The lme4 package is still in development. I can't guarantee the
evaluation of the deviance for the quasipoisson family. There is a
certain amount of mystery about the role of the dispersion parameter
and the null deviance in families like quasipoisson and quasibinomial.
For the time being don't
On Mon, Feb 25, 2008 at 1:46 PM, Peter Dalgaard
[EMAIL PROTECTED] wrote:
Ben Bolker wrote:
stian at mail.rockefeller.edu stian at mail.rockefeller.edu writes:
Hi,I am wondering how to conduct Kenward-Roger correction in
the linear mixed model using R. Any idea?
Thanks a lot,
On Thu, Feb 28, 2008 at 7:52 AM, Nauta, A.L. [EMAIL PROTECTED] wrote:
Hi,
I have an unbalanced dataset on which I would like to perform a one-way
anova test using R (aov). According to Wannacott and Wannacott (1990) p. 333,
one-way anova with unbalanced data is possible with a few
.
If in doubt about which sum of squares to use, the general rule is
that you should only pay attention to the F ratio and p-value for the
last term in the model.
From: [EMAIL PROTECTED] on behalf of Douglas Bates
Sent: Fri 29-2-2008 0:39
To: Nauta, A.L.
Cc: r-help@r
.
From: [EMAIL PROTECTED] on behalf of Douglas Bates
Sent: Fri 29-2-2008 15:38
To: Nauta, A.L.
Cc: R Help
Subject: Re: [R] unbalanced one-way ANOVA
On Fri, Feb 29, 2008 at 4:47 AM, Nauta, A.L. [EMAIL PROTECTED]
wrote:
Thank you for your reply,
is your answer (that the approach
On Mon, Mar 3, 2008 at 8:25 AM, Duncan Murdoch [EMAIL PROTECTED] wrote:
On 3/3/2008 9:10 AM, Rogers, James A [PGRD Groton] wrote:
As someone of partly French heritage, I would also ask how this
distribution came to be called Gaussian. It seems very unfair to de
Moivre, who discovered the
On Mon, Mar 3, 2008 at 9:57 AM, Charilaos Skiadas [EMAIL PROTECTED] wrote:
Nothing's wrong. It just means that the package or one of its
dependencies, has its own xtabs function, which hides the default
xtabs function, since it comes first in the search path. So when you
next write
On Tue, Mar 4, 2008 at 10:35 AM, Erika Frigo [EMAIL PROTECTED] wrote:
Good evening to everybody,
I have problems to import in R a really big dataset (more than 100
values). Which is the best package to install?
Is there someone who works with this kind of dataset and can help me,
On Tue, Mar 4, 2008 at 10:52 AM, John Sorkin
[EMAIL PROTECTED] wrote:
R 2.6.0
Windows XP
At the risk of raising the ire of the R gods . . .
I am looking for a package that will allow me to perform a poisson,
quasipoisson, or negative binomial regression with adjustment for repeated
On Wed, Mar 5, 2008 at 7:43 AM, Duncan Murdoch [EMAIL PROTECTED] wrote:
On 3/5/2008 8:21 AM, gerardus vanneste wrote:
Hello
I've stumbled upon a problem for inversion of a matrix with large values,
and I haven't found a solution yet...
Someone with experience in numerical linear
)
Douglas Bates [EMAIL PROTECTED] 3/4/2008 5:13 PM
On Tue, Mar 4, 2008 at 10:52 AM, John Sorkin
[EMAIL PROTECTED] wrote:
R 2.6.0
Windows XP
At the risk of raising the ire of the R gods . . .
I am looking for a package that will allow me to perform a poisson,
quasipoisson
On Sat, Mar 8, 2008 at 2:57 AM, Alexandra Bremner
[EMAIL PROTECTED] wrote:
I am attempting to model data with the following variables:
timepoint - n=48, monthly over 4 years
hospital - n=3
opsn1 - no of outcomes
total.patients
skillmixpc - skill mix percentage
nurse.hours.per.day
On Sat, Mar 8, 2008 at 11:00 AM, Manuel Morales
[EMAIL PROTECTED] wrote:
On Sat, 2008-03-08 at 08:07 -0600, Douglas Bates wrote:
On Sat, Mar 8, 2008 at 2:57 AM, Alexandra Bremner
[EMAIL PROTECTED] wrote:
I am attempting to model data with the following variables:
timepoint
On Sun, Mar 16, 2008 at 6:39 AM, Gavin Simpson [EMAIL PROTECTED] wrote:
On Sat, 2008-03-15 at 12:48 -0500, daniel jupiter wrote:
Hi all,
I apologize for what might be a silly question.
I am interested in doing a one way anova.
This is not too hard in and of itself, either with
Usually a captcha is used to prevent creation of email accounts for
use by spammers. (There was an interesting article recently on
whether the Gmail captcha scheme had been broken so that spammers
could create masses of gmail accounts. The general conclusion is that
the capcha scheme is intact
On Wed, Mar 19, 2008 at 3:02 PM, Ben Bolker [EMAIL PROTECTED] wrote:
Jean-Baptiste Ferdy Jean-Baptiste.Ferdy at univ-montp2.fr writes:
Dear R users,
I want to explain binomial data by a serie of fixed effects. My problem is
that my binomial data are spatially correlated. Naively,
On Thu, Mar 27, 2008 at 3:05 PM, Dimitris Rizopoulos
[EMAIL PROTECTED] wrote:
try this:
dat - data.frame(x = rnorm(10), y = rexp(10), z = letters[1:10])
colMeans(data.matrix(dat[sapply(dat, is.numeric)]))
Alternatively
sapply(dat, mean)
x y z
-0.5260131
On Thu, Mar 27, 2008 at 7:01 AM, Aberg Carl [EMAIL PROTECTED] wrote:
Hi,
Im using lme to calculate a mixed factors ANOVA according to:
px_anova = anova(lme(dep~music*time*group, random = ~1|id, data = px_data))
where
dep is a threshold,
time is a repeated measures variable (2 levels)
On Mon, Mar 31, 2008 at 7:13 AM, Boikanyo Makubate
[EMAIL PROTECTED] wrote:
I am using the lmer function from the lme4 package. I wrote the
following statement, specifying the method to be adaptive Gaussian
quadrature. I am getting an error saying method = AGQ not yet
implemented for
getting an error saying method = AGQ not yet
BM implemented for supernodal representation. Please help. How can i
BM implement AGQ.
This has been answered yesterday by Douglas Bates who is the lme4 developer:
http://www.nabble.com/lmer-function.-td16398022.html#a16398022
Why do you
On Mon, Jun 22, 2009 at 7:12 AM, Martin
Maechlermaech...@stat.math.ethz.ch wrote:
TobiasV == Tobias Verbeke tobias.verb...@openanalytics.be
on Sun, 21 Jun 2009 08:25:07 +0200 writes:
TobiasV Hi Ken,
I have been using R for a while. Recently, I have begun converting my
package
On Wed, Jul 15, 2009 at 3:42 AM, Nair, Murlidharan Tmn...@iusb.edu wrote:
Hi!!
I am trying to multiply 5 matrices and then using the inverse of that matrix
for further computation. I read about precision problems from the archives
and the suggestion was to use as.numeric while computing the
On Fri, Jul 17, 2009 at 9:15 AM, Saptarshi Guhasaptarshi.g...@gmail.com wrote:
Hello,
I tried this pseudo-generator style experiment (see below). The -
operator assigns to in the calling environment which would be the
environment of getN.
Yes.
Yet when the function incr is returned, isn't
On Sun, Jul 19, 2009 at 11:32 PM, Marujo A.a.mar...@soton.ac.uk wrote:
Dear R-helpers
I have 2 variables
x1=rgamma(6000, 2, 1) and x2=rgamma(6000, 3,2). I have to sort (descending)
each one and split it into groups. After this each two groups must be merged
into one until all population
On Mon, Jul 20, 2009 at 5:18 AM, Jie TANGtotang...@gmail.com wrote:
Hi ,everyone ,
I draw some boxplot figure with the command boxplot.But in the
figure,there are some bubbles at the top part of the figure.
Can anyone tell me what the correct meaning of these bubbles?and how to
remove it?
On Sun, Aug 9, 2009 at 11:32 AM, Ted
Hardingted.hard...@manchester.ac.uk wrote:
On 09-Aug-09 16:06:52, Peng Yu wrote:
Hi,
I know '.' is not a separator in R as in C++. I am wondering where it
discusses the detailed usage of '.' in R. Can somebody point me a
webpage, a manual or a book that
On Mon, Aug 18, 2008 at 11:20 AM, Aaron Mackey [EMAIL PROTECTED] wrote:
I have a fairly large model:
length(Y)
[1] 3051
dim(covariates)
[1] 3051 211
All of these 211 covariates need to be nested hierarchically within a
grouping class, of which there are 8. I have an accessory vector,
On Mon, Aug 18, 2008 at 9:27 AM, Ben Bolker [EMAIL PROTECTED] wrote:
Fränzi Korner fraenzi.korner at oikostat.ch writes:
Have you got an answer? I am now working with R 2.7.1.. This R-version does
not give the scale parameter in the summary of an lmer-object.
Therefore, I would like to
On Mon, Aug 18, 2008 at 7:55 PM, [EMAIL PROTECTED] wrote:
Hello,
I have compared the potentials of R and Stata about GLMM, analysing the
dataset 'ohio' in the package 'faraway' (the same dataset is analysed with
GEE in the book 'Extending the linear model with R' by Julian Faraway).
On Fri, Aug 22, 2008 at 2:16 PM, John Tillinghast [EMAIL PROTECTED] wrote:
I'm trying to figure this out with Writing R Extensions but there's not a
lot of detail on this issue.
I want to write a (very simple really) C external that will be able to take
... as an argument.
(It's for
On Sun, Aug 24, 2008 at 11:54 AM, Ben Bolker [EMAIL PROTECTED] wrote:
Wade Wall wade.wall at gmail.com writes:
I am trying to look for a way to eliminate columns that sum to zero. Any
help would be appreciated.
x_without_zero_cols - x[,colSums(x)!=0]
Of course, depending on the nature of
On Mon, Aug 25, 2008 at 12:28 PM, John Tillinghast [EMAIL PROTECTED] wrote:
On Sat, Aug 23, 2008 at 11:46 AM, Douglas Bates [EMAIL PROTECTED] wrote:
I don't think it is necessary to go through the agonies of dealing
with the argument list in a .External call., which is what I assume
you
On Tue, Aug 26, 2008 at 6:07 AM, Henrique Dallazuanna [EMAIL PROTECTED] wrote:
I think you need assign, see ?assign for more details.
On Tue, Aug 26, 2008 at 6:02 AM, Antje [EMAIL PROTECTED] wrote:
Hi there,
I try to understand the usage of environments but I'm not sure if I get it.
I wrote
On Fri, Aug 29, 2008 at 6:46 PM, David Huffer [EMAIL PROTECTED] wrote:
I'm looking for something along the lines of
which ( table ( x ) == max ( table ( x ) ) )
to find the most common level of one factor
by several other factors. For instance, I've got
X - data.frame (
+ x = factor
On Wed, Sep 24, 2008 at 11:08 AM, [EMAIL PROTECTED] wrote:
Thank you for all of you. Intuitively, 7 is an integer for people who live
in this planet. It is just very difficult for me to believe that R does not
think 7 is an integer but 7L is.
is.integer(7) # R 2.7.2
[1] FALSE
Thus, based
On Wed, Sep 24, 2008 at 4:30 PM, Wacek Kusnierczyk
[EMAIL PROTECTED] wrote:
Douglas Bates wrote:
On Wed, Sep 24, 2008 at 11:08 AM, [EMAIL PROTECTED] wrote:
Thank you for all of you. Intuitively, 7 is an integer for people who live
in this planet. It is just very difficult for me to believe
On Wed, Sep 24, 2008 at 2:54 PM, getulio coutinho figueiredo
[EMAIL PROTECTED] wrote:
Hello, everyone!
I would like to know how to calculate the F-value and P-value for a
non-linear regression: y ~ a * X^b * W^c ?
Note: a, b and c are coefficients of adjustment of the equation and X and W
On Thu, Sep 25, 2008 at 8:15 AM, Chuck Cleland [EMAIL PROTECTED] wrote:
On 9/25/2008 7:43 AM, Stefan Fritsch wrote:
Dear R Users,
I want to exclude elements in a vector by:
vector[-exclude]
is it intended to cause an error if no elements are excluded?
vector - 1:10
exclude - NULL
On Thu, Sep 25, 2008 at 4:23 PM, Wacek Kusnierczyk
[EMAIL PROTECTED] wrote:
Rolf Turner wrote:
On 26/09/2008, at 1:27 AM, Petr PIKAL wrote:
Hi
Sorry but I can not agree. If you measure something and your values in a
vector are
c(5.1, 5.4, 4.8, 5.0)
do you think the first three numbers
On Thu, Sep 25, 2008 at 5:07 PM, Douglas Bates [EMAIL PROTECTED] wrote:
On Thu, Sep 25, 2008 at 4:23 PM, Wacek Kusnierczyk
[EMAIL PROTECTED] wrote:
Rolf Turner wrote:
On 26/09/2008, at 1:27 AM, Petr PIKAL wrote:
Hi
Sorry but I can not agree. If you measure something and your values
, check
?which
I can use lists now, and stop thrashing :)
Thx again for the assistance!
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Douglas
Bates
Sent: Monday, June 09, 2008 1:08 PM
To: Dumblauskas, Jerry
Cc: r-help@r-project.org
Subject: Re
nlminb provides unconstrained optimization and optimization subject to
box constraints (i.e. upper and/or lower constraints on individual
elements of the parameter vector). The nlm function provides
unconstrained optimization.
I created the nlminb function because I was unable to get reliable
We may want to move this discussion to the R-SIG-Mixed-Models list,
which I have cc:'d on this reply.
On Sun, Jun 15, 2008 at 6:16 PM, eugen pircalabelu
[EMAIL PROTECTED] wrote:
Hi R users!
I am trying to learn some multilevel analysis, but unfortunately i am now
very confused. The reason:
On Fri, Jun 20, 2008 at 11:33 AM, Ben Fairbank [EMAIL PROTECTED] wrote:
I bogged down about half way through reading the Green Book, in part
because it became increasingly difficult to understand how some of the
ideas related to R, as opposed to S (which I have not used). Does any
reader know
I am indebted to Deepayan Sarkar for lattice graphics, Fritz Leisch
for Sweave and the authors of the beamer package for LaTeX. For me
these are a killer app combination. I wouldn't want to go back to
creating presentations in any other way.
When I create a presentation I use a Makefile that
On Tue, Jun 24, 2008 at 7:43 PM, Deepayan Sarkar
[EMAIL PROTECTED] wrote:
On 6/24/08, Douglas Bates [EMAIL PROTECTED] wrote:
I am indebted to Deepayan Sarkar for lattice graphics, Fritz Leisch
for Sweave and the authors of the beamer package for LaTeX. For me
these are a killer app
On Wed, Jul 9, 2008 at 12:01 PM, Ulrike Grömping [EMAIL PROTECTED] wrote:
Dear R-helpers,
I have a question regarding LU-decomposition with function lu in package
Matrix. The following simple example confuses me: Why is as.matrix(elu$U)
not an upper triangular matrix?
u3 -
On Sat, Jul 12, 2008 at 6:23 AM, Lan Wei [EMAIL PROTECTED] wrote:
Hi all,
I have a problem when running lmer.
In my data set, Agree is a binary(0/1) response. WalkerID and ObsID is
the identification number of the subjects. the description of the
other variables are as follows:
By the way, did you notice that the levels of Emotion include both
joy and joy . You may want to correct that.
On Sat, Jul 12, 2008 at 7:47 AM, Douglas Bates [EMAIL PROTECTED] wrote:
On Sat, Jul 12, 2008 at 6:23 AM, Lan Wei [EMAIL PROTECTED] wrote:
Hi all,
I have a problem when running lmer
On Tue, Jul 15, 2008 at 10:25 AM, Patrick Burns
[EMAIL PROTECTED] wrote:
That can be accomplished with 8 keystrokes.
A hint is to do the 4 keystrokes:
?lm
Umm - unless you are counting the implicit Enter, that's only 3
keystrokes isn't it?
Angila Albaros wrote:
Hello all,
On Thu, Jul 17, 2008 at 2:50 AM, Rune Haubo [EMAIL PROTECTED] wrote:
2008/7/16 Dimitris Rizopoulos [EMAIL PROTECTED]:
well, for computing the p-value you need to use pchisq() and dchisq() (check
?dchisq for more info). For model fits with a logLik method you can directly
use the following
effects for
thousands of levels of a factor.
-- Bert Gunter
Genentech, Inc.
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On
Behalf Of Doran, Harold
Sent: Monday, July 21, 2008 3:16 PM
To: [EMAIL PROTECTED]; r-help@r-project.org
Cc: Douglas Bates
Subject: Re: [R
You have a mismatch between glht and the model fit by lmer. A model
fit by lmer is an object of an S4 class (that's what the 4 in the
package name lme4 is to indicate). The glht function, or possibly a
default method for that generic, is treating the model as an S3 class
object.
Also, you
On Sun, Jul 27, 2008 at 9:06 PM, Rolf Turner [EMAIL PROTECTED] wrote:
I continue to struggle with mixed models. The square zero version
of the problem that I am trying to deal with is as follows:
A number (240) of students are measured (tested; for reading comprehension)
on 6 separate
On Fri, Aug 1, 2008 at 10:56 AM, Doran, Harold [EMAIL PROTECTED] wrote:
First off, Marc Schwartz posted this link earlier today, read it.
http://cran.r-project.org/doc/FAQ/R-FAQ.html#Why-are-p_002dvalues-not-di
splayed-when-using-lmer_0028_0029_003f
Second, your email is not really
Martin Maechler [EMAIL PROTECTED], who oversees the mailing
lists, would be the best person to start with.
On 4/10/08, [EMAIL PROTECTED]
[EMAIL PROTECTED] wrote:
Dear list,
After some extensive searching, I have drawn a blank on this. So ...
Who is the best contact for questions
On 4/21/08, Michael Kubovy [EMAIL PROTECTED] wrote:
To help Kedar a bit:
Here is one way:
recall - c(10, 13, 13, 6, 8, 8, 11, 14, 14, 22, 23, 25, 16, 18, 20,
15, 17, 17, 1, 1, 4, 12, 15, 17, 9, 12, 12, 8, 9, 12)
fr - data.frame(rcl = recall, time = factor(rep(c(1, 2, 5), 10)),
subj =
On 4/22/08, Prof Brian Ripley [EMAIL PROTECTED] wrote:
On Tue, 22 Apr 2008, Peter Dalgaard wrote:
Doran, Harold wrote:
Dear List:
I am very much a unix neophyte, but recently had a Ubuntu box installed
in my office. I commonly use Windows XP with 3 GB RAM on my machine and
the
On 4/22/08, Ista Zahn [EMAIL PROTECTED] wrote:
Hello,
This is a follow up question to my previous one
http://tolstoy.newcastle.edu.au/R/e4/help/08/02/3600.html
I am attempting to model relationship satisfaction (MAT) scores
(measurements at 5 time points), using participant (spouseID)
On 4/25/08, Wilfried Cools [EMAIL PROTECTED] wrote:
Dear list-members,
a model is fit with lmer, but I want to force the variance parameter values
to be as defined by me
I thought, use 'start' to specify initial values and only allow for one
iteration ?
my question is how to do that ?
On 5/1/08, Shige Song [EMAIL PROTECTED] wrote:
Will the use of jit improve performance of use contributed packages such as
lme4? Thanks.
A technology like a byte-compiler or a just-in-time compiler will
change the performance of interpreted code. It will not change the
performance of compiled
On Sat, May 10, 2008 at 5:27 AM, amarkos [EMAIL PROTECTED] wrote:
An indicator matrix is a binary matrix with orthogonal columns whose
rows sum to 1. A row of this matrix could be [0 1 0 0]. My problem is
to group the similar rows (profiles) so that to create a compact form
of the matrix.
I'm
On Sun, May 11, 2008 at 9:49 AM, amarkos [EMAIL PROTECTED] wrote:
On May 11, 4:47 pm, Douglas Bates [EMAIL PROTECTED] wrote:
Do you mean that you want to collapse similar rows into a single row
and perhaps a count of the number of times that this row occurs?
Let me rephrase the problem
I'm entering this discussion late so I may be discussing issues that
have already been addressed.
As I understand it, Federico, you began by describing a model for data
in which two factors have a fixed set of levels and one factor has an
extensible, or random, set of levels and you wanted to fit
suggest that you continue to cc: the R-help list on the
discussion. I can't always respond rapidly to requests and there are
many who read the list that can.
On May 12, 4:30 pm, Douglas Bates [EMAIL PROTECTED] wrote:
On Sun, May 11, 2008 at 9:49 AM, amarkos [EMAIL PROTECTED] wrote:
On May 11, 4:47
On Mon, May 12, 2008 at 11:22 AM, Federico Calboli
[EMAIL PROTECTED] wrote:
On 12 May 2008, at 17:09, Douglas Bates wrote:
I'm entering this discussion late so I may be discussing issues that
have already been addressed.
As I understand it, Federico, you began by describing a model for data
On Tue, May 13, 2008 at 1:40 PM, James Hudson [EMAIL PROTECTED] wrote:
Please advise the proper format for coding the random effects of a
split-plot experiment WITH repeated measures. I have been unable to
figure out how to use either lme or lmer's grouping to properly
assign the error terms.
Did you happen to notice the part at the bottom of every message about
provide commented, minimal, self-contained, reproducible code?
Considering that the result you quote from 251 has 2 coefficients
and the result from 171 has 3 coefficients one might contemplate the
possibility that you are
On Thu, May 15, 2008 at 9:22 AM, Luis Cayuela [EMAIL PROTECTED] wrote:
Hi everybody,
I am trying to fit a model with the lmer function for mixed effects. I have
an experimental design consisting of 5 field plots. Each plot is divided in
12 subplots where the influence of three factors on
There is a very good book called Data Manipulation with R by Phil
Spector that just became available. It is brief and concise. I would
recommend that book for learning about manipulating data in tables.
For anyone interested in data exploration and graphics I would also
recommend Deepayan
It looks like you want to stop the function execution on detecting an
error condition, in which case the appropriate function to call is
stop(), as in
if (nAssetPositions != nAssetPrices)
stop(Different number of assets!)
An alternative, if you don't want to write the error messages for each
See also
?rowMeans
On Fri, Jun 6, 2008 at 1:56 PM, [EMAIL PROTECTED] wrote:
TABLE-matrix(data=c(12,13,14,15,24,10),byrow=T,nrow=2,ncol=3)
TABLE
[,1] [,2] [,3]
[1,] 12 13 14
[2,] 15 24 10
apply(TABLE,1,mean)
[1] 13.0 16.3
Chunhao
Quoting Marco Chiapello
On Fri, Jun 6, 2008 at 1:13 PM, steven wilson [EMAIL PROTECTED] wrote:
Dear all;
I'm planning to install Linux on my computer to run R (I'm bored of
W..XP). However, I haven't used Linux before and I would appreciate,
if possible, suggestions/comments about what could be the best option
-matrix to compute the effects; you could also get standard errors
by using the covariance matrix for the fixed effects.
Douglas Bates:
https://stat.ethz.ch/pipermail/r-sig-mixed-models/2007q2/000222.html
My big problem with lsmeans is
that I have never been able
Thanks for sending that, Ben. I have incorporated a slightly modified
version, with attribution, in the lme4 sources.
On Tue, Apr 28, 2009 at 8:03 AM, Ben Bolker bol...@ufl.edu wrote:
I think the following works, but use with caution -- I just
wrote it last night.
setMethod(refit,
On Thu, May 7, 2009 at 9:56 AM, Sarah Goslee sarah.gos...@gmail.com wrote:
It probably has less to do with paste() than with Theoph, but since
we have no idea what that might be, it's hard to tell.
See the bit about reproducible example, please.
Well, actually Theoph is one of the datasets in
On Fri, May 8, 2009 at 7:07 AM, Boikanyo Makubate
boika...@stats.gla.ac.uk wrote:
Can anyone help me on how to get the nodes and weights of the adaptive
quadrature
using R.
You need to be more specific about which quadrature formula. I'm
guessing that you probably have Gauss-Hermite
On Wed, May 13, 2009 at 5:21 PM, avraham.ad...@guycarp.com wrote:
Hello.
I am trying to optimize a set of parameters using /optim/ in which the
actual function to be minimized contains matrix multiplication and is of
the form:
SUM ((A%*%X - B)^2)
where A is a matrix and X and B are
On Sat, May 16, 2009 at 10:21 AM, mcnda...@mncn.csic.es wrote:
Thanks a lot for all of you that have reply me about opening and ending R
workspaces in BATCH mode. However replies were a king general and I’m afraid
I could not take the entire message from them. Therefore I chose to expose
here
On Mon, May 18, 2009 at 9:22 AM, Thomas Lumley tlum...@u.washington.edu wrote:
On Mon, 18 May 2009, Debbie Zhang wrote:
Based on a set of binomial sample data, how would you utilize the nlm
function in R to estimate the true proportion of the population?
I can't see why anyone would want to
On Tue, May 19, 2009 at 2:01 PM, Michael Hannon jm_han...@yahoo.com wrote:
Greetings. I'm trying to learn to program in R. (I'm definitely NOT new to
programming, just to R.) A colleague suggested that I have a look at the
book:
An Introduction to S and S-Plus
by:
Phil Spector
Hi Bill,
I'm about to take a look at this. If I understand the issue, very
long expressions for what I call the grouping factor of a random
effects term (the expressions on the right hand side of the vertical
bar) are encountering problems with deparse. I should have realized
that, any time one
On Wed, May 27, 2009 at 9:17 AM, Ben Bolker bol...@ufl.edu wrote:
Johan Stenberg-2 wrote:
Dear members of the R help list,
I want to do a hierarchical glm with binomial family but am unsure
about how to write the syntax which involves nesting.
I want to test whether the risk of being
On Fri, May 29, 2009 at 7:50 AM, DanielWC daniel.carsten...@gmail.com wrote:
Hello
I am working with a biological data including variables called Habitat and
Site, example:
Habitat Site
Forest Low
Forest Low
Forest High
Forest High
I want to tell R that the
On Wed, Jun 17, 2009 at 2:02 PM, Albyn Jonesjo...@reed.edu wrote:
As you seem to be aware, the matrix is poorly conditioned:
kappa(PLLH,exact=TRUE)
[1] 115868900869
It might be worth your while to think about reparametrizing.
Also, if it is to be a variance-covariance matrix then it must be
On Nov 20, 2007 10:29 AM, Gabor Grothendieck [EMAIL PROTECTED] wrote:
update already has formula and packageStatus methods so its
being extended beyond models already even within core packages.
Also, update methods are extensively used for the other kind of
graphs in the lattice package.
On Nov 29, 2007 8:09 PM, M-J Milloy [EMAIL PROTECTED] wrote:
Hello all,
I'm attempting to fit a generalized linear mixed-effects model using lmer
(R v 2.6.0, lmer 0.99875-9, Mac OS X 10.4.10) using the call:
vidusLMER1 - lmer(jail ~ visit + gender + house + cokefreq + cracfreq +
herofreq +
On Dec 1, 2007 9:26 AM, Douglas Bates [EMAIL PROTECTED] wrote:
On Nov 29, 2007 8:09 PM, M-J Milloy [EMAIL PROTECTED] wrote:
Hello all,
I'm attempting to fit a generalized linear mixed-effects model using lmer
(R v 2.6.0, lmer 0.99875-9, Mac OS X 10.4.10) using the call:
vidusLMER1
On Dec 3, 2007 1:45 PM, David Park [EMAIL PROTECTED] wrote:
I'm working with Andrew Gelman on a book project and we're having some
difficulties getting coef() to work in some lmer() calls.
Some versions of the model work and some do not. For example, this works
(in that we can run the model
On Dec 13, 2007 4:15 PM, Ilona Leyer [EMAIL PROTECTED] wrote:
Dear All,
I want to analyse treatment effects with time series
data: I measured e.g. leaf number (five replicate
plants) in relation to two soil pH - after 2,4,6,8
weeks. I used mixed effects models, but some analyses
didn´t
On Dec 28, 2007 9:35 AM, Sharon Goldwater [EMAIL PROTECTED] wrote:
I have a question about some strange results I get when using lmer to
build a logistic mixed effects model. I have a data set of about 30k
points, and I'm trying to do backwards selection to reduce the number
of fixed effects
On Jan 4, 2008 6:21 PM, Andrea Previtali [EMAIL PROTECTED] wrote:
Sorry, I realized that somehow the message got truncated. Here is the
remaining part of the SAS output:
Solutions for Fixed Effects:
Effect DIST DW ELI SEX SEAS Estimate Std. Error
DF t Value Pr
On Jan 8, 2008 12:34 AM, suman Duvvuru [EMAIL PROTECTED] wrote:
Hello,
I have a dataset with 20,000 variables.and I would like to compute a pearson
correlation matrix which will be 2*2. The cor() function doesnt work
in this case due to memory problem. If you have any ideas regarding
On Wed, Mar 11, 2009 at 11:11 AM, Terry Therneau thern...@mayo.edu wrote:
I fired up a new machine last night and loaded Ubuntu 8.10 on it. I then had
to add in the usual compiler stuff which is not loaded by default: make,
emacs,
fortran, c++, etc.
I'm having trouble compiling R 2.8
On Fri, Mar 13, 2009 at 2:39 PM, Martín Quiroga mquir...@ssdfe.com.ar wrote:
Hi everyone! I am a biologist from Argentina and have to solve this problem.
I have an insect population obtained from 10 different nests and need to
know its sex ratio. But as I cannot ensure insects independence I
On Mon, Mar 23, 2009 at 2:18 PM, Kingsford Jones
kingsfordjo...@gmail.com wrote:
On Mon, Mar 23, 2009 at 11:26 AM, Ben Domingue ben.domin...@gmail.com wrote:
Hello,
How do I get the standard deviations for the random effects out of the
lme object? I feel like there's probably a simple way of
On Mon, Mar 23, 2009 at 2:35 PM, Lawrence Hanser lhan...@gmail.com wrote:
Dear Colleagues,
I have what Roger Kirk (Experimental Design: Procedures for the Behavioral
Sciences, 1968) refers to as a randomized block factorial design. The anova
table would look like this:
On Tue, Mar 24, 2009 at 5:25 AM, LiatL liat.lam...@gmail.com wrote:
I've built a poisson regression model for multiple subjects by using the
GLMER function. I've also developed some curves for defining its limits but
I did not succeed in developing confidence interval for the model's curve
On Sat, Mar 28, 2009 at 2:33 AM, Jim Silverton jim.silver...@gmail.com wrote:
Can someone explain why I am getting the following error: in the r code
below?
Are you asking what the error message means or how you are getting a
computationally singular system? (My guess is that currvar is very
,
which compares timings of various methods for least squares
computations.
Douglas Bates. Least squares calculations in R. R News, 4(1):17-20, June
2004.
A Cholesky decomposition solution proved fastest in base R code, with an
even faster version developed using sparse matrices and the Matrix
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