw (and also look in Frank's book Regression
In message [EMAIL PROTECTED], r-help-
[EMAIL PROTECTED] writes
Dear R Users,
I'm very very interested in learning how to use R to carry out a
classification of data using discriminant function analysis. I've
found the MASS package and the lda function, but the examples in the
help system are
On Wed, 2005-03-30 at 11:06 +0100, Steven J. Murdoch wrote:
I would like to draw only the ticks of an axis, but not the axis
itself. I don't think this can be done using axis(), so I am trying to
write a cut-down version in R, which only draws ticks.
The point at which I am stuck is that the
I doubt it's possible to use Recall inside a sapply like this. sapply
(and lapply) make a copy of the function (FUN - match.fun(FUN)) before
passing it inside an internal function (rval - .Internal(lapply(X,
FUN)). So, while I'm not precisely sure how Recall is coded up, I bet
that once it is
I believe that the function that Recall executes is the
function in which Recall, itself, is evaluated -- not the
function in which Recall appears. In normal cases these are
the same but if you pass Recall to another function then
they are not the same. Here Recall is being passed to
sapply
[EMAIL PROTECTED] ulimit -a
core file size(blocks, -c) 0
data seg size (kbytes, -d) unlimited
file size (blocks, -f) unlimited
max locked memory (kbytes, -l) unlimited
max memory size (kbytes, -m) unlimited
open files(-n) 1024
pipe size
Hi, all,
I have a question about multiple comparison of analysis of covariance using
SPSS 10.
The way I used was in the menu 'Analyze-General Linear Model-Mutivariate'.
When I only chosed 'Dependent Variables' and 'Fixed Factor(s)', the button of
'Post Hoc' can be pressed and I can chose some
Dear Johannes
I have noticed the same complaint, and you are right that it can be
unconnected with faulty S3 methods, etc., in your package.
For example, in my relimp package (current version 0.9-1, new on CRAN
today) the DESCRIPTION file has
Suggests: tcltk
and that works fine (ie it passes
Hie,
I have written before and probably missed the reply.
1.) I have my figures in a 3X3 array and want to fit them onto a A4 size
page. I have written commands to try a represent them in eps format but
still their cutting out information.
2.) I have an odd number of years and wanted to
Hie,
I have written before and probably missed the reply.
1.) I have my figures in a 3X3 array and want to fit them onto a A4 size
page. I have written commands to try a represent them in eps format but
still their cutting out information.
2.) I have an odd number of years and wanted to
hclust creates a distance matrix. In your case it is 10,000 x 10,000. For
various reasons several copies are created, so you probably need at least
100M x 8 bytes per entry x 3 copies = 2.4 GB
just for the distance matrix. If you don't have that much RAM the
computation will probably take
Peter Flom wrote:
Hello
I am running R 2.0.1 on Windows, I am attempting to use Frank Harrell's
'fastbw' function (from the Design library), but I get an error that the
fit was not created with a Design library fitting function; yet when I
go to the help for fastbw (and also look in Frank's book
hello!
what's wrong???
i use 32 bit machine.
every time i 'm connecting the server to do my work with R on it ,
after having done
R --max-vsize=4000M --max-nsize=4000M
i become wrong limits specification for Ncells:
.
gc()
used(Mb) gc
On Wed, 30 Mar 2005, Robin Hankin wrote:
Hi.
I'm having difficulty following the advice given in help(Recall). Consider
the two
following toy functions:
f1 - function(n){
if(length(n)1){return(sapply(n,f1))}
matrix(n,n,n)
}
f2 - function(n){
if(length(n)1){return(sapply(n,Recall))}
Finally,
I found a way to make fix() and edit() work with gnuclient
in ESS-5.2.6/R-2.0.1/Xemacs-21.4.15-r3 on gentoo-linux.
When invoking R/ESS the following is induced by ESS
options(STERM='iESS', editor='gnuclient -q')
It appears as if the problem is with 'gnuclient -q'
(whatever does -q
Dear Qian,
You might try the S+Resample library, which has built-in support
for both sampling by subject and stratified sampling.
If you are a student, there is a free student version of S+.
See
www.insightful.com/downloads/libraries (S+Resample)
www.insightful.com/Hesterberg/bootstrap (has
I'm in the process of packaging R (and R modules) for future inclusion
in Fedora Extras, and I've managed to get several hundred modules
installed without issue, however, the GO metadata package is refusing to
comply.
Since I'm packaging this in rpm format, I can't use any of the automated
Also look at ?readline
Greg Snow, Ph.D.
Statistical Data Center
[EMAIL PROTECTED]
(801) 408-8111
Uwe Ligges [EMAIL PROTECTED] 03/29/05 11:43PM
Cuichang Zhao wrote:
Hello,
Could you please tell me how i can get an input from the user in R?
Depends on the kind of input.
See, e.g., ?scan or
Yes, you may need more memory unless you can somehow free a good amount of RAM
or find a more memory-efficient method for clustering. If I'm reading it
correctly, R wanted to allocate about 382 MB memory on top of what it had
already taken but your computer had only about 98 MB swap plus about
Hi Tom,
I'm cc'ing to Bioconductor as that is probably a better place for the
discussion.
Tom 'spot' Callaway [EMAIL PROTECTED] writes:
I'm in the process of packaging R (and R modules) for future inclusion
in Fedora Extras, and I've managed to get several hundred modules
installed without
Gerard Tromp [EMAIL PROTECTED] writes:
Greetings,
this is a follow-up to the mailing below. Seth Falcon replied and indicated
that he and several others were unable to replicate the problem.
Specifically he requested:
We are not able to reproduce this issue. If you reinstall
If you are on Windows and want to go GUI, see ?choose.files, ?winMenuAdd,
?winDialog, ?select.list
-- Bert Gunter
Genentech Non-Clinical Statistics
South San Francisco, CA
The business of the statistician is to catalyze the scientific learning
process. - George E. P. Box
-Original
Could anyone tell me what am I doing wrong?
pro-function(indep,dep){
+ d-data.frame(indep)
+ form-formula(lm(dep~.,data=d))
+
forward-step(lm(dep~X1,data=d),scope=form,trace=0,direction='f')
+ return(forward)
+ }
pro(m,q)
Error in inherits(x, data.frame) : Object d not
found
Where q is a
Dear Sir/Madam:
I have a question about computing adjusted mean using R. I am really new to
this area.
Suppose I have a response Y, and covariate: treat (binary), sex (binary) race
(catogorical ) and age (continuous).
the model: Y~treat+sex+race+age;
I am asked to compute the adjusted mean of
I'm using R 2.0 on Redhat Linux 9. When I try to produce PDF or PS
output, the files are corrupted -- they won't open in Acroread, xpdf,
ggv, and on attempting to convert to PNG, I get message This file has
corrupted %%EOF marker. Perhaps I am just doing something wrong. I
did:
pdf()
Dear Tim,
Thank you very much for your information. I will try to play with S+ as
you suggested. At the same time, I would like to share our idea with you
about the stratified bootstrapping for my scenario. I am not sure if it is
correct. I am playing with it now.
We created a new dataset
Ach -- such a simple mistake. Thank you for pointing out my error,
and I apologize for wasting your time.
Best wishes,
Hans
Peter Dalgaard [EMAIL PROTECTED] writes:
Hans Halvorson [EMAIL PROTECTED] writes:
I'm using R 2.0 on Redhat Linux 9. When I try to produce PDF or PS
output, the
Hi:
dev.off()
Check your file now...
That's it!
Hans Halvorson wrote:
I'm using R 2.0 on Redhat Linux 9. When I try to produce PDF or PS
output, the files are corrupted -- they won't open in Acroread, xpdf,
ggv, and on attempting to convert to PNG, I get message This file has
corrupted %%EOF
Dear Tim,
Thank you so much for your help. My random mixed model is as follows:
b.lme - lme(sbp ~ age + gender, data=bdat, random=~1/clinic/id,
na.action=na.omit)
When doing bootstrap with stratum clinic, a patient's data may appear
multiple times in the boostrap dataset and all of
Dear R experts,
Did someone implemented French Curve yet? Or can anyone point me some
papers that I can follow to implement it?
thanks in advance for your help.
Paul
__
R-help@stat.math.ethz.ch mailing list
Hi
Deepayan Sarkar wrote:
On Tuesday 29 March 2005 22:32, John Maindonald wrote:
Although base graphics does not mix with lattice in the one graph,
I've found that print.trellis(position=..., ) and the use of
par(fig=...)
to put regular and trellis graphics on the one graphics page works
like a
Hello Gerard, all,
The annotation packages breaking help.search was due to improperly
built annotation packages.
We have posted updated annotation packages to the Bioconductor meta
data repository.
Reinstalling the annotation data packages should resolve the issue and
allow help.search to
Your message doesn't help us very much. You haven't said what kind of
calculation it is you want to do, and that certainly matters. For
example, for some kinds of computations the solution you started below
would work fine:
M - matrix(1:16, 4, 4)
is.na(diag(M)) - TRUE
M
[,1] [,2] [,3]
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)
palette(rainbow(n))
barplot(1:25,col = 1:25)
palette(rgb((0:15)/15, g=0,b=0,
Hello,
I have used the functions agnes and cutree to cluster my data (4977
objects x 22 variables) into 8 clusters. I would like to refine the
solution using a k-means or similar algorithm, setting the initial
cluster centres as the group means from agnes. However my data matrix
has NA's in it
See upper.tri and lower.tri.
I think that you might also look for specific packages that function using
matrices, from what I have seen these often have the capacity to ignore the
diagonal or use just the upper or lower triangle. This is not an area that I
use very much, but I have seen
Does ?na.omit help
x - kmeans(na.omit(data),centres)
of course if you have too many NAs you need to be sure that their removal does
not unduly influence the results.
Although I am a bit confused as I thought that agnes did not allow NAs. I
assume that you are running an alternative clustering
I am sorry about that.
I like to do column mean, sd, var
as well as kmeans on the matrix
does this na.rm = TRUE work for such fuctions and only the diagonal is
ignored?
From: [EMAIL PROTECTED]
To: [EMAIL PROTECTED],r-help@stat.math.ethz.ch
Subject: RE: [R] NA's?
Date: Thu, 31 Mar 2005 11:42:05
i have not answered your query in the last mail.
I hoped na.omit(M) will just ingnore the diagonal elements. i learnt by
practice that it removes the whole row which has atleast one NA!! (that is
not the case in Perl)
Since I am bit new to R, i did not knew how to just ignore those elements in
x - c(5, 5, 8, 8, 8, 27)
table(x)
x
5 8 27
2 3 1
I want a way to use only 2, 3, 1, nomatter table or what other function used.
Thanks.
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the
Terry Mu wrote:
x - c(5, 5, 8, 8, 8, 27)
table(x)
x
5 8 27
2 3 1
I want a way to use only 2, 3, 1, nomatter table or what other function used.
as.vector() removes the attributes, if that is your question.
Uwe Ligges
Thanks.
__
Thank you.
mycols - c(brown,orange,tomato)
plot(x,col = mycols[cl$cluster])
this works. I can define distinct colours and check the graph.
the rest of the examples does not give a wide palette to choose from
Asha
From: Mulholland, Tom [EMAIL PROTECTED]
To: Asha Jayanthi [EMAIL
I'm not sure that I understand you comment about the other examples not giving
a wide palette. Are you using wide to refer to the difference in colours rather
than the number of choices in the palette? If this is your issue you should
look at the dichromat package that I referred to, in
is.na(diag(M)) - TRUE
cmeans - colMeans(M, na.rm = TRUE)
csd - apply(M, 2, sd, na.rm = TRUE)
cvar - csd ^2
(or
cvar - apply(M, 2, var, na.rm = TRUE)
)
Using 'kmeans' on a matrix but 'ignoring the diagonal entries' just
doesn't make sense as it stands, so I can't help you there.
V.
BertG == Berton Gunter [EMAIL PROTECTED]
on Wed, 30 Mar 2005 10:09:38 -0800 writes:
BertG If you are on Windows and want to go GUI, see
BertG ?choose.files, ?winMenuAdd, ?winDialog, ?select.list
with the big drawback that it will only work on Windows.
As Uwe says below, it depends
Unfortunately, I can't tell you how to solve this problem. However, I can
confirm that this crash happens also on my machines (R 2.0.1 on Debian Sarge,
AMD Athlon, 750 MHz, 256 MB RAM and R 2.0.0 on SuSE 9.0, Intel P4, 2.6 GHz,
512 MB RAM):
R aaa(1000)
alloc of 8 bytes failed
alloc of 4
Thanks for your reply.
On Wed, Mar 30, 2005 at 08:03:10AM -0600, Marc Schwartz wrote:
or even something like this:
plot(1:5, axes = FALSE)
axis(1, col.axis = white, col = red, tcl = 1)
axis(1, col.axis = white, col = white, tcl = 0)
axis(2, col.axis = white, col = red, tcl = 1)
Dear all,
I have a beginner's R question for coxph() and survfit().
I have a data set with survival time (no censoring) and treatment
indicator(0/1). I did something like
fit-coxph( Surv(t)~treat, method=breslow,data=data)
fit
Call:
coxph(formula = Surv(t) ~ treat, data = data, method =
Hi
Steven J. Murdoch wrote:
Thanks for your reply.
On Wed, Mar 30, 2005 at 08:03:10AM -0600, Marc Schwartz wrote:
or even something like this:
plot(1:5, axes = FALSE)
axis(1, col.axis = white, col = red, tcl = 1)
axis(1, col.axis = white, col = white, tcl = 0)
axis(2, col.axis = white, col = red,
I think you need to read the posting guide (see the bottom of each post made)
and once you have done this take some time to compose your message.
The issue is that I have too little information about what you have done. It
looks to me as if you are using postscript, but I am not sure if you
Thank you very much.
the code
plot(x, col = s)
points(cl$centers, col = s, pch = 8, cex=2)
does not plot the points according to the group colors. The plots are used
to identify the groups by colors
That could be done by
plot(x, col = cl$cluster)
This means that we need to set the default
I have a large matrix of data .
The size of the matrix ranges from 100 x 100 to 1000 x 1000
Now i have to do computations on that. And should not consider the diagonal
elements.
I tried setting diag(M) = NA and M = na.omit(M).
But this omits all the rows. I only want to omit that diagonal
Hi,
I am analyzing a data set with greater than 1000 independent cases
(collected in an unrestricted manner), where each case has 3 variables
associated with it: one, a factor variable with 0/1 levels (called XX),
another factor variable with 8 levels (X) and a third response variable
with two
Oops, I corrected some errors in the first paragraph; sorry for the
repeated posting.
Suresh
~~
Hi,
I am analyzing a data set with greater than 1000 independent cases
(collected in an unrestricted manner), where each case has 3
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