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++
sessionInfo()
R version 2.4.0 Patched (2006-10-29 r39744)
i686-pc-linux-gnu
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application!
Göran
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problems, R or latex. How can I get rid of it?
This is on linux (ubuntu), with R-2.4.0.
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On 10/7/06, Gregor Gorjanc [EMAIL PROTECTED] wrote:
Göran Broström goran.brostrom at gmail.com writes:
When I am using Sweave to produce reports I get a strange Warning from
latex:
LaTeX Warning: You have requested package
`/usr/local/lib/R/share/texmf/Sweave
On 8/21/06, Martin Maechler [EMAIL PROTECTED] wrote:
Hi Göran,
GB == Göran Broström [EMAIL PROTECTED]
on Mon, 21 Aug 2006 11:12:49 +0200 writes:
GB A new version, 0.65-1, of glmmML is now on CRAN. It is a major rewrite
GB of the inner structures, so frequent updates (bug fixes
A new version, 0.65-1, of glmmML is now on CRAN. It is a major rewrite
of the inner structures, so frequent updates (bug fixes) may be
expected for some time.
News:
* The Laplace and adaptive Gauss-Hermite approximations to the log
likelihood function are fully implemented. The Laplace method is
On 7/21/06, Thomas Lumley [EMAIL PROTECTED] wrote:
On Fri, 21 Jul 2006, Valentin Dimitrov wrote:
Dear Leaf,
I modified your code as follows:
gamma.fun - function(mu,sd,start=100)
{
f.fn - function(alpha)
On 7/15/06, Douglas Bates [EMAIL PROTECTED] wrote:
Hi Spencer,
[]
rant
Some software, notably SAS PROC MIXED, does produce standard errors
for the estimates of variances and covariances of random effects. In
my opinion this is more harmful than helpful. The only use I can
imagine for
the 'conditional'
approach.
As usual, comments, and error and bug reports are welcome.
Göran
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Göran
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intercepts for binomial and poisson models, (ii) the
p-value is calculated thru bootstrapping (can be slow with large data sets).
Göran
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On 6/19/06, Rick Bilonick [EMAIL PROTECTED] wrote:
On Sun, 2006-06-18 at 13:58 +0200, Douglas Bates wrote:
If I understand correctly Rick it trying to fit a model with random
effects on a binary response when there are either 1 or 2 observations
per group.
If you look at Rick's examples,
- factor(x)
x
[1] 1 2 b
Levels: 1 2 b
?
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I am trying to write a lesson on maximum likelihood with Sweave. I get
a surprising result with the following code, lec4.Snw:
\documentclass[a4paper,12pt]{article}
\usepackage[latin1]{inputenc}
\title{Maximum likelihood}
\author{Göran Broström}
\begin{document}
\maketitle
fig=TRUE
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such instance.
)
But it doesn't work with R code (with C code it works). So what is missing?
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to an event
indicator, what relation do you mean it has to 'interval censor data'?
You have to give more detail and be more precise in order to get a
valuable answer.
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On Mon, Sep 26, 2005 at 07:05:33PM +0200, Göran Broström wrote:
On Mon, Sep 26, 2005 at 09:27:56AM +0200, Martin Maechler wrote:
I'm crossposting to the ESS-help mailing list which is slightly
more appropriate here. [This may be a rare case where
crossposting seems to make much sense
On Mon, Sep 26, 2005 at 09:27:56AM +0200, Martin Maechler wrote:
I'm crossposting to the ESS-help mailing list which is slightly
more appropriate here. [This may be a rare case where
crossposting seems to make much sense.]
PD == Peter Dalgaard [EMAIL PROTECTED]
on 25 Sep 2005
On Mon, Sep 05, 2005 at 06:55:26PM -0400, Duncan Murdoch wrote:
Göran Broström wrote:
I'm looking for a Windows distribution of TeX that works with R, after a
few years' absence from Windows. On Duncan Murdoch's Rtools page fptex is
still recommended, but it turns out that fptex is defunct
is suggested? TUG (tug.org) recommends something called proTeXt,
which is said to be based on MiKTeX, for Windows users. Since MikTeX
could be used with R, that sounds like a good alternative.
Any comments to that?
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On Tue, Sep 06, 2005 at 12:07:21AM +1000, Ko-Kang Kevin Wang wrote:
Slightly off topic, if you want to get MikTeX working with Emacs and
ESS, the Claus Dethlefsen has a wonderful web site (in fact, best
website on this topic IMHO) http://www.math.auc.dk/~dethlef/Tips/
Thanks for that tips,
On Mon, Sep 05, 2005 at 01:55:39PM -0400, Peter Flom wrote:
Goran wrote
The consensus (so far) seems to be to stick to MikTeX and skip proTeXt.
Thanks for all the input.
Well, nothing against MikTeX, but ProteXt also works fine with R.
I have made some studying; it seems as if proTeXt
On Fri, Aug 19, 2005 at 01:35:45PM +0200, Peter Dalgaard wrote:
Göran Broström [EMAIL PROTECTED] writes:
I have a problem with some functions handling dates, in packages 'date' and
'survival' (they seem to be identical). For instance, from the
documentation
8330 CALL ZAXPY( N-I, ALPHA, A( I+1, I ), 1, TAU( I ), 1 )
Current language: auto; currently fortran
---
[...]
Göran
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On Tue, Aug 02, 2005 at 09:33:45AM +0100, Prof Brian Ripley wrote:
On Tue, 2 Aug 2005, Göran Broström wrote:
[...]
Incidentally, I have just tried building R on a Fujitsu Amilo amd64 with
debian-amd64 (unstable) and ATLAS. Both 'make' and 'make check' worked
without complaints with gcc-3.4.5
On Tue, Aug 02, 2005 at 10:58:31AM +0100, Prof Brian Ripley wrote:
The problems we are seeing with gcc4 are mainly (but not
entirely) with gfortran: it seems not quite ready for production use.
-4.0.1 is already a considerable improvement over -4.0.0.
There is another project (www.g95.org)
On Thu, Jul 07, 2005 at 11:18:09AM +0100, Ted Harding wrote:
My first reaction to Duncan's example was Touché -- with apologies
to Göran for suspecting on over-trivial example!
No need to apologize; that was of course my first reaction to Thomas'
statement.
I had not thought
long enough
On Wed, Jul 06, 2005 at 10:06:45AM -0700, Thomas Lumley wrote:
(...)
If X, Y, and Z are
independent and Z takes on more than one value then X/Z and Y/Z can't be
independent.
Not really true. I can produce a counterexample on request (admittedly
quite trivial though).
Göran Broström
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elementary.
I have a vague memory saying that such books exist, but I cannot find any
for the moment. Any suggestions are welcome.
Thanks,
Göran
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. (I really have no idea of what is going on!)
This is
R : Version 2.1.0 Under development (unstable) (2005-01-19)
on Debian.
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this is
common knowledge.
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On Wed, Jan 26, 2005 at 11:01:03AM +0100, Peter Dalgaard wrote:
Göran Broström [EMAIL PROTECTED] writes:
Try it with
b=c(rep(0,8),rmultinom(1,24,rep(1/8,8)))
This is the conditional distribution, given the sufficient statistic.
Yes (and that was of course the point). I
On Wed, Jan 26, 2005 at 02:03:25PM +0100, Peter Dalgaard wrote:
Göran Broström [EMAIL PROTECTED] writes:
On Wed, Jan 26, 2005 at 11:01:03AM +0100, Peter Dalgaard wrote:
Göran Broström [EMAIL PROTECTED] writes:
Try it with
b=c(rep(0,8),rmultinom(1,24,rep(1/8,8
(although it has one, at
least in R-2.1.0, 2005-01-19). Another aspect is that this code relies on
m.id being numeric; I would have to change it if the type of m.id changes
to, eg, character.
So, question: Is there a better way of doing this?
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ratio test gives a p-value of 8.017e-09, while the Wald p-value is 1 !
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On Tue, Jan 25, 2005 at 10:43:24AM -0500, Liaw, Andy wrote:
From: Göran Broström
I have a data frame containing children, with variables 'year' = birth
year, and 'm.id' = mother's id number. Let's assume that all
the births of
each mother is represented in the data frame.
Now I
the likelood
of the model under
HA: location parameters are not equal (i.e. each stress level has its
slope and intercept).
How can I do this?
Stratify on stress level.
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using coxph(non
parametric model) and survreg(parametric model) ?
One way of avoiding this problem is to fit the Weibull model with 'weibreg'
in the package eha.
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to the uniform distribution thru
F(X) = U ~ uniform(0, 1),
where X is Pareto with cdf F. Solve for X and you have just reinvented the
inverse method of generating random numbers from a cdf F.
Remigijus made that explicit for you.
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for that
value. I don't mind which of the rows now..)
something like this, however, this gives me the complete df.
df[df$colname %in% unique(df$colname),]
or this, which doesnt work
df[df$colname == unique(df$colname),]
Use 'duplicated':
df[!duplicated(df$colname), ]
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that I got what I
should have.
Thanks,
Göran
And, I'm using R-2.0.1 on Debian testing (from source).
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can't have a mix of integer and
non-integer elements. With a list it's a different story.
Göran
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{equation*}
3. Join a latex mailing list?
Göran
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On Mon, Oct 18, 2004 at 12:57:09PM -0700, Thomas Lumley wrote:
On Mon, 18 Oct 2004, Göran Broström wrote:
On Mon, Oct 18, 2004 at 08:48:40AM -0700, Thomas Lumley wrote:
However, all the distributions in survreg are
location-scale families,
But only after a time
.)
Göran
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will that work?
?factor
?as.factor
Thanks
Neil
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] is a data frame of length 4; iris[, 5] is a vector of length 150.
You probably need to loop over the four first columns and apply tapply(!)
four times, but I'm sure there is a smarter way. Others will tell you.
Göran
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Warning message:
NAs introduced by coercion
What am I doing wrong? This is R-1.9.1, Linux (debian installation)
Another question: I have a factor with four levels, which I want
to collapse to two. How do I do it in the simplest possible way?
Thanks,
Göran
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On Wed, Aug 18, 2004 at 09:30:50AM +0100, Prof Brian Ripley wrote:
On Wed, 18 Aug 2004, Göran Broström wrote:
I'm trying a recommendation on the help page for 'factor':
x - c(1, 2, 1, 2)
x - factor(x, labels = c(one, two))
x
[1] one two one two
Levels: one two
as.numeric
be Poisson regression with riskset size as an offset.
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effect 'sd' in the two lme4
runs! Note further how close to each other the corresponding estimates for
the second run of lme4 and of glmmML are.
[...]
Göran
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in
general?
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is going on there. I use only standard linpack routines
(found in R) for solving linear equations, and matrix inversion at the
end. I think 'coxph' has its own optimizing routines.
Peter D. explained why scaling can be a problem.
Göran
[...]
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, though. Efron's method is quite
robust. (You might check if there are any differences with 'breslow')
Best,
Göran
[...]
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this helps,
Henric
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On Wed, Apr 28, 2004 at 11:18:38AM +0200, Göran Broström wrote:
On Wed, Apr 28, 2004 at 11:46:51AM +0300, Renaud Lancelot wrote:
Martin Maechler a écrit :
kjetil == kjetil [EMAIL PROTECTED]
on Tue, 27 Apr 2004 19:19:59 -0400 writes:
kjetil On 27 Apr 2004 at 16:46, Raubertas
On Wed, Apr 28, 2004 at 12:59:54PM +0200, Göran Broström wrote:
On Wed, Apr 28, 2004 at 11:18:38AM +0200, Göran Broström wrote:
On Wed, Apr 28, 2004 at 11:46:51AM +0300, Renaud Lancelot wrote:
Martin Maechler a écrit :
kjetil == kjetil [EMAIL PROTECTED]
on Tue, 27 Apr 2004 19:19:59
)
Delete downloaded files (y/N)? y
warnings()
NULL
---
Where did the warnings go? (R-1.9.0, Debian testing/unstable)
Göran
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:-(
[...]
The Design package by default computes inter-quartile-range effects.
[...]
Interesting idea... is this a common procedure in biostatistics?
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/contrib/1.7/PACKAGES'
^^^
[...]
Try upgrading to R 1.9.0 first (it seems as if 'mvtnorm' is missing in 1.7)
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)
}
A word of warning: Not well tested; I only noticed that the censoring
fraction seemed to be correct in some experiments.
Göran
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(ESS 5.1.24), my '_' are changed to ' - '!
What can I do? Upgrade to a beta version of ESS? (I want to continue
using ESS!)
Göran
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for Matlab?
I think there was a group at U.of Apraphulia working on it.
Peter, I think it was Aprilfoolia.
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On Wed, Jan 14, 2004 at 10:45:56PM +0100, Göran Broström wrote:
On Wed, Jan 14, 2004 at 09:10:51PM +0100, Fredrik Lundgren wrote:
Dear R experts,
How should lambda and gamma (with std.errors) be calculated for a weibull model
with age as an independent predictor? I have assumed
of Wisconsin - Madisonhttp://www.stat.wisc.edu/~bates/
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changed to conform with R-1.8.0 (and later).
-
As usual, comments and bug reports are welcome!
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it out)
You can also use 'plot.Surv' in package 'eha' (for plotting).
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'formatC':
formatC(p)
[1] 0.0001
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and tried this advice, but got rsync not found.
I searched CRAN, and found links to 'rsync.r-project.org' and
'www.rsync.org', none of which worked. Where and how do I get 'rsync'?
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On Wed, Dec 31, 2003 at 11:02:36AM +0100, Göran Broström wrote:
On Wed, Dec 31, 2003 at 07:40:23AM +, Prof Brian Ripley wrote:
[...]
lda is still in Venables and Ripley's MASS. Perhaps you forgot to rsync
up the recommended packages? (Run tools/rsync-recommended in the
top level
4.5e-5).
What is the 'right' way of doing this in R?
--
Göran Broströmtel: +46 90 786 5223
Department of Statistics fax: +46 90 786 6614
Umeå University http://www.stat.umu.se/egna/gb/
SE-90187 Umeå, Sweden e-mail: [EMAIL PROTECTED
On Thu, Dec 18, 2003 at 12:04:31PM +0100, Peter Dalgaard wrote:
Göran Broström [EMAIL PROTECTED] writes:
Dear R-helpers,
In a data set I got from a medical doctor there are six treatment groups
and (about) 5 bivariate responses in each group. Using 'manova', it is
easy to see
:length(x))
0.5 0.8
and
identical(1:4, c(1:4))
[1] TRUE
Should I report this as a bug?
Göran
--
Göran Broströmtel: +46 90 786 5223
Department of Statistics fax: +46 90 786 6614
Umeå University http://www.stat.umu.se/egna
On 0, Uwe Ligges [EMAIL PROTECTED] wrote:
Göran Broström wrote:
I recently ran into the following:
x - c(1,2,4,3)
lm(x ~ 1:length(x))
Error in model.frame(formula, rownames, variables, varnames, extras,
extranames, : variable lengths differ
but
lm(x ~ c(1:length(x
3
[5,]123
G.
Thanks,
David
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--
---
Göran Broströmtel: +46 90 786 5223
Department of Statistics fax: +46 90
Seems to work. What is happening?
Göran
---
Göran Broströmtel: +46 90 786 5223
Department of Statistics fax: +46 90 786 6614
Umeå University http://www.stat.umu.se/egna/gb/
SE-90187
On Wed, 18 Jun 2003, Dowkiw, Arnaud wrote:
How do you install a package from CRAN ? I want to install pls.pcr, so I have
downloaded pls.pcr_0.1.1.tar.gz but when I try to install it using the install
package(s) from local zip file(s) option it says :
.
Göran
---
Göran Broströmtel: +46 90 786 5223
Department of Statistics fax: +46 90 786 6614
Umeå University http://www.stat.umu.se/egna/gb/
SE-90187 Umeå, Sweden e-mail: [EMAIL PROTECTED
On Mon, 9 Jun 2003, Prof Brian Ripley wrote:
On Sun, 8 Jun 2003, Göran Broström wrote:
On Sun, 8 Jun 2003, Thomas Lumley wrote:
On Sat, 7 Jun 2003, [ISO-8859-1] Göran Broström wrote:
I need to order a long vector of integers with rather few unique values.
This is very
On Sat, 7 Jun 2003, Göran Broström wrote:
I need to order a long vector of integers with rather few unique values.
This is very slow:
x - sample(rep(c(1:10), 5))
system.time(ord - order(x))
[1] 189.18 0.09 190.48 0.00 0.00
But with no ties
y - sample(50
On Sun, 8 Jun 2003, Thomas Lumley wrote:
On Sat, 7 Jun 2003, [ISO-8859-1] Göran Broström wrote:
I need to order a long vector of integers with rather few unique values.
This is very slow:
I think the culprit is
src/main/sort.c: orderVector1
/* Shell sort isn't stable
or with 1.7.0? I have seen the reports on failures
with bundles, but 'eha' is not a bundle.
Thanks,
Göran
---
Göran Broströmtel: +46 90 786 5223
Department of Statistics fax: +46 90 786 6614
Umeå University http://www.stat.umu.se/egna/gb/
SE-90187
On Thu, 29 May 2003, John Fox wrote:
Dear Goran,
I've noticed this problem with recent versions of R when I've zipped an R
package for Windows using a zip utility different from the recommended
Info-Zip. If you build the package under Windows with the --binary switch,
then a usable zip
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