Marc == Marc Schwartz [EMAIL PROTECTED]
on Mon, 08 Nov 2004 22:27:47 -0600 writes:
Marc On Mon, 2004-11-08 at 21:56, Dr. John R. Vokey wrote:
Yes, I am a newbie at R, but it is not the complex
commands in R that have me baffled, but simple data
commands. For example, why
Hi users,
I am not sure to understand the help page about do.call.
--
do.call(what, args)
args: a _list_ of arguments to the function call. The 'names'
attribute of 'args' gives the argument names.
--
If we take the following sample data:
(tab=as.data.frame(table(factor(1:10
On Tue, 9 Nov 2004, Eric Lecoutre wrote:
I am not sure to understand the help page about do.call.
I think you do, just not how to construct a list.
--
do.call(what, args)
args: a _list_ of arguments to the function call. The 'names'
attribute of 'args' gives the argument
Hi Eric,
you could try it this way:
tab - as.data.frame(table(factor(1:10)))
do.call(paste, c(tab, list(sep=:)))
[1] 1:1 2:1 3:1 4:1 5:1 6:1 7:1 8:1 9:1
10:1
since `tab' is already a list
Best,
Dimitris
Dimitris Rizopoulos
Ph.D. Student
Biostatistical Centre
School of Public Health
Dear All,
I got these results from the example in the function dbeta:
x - seq(0, 1, length=21)
dbeta(x, 1, 1)
[1] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
Any Idea?
TIA
Giovanni
dr. Giovanni Parrinello
Section of Medical Statistics
Department of Biosciences
University of Brescia
25127
Hi Louize
On 8 Nov 2004 at 22:58, Louize Hill wrote:
Hello,
I have a large data frame and am aiming to create a summary data frame
in order to plot quarterly means by age. However, it seems as though I
am taking a very long winded approach to this - can anybody point me
in the direction
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Why strange? It is known that Beta(1, 1) = Uniform(0,1) whose density
is 1/(1-0)=1
Best,
Dimitris
Dimitris Rizopoulos
Ph.D. Student
Biostatistical Centre
School of Public Health
Catholic University of Leuven
Address: Kapucijnenvoer 35, Leuven, Belgium
Tel: +32/16/396887
Fax: +32/16/337015
On Tue, 9 Nov 2004 [EMAIL PROTECTED] wrote:
I got these results from the example in the function dbeta:
x - seq(0, 1, length=21)
dbeta(x, 1, 1)
[1] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
Any Idea?
What does help page say the density is?
A Beta(1,1) distribution is U(0, 1), and
On 09-Nov-04 [EMAIL PROTECTED] wrote:
Dear All,
I got these results from the example in the function dbeta:
x - seq(0, 1, length=21)
dbeta(x, 1, 1)
[1] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
Any Idea?
The density function for Beta(p,q) is (x^(p-1))*((1-x)^(q-1))/B(p,q).
In your
Hi, sorry for this lengthy post.
I am using R-2.0.0 on Unix, compiled.
Overview:
A) R CMD check: Unaccounted top-level text
B) In which sections of *.Rd is LaTeX notation allowed, where *not*?
C) Codoc mismatches and polyvalent parameters
D) Successful R CMD INSTALL and R CMD build
E) cp
Dear All,
I would like to ask clarifications on the gower distnce matrix calculated by
the function gdistin the library mvpart.
Here is a dummy example:
library(mvpart)
Loading required package: survival
Loading required package: splines
mvpart package loaded: extends rpart to include
Hello all R-user
I am relative new to the R-environment and also to GLMM, so please don't be
irritated if some questions don't make sense.
I am using R 2.0.0 on Windows 2000.
I investigated the occurrence of insects (count) in different parts of
different plants (plantid) and recorded as well
Dear useRs,
it's quite difficult for me to find `Error:'s in my R code, because R does
say about error itself, but say nothing about its location, say, string
number and file with an error (which may be `source'd from another file).
Are there any option for turning of the similar feature, or R
Hi,
Id like to know if it's possible to mail a file (image generated with R) in
attachments a similar to bug.report
Thanks in advance.
TEMANNI Ramzi
PhD Student
LimBio
http://www.limbio-paris13.org
UFR de Santé, Médecine et Biologie Humaine (SMBH)
Léonard de Vinci 74, rue Marcel Cachin
93017
Will R run under Windows Pocket PC?
Yours
Lars Strand
[[alternative HTML version deleted]]
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You are probably interested in traceback(). See ?traceback. Also, the
debugger is your friend. See ?debug.
Sean
On Nov 9, 2004, at 6:52 AM, Timur Elzhov wrote:
Dear useRs,
it's quite difficult for me to find `Error:'s in my R code, because R
does
say about error itself, but say nothing about
Sorry , I had to think a little bit more about..
But I think that the example is strange. generally an example ir related to a
quite
general condition, not to a special case..
Thanks
dr. Giovanni Parrinello
Section of Medical Statistics
Department of Biosciences
University of Brescia
25127
Hi,
Check R's manual R Language Definition.
Regards
EJ
On Tue, 2004-11-09 at 11:52, Timur Elzhov wrote:
Dear useRs,
it's quite difficult for me to find `Error:'s in my R code, because R does
say about error itself, but say nothing about its location, say, string
number and file with an
On Tue, 9 Nov 2004, Timur Elzhov wrote:
it's quite difficult for me to find `Error:'s in my R code, because R does
say about error itself, but say nothing about its location, say, string
number and file with an error (which may be `source'd from another file).
Are there any option for turning
On Tue, 9 Nov 2004, Lars Strand wrote:
Will R run under Windows Pocket PC?
We don't know!
There are no binary versions of R for that platform, but perhaps you could
find a suitable compiler and manage to build the sources.
Outside pure mathematics it is usually very hard to establish that
I've just starting using the prcomp function, and I want to be able to extract
individual principal components (e.g. PC1, PC2) in vector format. I haven't
been able to find any documentation that explains how to do this (or even if it
is possible). Any help on the subject would be greatly
It would work if you modified as follows:
plot(lm(Girth~Height))
Or alternatively,
fm1-lm(Girth~Height);plot(fm1)
Harold
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Dr. John R. Vokey
Sent: Monday, November 08, 2004 10:56 PM
To: [EMAIL PROTECTED]
Hi,
I make an analysis sequence on R. In some cases the function glm.nb fail to
ajust the model. Its Ok. The problem is that this error stop the program. I
need treat this error and not stop the program. Something like this:
...
model - glm.nb(y~x,maxit=1000)
if(glm.nb fail) {
teste[i] - 0
}
On Tue, 9 Nov 2004, Deirdre Toher wrote:
I've just starting using the prcomp function, and I want to be able to extract
individual principal components (e.g. PC1, PC2) in vector format. I haven't
been able to find any documentation that explains how to do this (or even if
it
is possible).
You need to be more specific when you say it works =) strptime()
returns a POSIXlt object whose printed representation appears to be a
string (but it is a list). What you want, I think, is either
as.POSIXct() or as.Date(). See ?DateTimeClasses.
-roger
João Mendes Moreira wrote:
Hello,
I
On Tue, 2004-11-09 at 12:59, Alessio Boattini wrote:
Dear All,
I would like to ask clarifications on the gower distnce matrix calculated by
the function gdistin the library mvpart.
Here is a dummy example:
library(mvpart)
Loading required package: survival
Loading required package:
Hi
I'm able to create multiple plots from a dataset using a for loop to
change variables, but when I try with stripchart it doesn't work.
Standard boxplot:
for(i in 2:14){boxplot(klk[,i]~Group,main=colnames(klk)[i])
Stripchart:
for(i in 2:14){stripchart(klk[,i]~Group,main=colnames(klk)[i])
On Mon, 8 Nov 2004, Mark White wrote:
Any idea what might be causing a compressed file read?
Prof Brian Ripley writes:
It's not a compressed file read, but rather from the interface for unz()
connections to zip files. That is very unlikely to be used on a
non-Windows system, so if
On Tue, 2004-11-09 at 02:07, Martin Maechler wrote:
SNIP
Further note that many of us try to avoid attach()ing data frames
(most of the time; not always) and we have provided the nice alternative
with( data , expression_body )
So, for the current example, you could also say
To Danardonos concern of splitting time for records with delayed entry:
This can fairly easily be accomodated, by simply splitting time in small
intervals of time since entry into the study, and then compute the value
of the other timescales for each of these e.g.:
current.age - time.from.entry
How can I specify the repositories for upgrade()?
x - packageStatus(repositories =
http://cran.us.r-project.org//bin/windows/contrib/2.0;)
upgrade(x, ask = FALSE)
Error in update[, 3] : incorrect number of dimensions
x, the object of class packageStatus, prints and summarizes fine. I also
ran
On Tue, 9 Nov 2004, BXC (Bendix Carstensen) wrote:
To Danardonos concern of splitting time for records with delayed entry:
There was actually no intention of supporting counting-process input, but
it turns out to be a one-line change: from
starttime - c(starttime, rep(cut, each = n))
to
Jan Hattendorf wrote:
Hello all R-user
I am relative new to the R-environment and also to GLMM, so please don't be
irritated if some questions don't make sense.
I am using R 2.0.0 on Windows 2000.
I investigated the occurrence of insects (count) in different parts of
different plants (plantid)
Ooops. Make that subject line 'upgrade', not 'update!' Sorry. -AB
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] Behalf Of Andy Bunn
Sent: Tuesday, November 09, 2004 9:23 AM
To: R-Help
Subject: [R] Error in update() when repositories is specified.
How can I
On Tue, 9 Nov 2004, F Z wrote:
Hi,
I have a data.frame with several variables and 50,000 observations.
i.e.
data[1:2,1:7]
Iteration Day Production.Type tsUSusc tsASusc tsULat tsALat
1 0 Generic 17965 8833053 0 0
1 1 Generic 17965 8833053 0
Prof Brian Ripley [EMAIL PROTECTED] writes:
On Tue, 9 Nov 2004, Lars Strand wrote:
Will R run under Windows Pocket PC?
We don't know!
There are no binary versions of R for that platform, but perhaps you could
find a suitable compiler and manage to build the sources.
The PDA idea is
Hi all,
there is environment-list coercion, i.e. as.list.environment.
Is there any list-environment coercion?
thank you.
--
Valery.
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On 9 Nov 2004, at 12:27 pm, Prof Brian Ripley wrote:
On Tue, 9 Nov 2004, Lars Strand wrote:
Will R run under Windows Pocket PC?
We don't know!
There are no binary versions of R for that platform, but perhaps you
could
find a suitable compiler and manage to build the sources.
Outside pure
Em Tuesday 09 November 2004 12:12, Vito Muggeo escreveu:
if(class(model)==try-error)
Thanks
it works fine :)
Ronaldo
--
O importante não é ganhar. O que importa é competir
sem perder nem empatar.
--
| // | \\ [***]
| ( õ õ ) [Ronaldo Reis Júnior
Is there any way I can increase memory size for R under Unix? I tried
Memory function, which was not working.
Thanks,
Hua Li
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Hi there,
I have a question on the frailty model for gap times with distinct baseline
hazard for each gap. Can I use R coxph function to do it? For example, the
following code assumes an identical baseline hazard for every gap time, but
what if I want a distinct baseline hazard for each gap?
Hi Valery,
a simple way to do it might be the following:
lis - list(a=10, b=20, d=x)
e1 - new.env()
for(i in 1:length(lis)) assign(names(lis)[i], lis[[i]], envir=e1)
d
get(d, env=e1)
I hope it helps.
Best,
Dimitris
Dimitris Rizopoulos
Ph.D. Student
Biostatistical Centre
School of Public
On Tue, 9 Nov 2004, Tim Cutts wrote:
On 9 Nov 2004, at 12:27 pm, Prof Brian Ripley wrote:
On Tue, 9 Nov 2004, Lars Strand wrote:
Will R run under Windows Pocket PC?
We don't know!
There are no binary versions of R for that platform, but perhaps you
could
find a suitable
Peter Dalgaard [EMAIL PROTECTED] writes:
Prof Brian Ripley [EMAIL PROTECTED] writes:
On Tue, 9 Nov 2004, Lars Strand wrote:
Will R run under Windows Pocket PC?
We don't know!
There are no binary versions of R for that platform, but perhaps you could
find a suitable
On Tue, 9 Nov 2004, Hua Li wrote:
Is there any way I can increase memory size for R under Unix? I tried Memory
function, which was not working.
Possibly because there is no Memory function.
The standard configuration of R under Unix uses all the memory the
operating system will give it. If
I don't think that has ever been tested under Windows: until recently
packageStatus did not work under Windows at all.
The problem seems to be in ask=FALSE, which looks completely broken.
ask=TRUE seems to work. This was true of Unix, 1.9.1 as well so I guess
no one ever uses it
On Tue, 9
On Monday 08 November 2004 19:56, Dr. John R. Vokey wrote:
Yes, I am a newbie at R, but it is not the complex commands in R that
have me baffled, but simple data commands. For example, why does
something like:
plot(Girth ~ Height)
*not* work after a command that allegedly loads the data:
Tim Cutts [EMAIL PROTECTED] writes:
Technically, I don't suppose there's much to stop R running on some
PDAs, especially those based on Linux like the Sharp Zaurus, other
than storage and memory requirements. If there's a Qt graphical
interface available for R, you could even get graphics
Greetings:
In a function I'm trying to write I am multiplying each row in a matrix by a
vector. When the vector extends beyond the end of the matrix I need to have
the multiplication wrap around (continue with column 1 of the matrix).
Initially I got this to work with a loop (old programming
Prof Brian Ripley [EMAIL PROTECTED] writes:
The Windows API on Pocket PC is quite a reduced subset
compared to full Windows, so you might have problems with that.
But that was. However, as I said, you would have to find a suitable
compiler or cross-compiler, that supports enough
David Whiting david.whiting at ncl.ac.uk writes:
: It is interesting this has come up at this time. Two days ago I
: installed Linux on a Psion 5MX (16Mb RAM) and am tickled pink by
: it. Installation is easy. At the moment I only have a small
: compactflash disk so I have not been able to
The RPM for Fedora Core 2 seems to work just fine on Core 3.
(The graphics window got smaller, but I'm sure there is a setting
for that.)
Jon
--
Jonathan Baron, Professor of Psychology, University of Pennsylvania
Home page: http://www.sas.upenn.edu/~baron
R search page:
On 9 Nov 2004, at 19:44, Jonathan Baron wrote:
The RPM for Fedora Core 2 seems to work just fine on Core 3.
(The graphics window got smaller, but I'm sure there is a setting
for that.)
That would be good news. I really don't know how the graphics window
became so big at some stage. (MacOS X is
On 11/09/04 20:37, Jari Oksanen wrote:
On 9 Nov 2004, at 19:44, Jonathan Baron wrote:
The RPM for Fedora Core 2 seems to work just fine on Core 3.
(The graphics window got smaller, but I'm sure there is a setting
for that.)
That would be good news. I really don't know how the graphics
Many thanks to Gabor Grothendieck, Thomas Lumley and James Holtman for their
useful answers on this thread. The three solutions worked for the problem.
Here is a sumary of their responses (modified for consistency on notations):
F Z gerifalte28 at hotmail.com writes:
: Hi,
:
: I have a
Shalom.
I have some problems in the BsProb procedure.
I construct a full orthogonal factorial experimental design of 26 when the
response is from random sampling from normal distribution with expectancy
that depends on factor A (equal 2 when A=-1 and equal 0.5 when A=1).
On primary analysis using
Gabor Grothendieck [EMAIL PROTECTED] writes:
David Whiting david.whiting at ncl.ac.uk writes:
: It is interesting this has come up at this time. Two days ago I
: installed Linux on a Psion 5MX (16Mb RAM) and am tickled pink by
: it. Installation is easy. At the moment I only have a small
Hi,
Would like to use to the hexbin package to plot a 2D hist - because it looks
really _cool_.
My problem is related to drawing a pdf hexbin graphic in series of other
graphics.
All other figures have a par(mar=c(3.2,3.2,1,1)). So the gplot.hexbin figure in
this series looks a little
You might want to check out the debug package on CRAN:
debug: MVB's debugger for R
Debugger for R functions, with code display, graceful error recovery,
line-numbered conditional breakpoints, access to exit code, flow
control, and full keyboard input.
Version:1.0.1
Depends:R (=
How can I set the plot range for a boxplot using the boxplot() function?
For example, the values in the boxplot go from -3 to 3 (outliers plotted),
but I'd like the y axis to go from -5 to 5.
Thanks much
Scott dot Rifkin at yale dot edu
__
[EMAIL
From: Scott Rifkin
How can I set the plot range for a boxplot using the
boxplot() function?
For example, the values in the boxplot go from -3 to 3
(outliers plotted),
but I'd like the y axis to go from -5 to 5.
as in:
boxplot(rnorm(30), ylim=c(-5, 5))
?
Andy
Thanks much
Scott
How about using ylim?
foo - rnorm(100, 0, 1)
boxplot(foo, ylim = c(-5, 5))
HTH, Andy
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] Behalf Of Scott Rifkin
Sent: Tuesday, November 09, 2004 2:43 PM
To: [EMAIL PROTECTED]
Subject: [R] Boxplot plot range
How
Needed to redefine function sum for my MATLAB package.
There's something similar in Chambers's Green Book (pg 351)
so I modified it as such:
library(methods)
setGeneric(sum, function(x, ..., na.rm = FALSE) {
if (nDotArgs(...) 0)
sum(c(sum(x, na.rm = na.rm),
sum(...,
I'm seeing various things fail when I try to next braces inside \eqn.
This source
\eqn{{\bf\beta}_j}{b(j)} is the vector
produces this error
--
[4]
! Missing $ inserted.
inserted text
$
l.258 \eqn{{\bf\beta}_j}{\bf\beta}_
Is there any way besides looping to remove complete rows from a matrix
or data frame where there is at least one NA in any of the columns?
For example
a
[,1] [,2]
[1,] 02.6875
[2,] 8.37 6.625
[3,] 15.6 4.375
[4,] 23.4 6.25
[5,] 29 5.09375
[6,] 18
How about the following:
(A - array(c(1, NA, 3, NA, 4, 5), dim=c(3,2)))
[,1] [,2]
[1,]1 NA
[2,] NA4
[3,]35
A[apply(A, 1, function(x)!any(is.na(x))), , drop=F]
[,1] [,2]
[1,]35
hope this helps. spencer graves
William Briggs wrote:
Is there any way
Something is not as it seems:
a - matrix(scan(),,2,byrow=T)
1: 02.6875
3: 8.37 6.625
5: 15.6 4.375
7: 23.4 6.25
9: 29 5.09375
11: 18 NA
13: 04.15625
15: 9.37 6.25
17: 14.7 5.875
19: 31.26667 6.15625
21: NA 2.357
23: NA
?na.omit
as in A-na.omit(A)
-- 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 Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On
You might be interested in complete.cases(), as in:
use - complete.cases(a)
a[use, ]
-roger
William Briggs wrote:
Is there any way besides looping to remove complete rows from a matrix
or data frame where there is at least one NA in any of the columns?
For example
a
[,1] [,2]
[1,]
Hello,
I would like to know if there is a function in R that will test for
normality and handle censored data sets. Currently, I evaluate each
censored data set by the extent to which a normal scores plot
approximate a straight line. For complete data sets I use
shapiro.test().
Below is an
I don't know much about censored data, but what you described doesn't sound
like censored data, but rather truncated data.
I think normality tests are over-(ab)used, and would suggest inspection of
normal QQ plots instead (as you already do). For formal tests, you might be
able to cook up
I stand corrected! Hope Bert doesn't mind me CC'ing the list.
Andy
From: Berton Gunter
No Andy, they're (left) censored alright: their values are
known to be below
2.4, but not how far below. Truncated data arise when
observations are
actually observed only when they take on values in
On Tue, 9 Nov 2004, Lei Liu wrote:
Hi there,
I have a question on the frailty model for gap times with distinct baseline
hazard for each gap. Can I use R coxph function to do it? For example, the
following code assumes an identical baseline hazard for every gap time, but
what if I want a
Hi,
I wrote a function that worked well in R, but not in
S-Plus, can anyone suggest a solution?
f.coxph.zph-function(x)
{
cox.fit - coxph(Surv(time.cox, status.cox) ~ x,
na.action = na.exclude, method = breslow)
fit.zph-cox.zph(cox.fit,transform='log')
fit.zph$table[,3]
Hi all: Are thare anyones that use vsn?Some questions need your help.Thanks a
lot 1.If e1(raw data) contain 2419 genes, after e2-vsn(e1),e2 contains 2419*2
genes. Why does it happen?
2.How the ¡°calibrated and glog-transformation¡± is perform. In other words,
what¡¯s the calculation method
The following works, you need to include x=TRUE in the call to coxph.
Passing the time and status variables as additional arguments is a matter of
personal preference.
f.coxph.zph-function(x, timeVar, statusVar)
{
cox.fit - coxph(Surv(timeVar, statusVar) ~ x, na.action =
na.exclude,
Greetings R community,
I am curious about the following behaviour: if I define a factor, and
then store a subset of it in a list, the stored version seems to drop
levels that were not included in the subset. E.g. ..
mask - c(T, F)
grp.1 - factor(c(1,2))
list(grp.1)
[[1]]
[1] 1 2
Levels: 1 2
I don't get the same result, do you have a package loaded that would change
the default behavior (such as Hmisc)?
list(grp.1)
[[1]]
[1] 1 2
Levels: 1 2
list(grp.1[mask])
[[1]]
[1] 1
Levels: 1 2
library(Hmisc)
snip
list(grp.1[mask])
[[1]]
[1] 1
Levels: 1
--Matt
version
_
Andrew Robinson wrote:
Greetings R community,
I am curious about the following behaviour: if I define a factor, and
then store a subset of it in a list, the stored version seems to drop
levels that were not included in the subset. E.g. ..
mask - c(T, F)
grp.1 - factor(c(1,2))
list(grp.1)
[[1]]
Matt,
very astute - thanks. I did indeed have Hmisc loaded.
Andrew
On Tue, Nov 09, 2004 at 08:12:57PM -0800, Austin, Matt wrote:
I don't get the same result, do you have a package loaded that would change
the default behavior (such as Hmisc)?
list(grp.1)
[[1]]
[1] 1 2
Levels: 1 2
Hallo
I can not reproduce your result with artificial data (R2.0.0). Error
says that some of your data have infinite values somewhere. Try to
figure out in which cycle it gives this error and inspect your data
from this cycle. I suppose you have all of them missing, but I
wonder why boxplot
One concern I recall from looking into this a while back (hopefully
not founded) was the issue with floating point handling on the ARMs
and similar PDA CPUs.
This was relevant to the familiar/intimate linux distro's around 18-24
months ago, when I was considering an IPAQ or Zaurus to replace my
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