On 8/30/07, Douglas Bates <[EMAIL PROTECTED]> wrote:
> On 8/29/07, Fränzi Korner <[EMAIL PROTECTED]> wrote:
>
> > how can I specify a correlation structure in the lmer-function as it is
> > possible in lme(formula, ..., corr=corAR1(form=...))?
>
> The short ans
On 8/29/07, hui xie <[EMAIL PROTECTED]> wrote:
> Thanks very much for all your advice. To be clear, my OS is window XP. I
> bought this server last year. It's Dell Precision PWS690. THe processor is
> Xeon(TM) CPU 3GHZ, 2G RAM. I am not sure how to check more details of
> processor on my compute
On 8/29/07, Fränzi Korner <[EMAIL PROTECTED]> wrote:
> how can I specify a correlation structure in the lmer-function as it is
> possible in lme(formula, ..., corr=corAR1(form=...))?
The short answer is "you can't".
__
R-help@stat.math.ethz.ch mailing
On 8/22/07, Greg Tarpinian <[EMAIL PROTECTED]> wrote:
> R2.3, WinXP
> Dear all,
> I am using the following functions:
> f1 = Phi1+(Phi2-Phi1)/(1+exp((log(Phi3)-log(x))/exp(log(Phi4)))
> f2 = Phi1+(Phi2-Phi1)/(1+exp((log(Phi3)-log(r)-log(x))/exp(log(Phi4)))
> subject to the residual weight
On 8/21/07, Horace Tso <[EMAIL PROTECTED]> wrote:
> Deepayan, you're right. Now I realize anyone could write a densityplot
> function to apply on a different class of objects. I guess I should write to
> the author of lme4 which from what I could see does not describe a
> densityplot. By the way
On 8/14/07, Jiao Yang <[EMAIL PROTECTED]> wrote:
> Tir,
> Thank you very much for the note. I'm using an algorithm to analyze a data
> set of 400 variables and the algorithm uses the inverse of a 16x16
> positive definite matrix. The matrix is stored as a text file.
A meta-theorem in
On 8/7/07, Daniel Caro <[EMAIL PROTECTED]> wrote:
> Dear all,
>
> I want to estimate a crossed-random-effects model (i.e., measurements,
> students, schools) where students migrate between schools over time.
> I'm interested in the fixed effects of "SES", "age" and their
> interaction on "read" (re
On 7/30/07, Gregory Gentlemen <[EMAIL PROTECTED]> wrote:
>
>
> Douglas Bates <[EMAIL PROTECTED]> wrote:
> On 7/27/07, Gregory Gentlemen wrote:
> > Greetings,
>
> > I have a seemingly simple task which I have not been able to solve today.
> I want to cons
On 7/27/07, Gregory Gentlemen <[EMAIL PROTECTED]> wrote:
> Greetings,
> I have a seemingly simple task which I have not been able to solve today. I
> want to construct a symmetric matrix of arbtriray size w/o using loops. The
> following I thought would do it:
> p <- 6
> Rmat <- diag(p)
> dat.c
On 7/12/07, JVVerkuilen <[EMAIL PROTECTED]> wrote:
> Hello all,
> I am using lme4 to fit some mixed logistic regressions. I need to
> impose an identification constraint of the following form:
> (1sig12)
> (sig12 sig22)
> and have not figured out how to do it, i.e., sig11 = 1 but the re
On 7/12/07, Atte Tenkanen <[EMAIL PROTECTED]> wrote:
> Seems to work, if I unlist the argument at first ;-)
> Atte
> > Hi,
> > What's wrong here?:
> > > v=c(`-`,`+`,1,`^`,`^`,NA,NA,"X",9,"X",2)
> > > i2=16
> > > v[i2]
> > [[1]]
> > NULL
> > > is.null(v[i2])
> > [1] FALSE
> > Is it a bug or h
On 7/11/07, Helin Gai <[EMAIL PROTECTED]> wrote:
> Hi all,
> I'm wondering whether anyone has installed R on Mac OS X leopard with
> success. I downloaded the latest version, but couldn't have it installed.
> Any idea as to how I get around the problem? Thanks!
Simon Urbanek has comments about R f
On 6/27/07, ivo welch <[EMAIL PROTECTED]> wrote:
> Dear R experts---I would like to write a replacement for the read.csv
> function that is less general, but also more efficient.
>
> could someone please provide me with a skeleton function that shows me
> how to read the arguments and return a data
On 6/22/07, Zhang Jian <[EMAIL PROTECTED]> wrote:
> I have some programs which were writen in mathematica or c language, but I
> donot know how to use these software. So I want to run them in R.
> Can I do it ?
> How to run "mathematica" or "c" programs in R?
To paraphrase Thomas Lumley,
Sure.
On 6/21/07, [EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote:
> Dear list,
> I would like to do a huge number of lme's using the same design matrix
> (and fixed and random effects). Is it possible to do this efficiently?
> Doing otherwise is not an option for my example.
> Basically, I am wanting to d
On 6/18/07, Julia Proudnikova <[EMAIL PROTECTED]> wrote:
> Hello,
>
> We have a problem with function lmer. This is our code:
>
> Get_values<-function(ff_count, fixed_factors, rf_count, random_factors,
> y_values)
> {
> SA<-matrix(as.array(c(fixed_factors, random_factors)), ncol=3)
> data<-as.
On 6/16/07, Ronaldo Reis Junior <[EMAIL PROTECTED]> wrote:
> When I using Xemacs+ESS to write a R code, I need to comment out a code line
> by line putting #
> It is possible to configure ESS to comment and uncomment a selected block of
> code.
This question probably belongs on the ESS-help mail
On 6/14/07, Greg Snow <[EMAIL PROTECTED]> wrote:
>
> Try:
>
> > lm( formula( paste( Ytext, '~ Xvar' ) ), data=X)
That type of construction is perilously close to parse(paste(...)) and
we know what Thomas said about that (see fortune("parse")).
A safer way of constructing a formula from names stor
On 6/15/07, Nicholas Lewin-Koh <[EMAIL PROTECTED]> wrote:
> Hi,
> I just saw this thread. This issue, and the larger scale issue of open
> source in industry
> is being addressed. One has to realize that the behemoth that is the
> clinical aperatus
> of the pharma industry is very conservative and
On 6/13/07, David Daniel <[EMAIL PROTECTED]> wrote:
> Running the Chapter 4 examples in Pinheiro & Bates' "Mixed-Effects
> Models in S and S-PLUS" (2000), I get a message that the default
> optimizer doesn't converge, but using "optim" for the optimizer
> results in convergence:
>
> > > library(nlm
On 6/7/07, Robert Wilkins <[EMAIL PROTECTED]> wrote:
> As noted on the R-project web site itself ( www.r-project.org ->
> Manuals -> R Data Import/Export ), it can be cumbersome to prepare
> messy and dirty data for analysis with the R tool itself. I've also
> seen at least one S programming book (
On 6/4/07, Stan Hopkins <[EMAIL PROTECTED]> wrote:
> I'm new to R and am trying to extract the factors of a dataframe using
> numeric indices (e.g. df[1]) that are input to a function definition instead
> of the other types of references (e.g. df$out). df[1] is a list(?) whose
> class is "dataf
On 6/1/07, [EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote:
> I was reading the help but just did not get how to specify starting values for
> varIdent() of the lme() function, although I managed to do it for corSymm().
> Do I specify the values just as they are printed out in an output, like c(1,
> 1
It looks like your C++ compiler is mangling the name
R_RegisterCCallable. Move the
extern "C"
before the
#include
On 6/1/07, Alex Chen <[EMAIL PROTECTED]> wrote:
> Hi,
>
>
>
> I want to make use of some C routines from other packages to write extensions
> in C.
>
>
>
> In "Writing R Extension
On 6/1/07, emine özgür Bayman <[EMAIL PROTECTED]> wrote:
> Dear R users,
> I'm pretty new on using lmer package. My response is binary and I have fixed
> treatment effect (2 treatments) and random center effect (7 centers). I want
> to test the effect of treatment by fitting 2 models:
>
> Model 1:
On 5/28/07, [EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote:
> Hi All
> Had anyone of you seen if it is possible to split a large lme() job to be
> processed by multiple cpus/computers?
> I am just at the very beginning to understand related things, but does the
> lme()
> use solution finding functi
On 5/24/07, Ken Nussear <[EMAIL PROTECTED]> wrote:
> > Ken Nussear mac.com> writes:
> >
> > > I'm running a series of mixed models using lme, and I wonder if
> > there
> > > is a way to sort them by AIC prior to testing using anova
> > > (lme1,lme2,lme3,lme7) other than by hand.
> >
> > You ca
On 5/22/07, Adrian Dusa <[EMAIL PROTECTED]> wrote:
> Dear all,
> Is it possible to add a list in the data folder when creating a new package?
Yes.
> In other words, is data in packages restricted to data.frame only?
Well section 1.1.3 of the manual "Writing R Extensions" say, in part,
"Currentl
On 5/20/07, [EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote:
> I was wondering how to get the same results with gls and lme. In my lme, the
> design matrix for the random effects is (should be) a identity matrix and
> therefore G should add up with R to produce the R matrix that gls would report
> (V=
On 5/15/07, Jose Quesada <[EMAIL PROTECTED]> wrote:
> Hi,
>
> I'm finding that readMM() cannot read a file written with writeMM().
> Example:
>
> library(Matrix)
> a = Matrix(c(1,0,3,0,0,5), 10, 10)
> a = as(a, "CsparseMatrix")
> writeMM(a, "kk.mm")
> b = readMM("kk.mm")
>
> Error in validObject(.O
On 5/16/07, Thomas Adams <[EMAIL PROTECTED]> wrote:
> Marc,
>
> That did it! Thank you so much for your help…
>
> Regards,
> Tom
>
>
> Marc Schwartz wrote:
> > On Wed, 2007-05-16 at 16:34 -0400, Thomas Adams wrote:
> >
> >> I am generating a single graphic containing about 31 Boxplots; the issue
>
On 5/16/07, Rick DeShon <[EMAIL PROTECTED]> wrote:
> Hi All.
>
> I'm trying to run a simple model from Baayan, Davidson, & Bates and getting
> a confusing error message. Any ideas what I'm doing wrong here?
>
> # Here's the data.
> Subj<- factor(rep(1:3,each=6))
> Item<- factor(rep(1:3
-- Original Message
From: Douglas Bates <[EMAIL PROTECTED]>
To: Steven McKinney <[EMAIL PROTECTED]>
Cc: Iasonas Lamprianou <[EMAIL PROTECTED]>; r-help@stat.math.ethz.ch
Sent: Tuesday, 15 May, 2007 2:17:34 AM
Subject: Re: [R] lmer function
On 5/14/07, Steven McKin
On 5/16/07, Vittorio De Martino <[EMAIL PROTECTED]> wrote:
> After upgrading to 2.5.0 under freebsd 6.2 I updated all the add-on packages
> in an R session via update.packages(...). R was unable to install
> the "Matrix" package because it couldn't find the package.
> Therefore I downloaded the *.t
On 5/15/07, Seyed Reza Jafarzadeh <[EMAIL PROTECTED]> wrote:
> It should be
>
> > lmer(success ~ yearF + (1 | bandnumb), data=quality, family = binomial,
> > method = PQL)
It has to be method = "PQL" (the quotes are important) except that the
PQL method is no longer an option in lmer. Beginning
gt;lme4 Matrix lattice
> "0.9975-13" "0.9975-11""0.15-4"
> >
>
> Steven McKinney
>
> Statistician
> Molecular Oncology and Breast Cancer Program
> British Columbia Cancer Research Centre
>
> email: [EMAIL PROTECTED]
On 5/14/07, Brian Riordan <[EMAIL PROTECTED]> wrote:
> I'm trying to specify a model using lmer with a binary response and
> interaction term, but I get an error I can't parse (see below).
>
> Here is some sample data:
>
> SubjectConcordAgeDisc
> SVC999MX148SU-Fyesuint
> TOU
On 5/14/07, Iasonas Lamprianou <[EMAIL PROTECTED]> wrote:
> Does anyone know if the lmer function of lme4 works fine for unbalanced
> designs? I have the examination results of 1000 pupils on three subjects, one
> score every term. So, I have three scores for English (one for every term),
> thre
On 5/14/07, Martin Henry H. Stevens <[EMAIL PROTECTED]> wrote:
> Hi Cleber,
> By "full" I simply meant "not REML." the function assumes that the
> fixed effects were estimated using REML criteria, and using update()
> simply changes that to ML. If the model was fit originally with ML,
> it shouldn
On 5/11/07, Benilton Carvalho <[EMAIL PROTECTED]> wrote:
> Hi everyone,
>
> sorry if this was discussed before (and in this situation, could you
> please point me to the discussion in the archive? My search didn't
> seem to be effective).
>
> Is there a way of getting the names of objects in a .rda
On 5/4/07, ivo welch <[EMAIL PROTECTED]> wrote:
hi doug: yikes. could I have done better? Oh dear. I tried to make
my example clearer half-way through, but made it worse. I meant
set.seed(1);
fe = as.factor( as.integer( runif(100)*10 ) ); y=rnorm(100); x=rnorm(100);
print(summary(lm( y ~
On 5/3/07, ivo welch <[EMAIL PROTECTED]> wrote:
> dear R experts:
>
> sorry, I have to ask this again. I know that the answer is in section
> 7.2 of "S Programming," but I don't have the book (and I plan to buy
> the next edition---which I hope will be titled S/R programming ;-) ).
> I believe th
On 5/4/07, Adrian J. Montero Calvo <[EMAIL PROTECTED]> wrote:
> Can anybody explain me how do i get Correlation Coefficient R² in a
> non-linear regresion analisys performed with nls()?. Thanks in advance.
It may seem "obvious" how to define the multiple correlation
coefficient R^2 for a non-linea
On 4/27/07, Michael Kubovy <[EMAIL PROTECTED]> wrote:
> Hi,
>
> I would appreciate help with the following model
>
> <<1>>=
> gunload <- read.table(hh('datasets/gunload.dat'), header = T)
> gunload$method <- factor(gunload$method, labels = c('new', 'old'))
> gunload$physique <- factor(gunload$group
On 4/28/07, John Kane <[EMAIL PROTECTED]> wrote:
> IIRC you have a yes/no smoking variable scored 1/2 ?
>
> It is possibly being read in as a factor not as an
> integer.
>
> try
> class(df$smoking.variable)
> to see .
Good point. In general I would recommend using
str(df)
to check on the class
On 4/28/07, Ajit Pawar <[EMAIL PROTECTED]> wrote:
> Greetings,
> This might be something very simple but a nice solution eludes me!!
>
>I have a function that I call within sapply that generates data frame
> in each call. Now when sapply returns me back the result - it's in the form
>
On 4/24/07, Gardar Johannesson <[EMAIL PROTECTED]> wrote:
> I have been playing around with sparse matrices in the Matrix
> package, in particularly with the Cholesky factorization of matrices
> of class dsCMatrix. And BTW, what a fantastic package.
>
> My problem is that I have to carry out repeat
On 4/18/07, Bernhard Klingenberg <[EMAIL PROTECTED]> wrote:
> Consider the code:
>
> x <- seq(0,1,0.2)
> y <- seq(0,1,0.01)
> cbind(match(y,x),y)
>
> which, surprisingly, doesn't show a match at 0.6! (It gives correct
> matches at 0, 0.2, 0.4, 0.8 and 1, though)
>
> In addition,
>
> x[4]==y[61]
>
>
On 4/18/07, Helmut Schütz <[EMAIL PROTECTED]> wrote:
> Dear group members,
>
> I want to compare response variables ("logAUC") of two groups (treatment
> "Test", "Reference") of a subset ("period == 1") in dataframe "resp"
> (below):
>
>sequence subject period treatment AUC logAUC
> 1
May I suggest the Exam data from the mlmRev package as an example.
If you wish to have a random effect for Sex by school you could write
the model as
lmer(test.result ~ homework + Sex + (Sex|school))
which gives correlated random effects for the overall achievement in
schools and the differentia
On 4/13/07, Michael Stevens <[EMAIL PROTECTED]> wrote:
Hi,
I have sort of a newbie question. I've seriously put a lot of effort into how
to handle simple replicates in a repeated ANOVA design, but haven't had much
luck.
I really liked reading "Notes on the use of R for psychology experiments an
On 4/12/07, Izmirlian, Grant (NIH/NCI) [E] <[EMAIL PROTECTED]> wrote:
> Hi:
>
> I've been reading "Computational Methods for Multilevel Modeling" by Pinheiro
> and Bates, the idea of embedding the technique in my own c-level code. The
> basic idea is to rewrite the joint density in a form to mimi
On 4/11/07, Brendan Connors <[EMAIL PROTECTED]> wrote:
> Hi R-users:
>
> New to R and I am trying to run a GLM with random effects.
>
> I have 3 replicates ('Replicate) of counts of parasites ('nor.tot.lep')
> before and after an experiment ('In.Out'). When I run lmer I get the
> error messages (16
On 4/11/07, Robert Duval <[EMAIL PROTECTED]> wrote:
> So I guess my question is...
>
> Is there any hope of R being modified on its core in order to handle
> more graciously large datasets? (You've mentioned SAS and SPSS, I'd
> add Stata to the list).
>
> Or should we (the users of large datasets)
On 4/11/07, Åsa Granberg <[EMAIL PROTECTED]> wrote:
> Hi all!
>
> My question is why, and what I can do about that
> I sometimes, but not always, get warning-messages like
>
> nlminb returned message singular convergence (7)
> in: LMEopt(x = mer, value = cv)
>
> or
>
> IRLS iterations for PQL did
On 4/11/07, Jeann S <[EMAIL PROTECTED]> wrote:
> Dear all,
>
> Sorry for bringing up an old issue:
>
> >pexp(50, 0.5)
> [1] 1
>
> In some cases, pexp() gives CDF=1. I read some discussion in 2002 saying it
> has been patched. However it's not working in "R2.4.1Patched". Could anyone
> help
On 4/11/07, Tu Yu-Kang <[EMAIL PROTECTED]> wrote:
> Dear R experts,
>
> I had a question which may not be directly relevant to R but I will be
> grateful if you can give me some advices.
>
> I ran a two-level multilevel model for data with repeated measurements over
> time, i.e. level-1 the repeate
On 4/10/07, Wensui Liu <[EMAIL PROTECTED]> wrote:
> Greg,
> As far as I understand, SAS is more efficient handling large data
> probably than S+/R. Do you have any idea why?
SAS originated at a time when large data sets were stored on magnetic
tape and the only reasonable way to process them was s
On 4/4/07, [EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote:
> Hello,
>
> Is there any function "argmax" in R ?
>
> For example, if I have the vector x=c(1,4,15,7,6), max(x)=15.
> But I need a function f such that f(x)=3, 3 being the number where 15 is.
which.max
__
istance.
> -----Original Message-
> From: [EMAIL PROTECTED] on behalf of Douglas Bates
> Sent: Tue 4/3/2007 5:57 PM
> To: Fang, Yongxiang
> Cc: r-help@stat.math.ethz.ch
> Subject: Re: [R] the numimum number of fixed factors lme package can deal with
>
> On 4/3/07, Fan
On 4/2/07, Seyed Reza Jafarzadeh <[EMAIL PROTECTED]> wrote:
> Hi,
>
> I am getting a warning message when I am fitting a generalized linear
> mixed model (m1.2 below).
>
>
> CHOLMOD warning: matrix not positive definite
> Error in objective(.par, ...) : Cholmod error `matrix not positive
> definit
On 4/3/07, Fang, Yongxiang <[EMAIL PROTECTED]> wrote:
> In my study, mixed effects model is required and the number of fixed
> effects is very large. When lme package is employed, a model error is
> displayed once the number of fixed factors in the formula reaches 200. Is
> this the maximum numbe
I did read your second message about the problem symptoms disappearing
but I thought that I might make a couple of suggestions about your
code anyway.
There are a number of helper functions declared in Rinternals.h such
as ScalarReal, which is equivalent to your mkans. (Also
ScalarInteger, Scalar
On 3/28/07, Marc Schwartz <[EMAIL PROTECTED]> wrote:
> On Wed, 2007-03-28 at 02:42 -0700, francogrex wrote:
> > Does anyone know of an R package that is equivalent of S+SeqTrial for
> > analysis of clinical trials using group sequential methods? Thanks.
>
> I don't know that there are fully functio
On 3/22/07, Muenchen, Robert A (Bob) <[EMAIL PROTECTED]> wrote:
> Perhaps I'm stating the obvious, but to increase the use of R in places
> where SAS & SPSS dominate, it's important to make getting the same
> answers as easy as possible. That includes things like lsmeans and type
> III sums of squ
On 3/22/07, Hufkens Koen <[EMAIL PROTECTED]> wrote:
> Is there a means of getting an F-statistic (p-value) out of all of this.
> Because least-square criterion / r-square only tell me how good the fit is
> and not necessarily how solid this fit is. An F-statistic (p-value) would be
> nice...
Wh
On 3/21/07, Doran, Harold <[EMAIL PROTECTED]> wrote:
> The function integrate() uses AGQ. There are other functions for
> gaussian quadrature in the statmod() package that I really like.
I think that integrate does adaptive quadrature but not adaptive
Gaussian quadrature (which probably should hav
On 3/20/07, Mike Lawrence <[EMAIL PROTECTED]> wrote:
> Hi all,
>
> Trying to understand the logistic regression performed by glm (i.e. when
> family='binomial'), and I'm curious to know how it treats perfect
> success. That is, lets say I have the following summary data
>
> x=c(1,2,3,4,5,6)
On 3/7/07, Bricklemyer, Ross S <[EMAIL PROTECTED]> wrote:
>
> I was finally able to get R to 'configure', 'make', and 'install' on Mandriva
> 2007. Itried to install gnomeGUI and I received an error. See below. At
> what step do I make R a shared library? Where did I go wrong?
At the configu
On 3/8/07, Andrew Robinson <[EMAIL PROTECTED]> wrote:
> Hi Kyle,
>
> not yet! At least not as far as I know.
Not as far as I know either.
> On Thu, Mar 08, 2007 at 03:08:19PM -0600, Roberts, J. Kyle wrote:
> > I read the posts about augPred with lme, but does anyone know if there is a
> > corre
On 3/6/07, Peter Dalgaard <[EMAIL PROTECTED]> wrote:
> Bert Gunter wrote:
> > Folks:
> >
> > In the past 2 days I have seen a large increase of spam getting into
> > R-help. Are others experiencing this problem? If so, has there been some
> > change to the spam filters on the R-servers? If not, is
On 3/6/07, Bert Gunter <[EMAIL PROTECTED]> wrote:
> In the past 2 days I have seen a large increase of spam getting into
> R-help. Are others experiencing this problem? If so, has there been some
> change to the spam filters on the R-servers? If not, is the problem on my
> end?
There has indeed
On 3/6/07, Laura Hill <[EMAIL PROTECTED]> wrote:
> Can the expm function be used to calculate the exponential of a matrix where
> the matrix is multiplied by a vector in a data frame?
I don't quite understand the question. The exponential of a matrix is
only defined for square matrices.
> For ex
On 3/2/07, Beth Gifford <[EMAIL PROTECTED]> wrote:
> Hey there
> I am estimating a multilevel model using lmer. I have 5 imputed datasets so
> I am using mitools to pool the estimates from the 5
> datasets. Everything seems to work until I try to use
> MIcombine to produced pooled estimates. Doe
On 2/28/07, Ralf Sommerfeld <[EMAIL PROTECTED]> wrote:
> Dear R-help list readers,
>
> I am fitting a mixed model using the lme function (R V 2.3.1 for
> Windows). This is an example:
>
> dep<-c(25,40,33.33,60,70.83,72,71.43,50,40,53.33,64,54.17,60,53.57)
> yes<-c(0,1,2,3,4,5,6,0,1,2,3,4,5,6)
> tre
On 2/27/07, Bricklemyer, Ross S <[EMAIL PROTECTED]> wrote:
> All,
>
> I am a new user to Linux but I am familiar with R. I have previously
> used and installed R on a Windows platform without problems. I recently
> set up a dual boot system (XP_64, Mandriva) to run R on a Linux platform
> in orde
On 2/23/07, Ronaldo Reis Junior <[EMAIL PROTECTED]> wrote:
> Em Quinta 22 Fevereiro 2007 20:36, Andrew Robinson escreveu:
> > Hi Ronaldo,
> >
> > I suggest that you send us a small, well-documented, code example that
> > we can reproduce. It certainly looks as though there is a problem,
> > but gi
On 2/21/07, joerg van den hoff <[EMAIL PROTECTED]> wrote:
> On Wed, Feb 21, 2007 at 11:09:52AM +, Prof Brian Ripley wrote:
> > Well, the algorithm used does not affect the confidence interval (provided
> > it works correctly), but what is nls.ml (presumably in some package you
> > have not ment
On 2/19/07, Nils Höller <[EMAIL PROTECTED]> wrote:
> Hi,
>
> I have some big calculations in R to be done.
> Since I can use R on a server with ssh, i was wondering if I can reopen
> a R Shell after exiting ssh.
>
> I don't want to use the batch mode and nohup doesn't work.
>
> I want to use someth
On 2/16/07, Jari Oksanen <[EMAIL PROTECTED]> wrote:
> Gerard Smits g_smits at verizon.net Fri Feb 16 00:46:09 CET 2007:
> > just noticed that two key pieces of information are not given by
> > the summary() command: N and SD. we are given the N missing, but
> > not the converse. I know these sum
On 2/13/07, shirley zhang <[EMAIL PROTECTED]> wrote:
> I'm working with a nested model (mixed).
>
> I have four factors: Patients, Tissue, sex, and tissue_stage.
>
> Totally I have 10 patients, for each patient, there are 2 tissues
> (Cancer vs. Normal).
>
> I think Tissue and sex are fixed. Patien
old. If it didn't install on a stock version of R-2.4.1
I imagine we would have heard about it before now. I think you may
need to check if somehow you have an old version of the methods
package on your search path or just install a fresh copy of R-2.4.1
>
> Douglas Bates wrote:
>
On 2/11/07, Andrew Gelman <[EMAIL PROTECTED]> wrote:
> I decided to update my packages and then had a problem with loading the
> Matrix package
> http://cran.at.r-project.org/bin/windows/contrib/2.4/Matrix_0.9975-9.zip
> This is what happened when I tried to load it in:
>
> > library("Matrix")
> E
uasi() allows user-specified variance functions.
>
> I thought that was the point of the example on the family help page.
>
> ken
>
>
> Douglas Bates a écrit :
> Look at the 'link' component of the two lists. In the binomial family
> object the link componen
On 2/11/07, Milton Cezar Ribeiro <[EMAIL PROTECTED]> wrote:
> How can I delete rows from a data.frame where almost one column is.na()?
The na.omit function does this.
> set.seed(123454321)
> x <- matrix(rnorm(50, mean = 1), ncol = 5)
> x[x < 0] <- NA
> df <- data.frame(x)
> df
X1
ideta : NULL
> - attr(*, "class")= chr "family"
>
>
> So, could this be the root of the problem?
>
> Here again is the logexp function:
> logexp <- function(days = 1)
> {
> linkfun <- function(mu) qlogis(mu^(1/days))
> linkinv <
On 2/10/07, Jessi Brown <[EMAIL PROTECTED]> wrote:
> Greetings, everyone. I've been trying to analyze bird nest survival
> data using generalized linear mixed models (because we documented
> several consecutive nesting attempts by the same individuals; i.e.
> repeated measures data) and have been u
On 2/9/07, [EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote:
> Does someone know how to use TA-Lib in R (http://ta-lib.org/)?
Simple. Read the documentation for TA-Lib, then read the manual
"Writing R Extensions", then write and test the necessary interface
routines.
___
On 2/9/07, Prof Brian Ripley <[EMAIL PROTECTED]> wrote:
> The other reason why pmin/pmax are preferable to your functions is that
> they are fully generic. It is not easy to write C code which takes into
> account that <, [, [<- and is.na are all generic. That is not to say that
> it is not worth
On 2/8/07, Albrecht, Dr. Stefan (AZ Private Equity Partner)
<[EMAIL PROTECTED]> wrote:
Dear all,
Thanks a lot for your comments.
I very well agree with you that writing efficient code is about optimisation.
The most important rules I know would be:
- vectorization
- pre-definition of vectors,
On 2/8/07, Manuel Morales <[EMAIL PROTECTED]> wrote:
> On Thu, 2007-02-08 at 16:53 +0100, Martin Maechler wrote:
> > > "Albr" == Albrecht, Dr Stefan (AZ Private Equity Partner) <[EMAIL
> > > PROTECTED]>
> > > on Thu, 8 Feb 2007 16:38:18 +0100 writes:
>
> > Albr> And, I was ver
On 2/8/07, Zembower, Kevin <[EMAIL PROTECTED]> wrote:
> In Henric's recent post, he included this output:
>
> @BOOK{R:Harrell:2001,
> AUTHOR = {Frank E. Harrell},
> TITLE = {Regression Modeling Strategies, with Applications to
> Linear Models, Survival Analysis and Logistic
>
On 2/7/07, This Wiederkehr <[EMAIL PROTECTED]> wrote:
> I tried to fit data with the following function:
>
> fit<-nls(y~ Is*(1-exp(-l*x))+Iph,start=list(Is=-2e-5,l=2.3,Iph=-0.3
> ),control=list(maxiter=500,minFactor=1/1,tol=10e-05),trace=TRUE)
> But I get only a singular Gradient warning...
Di
On 2/3/07, pu chen <[EMAIL PROTECTED]> wrote:
> hello,
> I have to calculate the determinants of near singular matrices. Presently R
> just stop at the precision of 2.16 e-16.
I'm not sure what you mean by that. Can you explain how you
determined that number, perhaps including some code?
It h
On 1/31/07, Jon Stearley <[EMAIL PROTECTED]> wrote:
> I need to sum the columns of a sparse matrix according to a factor -
> ie given a sparse matrix X and a factor fac of length ncol(X), sum
> the elements by column factors and return the sparse matrix Y of size
> nrow(X) by nlevels(f). The appen
On 1/27/07, gallon li <[EMAIL PROTECTED]> wrote:
> actually there are too many subjects.
>
> is there a way that i can make a table such that it can tell me the
> frequency of number of observations?
>
> Like
>
> 3 4 5
>
> 30 40 60
>
> which means there are 30 subjects which each has 3
Version 0.9975-11 of the lme4 package has been uploaded to CRAN. The
source package should be available on the mirrors in a day or two and
binary packages should follow soon after.
There are several changes in this release of the package. The most
important is the availability of a development v
On 1/18/07, w jj <[EMAIL PROTECTED]> wrote:
> I have a question about the function lme() in R.
>
> I have a 2*2*3 layout with some missing data (labelled as *). These 3
> factors are labelled as A,B,C, the response is Score. The layout is as
> follows:-
>
> A B C
On 1/3/07, Martin Henry H. Stevens <[EMAIL PROTECTED]> wrote:
> Hi folks,
> I have assumed that ratios of variance components (Fst and Qst in
> population genetics) could be estimated using the output of mcmcsamp
> (the series on mcmc sample estimates of variance components).
> What I have started
On 12/17/06, Guojing Yang <[EMAIL PROTECTED]> wrote:
> Dear R users,
> We have encountered a slight problem when using the lmer()
> function:
>
> 1. Data description: 11 locations; Nt: monthly mosquito population
> density from 1994-2005 in each location.
> 2. Question: to examine the degr
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