Hi,
I was wondering if I might be able to ask some advice about doing residual
plots for the lmer function in the lme4 package.
Our group's aim is to find if the expression staining of a particular gene
in a sample (or "core") is related to the pathology of the core.
To do this, we use
Hi all,
I would appreciate your advice how to model the survival model for the
following data, especially if it can be modeled in one model or if I should
(have to) break it up (i.e. assume that some events are independent of each
other, etc.). Data is on an experimental stock market simulation.
On Wed, 15 Aug 2007, Pijus Virketis wrote:
> Thank you.
>
> When I tried to set as.list() in baseenv(), I learned that its bindings
> are locked.
Of course. Did you not see my comment about 'to protect code against
redefining functions'?
> Does this mean that the thing to do is just to write m
I'm working with a very large matrix ( 22k rows x 2k cols) of RNA
expression data with R v.2.5.0 on a RedHat Enterprise machine, x86_64
architecture.
The relevant code is below, but I call a function that takes a cluster
of this data ( a list structure that contains a $rows e
In my output, I should see the last few lines.
If you want to track the output, you can try:
for (i in 1:1)
{
# print("Who is this?")
print (i)
flush.console ()
}
Xiaohui
[EMAIL PROTECTED] wrote:
> Hi,
>
> I have a small question about RGui. I have a piece of code that
Thank you - I wasn't aware of this function.
One can even use lchoose which allows really huge
arguments (more than 2^1000)!
--- "Lucke, Joseph F" <[EMAIL PROTECTED]>
wrote:
> C is an R function for setting contrasts in a
> factor. Hence the funky
> error message.
> ?C
>
> Use choose() for your
Hi,
I have a small question about RGui. I have a piece of code that I run out of
TinnR. Says.
for (i in 1:1)
print("Who is this?")
When I send this code to RGui. On RGui output, I can only see the first,
perhaps 10-20 lines, and the rest I have to scroll down to see them. How can I
se
On 15-Aug-07 21:16:32, Rolf Turner wrote:
>
> I have a data matrix X (n x k, say) each row of which constitutes
> an observation of a k-dimensional random variable which I am willing,
> if not happy, to assume to be Gaussian, with mean ``mu'' and
> covariance matrix ``Sigma''. Distinct rows of X
Thank you ***very*** much Ted and Chuck. I will install these two
packages and study
them over, and then in all probability pester you with more questions
when I find things
that I don't understand!
Thanks again.
cheers,
Rolf
On 16
Pijus,
My 2 cents, which might be post-hoc rationalization.
If your class 'is' a list, with additional information, then
setClass("Test", contains="list")
and you're ready to go.
On the other hand, if your class 'has' a list, along with other
information, create an accessor
setGeneric("test",
Ted Harding wrote:
> Hi Rolf!
>
> Have a look at the 'norm' package.
>
> This does just what you;re asking for (assuming multivariate
> normal, and allowing CAR missingness -- i.e. probability of
> missing may depend on observed values, but must not depend on
> unobserved).
>
> Read the document
Hi Rolf!
Have a look at the 'norm' package.
This does just what you;re asking for (assuming multivariate
normal, and allowing CAR missingness -- i.e. probability of
missing may depend on observed values, but must not depend on
unobserved).
Read the documentation for the various function *very* c
Thank you.
When I tried to set as.list() in baseenv(), I learned that its bindings
are locked. Does this mean that the thing to do is just to write my own
"lapply", which does the coercion using my "private" as.list(), and then
invokes the base lapply()?
-P
-Original Message-
From: Prof
I have a data matrix X (n x k, say) each row of which constitutes an
observation of
a k-dimensional random variable which I am willing, if not happy, to
assume to be
Gaussian, with mean ``mu'' and covariance matrix ``Sigma''. Distinct
rows of X may
be assumed to correspond to independent re
Hi Daniel,
You might want to review further advances by Doug Bates with lme4
since the post you show in your email.
http://tolstoy.newcastle.edu.au/R/e2/help/06/10/3565.html
In this thread Doug Bates discusses fitting using maximum
likelihood for testing purposes. There is now an anova()
method
On Wed, 15 Aug 2007, Pijus Virketis wrote:
> I would like to get lapply() to work in the natural way on a class I've
> defined.
What you have not said is that this is an S4 class.
> As far as I can tell, lapply() needs the class to be coercible
> to a list. Even after I define as.list() and as.v
Hello,
I installed RGui 2.5.1 and package DBI on Windows XP and tried to connect to
Oracle database which is on a Linux server. When I tried to use
dbDriver("Oracle"), I got an error as follows:
> drv <- dbDriver("Oracle")
Error in do.call(as.character(drvName), list(...)) :
co
Dear R users,
I am using 'R' version 2.2.1 and 'S-PLUS' version 6.0; and I loaded the
MASS library in 'S-PLUS'.
I am running a logistic regression using glm:
---
> mydata.glm<-glm(COMU~MeanPycUpT+MeanPycUpS, family=binomia
On Wed, 2007-08-15 at 12:06 -0600, Natalie O'Toole wrote:
> Hi,
>
> I do want to use the Mann-Whitney test which ranks my data and then
> uses
> those ranks rather than the actual data.
>
> Here is the R code i am using:
>
> group1<-
> c(1.34,1.47,1.48,1.49,1.62,1.67,1.7,1.7,1.7,1.73,1.81,1.8
On 16/08/2007, at 12:26 AM, Petr PIKAL wrote:
> Dear all
>
> Please help me with analysis of some periodic data.
>
> I have an output from measurement each minute and this output is
> modulated
> by rotation of the equipment (approx 6.5 min/revolution). I can easily
> spot this frequency from
>
Hi,
I would like to get lapply() to work in the natural way on a class I've
defined. As far as I can tell, lapply() needs the class to be coercible
to a list. Even after I define as.list() and as.vector(x, mode="list")
methods, though, I still get an "Error in as.vector(x, "list") : cannot
coerce
Lucke, Joseph F wrote:
> R and SPSS are using different but equivalent statistics. R is using
> the rank sum of group1 adjusted for the mean rank. SPSS is using the
> rank sum of group2 adjusted for the mean rank.
>
>
Close: It is the _minimum_ possible rank sum that is getting subtracted.
If
Thanks everyone!
NC
On 15/08/07, Ted Harding <[EMAIL PROTECTED]> wrote:
>
> On 15-Aug-07 18:17:27, Greg Snow wrote:
> >
> >
> >
> > Ted Harding wrote:
> > [snip]
> >
> >> So you if you want the density plot, you would need to calculate
> >> this for yourself. E.g.
R and SPSS are using different but equivalent statistics. R is using
the rank sum of group1 adjusted for the mean rank. SPSS is using the
rank sum of group2 adjusted for the mean rank.
Example.
> G1=group1
> G2=group2[-length(group2)] #get rid of the NA
> n1=length(G1) #n1=28
> n2=length(G2) #n2
Hi,
I do want to use the Mann-Whitney test which ranks my data and then
uses
those ranks rather than the actual data.
Here is the R code i am using:
group1<-
c(1.34,1.47,1.48,1.49,1.62,1.67,1.7,1.7,1.7,1.73,1.81,1.84,1.9,1.96,2,
2,2.19,2.29,2.29,2.41,2.41,2.46,2.5,2.6,2.
On 15-Aug-07 18:17:27, Greg Snow wrote:
>
>
>
> Ted Harding wrote:
> [snip]
>
>> So you if you want the density plot, you would need to calculate
>> this for yourself. E.g.
>>
>> H1$density <- counts/sum(counts)
>> plot.histogram(H1,freq=FALSE)
>
> shouldn't th
You might want to specifically look at R Windows FAQ:
http://cran.r-project.org/bin/windows/base/rw-FAQ.html#R-can_0027t-find-my-file
In Windows, you need to use double back-slashes or use Unix-like
forward-slashes. So, for example, use:
read.xport("D:\\Databases\\nameoffile.xpt")
Additionall
JMP can write CSV, and that's probably a safer choice than XPT.
Andy
From: Diana C. Dolan
>
> Hi,
> I know how to use SPSS and JMP, and have quite a few
> JMP files I would like to use in R. I converted them
> to .xpt files, downloaded the 'foreign' library then
> tried this command:
>
> >rea
Basically the random forest algorithm can generate a proximity
matrix of the data, and it's up to you how you would want to
proceed from there. You can feed that into clustering
algorithms that accept a similarity matrix, or turn it into a
distance matrix for clustering algorithms that need a
On Wed, 15 Aug 2007, Werner Wernersen wrote:
> Hi,
>
> I have a supposedly representative sample from a
> stratified survey. Hence, all observations have an
> associated sample weight each which inflate the sample
> to population size.
>
> I want to run a glm probit regression on the data but
> I
Hi,
I know how to use SPSS and JMP, and have quite a few
JMP files I would like to use in R. I converted them
to .xpt files, downloaded the 'foreign' library then
tried this command:
>read.xport("D:\\Databases\nameoffile.xpt")
to which I get:
>Error in lookup.xport(file) : unable to open file
On Wed, 15 Aug 2007, Giovanni Petris wrote:
>
> Hello,
>
> I am upgrading to the current R 2.5.1 under Sun Solaris 8.
Actually, 2.5.1 is not current: '2.5.1 patched' aka R-patched is and this
has already been addressed there.
> I call the configure script with the --without-readline flag, and
Hi,
I am trying to extract MARS' component analysis from the model.
Essentially, for an input matrix where each row is a different device, and
each column is a different measurement, I'd like to know which columns were
selected as most important for making the model.
I saw the all.terms and s
On Wednesday 15 August 2007 12:27 pm, Szymon Plucinski wrote:
> Hello,
>
> I was wondering if it is possible to create a live data feed from Yahoo
> Finance stock data into an R program? Do any such modules already exist?
> Thanks for any help.
>
> Szymon
>
> [[alternative HTML version delete
Hello,
I am upgrading to the current R 2.5.1 under Sun Solaris 8. I call the
configure script with the --without-readline flag, and it works
fine. Then, when I invoke make, I get this kind of error messages:
make[2]: Entering directory `/usr/local/R/R-2.5.1-inst/src/library'
>>> Building/Upda
Ted Harding wrote:
[snip]
> So you if you want the density plot, you would need to calculate
> this for yourself. E.g.
>
> H1$density <- counts/sum(counts)
> plot.histogram(H1,freq=FALSE)
shouldn't that be:
H1$density <- counts/sum(counts)/diff(brkpts)
?
Hi,
I do want to use the Mann-Whitney test which ranks my data and then uses
those ranks rather than the actual data.
Here is the R code i am using:
group1<-
c(1.34,1.47,1.48,1.49,1.62,1.67,1.7,1.7,1.7,1.73,1.81,1.84,1.9,1.96,2,2,2.19,2.29,2.29,2.41,2.41,2.46,2.5,2.6,2.8,2.8,3.07,3.3)
> group
Lamac,
The ANOVA shown in 'pamph14' may not be suitable for your data.
If the replicates are separate experiments or blocks, you will need to
become familiar with the nlme package and the lme function in it. ( Your
labelling of replicates suggests that this is the case, viz. no
A==1 & B == 3
Hello,
I was wondering if it is possible to create a live data feed from Yahoo
Finance stock data into an R program? Do any such modules already exist?
Thanks for any help.
Szymon
[[alternative HTML version deleted]]
__
R-help@stat.math.ethz.c
Here is another solution that gets around the non-standard
way that subset= is handled in lm. It has the advantage that unlike
the previous solution where formula1 and group == x appear literally
in the output, in this one the formula appears written out and
group == "A" and group == "B" appear:
On Wed, 2007-08-15 at 09:44 -0700, David Katz wrote:
> Several searches turned up nothing. Perhaps I will try to implement it if
> nobody else has. Thanks.
You can do this with Andy Liaw's randomForest package can do this and
the first hit on a Google search (on term "RFclustering") was this:
htt
try this:
> x = predict(z, Iris[-train, ])
> x1 <- rnorm(100,1)
> x2 <- rnorm(100,1)
> y <- rnorm(100,1)
> group <- rep(c("A","B"),c(40,60))
> group <- factor(group)
> df <- data.frame(y,x1,x2,group)
> resf1 <- lapply(levels(df$group),function(x) {formula1 <- as.formula(y~x1);
> lm(formula1,df,
It can't find x since the environment of formula1 and of formula2 is the Global
Environment and x is not there -- its local to the function.
Try this:
#generating data
set.seed(1)
DF <- data.frame(y = rnorm(100, 1), x1 = rnorm(100, 1), x2 = rnorm(100, 1),
group = rep(c("A", "B"), c(40, 60)))
f
try this:
lapply(levels(df$group), function(x)lm(formula1, data=df[group==x,]))
--
Henrique Dallazuanna
Curitiba-Paraná-Brasil
25° 25' 40" S 49° 16' 22" O
On 15/08/07, Li, Yan (IED) <[EMAIL PROTECTED]> wrote:
>
> I am trying to run separate regressions for different groups of
> observations usi
Several searches turned up nothing. Perhaps I will try to implement it if
nobody else has. Thanks.
--
View this message in context:
http://www.nabble.com/RFclustering---is-it-available-in-R--tf4274225.html#a12165636
Sent from the R help mailing list archive at Nabble.com.
__
I am helping my wife do some statistical analysis. She is a biologist,
and she has performed some measurements on various genotypes of
mice. My background is in applied mathematics and engineering, and I
have a fairly good statistics background, but I am by no means a PhD
level expert in statistica
Hi Folks,
I'm playing with glm.nb() in MASS.
Reference: the negative binomial distribution
P(y) = (Gamma(theta+y)/(Gamma(theta)*y!))*(p^theta)*(1-p)^y
y = 0,1,2,...
in the notation of the MASS book (section 7.4), where
p = theta/(mu + theta) so (1-p) = mu/(mu + theta)
where mu is the
I am trying to run separate regressions for different groups of
observations using the lapply function. It works fine when I write the
formula inside the lm() function. But I would like to pass formulae into
lm(), so I can do multiple models more easily. I got an error message
when I tried to do th
C is an R function for setting contrasts in a factor. Hence the funky
error message.
?C
Use choose() for your C(N,k)
?choose
choose(200,2)
19900
choose(200,100)
9.054851e+58
N=200; k=100; m=50; p=.6; q=.95
choose(N,k)*p^k*(1-p)^(N-k)*choose(k,m)*q^m*(1-q)^(k-m)
6.554505e-41
-Original Me
Hi everybody!
I'm looking some way to do in R a polynomial fit, say like polyfit
function of Octave/MATLAB.
For who don't know, c = polyfit(x,y,m) finds the coefficients of a
polynomial p(x) of degree m that fits the data, p(x[i]) to y[i], in a
least squares sense. The result c is a vector of len
I found a solution to my problem.
It is describe here.
http://kb.mozillazine.org/Windows_error_opening_Internet_shortcut_or_local_HTML_file_-_Firefox
Essentially, it involves switching off DDE for some file associations
in Windows Explorer.
It really is a Firefox bug.
Erich Neuwirth wrote:
> My
Hi all,
I am trying to use the functions in the plm package with multiply
imputed datasets. I had tried to combine the datasets using the
imputationList() function of mitools. plm, however, requires a data
argument, and I don't know where to point it to. I'd appreciate any
Hi,
I have a supposedly representative sample from a
stratified survey. Hence, all observations have an
associated sample weight each which inflate the sample
to population size.
I want to run a glm probit regression on the data but
I am not clear about if or better how I can use the
weights in
Dear useRs,
I wanted to have a function that allows me to get the font.lab-font,
especially italic font,
in plotmath-annotation. Consulting the R-Help-list did not reveal a
solution,
but other requests, so I wrote a little function, which I would like to
share:
## code begin
math <- function (..
Hello Nick,
Wednesday, August 15, 2007, 1:18:34 PM, you wrote:
NC> On 15/08/07, Vladimir Eremeev <[EMAIL PROTECTED]> wrote:
NC> Nick Chorley-3 wrote:
>>
>> I have a large amount of data that I would like to create a histogram of
>> and
>> plot and do things with in R. It is pretty much impossible
My reason for setting stringsAsFactors = FALSE is more
that I really dislike having R convert what I "think"
are character variables to factors when I import data.
I suspect that it takes quite a few new users by
surprise that what they had intended to be a character
variable has become a factor.
> "JK" == John Kane <[EMAIL PROTECTED]>
> on Wed, 15 Aug 2007 08:55:59 -0400 (EDT) writes:
JK> I think we need more information about your system.
JK> Please run
JK> sessionInfo()
JK> and include the information in another posting.
Yes, indeed.
However R version 2.3.1
Dear all,
I just want to integrate an offset in a linear mixed model applying
functions lmer and lmer2 from library(lme4). It seems that lmer just
ignores the offset term and lmer2 does the fit but replies an error if
calling the fitted object:
#lmer with offset
lmeTNr_offset<-lmer(res_id~1+of
I think we need more information about your system.
Please run
sessionInfo()
and include the information in another posting.
--- "Mag. Ferri Leberl" <[EMAIL PROTECTED]> wrote:
> Dear everybody,
> excuse me if this question ist trivial, however, I
> have now looked for
> an answer for quite a whi
Dear everybody,
excuse me if this question ist trivial, however, I have now looked for
an answer for quite a while and therefore dare placing it here.
I want to export .svg-files and got here the advice to employ the
cairo-library.
I downloaded the *current*-version here and expanded it
to /usr/loc
Hello,
I encountered the following problem with the parameter scaled in ksvm()
from package kernlab:
[Package kernlab version 0.9-5]
library(kernlab)
> svp =ksvm(x=mydata,y=y,scaled=T)
Using automatic sigma estimation (sigest) for RBF or laplace kernel
> svp
Dear all
Please help me with analysis of some periodic data.
I have an output from measurement each minute and this output is modulated
by rotation of the equipment (approx 6.5 min/revolution). I can easily
spot this frequency from
spectrum(mydata, some suitable span)
However from other anal
Hello,
I am using the function mda of the mda library in order to discriminate
4 groups with 8 explanatory variables. I only have 66 observations.
I tested all possible combinations of those variable and run for each
the Mixture Discriminant Analysis.
For some iterations, I got an error message
On 15-Aug-07 08:30:08, Nick Chorley wrote:
> Hi,
>
> I have a large amount of data that I would like to create a
> histogram of and plot and do things with in R. It is pretty
> much impossible to read the data into R, so I have written a
> program to bin the data and now have a list of counts in e
On 15-Aug-07 10:15:13, Nick Chorley wrote:
>>[...]
>> Now create a histogram template (any silly old data will do):
>>
>> H1 <- hist(c(1,2))
>>
>> Next, attach your variables to it:
>>
>> H1$breaks <- brkpts
>> H1$counts <- counts
>>
>> and you have your histogram in R. Also, you can use the data
>
Never mind, using scan() and putting it into an array
of the specific dimensions is sufficient for my case.
But it still would be interesting to know if there is
some function to read in more complex data objects.
Thanks,
Werner
> Hi,
>
> I was wondering if there is already some function
>
My configuration is Windows XP, R-2.5.1patched.
My standard browser in Windows is Firefox 2.0.6,
and I am using htmlhelp.
I have problems with starting the browser for displaying help.
help("lm") works as it should when Firefox is already running.
When I do help("lm") and the browser is not yet st
On 15/08/07, Ted Harding <[EMAIL PROTECTED]> wrote:
>
> On 15-Aug-07 08:30:08, Nick Chorley wrote:
> > Hi,
> >
> > I have a large amount of data that I would like to create a
> > histogram of and plot and do things with in R. It is pretty
> > much impossible to read the data into R, so I have writt
On 15/08/07, Vladimir Eremeev <[EMAIL PROTECTED]> wrote:
Nick Chorley-3 wrote:
>
> I have a large amount of data that I would like to create a histogram of
> and
> plot and do things with in R. It is pretty much impossible to read the
> data
> into R, so I have written a program to bin the data
Nick Chorley-3 wrote:
>
> I have a large amount of data that I would like to create a histogram of
> and
> plot and do things with in R. It is pretty much impossible to read the
> data
> into R, so I have written a program to bin the data and now have a list of
> counts in each bin. Is it possib
Hi,
I have a large amount of data that I would like to create a histogram of and
plot and do things with in R. It is pretty much impossible to read the data
into R, so I have written a program to bin the data and now have a list of
counts in each bin. Is it possible to somehow import this into R a
"Lawrence D. Brenninkmeyer" <[EMAIL PROTECTED]> writes:
> I am trying to find a way to diffuse GIS data on a European map. I have a
> dataset consisting of particular locations scattered across Europe,
> along with magnitude and value information.
The dataset is a spatial point pattern, where the
Hi,
I was wondering if there is already some function
implemented into R that reads in tables with more than
2 dimensions. There is probably something neat out
there...
Thanks,
Werner
Wissenswertes zum Thema PC, Zubehör oder Programme. BE A BETTER
INTERNET-GURU! www.yahoo.de/clever
_
Hi Yuchen,
First of all please notice that you may not have more
than 2^8 = 256 columns in Excel, so if you have more
than 256 time-series you can not put them all in one
Excel sheet. I also believe that you can not have more
than 2^16 = 65536 rows.
If you do not have more than 256 time-series, I
Thank you very much Professor Ripley! Afterwards it seems obvious where to
look.
Have a nice day,
Maciej
PS: Yes, my machine has not much memory, but it is sufficient for the smaller
trial data.
-Ursprüngliche Nachricht-
Von: Prof Brian Ripley [mailto:[EMAIL PROTECTED]
Gesendet: Di
No wonder that you are getting overflow, since
gamma(N+1) = n! and 200! > (200/e)^200 > 10^370.
There exists another way to compute C(N,k). Let me
know if you need this and I will explain to you how
this can be done.
But do you really need to compute the individual
probabilities? May be you need so
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