Although I know there is another message in this thread I am replying
to this message to be able to include the whole discussion to this
point.
Gregor mentioned the possibility of extending the compiled code for
cumsum so that it would handle the matrix case. The work by Dirk
Eddelbuettel and
On Fri, Oct 22, 2010 at 9:13 AM, Czerminski, Ryszard
ryszard.czermin...@astrazeneca.com wrote:
I want to fit a linear model with fixed slope e.g. y = x + b
(instead of general: y = a*x + b)
Is it possible to do with lm()?
Yes. The simplest way is to fit
lm(y - a*x ~ 1)
which will give you
On Thu, Oct 21, 2010 at 2:00 PM, Ben Bolker bbol...@gmail.com wrote:
Michal Figurski figurski at mail.med.upenn.edu writes:
I have a data set of roughly 10 million records, 7 columns. It has only
about 500MB as a csv, so it fits in the memory. It's painfully slow to
do anything with it, but
On Tue, Oct 26, 2010 at 12:27 PM, Dimitri Liakhovitski
dimitri.liakhovit...@gmail.com wrote:
Hello,
and sorry for asking a question without the data - hope it can still
be answered:
I've run two things on the same data:
# Using lme:
mix.lme - lme(DV ~a+b+c+d+e+f+h+i, random = random = ~
On Sun, Oct 31, 2010 at 2:35 AM, Carabiniero ja...@troutnut.com wrote:
I haven't been able to fully make sense of the conflicting online information
about whether and how to specify nesting structure for a nested, mixed
model. I'll describe my experiment and hopefully somebody who knows lme4
On Mon, Nov 1, 2010 at 11:04 PM, Santosh Srinivas
santosh.srini...@gmail.com wrote:
Hello Group,
This is an open-ended question.
Quite fascinated by the things I can do and the control I have on my
activities since I started using R.
I basically have been using this for analytical related
I don't know about the statmod package and the gauss.quad function but
generally the definition of Gauss-Hermite quadrature is with respect
to the function that is multiplied by exp(-x^2) in the integrand. So
your example would reduce to summing the weights.
On Sun, Nov 14, 2010 at 11:18 AM,
On Tue, Nov 16, 2010 at 10:30 AM, poko2000 quan.poko2...@gmail.com wrote:
Hi I am a newbie in R.
I have data with dim of 20.
How to use lm if i want to do regression with the whole design matrix? My y
is the first column.
the left are xs.
Thanks a lot.
Do you have the data stored in a
On Tue, Nov 16, 2010 at 11:09 AM, skan juanp...@gmail.com wrote:
What's the differente betwen using plot and using print in order to
plot a graph?
For example in order to plot the result of a histogram.
Could you give an example?
It seems that you are referring to graphics functions in
It is often more effective to send questions about lmer or glmer to
the r-sig-mixed-mod...@r-project.org mailing list, which I am cc:ing
on this response.
On Tue, Nov 16, 2010 at 3:25 AM, Annika annika.opperb...@jyu.fi wrote:
Dear list,
I am new to this list and I am new to the world of R.
I am cc:ing the r-sig-mixed-mod...@r-project.org mailing list on this
reply as such questions are often answered more quickly on that list.
On Tue, Nov 16, 2010 at 2:00 PM, Daniel Jeske daniel.je...@ucr.edu wrote:
Dear R Help,
I believe the glmer() function in lme4 automatically fits an
On Wed, Jul 14, 2010 at 4:23 PM, paul s r-project@queuemail.com wrote:
hi -
i just started using R as i am trying to figure out how perform a linear
regression on a huge matrix.
i am sure this topic has passed through the email list before but could not
find anything in the archives.
On Wed, Aug 4, 2010 at 2:09 PM, Erik Iverson er...@ccbr.umn.edu wrote:
Hello,
I have a problem which has bitten me occasionally. I often need to
prepare graphs for many variables in a data set, but seldom for all.
or for any large number of sequential or sequentially named variables.
Often
On Thu, Aug 5, 2010 at 9:31 AM, rod84 ngueye...@hotmail.com wrote:
Dear R users,
I recently downloaded the library lme4a by
svn checkout svn://svn.r-forge.r-project.org/svnroot/lme4.
I tried to install the library lme4a by copying the downloaded document in
the location where all the R
On Wed, Sep 15, 2010 at 3:48 PM, Matias Salibian-Barrera
msalib...@yahoo.ca wrote:
Hi there,
I'm trying to install the package RcppArmadillo in my R 2.11.1 which I
installed
and regularly update via Ubuntu's repositories.
When I try to install RcppArmadillo from CRAN I get:
I haven't had the time to keep up with this discussion, or many of the
other discussions on the R-SIG-Mixed-Models email list. I swamped
with other duties at present.
It is important to remember that the nlme and lme4 packages take a
model specification and provide code to evaluate the deviance.
On Tue, Sep 21, 2010 at 1:39 PM, Douglas Bates ba...@stat.wisc.edu wrote:
I haven't had the time to keep up with this discussion, or many of the
other discussions on the R-SIG-Mixed-Models email list. I swamped
with other duties at present.
It is important to remember that the nlme and lme4
On Tue, Sep 21, 2010 at 4:21 PM, Peter Dalgaard pda...@gmail.com wrote:
On 09/21/2010 09:02 PM, Douglas Bates wrote:
On Tue, Sep 21, 2010 at 1:39 PM, Douglas Bates ba...@stat.wisc.edu wrote:
I haven't had the time to keep up with this discussion, or many of the
other discussions on the R-SIG
On Mon, Sep 27, 2010 at 3:04 AM, Petr PIKAL petr.pi...@precheza.cz wrote:
Hi
I noticed that nobody answered your question yet so here is my try.
If you want to see what objects are in your environment you can use ls()
but its output is only names of objects. Here is a function I use a long
An interesting, and topical, example of multivariate data for
classroom illustrations are the American college football rankings.
Starting at the end of October (or week 8, the 8th week of the
football season) a set of rankings called the BCS (Bowl Championship
Series) will be published. This is
On Tue, Sep 29, 2009 at 7:56 AM, Douglas Bates ba...@stat.wisc.edu wrote:
An interesting, and topical, example of multivariate data for
classroom illustrations are the American college football rankings.
Starting at the end of October (or week 8, the 8th week of the
football season) a set
On Wed, Sep 30, 2009 at 2:42 PM, Douglas Bates ba...@stat.wisc.edu wrote:
On Wed, Sep 30, 2009 at 2:43 AM, Dieter Menne
dieter.me...@menne-biomed.de wrote:
Dear List,
creating factors in a given non-default orders is notoriously difficult to
explain in a course. Students love the ifelse
On Wed, Sep 30, 2009 at 2:32 PM, Peter Dalgaardp.dalga...@biostat.ku.dk wrote:
Martin Batholdy wrote:
hum,
can you explain that a little more detailed?
Perhaps I miss the background knowledge - but it seems just absurd to me.
0.1+0.1+0.1 is 0.3 - there is no rounding involved, is there?
I'm not sure if this is exactly what you are looking for but I would
generally create an interaction plot using the lattice 'dotplot' with
type = c(p,a) so I get both the original data and the lines
joining the averages for the different factor levels. I also prefer
the horizontal orientation to
On Fri, Oct 16, 2009 at 7:09 PM, Michael A. Gilchrist mi...@utk.edu wrote:
Hello,
I'm having problems creating and using a selfStart model with nlme.
Briefly, I've defined the model, a selfStart object, and then combined them
to make a selfStart.default model.
If I apply getInitial to the
On Thu, Oct 22, 2009 at 12:46 PM, Douglas M. Hultstrand
dmhul...@metstat.com wrote:
Hello,
I am generating .png images using the Cairo package in a for loop (looping
on the number of zones, number of zones equals the number of plots to create
based on different zone data). When I run the R
On Thu, Oct 22, 2009 at 1:39 PM, Ben Bolker bol...@ufl.edu wrote:
ROBARDET Emmanuelle wrote:
Dear R users,
I'm performing some GLMMs analysis with a negative binomial link.
I already performed such analysis some months ago with the lmer() function
but when I tried it today I encountered
Alternatively you could install the NRAIA package and collapse the
construction of the plot to a call to plotfit as shown in the
enclosed.
Note that this is a poor fit of a logistic growth model. There are no
data values beyond the inflection point so the Asym parameter (the
asymptote) is poorly
On Thu, Oct 22, 2009 at 10:26 AM, Ravi Varadhan rvarad...@jhmi.edu wrote:
Ted,
LAPACK is newer and is supposed to contain better algorithms than LINPACK.
It is not true that LAPACK cannot handle rank-deficient problems. It can.
It's not just a question of handling rank-deficiency. It's
On Thu, Oct 22, 2009 at 8:11 PM, Ista Zahn iz...@psych.rochester.edu wrote:
Hi everyone,
I'm sure this has been asked before, but I could not find the right
search terms to find it.
If I want to see what summarizing a model fit with lm() does, I can
write summary.lm. But what if I want to
On Sun, Nov 1, 2009 at 9:01 AM, wenjun zheng wjzhen...@gmail.com wrote:
Hi R Users,
When I use package lme4 for mixed model analysis, I can't distinguish
the significant and insignificant variables from all random independent
variables.
Here is my data and result:
Data:
, groups: Variety:Stand, 9; Variety, 3; Stand, 3
Fixed effects:
Estimate Std. Error t value
(Intercept) 7.1852 0.6919 10.38
2009/11/2 Douglas Bates ba...@stat.wisc.edu
On Sun, Nov 1, 2009 at 9:01 AM, wenjun zheng wjzhen...@gmail.com wrote:
Hi R Users,
When I use
-values from the likelihood ratio tests in that
transcript I sent.
The point of those tests is that a p-value can only be calculated when
you know both the null hypothesis and the alternative, which is why
those p-values are the result of comparing two nested model fits.
2009/11/2 Douglas Bates ba
On Thu, Nov 12, 2009 at 10:14 AM, milton ruser milton.ru...@gmail.com wrote:
Hi Ana,
I am not quite sure if it is the problem, but if you call your data.frame as
exp,
you will crash exp() function... try use another name for your data.frame.
By the way, I suggest you not use attach().
Try
On Sun, Nov 15, 2009 at 7:19 AM, Green, Gerwyn (greeng6)
g.gre...@lancaster.ac.uk wrote:
Dear all
this is a question of model specification in lme which I'd for which I'd
greatly appreciate some guidance.
Suppose I have data in long format
gene treatment rep Y
1 1 1 4.32
1
image applied to a sparseMatrix object uses lattice functions to
create the image. As described in R FAQ 7.22 you must use
print(image(x))
or
show(image(x))
or even
plot(image(x))
when a lattice function is called from within another function.
On Wed, Apr 28, 2010 at 1:20 PM, Gildas Mazo
Google the name dgesdd to get the documentation where you will find
that the error code indicates that the SVD algorithm failed to
converge. Evaluation of the singular values and vectors is done via
an iterative optimization and on some occasions will fail to converge.
Frequently this is
On Sun, May 23, 2010 at 5:09 AM, Peter Ehlers ehl...@ucalgary.ca wrote:
On 2010-05-23 0:56, john smith wrote:
Hi,
I am trying to implement Higham's algorithm for correcting a non positive
definite covariance matrix.
I found this code in R:
As Frank mentioned in his reply, expecting to estimate tens of
thousands of fixed-effects parameters in a logistic regression is
optimistic. You could start with a generalized linear mixed model
instead
library(lme4)
fm1 - glmer(resp ~ 1 + (1|f1) + (1|f2) + (1|f1:f2), mydata, binomial))
If you
On Mon, May 24, 2010 at 6:24 PM, Robin Jeffries rjeffr...@ucla.edu wrote:
I read somewhere (help list, documentation) that the random effects in lme4
uses sparse matrix technology.
Yes. That is why there is such a close link between the Matrix and
lme4 packages. The sparse matrix methods in
On Thu, Nov 26, 2009 at 10:03 AM, Rob Steele
freenx.10.robste...@xoxy.net wrote:
These are the ways that occur to me.
## This produces a logical vector, which will get converted to a numeric
## vector the first time a number is assigned to it. That seems
## wasteful.
x - rep(NA, n)
##
On Thu, Dec 24, 2009 at 1:03 PM, postava-davig.m
postava-davi...@husky.neu.edu wrote:
Hello,
I have been attempting to run a poisson glmm using lme4 for some time now
and have had a lot of trouble. I would say 9 times out of 10 I receive the
following warning:
CHOLMOD warning: %h
Error
On Tue, Dec 29, 2009 at 11:46 AM, Julia7 liujul...@yahoo.com wrote:
Hello,
How do I fit a mixed effect model with no intercept using lmer()?
Is the following syntax correct?
lmer(y ~ -1+x1+x2+(-1+x1+x2|id), data=dt)
Yes. An alternative, which I prefer, is
lmer(y ~ 0 + x1 + x2 + (0 + x1 +
I forgot to cc: the list on this response.
-- Forwarded message --
From: Douglas Bates ba...@stat.wisc.edu
Date: Wed, Dec 30, 2009 at 8:05 AM
Subject: Re: [R] glm error: cannot correct step size
To: John Sorkin jsor...@grecc.umaryland.edu
On Wed, Dec 30, 2009 at 7:50 AM, John
On Mon, Jan 4, 2010 at 6:24 AM, Walmes Zeviani
walmeszevi...@hotmail.com wrote:
AD Hayward wrote:
Dear all,
I'm attempting to use a piecewise regression to model the trajectory
of reproductive traits with age in a longitudinal data set using a
mixed model framework. The aim is to find
On Tue, Jun 8, 2010 at 7:10 AM, Enrico Colosimo enrico...@gmail.com wrote:
Hello,
I am having some trouble running a very simple
example. I am running a logistic regression entering the SAME data set
in two different forms and getting different values for the deviance residual.
Just look
The lm and aov functions can take a matrix response allowing you to
fit all of the responses for a single attribute simultaneously.
On Thu, Jun 10, 2010 at 8:47 AM, melissa mellep...@orange.fr wrote:
Dear all R users,
I want to realize 800 000 ANOVAS and to store Sum of Squares of the effects.
On Sat, Jun 12, 2010 at 6:18 AM, Tal Galili tal.gal...@gmail.com wrote:
Hello Gabor, Matt, Dirk.
Thank you all for clarifying the situation.
So if I understand correctly then:
1) Changing the BLAST would require specific BLAST per computer
configuration (OS/chipset).
It's BLAS (Basic
On Sat, Jun 12, 2010 at 8:37 AM, Dr. David Kirkby
david.kir...@onetel.net wrote:
R 2.10.1 is used in the Sage maths project. Several recommended packages
(Matrix, class, mgcv, nnet, rpart, spatial, and survival) are failing to
build on Solaris 10 (SPARC).
Have you checked the dependencies for
On Thu, Jun 17, 2010 at 10:50 AM, Barry Rowlingson
b.rowling...@lancaster.ac.uk wrote:
On Thu, Jun 17, 2010 at 3:33 PM, Doran, Harold hdo...@air.org wrote:
I have a function that is an iterative process for estimating some MLEs. I
want to print some progress to screen as the process iterates.
On Mon, Jun 21, 2010 at 8:38 PM, David Winsemius dwinsem...@comcast.net wrote:
On Jun 21, 2010, at 9:18 PM, Duncan Murdoch wrote:
On 21/06/2010 9:06 PM, G FANG wrote:
Hi,
I want to get the unique set from a large numeric k by 1 vector, k is
in tens of millions
when I used the matlab
On Mon, Jun 28, 2010 at 12:28 PM, Doran, Harold hdo...@air.org wrote:
Two things I think are some of the best developments in statistics and
production are the lattice package and the beamer class for presentation in
Latex. One thing I have not become very good at is properly sizing my
On OS X you need to install the source package for lme4 as the binary
package fails one of the tests. We have been unable to reproduce this
failure under other operating systems, which makes it hard to debug.
On Tue, Jul 6, 2010 at 11:09 AM, Alex Foley alex_foley_...@yahoo.com wrote:
Hi,
I
On Fri, Jan 15, 2010 at 10:00 AM, Ben Bolker bol...@ufl.edu wrote:
John Kane jrkrideau at yahoo.ca writes:
I've only been using R for about 2.5 years but and I'm not all that good but
I vote for - .
I think the deciding factor is in RSiteSearch() and the various manuals.
Almost
On Sat, Jan 16, 2010 at 8:20 AM, Walmes Zeviani
walmeszevi...@hotmail.com wrote:
Doug,
It appears you are mixing nlme and lme4 formulation type.
On nlme library you type
lme(y~x, random=~1|subjetc)
On lme4 library you type
lmer(y~x+(1|subject))
You mixed them.
At your disposal.
On Tue, Jan 19, 2010 at 9:26 AM, Martin Maechler
maech...@stat.math.ethz.ch wrote:
Scanning for 'Matrix' in old R-help e-mail, I found
GA == Gad Abraham gabra...@csse.unimelb.edu.au
on Fri, 27 Nov 2009 13:45:00 +1100 writes:
GA Hi,
GA I'd like to store large covariance matrices
On Sun, Jan 31, 2010 at 10:24 PM, Anton du Toit atdutoitrh...@gmail.com wrote:
Dear R-helpers,
I’m writing for advice on whether I should use R or a different package or
language. I’ve looked through the R-help archives, some manuals, and some
other sites as well, and I haven’t done too well
On Sat, Feb 6, 2010 at 4:45 AM, Martin Bulla bu...@centrum.cz wrote:
Does anybody knows what this error message means: Error in object$terms : $
operator not defined for this S4 class
The error message means what it says and it doesn't come from lmer, it
comes from the drop1 function being
On Sat, Feb 6, 2010 at 2:46 PM, David Winsemius dwinsem...@comcast.net wrote:
On Feb 6, 2010, at 3:29 PM, Ravi Ramaswamy wrote:
Hi - I am not familiar with R. Could I ask you a quick question?
When I read a file like this, I get an error. Not sure what I am doing
wrong. I use a MAC. How
On Sun, Feb 7, 2010 at 2:40 PM, Emmanuel Charpentier
charp...@bacbuc.dyndns.org wrote:
Note : this post has been motivated more by the hierarchical data
subject than the aside joke of Douglas Bates, but might be of interest
to its respondents.
Le vendredi 05 février 2010 à 21:56 +0100, Peter
On Tue, Feb 9, 2010 at 4:38 AM, Demirtas, Hakan demir...@uic.edu wrote:
Does lmer do three-level mixed-effects models?
Yes.
What forms of outcome
variables can it handle (continuous, survival, binary)? I'd appreciate any
help.
Continuous outcomes for lmer. glmer can handle binary
On Fri, Feb 12, 2010 at 9:22 AM, Arnaud Mosnier a.mosn...@gmail.com wrote:
Dear useRs,
Just a little post to provide the answer of a problem that took me
some time to resolve !
Hope that reading this will permit the others to avoid that error.
When using the subset function, writing
On Fri, Feb 12, 2010 at 4:25 PM, blue sky bluesky...@gmail.com wrote:
?'`' shows the following:
Single and double quotes delimit character constants. They can be
used interchangeably but double quotes are *preferred* (and character
constants are printed using double quotes), so single quotes
On Sat, Feb 13, 2010 at 7:09 PM, Daniel Malter dan...@umd.edu wrote:
It seems to me that your question is more about the econometrics than about
R. Any introductory econometric textbook or compendium on econometrics will
cover this as it is a basic. See, for example, Greene 2006 or Wooldridge
On Tue, Feb 16, 2010 at 9:05 AM, Shige Song shiges...@gmail.com wrote:
Dear All,
I am trying to fit a 2-level random intercept logistic regression on a
data set of 20,000 cases. The model is specified as the following:
m1 - glmer(inftmort ~ as.factor(cohort) + (1|code), family=binomial,
This is similar to another question on the list today.
On Tue, Feb 16, 2010 at 4:39 AM, Luisa Carvalheiro
lgcarvalhe...@gmail.com wrote:
Dear R users,
I am having problems using package lme4.
I am trying to analyse the effect of a continuous variable (Dist_NV)
on a count data response
,
Luisa
On Tue, Feb 16, 2010 at 5:35 PM, Douglas Bates ba...@stat.wisc.edu wrote:
This is similar to another question on the list today.
On Tue, Feb 16, 2010 at 4:39 AM, Luisa Carvalheiro
lgcarvalhe...@gmail.com wrote:
Dear R users,
I am having problems using package lme4.
I am trying
feel that I might get some very
basic specification wrong in my R model...
Best,
Shige
On Tue, Feb 16, 2010 at 10:29 AM, Douglas Bates ba...@stat.wisc.edu wrote:
On Tue, Feb 16, 2010 at 9:05 AM, Shige Song shiges...@gmail.com wrote:
Dear All,
I am trying to fit a 2-level random intercept
On Thu, Feb 18, 2010 at 12:36 PM, Bert Gunter gunter.ber...@gene.com wrote:
The key dates are 1938 and 1962. The FDC act of 1938 essentially mandated
(demonstration of) safety. The tox testing infrastructure grew from that.At
that time, there were no computers, little data, little statistics
On Sat, Feb 20, 2010 at 4:28 AM, Dieter Menne
dieter.me...@menne-biomed.de wrote:
Daniel-6 wrote:
Hello, I'm trying to add lme results in a table with lm coef results, but
as
I know, estout or xtabel cannot support lme objects.
I'm a new in R and I'll appreciate some helpful comments.
On Sat, Feb 20, 2010 at 10:27 AM, Dieter Menne
dieter.me...@menne-biomed.de wrote:
Douglas Bates-2 wrote:
On Sat, Feb 20, 2010 at 4:28 AM, Dieter Menne
For most other model fitting functions the sequence
coef(summary(mymodel))
works. Unfortunately, in the nlme package we assigned
On Wed, Feb 24, 2010 at 3:56 PM, Duncan Murdoch murd...@stats.uwo.ca wrote:
On 24/02/2010 4:31 PM, Georg Ehret wrote:
Dear R communtiy,
I do not understand why this does not work...:
betaS$SBP
[1] 0.03274 -0.04216 -0.08986 -0.45980 0.60320 -0.63070 -0.05682
0.20130
t-c(betaS$SBP)
An alternative to cross-compiling when you have a source package is to
use the Win-builder facility at win-builder.R-project.org
Thanks to Uwe for providing this facility. I find it much, much
easier than trying to cross-compile or to set up a Windows computer
for compiling R packages.
On
On 9/26/07, Rob Forsyth [EMAIL PROTECTED] wrote:
I would appreciate confirmation that the function vcov(model.nlme)
gives the var-cov matrix of the fixed effects in an nlme model.
It gives the approximate variance-covariance matrix for the
fixed-effects parameters in the model. (Exact
not sure it give the fitted values both for
the fixed and random or only the fixed. I looked in the r help and the r
list and I haven't not found much details about it excepted this
comments from Douglas Bates in January 2006 :
Would it help if there were an option in the fitted method to allow
outpm or outp in SAS).
..
Quoting Douglas Bates bates at stat.wisc.edu
The calculation of the level = 0 fitted values in the new
representation of the fitted model is quite easy. It is
[EMAIL PROTECTED] %*% fixef(fm1)
Douglas Bates replied
Yes.
Mmm.. If I consider a few
On 10/5/07, Bert Gunter [EMAIL PROTECTED] wrote:
Folks:
In the following mixed effect model, the x and residual variance
components are nonidentifiable. Yet lme() (or the equivalent in lmer())
happily produces an answer in which the sum of the variance components is
the correct estimate of
On 10/8/07, Abdus Sattar [EMAIL PROTECTED] wrote:
Hello EVERYONE,
I need an URGENT help from you please!
How can I see the estfun (empirical estimating function) and df (degree
of freedom) from the following mixed-model please?
(fm1 - lmer2(Reaction ~ Days + (Days|Subject), sleepstudy))
On 10/8/07, Achim Zeileis [EMAIL PROTECTED] wrote:
On Mon, 8 Oct 2007, Abdus Sattar wrote:
Hello EVERYONE,
I need an URGENT help from you please!
This type of requests is not considered to be very polite, please have a
look at the posting guide.
How can I see the estfun (empirical
On 10/11/07, David Reitter [EMAIL PROTECTED] wrote:
After upgrading to R 2.6.0, I'm having trouble running lmer:
model - lmer(primed ~ log(dist.time)*role + 1|target.utt,
data=data.utts)
Error in UseMethod(as.logical) : no applicable method for as.logical
That problem originates in the
On 10/11/07, Martin Ivanov [EMAIL PROTECTED] wrote:
Dear R users,
I need to to the the following. Let a= 1 2 3
4 5 6
and b= -1 -2 -3 be (2x3) matrices.
-4 -5 -6
I need to combine the two matrices into a new (2x6) matrix like this:
ab =
On 10/11/07, Douglas Bates [EMAIL PROTECTED] wrote:
On 10/11/07, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote:
Dear list, first accept my apologies for asking a non-R question.
Can anyone point me to a good reference on logistic regression? web or
book references would be great. I am
On 10/12/07, David Afshartous [EMAIL PROTECTED] wrote:
All,
Sorry for overly simplistic question, but I can't seem to remember how to
create the basic plot shown in Figure 1.1 of Pinheiro Bates (2004; p.4).
The y-axis delineates a factor (Rail) while the x-axis displays the
distribution of a
On 10/15/07, Doran, Harold [EMAIL PROTECTED] wrote:
?vcov
The vcov method returns the estimated variance-covariance matrix of
the fixed-effects only. I think Irene's question is about the
combination of the fixed-effects parameters and the BLUPs of the
random effects that is returned by the
I have reached the correlation section in a course that I teach and I
hit upon the idea of using data from the weekly Bowl Championship
Series (BCS) rankings to illustrate different techniques for assessing
correlation.
For those not familiar with college football in the United States
(where
On 10/26/07, Frank Thomas [EMAIL PROTECTED] wrote:
...
BTW: Contrary to some ideas both R SPSS can be programmed and the
algorithms for both have been published. So, no matter whether open
source or private property you know what you do (if you want).
This is off the point of Matt's original
On 10/24/07, Dimitris Rizopoulos [EMAIL PROTECTED] wrote:
you can wave a look at the gls() function in package nlme, and
specifically at the `weights' and `correlation' arguments; the same
arguments are also available in the lme() function.
That is certainly a way of fitting a correlation
I have created some slides on the Bowl Championship series data for my
class. Copies of just that part are available in
http://www.stat.wisc.edu/~bates/BCS.zip
Two interesting things about the analysis are that a parallel
coordinate plot shows the differences in agreement quite clearly and
that
On Nov 9, 2007 1:15 PM, Rick Bilonick [EMAIL PROTECTED] wrote:
On Fri, 2007-11-09 at 18:55 +, Prof Brian Ripley wrote:
I think Bert's point is important: I picked up a student on it in a case
study presentation on this week because I could think of three
interpretations, none strictly
On Nov 13, 2007 1:02 AM, Rick Bilonick [EMAIL PROTECTED] wrote:
On Tue, 2007-11-13 at 01:03 -0500, Rick Bilonick wrote:
Is there some way to get ranef with postVar=TRUE to show what the
variances are, or what the lower and upper bounds are? qqmath makes nice
plots but I need to obtain
2008/1/31 stephen sefick [EMAIL PROTECTED]:
the data is attached
Thanks.
I want to boxplot this data
y-read.table(afdmmgs.txt, header=T)
boxplot(y)
At this point you should use
str(y)
to examine the structure of the data.
str(y)
'data.frame': 4 obs. of 12 variables:
$ X215: num
On Feb 1, 2008 7:30 AM, Falco tinnunculus [EMAIL PROTECTED] wrote:
Dear all,
Is it possible with two random effects in lme()?
lmefit1- lme(Handling ~ Mass + factor(Prey)+ Mass*factor(Prey), random = ~
1 |Place+Age)
I assume that Place and Age are not nested. If so, it's possible to
fit
On Feb 6, 2008 11:28 AM, Tony Plate [EMAIL PROTECTED] wrote:
Bert Gunter wrote:
I strongly suggest you collaborate with a local statistician. I can think of
no circumstance where multiple regression on hundreds of thousands of
variables is anything more than a fancy random number generator.
On Feb 7, 2008 3:43 PM, Eric Imbert [EMAIL PROTECTED] wrote:
I am analyzing from a very simple experiment.
I have measured plants of two different colours (yellow and purple) in 9
different populations.
So, I have two different factors : a fixed effect (Colour with two
levels) and a random
On Feb 10, 2008 2:32 PM, Spencer Graves [EMAIL PROTECTED] wrote:
Hi, Erin:
Have you looked at Pinheiro and Bates (2000) Mixed-Effects Models
in S and S-Plus (Springer)?
As far as I know, Doug Bates has been the leading innovator in
this area for the past 20 years. Pinheiro was
On Feb 13, 2008 9:53 AM, Ista Zahn [EMAIL PROTECTED] wrote:
Dear R listers,
I know I'm breaking the rules by asking a homework related question--
I hope you'll forgive me. I am a social psychology graduate student,
and the only one in my department who uses R. I successfully completed
my
Could you tell us which version of the lme4 package you are using?
You can just send the output produced by
sessionInfo()
If you can make your data available so we can test it then please do
so. If the data set is large you could send it to me in private email
and I will make it available on a
Could you send us the output of sessionInfo() please so we can see
which version of the lme4 package you are using? In recent versions,
especially the development version available as
install.packages(lme4, repos = http://r-forge.r-project.org;)
the PQL algorithm is no longer used. The Laplace
On Fri, Feb 15, 2008 at 1:53 PM, Kathy Gerber [EMAIL PROTECTED] wrote:
Earlier today I sent a question to Frank Harrell as an R developer with
whom I am most familiar. He suggested also that I put my questions to
the list for additional responses. Next month I'll be giving a talk on
R as
On Feb 15, 2008 11:50 AM, Gabor Grothendieck [EMAIL PROTECTED] wrote:
Try fitting regressing log(WEIGHT) against log(TOTAL) using lm
and then transform the results into starting values for nls (or
possibly that is sufficient and you don't need the nls results).
Also, set the trace argument to
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