At 19:02 2004-07-12 -0700, you wrote:
If I had confint.glm, I could modify it so it could find data. and
size. However, its hidden.
Try
library(MASS)
MASS:::confint.glm
or navigate to /.../library/MASS/R and open the MASS file in your favourite
editor.
HTH,
Henric
Hi
I can recommend you two files
a) http://www.psych.upenn.edu/~baron/rpsych/rpsych.html
b) http://www.pallier.org/ressources/stats_with_R/stats_with_R.pdf (in
french)
cheers
let me know whether this helped you
cheers
christoph
Matthias Unterhuber wrote:
Hello,
My name is Matthias and I do look
Hello,
Not really regular expressions but you may also look at the first
version of my package ttda at
http://wwwpeople.unil.ch/jean-pierre.mueller/
and the functions:
ttda.get.text
ttda.segmentation
ttda.forms.frame
ttda.TLE
HTH.
--
Jean-Pierre Müller
SSP / BFSH2 / UNIL / CH - 1015 Lausanne
Is there something wrong with this URL?
Mark Palmer
Environmetrics Monitoring for Management
CSIRO Mathematical and Information Sciences
Private bag 5, Wembley, Western Australia, 6913
Phone 61-8-9333-6293
Mobile
Hi All,
I have looked through the following thread:
http://tolstoy.newcastle.edu.au/R/help/02b/4551.html
and would like to ask after 1.5 year the same question:
Are there any plans to involve multithread
computations in R?
Few word about my motivation:
I use R on my OpenSSI
Dear Sirs,
I am a R beginning user: by mean of R I would like to apply the bootstrap to my data
in order to test cost differences between independent or paired samples of people
affected by a certain disease.
My problem is that even if I am reading the book by Efron (introduction to the
[sorry if this arrives in duplo: it doesn't show up in the archives and it seems that
the address I posted this from originally is no longer functional]
Hello,
I think I could do with some suggestions concerning the following problem.
I have data from a set of experiments on motion sickness
Dear all!
I wrote my R-code with an editor and loaded it with source(my_file.R).
Everything works fine as expected.
When I try to start my code with:
R --no-save my_file.R
I do get a synatx error half way through. The version is 1.9.0 on a Linux
system. To start it with R --no-save
Hi
based on some code from Thomas Petzoldt, I have a question:
---
opar - par(mfrow = c(2,4))
slices - 8
m - matrix(runif(100),10,10)
my.list - list()
for (slice in 1:slices) {
my.list[[slice]] - m
}
for (slice in 1:slices) {
x - 1*(1:25)
y - 1*(1:25)
z - my.list[[slice]]
p - locator(1)
c(round(p$x), round(p$y))
---
how can I get the correct location in the sense of a
3d info: (a) which slice (p$slice) (b) p$x (c) p$y
Okay, purely off the top of my head here...
You can use par()$usr, par()$plt, and par()$fig to transform from
locator()'s coordinates to device
Dear expeRts
Is it possible to compare correlation coefficients or to normalize
different correlation coefficients?
Concretely, we have the following situation:
We have gene expression profiles for different tissues, where the
number of samples per tissue are different, ranging from 10 to 250.
Hi
On 13 Jul 2004 at 12:28, luciana wrote:
Dear Sirs,
I am a R beginning user: by mean of R I would like to apply the
bootstrap to my data in order to test cost differences between
independent or paired samples of people affected by a certain
disease.
My problem is that even if I am
Hi Tae-Hoon,
I am very surprise by your answers :
When I try to make an affybatch with bioconductor and R 1.9.1, I was unable
to read and normalise more than 80 HU-133A CEL file with a Linux 32 bits
computer and 4 GB of RAM + 8 GB of swap (Of course, without any other
process on the computer
just a hint for further bootstrapping examples (worked out with R):
Bootstrap Methods and Their Applications by A.C. Davison and D.V. Hinkley
cheers
christoph
luciana wrote:
Dear Sirs,
I am a R beginning user: by mean of R I would like to apply the bootstrap to my data
in order to test cost
You actually don't need to load the package first:
MASS:::confint.glm
function (object, parm, level = 0.95, trace = FALSE, ...)
{
pnames - names(coef(object))
if (missing(parm))
parm - seq(along = pnames)
else if (is.character(parm))
parm - match(parm, pnames,
Try subscripting, e.g.
# L holds numbers; its names hold lookup keys
L - 1:26; names(L) - letters
L[c(d,f)] # look up numbers of d and f
or merge, e.g.
merge(c(d,f), L, by.x = 1, by.y = 0)
Anne anne.piotet at urbanet.ch writes:
:
: Hello R helpers!
: I looked but did not find
Thank you! It should do the job... (it was jeust a question to know where to
look!)
Anne
- Original Message -
From: Adaikalavan Ramasamy [EMAIL PROTECTED]
To: Anne [EMAIL PROTECTED]
Sent: Tuesday, July 13, 2004 2:45 PM
Subject: Re: [R] table lookup n R
See match(), %in% and related
Hi
On 13 Jul 2004 at 14:34, Anne wrote:
Hello R helpers!
I looked but did not find a table-lookup R-utility. I could use a
loop to do the job (old FORTRAN/C habits die hard) but if I have a big
table in which I have to search for the values corresponding to a
vector, I end up logically
On Tue, 2004-07-13 at 07:28, Petr Pikal wrote:
Hi
On 13 Jul 2004 at 12:28, luciana wrote:
Dear Sirs,
I am a R beginning user: by mean of R I would like to apply the
bootstrap to my data in order to test cost differences between
independent or paired samples of people affected by a
Duncan Murdoch wrote:
On Mon, 12 Jul 2004 15:14:27 +0200, Uwe Ligges
[EMAIL PROTECTED] wrote :
Gabor Grothendieck wrote:
The objective should be that creating a package is as easy as this:
f - function()1; g - function()2; d - 3; e - 4:5
package.skeleton(list=c(f,g,d,e), name=AnExample)
Spencer == Spencer Graves [EMAIL PROTECTED]
on Mon, 12 Jul 2004 10:44:25 -0700 writes:
Spencer Please see: Brown, Cai and DasGupta (2001)
Spencer Statistical Science, 16: 101-133 and (2002) Annals
Spencer of Statistics, 30: 160-2001
Spencer They show that the
Hi, everyone
I am trying to estimate 3 parameters for my survival
function. It's very complicated. The negative
loglikelihood function is:
l- function(m1,m2,b) -sum(d*( log(m1) + log(m2)
+ log(1- exp(-(b + m2)*t)) ) + (m1/b - d)*log(m2 +
b*exp(-(b + m2)*t) ) + m1*t - m1/b*log(b+m2) )
Hi list,
I'm performing a series of confirmatory factor analysis on different
groupings of items from data collected with questionnaires. There are some
missing values.
For those sets with no missing values I call
factanal(datamatrix,factors=n)
where datamatrix is a table of all observations
Hi
On 13 Jul 2004 at 12:28, luciana wrote:
Dear Sirs,
I have a sample of diabetic people, matched (by age
and sex) with a
control sample. The variable I would like to compare
is their drug
and hospital monthly cost. The variable cost has a
very far from
gaussian distribution, but I need
Dear friends
I have recently migrated to R (8.0) for analysis of microarray data. I
am doing a loess (print-tip, perhaps scaled) normalization. I find that
there are 2 options to do this: using normalizeWithinArrays (Limma) and
stat.ma(sma). I find the objects returned by the two functions are
Hi R-developers,
R (unlike say C++) is rather interactive/interpreter language
with some high-order functions support. There is a nice project,
which able to bring exactly these type of language implementations
to a next performance level. I mean LLVM (http://llvm.cs.uiuc.edu/)
LLVM
Dear All,
I would like to ask how to add a table to a matrix of graphs.
I have three non linear regression graphs plotted together after:
par(mfrow=c(2,2))
which leaves an empty bottom right corner. I would like to use the space
to add a table (at the moment that's problem number one, adding a
-Original Message-
From: Federico Calboli
Sent: Tuesday, July 13, 2004 6:06 PM
To: r-help
Subject: [R] plotting a table together with graphs
Dear All,
I would like to ask how to add a table to a matrix of graphs.
I have three non linear regression graphs plotted
Hi
I would like to access compiled C code used in hclust and in dist functions
(in order to create my own functions using new methods). Is it possible ?
Thanks
Julie AUBERT
__
[EMAIL PROTECTED] mailing list
Have you considered estimating ln.m1, ln.m2, and ln.b, which makes
the negative log likelihood something like the following:
l.ln- function(ln.m1,ln.m2,ln.b){
m1 - exp(ln.m1); m2 - exp(ln.m2); b - exp(ln.b)
lglk - d*( ln.m1 + ln.m2
+ log1p(-exp(-(b+m2)*t)
+
Since both of the packages you mention are part of Bioconductor, you
would do well to re-post in the correct list
([EMAIL PROTECTED]).
Best,
Jim
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI
Dear Antonio,
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of
Antonio Prioglio
Sent: Tuesday, July 13, 2004 9:32 AM
To: [EMAIL PROTECTED]
Subject: [R] Help with factanal and missing values
Hi list,
I'm performing a series of confirmatory
Dear friends
I have recently migrated to R (8.0) for analysis of microarray data. I
am doing a loess (print-tip, perhaps scaled) normalization. I find that
there are 2 options to do this: using normalizeWithinArrays (Limma) and
stat.ma(sma). I find the objects returned by the two functions are
Thank you Andy.
It seems like this can be the reason for the confusion.
I never thought that there can be this kind of catches for using tune.*
functions.
For the record, I actually emailed to Dr. Friedrich Leisch the author
of this library.
When I get some reply, I will post it also.
Regards,
[EMAIL PROTECTED] wrote:
Hi
I would like to access compiled C code used in hclust and in dist
functions (in order to create my own functions using new methods). Is it
possible ?
Yes. Do you want to modify it or just use it? Using it is simple. Just
load the package and go ahead
Uwe Ligges
Philipp Heuser wrote:
Dear all!
I wrote my R-code with an editor and loaded it with source(my_file.R).
Everything works fine as expected.
When I try to start my code with:
R --no-save my_file.R
I do get a synatx error half way through. The version is 1.9.0 on a Linux
system. To start it with
Take a look at Textplot in the gregmisc package ...
Federico Calboli [EMAIL PROTECTED]
Sent by: [EMAIL PROTECTED]
07/13/2004 12:06 PM
Please respond to f.calboli
To: r-help [EMAIL PROTECTED]
cc:
Subject:[R] plotting a table together with graphs
Dear
Check out textplot in the gregmisc package ...
Federico Calboli [EMAIL PROTECTED]
Sent by: [EMAIL PROTECTED]
07/13/2004 12:06 PM
Please respond to f.calboli
To: r-help [EMAIL PROTECTED]
cc:
Subject:[R] plotting a table together with graphs
Dear All,
The handy function summary() doesn't work correctly with Date class
objects:
R.version.string
[1] R version 1.9.1, 2004-06-21
b - as.Date(c(2002-12-26, 2002-12-27, 2002-12-28, 2002-12-29, 2002-12-30))
b
[1] 2002-12-26 2002-12-27 2002-12-28 2002-12-29 2002-12-30
summary(b)
Min.
On Tue, 13 Jul 2004, John Fox wrote:
Two solutions are to use na.omit() to eliminate observations with missing
data -- factanal(na.omit(datamatrix), factors=n) -- or to use a formula
argument to factanal and pass the data as a data frame via the data argument
-- factanal(~ var1 + ... + vark,
Dear Antonio,
-Original Message-
From: Antonio Prioglio [mailto:[EMAIL PROTECTED]
Sent: Tuesday, July 13, 2004 12:50 PM
To: John Fox
Cc: [EMAIL PROTECTED]
Subject: RE: [R] Help with factanal and missing values
On Tue, 13 Jul 2004, John Fox wrote:
Two solutions are to use
Hi, R people,
I wonder if there is a statistics than can measure the correlation for more
than two random variables, instead of computing the correlation coefficient
matrix. If so, what R package should I use?
Right now I can only think of the mean of all pair-wise correlation
On 07/13/04 14:34, F Duan wrote:
Hi, R people,
I wonder if there is a statistics than can measure the correlation for more
than two random variables, instead of computing the correlation coefficient
matrix. If so, what R package should I use?
One possibility is Cronbach's alpha, which is in
On Tue, 13 Jul 2004, John Fox wrote:
Could you give an example on how to do CFA with sem?
Among the examples in ?sem is a second-order CFA.
Ok, sorry I forgot about the Thurstone example as I was focusing on Path
Analysis example when reading the sem doc.
I understand this is a model taken
Dear R users,
Im a beginner user of R and Ive a problem with permutations that I dont
know how to solve. Ive 12 elements in blocks of 3 elements and I want only
to make permutations inter-blocks (no intra-blocks) (sorry if the
terminology is not accurate), something similar to:
1 2 3 | 4 5
On Tue, 2004-07-13 at 14:07, Jordi Altirriba Gutirrez wrote:
Dear R users,
Im a beginner user of R and Ive a problem with permutations that I dont
know how to solve. Ive 12 elements in blocks of 3 elements and I want only
to make permutations inter-blocks (no intra-blocks) (sorry if the
On Tue, 2004-07-13 at 14:29, Marc Schwartz wrote:
On Tue, 2004-07-13 at 14:07, Jordi Altirriba Gutirrez wrote:
Dear R users,
Im a beginner user of R and Ive a problem with permutations that I dont
know how to solve. Ive 12 elements in blocks of 3 elements and I want only
to make
Hi all,
I've got clusters and would like to match individual records to each
cluster based on a sum of squares deviation. For each cluster and
individual, I've got 50 variables to use (measured in the same way).
Matrix 1 is individuals and is 25000x50. Matrix 2 is the cluster
centroids and
Marc Schwartz wrote (in response to a question from Jordi Altirriba):
You can use the permutations() function in the 'gregmisc' package on
CRAN:
# Assuming you installed 'gregmisc' and used library(gregmisc)
# First create 'groups' consisting of the four blocks
groups - c(1 2 3, 4 5 6, 7
This seems more like a STATS question than an R question - asking on a
list like STAT-L or ALLSTAT may result in more replies
Nevertheless, it seems to me that you need to describe (and maybe
decide) what you mean by 'summarize' the correlations. Certainly the
mean DOES summarize them, but is it
Hello,
I have used SAS for multi-factor ANOVA, and found the SLICE function of
LSMEANS to be valuable. Is there an equivalent function in R, and if so,
where might I find it? Thanks in advance for suggestions, and thanks for
access to this invaluable knowledge base.
Corey
I may be confused, but I think what you described will produce greater than
472 million permutations. I think your second permutation 1 2 4 | 3 5 6 |
7 8 9 | 10 11 12 YES-2nd permutation shows that you want more than
just a permutation of entire blocks.
There are a total of 12! (12
On Tue, 13 Jul 2004, John Fox wrote:
Among the examples in ?sem is a second-order CFA.
Thanks now I have it running, hopefully in a correct way.
By the way I notice in the output a GFI index that in your online appendix
to your 2002 book describe as an ad hoc measure.
Could you comment on
Tae-Hoon:
When we run tune.* for parameter tuning, we get performance value.
Can you tell me what the definition of it is?
The values returned by tune() are Mean Squared Errors in case of
regression, and simple rates (*no* percentages) in case of
classification. As Andy already suggested, you
Thank you David and Andy. Now, everything is clear.
For others, the problem is the one said in the subject, and the answer
is the one excerpted from reply from David.
TH.
On Jul 13, 2004, at 1:54 PM, David Meyer wrote:
Tae-Hoon:
When we run tune.* for parameter tuning, we get performance value.
In sas and matlab, I have been using a modified link
function.
I use a binomial distribution with the link log(p-.5/1-p)
instead of log(p/1-p) which is the usual logit link. This
allows the probabilities to go from .5 to 1 instead of 0 to
1. which is typical when probabilities vary between chance
As has been pointed out by Robert Baskin, your ``restricted''
permutations comprise the bulk of all permutations; i.e. the
restriction isn't as restrictive as one might have expected.
So constructing ***all*** restricted permutations is probably not
very useful.
However if you simply wish to
On Tue, 2004-07-13 at 15:02, Rolf Turner wrote:
Marc Schwartz wrote (in response to a question from Jordi Altirriba):
snip
This does not solve the problem that was posed. It only permutes the
blocks, and does not allow for swapping between blocks. For instance
it does produce the
Dear Antonio,
This example is (as stated) a second-order CFI, where each of the primary
factors, F1, F2, and F3 depends upon the second-order factor F4. To have no
second-order structure, simply define variances and (assuming that you're
specifying correlated factors) covariances among the
Dang!!! Forget it. My random restricted permutation generator
doesn't ``quite'' work. Further testing --- which I should've done
before posting (sigh) --- reveals that it can get into a situation in
which there's nothing left to sample from, and it still needs to fill
out the permutation. I.e.
Dear Antonio,
I'm afraid that you're asking the wrong person about this, because the
literature on goodness of fit measures in SEMs strikes me as mostly alchemy.
As I recall, there are several chapters discussing fit measures in Bollen
and Long, eds., Testing Structural Equation Models. Perhaps
Dear R users,
First of all, thanks for the incredibly fast answers and help of Rolf,
Marc and Robert.
Yes, I noticed that it was a lot of permutacions, but my intention was to
make this process automatic and take only 5.000 - 10.000 permutations.
Therefore, I wanted only to take that
For what it's worth, here is a mild revision of my restr.perm()
function, which seems NOT to fall over. I.e. it appears to
``reliably'' generate restricted permutations.
Whether these are genuinely ***random*** restricted permutations
(i.e. does each restricted permutation of 1:12 have the same
Kjetil and Andy,
Thanks for your helpful answers! The first two (mgcv and fda) seem to be in
the direction I'm looking for. I downloaded them both.
I'm running into a lot of implementation difficulties, though. I wonder if
there's anyone who tried to do a monotone spline using either the 'mgcv'
On Tue, 13 Jul 2004, John Fox wrote:
Dear Antonio,
This example is (as stated) a second-order CFI, where each of the primary
factors, F1, F2, and F3 depends upon the second-order factor F4. To have no
second-order structure, simply define variances and (assuming that you're
specifying
Hi.
I asked a question about lda() and got some answers. However, one
question remains (which is not independent of the earlier ones):
What output does lda() produce which I can use to compute the
posteriors? I know predict(lda())$posterior will give me precisely the
posteriors, but suppose
Dear Antonio,
-Original Message-
From: Antonio Prioglio [mailto:[EMAIL PROTECTED]
Sent: Tuesday, July 13, 2004 5:54 PM
To: John Fox
Cc: [EMAIL PROTECTED]
Subject: RE: [R] Help with factanal and missing values
On Tue, 13 Jul 2004, John Fox wrote:
Dear Antonio,
This
I have setup R 1.9.1 on my Dell laptop running windows XP. I have
installed it to C:\R\rw1091. Rgui runs fine, but Rcmd fails if run with
parameters (i.e. install). The windows dialog box cheerfully says R for
Windows front-end has encountered a problem and needs to close. We are
sorry for the
[EMAIL PROTECTED] wrote:
HI, sorry but i don't understand how to make a function with as.function()
formula-2+3*x
formu-as.symbol(formula)
formu
2+3*x
formul-as.function(alist(x=,formu))
curve(formul,1,5,col=blue)
Error in xy.coords(x, y, xlabel, ylabel, log) :
x and y lengths differ
Hola!
Experimenting a little, package fda seems very much under development,
and help pages are definitely not finished.
It would certainly help to read the book functional data analysis by
the author of fda, which is in our library.
On the other hand package mgcv is more mature, so it would
On Wed, 14 Jul 2004 10:12:45 +1000, [EMAIL PROTECTED] wrote:
I have setup R 1.9.1 on my Dell laptop running windows XP. I have
installed it to C:\R\rw1091. Rgui runs fine, but Rcmd fails if run with
parameters (i.e. install). The windows dialog box cheerfully says R for
Windows front-end has
I think I may know what you want. Try this :
# code
strata.restricted.sample - function( grp ){
K - length(unique(grp)) # number of levels
new.grp - sample(grp)
xtab- table(grp, new.grp)
propA - apply(xtab, 1, function(x) max(x) / sum(x))
no.A- sum( propA == 1 )
I remember doing this some time ago but forgot. Perhaps this might help
you
MASS:::predict.lda
On Tue, 2004-07-13 at 23:56, marzban wrote:
Hi.
I asked a question about lda() and got some answers. However, one
question remains (which is not independent of the earlier ones):
What output
Hello R People:
I have a data frame with 2 numeric variables and 1 factor.
There are 3 levels of the factor.
I would like to get sums/means/etc of the numeric variables with respect to
the factor level.
I tried table and subset but have not hit upon a solution.
I thought maybe apply would be the
?tapply
The examples there seem to describe what you want. hope this helps.
spencer graves
Laura Holt wrote:
Hello R People:
I have a data frame with 2 numeric variables and 1 factor.
There are 3 levels of the factor.
I would like to get sums/means/etc of the numeric variables with
respect to
Hi,
I'm using the SJava package and am trying to get event
handling to work, but no examples from
http://www.omegahat.org/RSJava/examples/ that have any event
handling work in R 1.9.0. I think the examples were all
written around 2001 so most probably used an older version
of R. The error
Hi,
I'm using the SJava package and am trying to get event
handling to work, but no examples from
http://www.omegahat.org/RSJava/examples/ that have any event
handling work in R 1.9.0. I think the examples were all
written around 2001 so most probably used an older version
of R. The error
I want to fit a piecewise nonlinear model in which the transition point is
an estimated parameter.
Something like:
F(x)=F1(x) when xalpha,
F(x)=F2(x) when x=alpha.
How can I solve for alpha within the nls call?
Thanks,
Rob
__
[EMAIL PROTECTED] mailing
solares at unsl.edu.ar writes:
HI, sorry but i don't understand how to make a function with as.function()
formula-2+3*x
formu-as.symbol(formula)
formu
2+3*x
formul-as.function(alist(x=,formu))
curve(formul,1,5,col=blue)
Error in xy.coords(x, y, xlabel, ylabel, log) :
x
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